CALIFORNIA, SAN DIEGO
UNIVERSITY OF
CALIFORNIA, SAN DIEGO
La Jolla, CA 92093-0332
TEL: (858) 534-5489
FAX: (858) 534-6693
Web: www-chem.ucsd.edu
Email: chair@chem.ucsd.edu
Department of Chemistry and Biochemistry
Robert E. Continetti, Chair.
Degrees Offered: B.A, B.S, M.S, Ph.D.
Fields of Specialization: MS and PhD in Chemistry
fields include Biochemistry, Biophysics, Analytical
Chemistry, Environmental and Atmospheric Chemistry, Inorganic Chemistry, Organic Chemistry, Computational Chemistry, Theoretical Chemistry, Materials Chemistry, and Physical Chemistry PhD in
Chemistry with specialization in Bioinformatics.
Interdisciplinary Program: Joint Doctoral Program
in Chemistry and San Diego State University and
University of California San Diego.
ALLISON, WILLIAM S. (b.1935) Professor, Emeritus. A.B, 1957, Dartmouth College; M.A, 1959, Dartmouth College; Ph.D, 1963, Brandeis University.
USPHS Fellow, 1964-1965, MRC, Laboratory Molecular
Biology, Cambridge, England. The molecular mechanism of ATP synthase. TEL: (858) 534-3057 FAX: (858)
822-0079
Web: www.chem.ucsd.edu
Email: wallison@ucsd.edu
wsa@checfs2.ucsd.edu
No publication information submitted for this edition.
ARNOLD, JAMES R.
No publication information submitted for this edition.
BAKER, TIMOTHY S. (b.1949) Professor. B.S,
1971, Duke University; Ph.D, 1976, University of California, Los Angeles. Jane Coffin Childs Fellow, 19761978; NIH Postdoc Fellow, 1979-1980; Charles A. King
Trust Postdoctoral Fellow, 1980-1982. Biochemistry.
Macromolecular, cryoelectron microscopy and three-dimensional, image-reconstruction techniques are used in
our research to visualize viruses and to determine how
viruses interact with their hosts. TEL: (858) 534-5845
FAX: (858) 534-5846
Web: www-biology.ucsd.edu/faculty/baker.html
Email: tsb@ucsd.edu
Said A. Ghabrial, Wendy F. Ochoa, Timothy S. Baker and
Max L. Nibert, Partitiviruses: General features, Encyclopedia
of Virology, 4, 68-75 (2008).
Xiaodong Yan, Zeyun Yu, Ping Zhang, Anthony J. Battisti,
Heather A. Holdaway, Paul R. Chipman, Chandrajit Bajaj,
Max Bergoin, Michael G. Rossmann and Timothy S. Baker,
The capsid proteins of a large icosahedral dsRNA virus, J.
Mol. Bio, 385, 1287-1299 (2008).
Hazel C. Levy, Valorie D. Bowman, Lakshmanan Govindasamy, Robert McKenna, Kevin Nash, Kenneth Warrington, Weijun Chen, Nicholas Muzyczka, Xiaodong Yan, Timothy S. Baker and Mavis Agbandje-McKenna, Heparin binding induces conformational changes in Adeno-associated virus serotype 2, J. Struct. Bio, 165, 146-156 (2008).
Jinghua Tang, Wendy F. Ochoa, Robert S. Sinkovits, Bonnie T. Poulos, Said A. Ghabrial, Donald V. Lightner, Timothy S. Baker and Max L. Nibert, Infectious myonecrosis virus has a totivirus-like, 120-subunit capsid, but with fiber
complexes at the fivefold axes, Proc. Natl. Acad. Sci. U. S. A,
105, 17526-17531 (2008).
Wendy F. Ochoa, Wendy M. Havens, Robert S. Sinkovits,
Max L. Nibert, Said A. Ghabrial and Timothy S. Baker, Partitivirus structure reveals a 120-subunit, helix-rich capsid
with distinctive surface arches formed by quasisymmetric
coat-protein dimers, Structure (Cambridge, MA, U. S.), 16,
776-786 (2008).
Jinghua Tang, Norman Olson, Paul J. Jardine, Shelley
Grimes, Dwight L. Anderson and Timothy S. Baker, DNA
poised for release in bacteriophage ␾29, Structure (Cambridge, MA, U. S.), 16, 935-943 (2008).
BALDRIDGE, KIM K. (b.1960) Adjunct Professor.
B.S, 1982, Minot State University; M.A, 1985, North
Dakota State University; Ph.D, 1988, North Dakota State
University. Postdoctoral Fellow, 1989, Wesleyan. Theoretical Chemistry. Direct application of quantum chemical software to problems in biomedical research and materials chemistry; development of new quantum chemical
algorithms for study of reaction processes including effects of the environment; development of visualization,
database, and grid middleware technologies for computational chemistry and biochemistry ; development of instructional codes for chemical curricula. TEL: (858) 534-
5149 FAX: (858) 822-5407
Web: www.sdsc.edu/~kimb
Email: kimb@oci.uzh.ch
kimb@sdsc.edu
Florian P. Seebeck, Angelo Guainazzi, Celine Amoreira
and Donald Hilvert, Stereoselectivity and expanded substrate
scope of an engineered PLP-dependent aldolase, Angewante.
Chemie. Int. Engl, 45, 6824-6826 (2006).
Toshiyuki Hamura, Yousuke Ibusuki, Hidehiro Uekusa,
Takashi Matsumoto, Jay S. Siegel and Kim K. Baldridge,
Dodecamethoxy- and Hexaoxo-tricyclobutabenzene: Synthesis and characterization, J. Am. Chem. Soc, 128, 1003210033 (2006).
Jay S. Siegel, Kim K. Baldridge, Anthony Linden and Reto
Dorta, D8 Rhodium and Iridium complexes of corannulene,
J. Am. Chem. Soc, 128, 10644-10645 (2006).
Michale DeClue, Kim K. Baldridge, Peter Kast and Donald
Hilvert, Experimental and computational investigatin of the
uncatalyzed elimination and rearrangement reactions of isochorismate, J. Am. Chem. Soc, 128, 2043 (2006).
Yao-Ting Wu, Tomoharu Hayama, Kim K. Baldridge, Anthony Linden and Jay S. Siegel, Synthesis of fluoranthenes
and indenocorannulenes: Elucidation of chrial stereoisomers
on the basis of static molecular bowls, J. Am. Chem. Soc,
128, 6870-6884 (2006).
Roie Yerushalmi, Alexander Brandis, Vada RosenbachBelkin, Kim K. Baldridge and Avigdor Scherz, Modulation
of fragmental charge transfer via hydrogen bonds; direct
measurement of electronic contributions, J. Phys. Chem, 110,
412 (2006).
Jose N. Onuchic, Chiguas Kobayashi, Osamu Miyashita,
Patricia Jennings and Kim K. Baldridge, Exploring biomolecular machines; energy landscape control of biological reactions, Philosophical Transactions of the Royal Society of
London, 361, 1439-1443 (2006).
Tomoharu Hayama, Yao-Ting Wu, Anthony Linden, Kim
K. Baldridge and Jay S. Siegel, Synthesis, Structure, and
Isomerization of Decapentynylcorannulene: Enediyne Cyclization/Interconversion of C40R10 Isomers, J. Am. Chem. Soc,
129, 12612-12613 (2007).
Giancarlo Terraneo, Donatella Potenza, Angeles Canales,
Jesus Jimenez-Barbero, Kim K. Baldridge and Anna Bernardi, A Simple Model System for the Study of CarbohydrateAromatic Interactions, J. Am. Chem. Soc, 129, 2890-2900
(2007).
Jan Andzelm, Adam M. Rawlett, Joshua A. Orlicki, James
F. Snyder and Kim K. Baldridge, Optical Properties of
Phthalocyanine and Naphthalocyanine Compounds, J. Chem.
Theory Comput, 3, 870-877 (2007).
He-Ping Wu, Daniel H. Ess, Seren Lanza, Timothy J. R.
Weakley, K. N. Houk, Kim K. Baldridge and Michael M.
Haley, Rearrangement of Iridabenzvalenes to Iridabenzenes
and/or ␩5-Cyclopentadienyliridium(I) Complexes: Experimental and Computational Analysis of the Influence of Silyl
Ring Substituents and Phosphine Ligands, Organometallics,
26, 3957-3968 (2007).
Simon Duttwyler, Quyen-Quyen Do, Anthony Linden,
Kim K. Baldridge and Jay S. Siegel, Synthesis of 2,6diarylphenyldimethylsilyl cations: polar-␲ distribution of cation character, Angew. Chem., Int. Ed, 47, 1719-1722 (2008).
Vincent Lemieux, M. Daniel Spantulescu, Kim K. Baldridge and Neil R. Branda, Modulating the Lewis acidity of
boron using a photoswitch, Angew. Chem., Int. Ed, 47, 50345037 (2008).
Tirath Ramdas, Gregory K. Egan, David Abramson and
Kim K. Baldridge, Uniting extrinsic vectorization and shell
structure for efficient SIMD evaluation of electron repulsion
integrals, Chem. Phys, 349, 147-157 (2008).
Tirath Ramdas, Gerald Egan, David Abramson and Kim K.
Baldridge, On ERI sorting for SIMD execution of large-scale
Hartree-Fock SCF, Comp. Phys. Comm, 178, 817-834
(2008).
Ryan L. Holland, Kevin D. Bunker, Christopher H. Chen,
Antonio G. Di Pasquale, Arnold L. Rheingold, Kim K. Baldridge and Joseph M. O’Connor, Reactions of a Metallacyclobutene Complex with Alkenes, J. Am. Chem. Soc, 130,
10093-10095 (2008).
Yao-Ting Wu, Davide Bandera, Roman Maag, Anthony
Linden, Kim K. Baldridge and Jay S. Siegel, Multiethynyl
Corannulenes: Synthesis, Structure, and Properties, J. Am.
Chem. Soc, 130, 10729-10739 (2008).
Tomoharu Hayama, Kim K. Baldridge, Yao-Ting Wu, Anthony Linden and Jay S. Siegel, Steric Isotope Effects
Gauged by the Bowl-Inversion Barrier in Selectively Deuterated Pentaarylcorannulenes, J. Am. Chem. Soc, 130, 15831591 (2008).
Jose N. Onuchic, Chigusa Kobayashi and Kim K. Baldridge, Quantum tunneling in biological reactions: the interplay between theory and experiments, J. Braz. Chem. Soc,
19, 206-210 (2008).
Roberto Peverati and Kim K. Baldridge, Implementation
and Performance of DFT-D with Respect to Basis Set and
Functional for Study of Dispersion Interactions in Nanoscale
Aromatic Hydrocarbons, J. Chem. Theory Comput, 4, 20302048 (2008).
Franco Cozzi, Rita Annunziata, Maurizio Benaglia, Kim
K. Baldridge, Gerardo Aguirre, Jesus Estrada, Yongsak Sritana-Anant and Jay S. Siegel, Through-space interactions between parallel-offset arenes at the van der Waals distance:
1,8-diarylbiphenylene syntheses, structure and QM computations, Phys. Chem. Chem. Phys, 10, 2686-2694 (2008).
1
Tirath Ramdas, Gerald Egan, David Abramson and Kim K.
Baldridge, Towards a special purpose computer for HartreeFock computations, Theor. Chem. Acc, 120, 133-135 (2008).
Kim K. Baldridge and Jay S. Siegel, Quantum chemical
prediction of the 13C NMR shifts in alkyl and chlorocorannulenes: correction of chlorine effects, Theor. Chem.
Acc, 120, 95-106 (2008).
L. Gregerson, Outlying charge, stability, efficiency, and
extensibility in quantum mechanical solvation methods: The
COSAB-GAMESS method. (D)
BERTRAM, TIMOTHY (b.1978) Assistant Professor. B.A, 2000, Colby College; Ph.D, 2006, UC Berkeley. NOAA C&GC; Postdoctoral Fellow, 2007-2009,
University of Washington. Atmospheric Chemistry; Environmental Chemistry. My research interests, in the field
of atmospheric chemistry, utilize both laboratory and
field-based approaches to provide constraints on chemical processes occurring in the atmosphere. Specifically,
my research focuses on providing measures of speciated
reactive nitrogen from various platforms (ground, aircraft and satellite). These observations are used to directly constrain both chemical mechanisms and transport
processes in the atmosphere. TEL: (510) 388-7600 FAX:
(858) 534-1697
Web: bertramgroup.ucsd.edu
Email: thbertram@ucsd.edu
E. C. Wood, T. H. Bertram, P. J. Wooldridge and R. C.
Cohen, Measurements of N2O5, NO2 and O3 East of the San
Francisco Bay, Atmos. Chem Phys, 5, 483-491 (2005).
T. H. Bertram, A. Heckel, A. Richter, J. Burrows and R. C.
Cohen, Satellite measurements of daily variations in soil
NOx emissions, Geophys. Res. Lett, (2005).
T. H. Bertram, P. M. Chu and R. C. Cohen, Comparison of
NIST ozone, nitric oxide and nitrogen dioxide standards, J.
Air and Waste Management Assoc, 55, 1473-1479 (2005).
C. S. Boxe, A. J. Colussi, M. R. Hoffman, J. G. Murphy, P.
J. Wooldridge, T. H. Bertram and R. C. Cohen, Photochemical production and release of gaseous NO2 from nitrate
doped water ice, J. Phys. Chem. B, (2005).
R. V. Martin, C. E. Sirois, K Chance, T. B. Ryerson, T. H.
Bertram, P. J. Wooldridge, R. C. Cohen, A. A. Neuman, A.
Swanson and F. M. Flocke, Evaluation of space based constraints on nitrogen oxide emissions with regional aircraft
measurements over and downwind of eastern North America,
J. Geophys. Res, (2006).
O. R. Cooper, A. Stohl, M. Trainer, A. Thompson, J. C.
Witte, S. J. Oltmans, B. J. Johnson, J. Merrill, J. L. Moody,
G. Morris, D. Tarasick, G. Forbes, P. Nedelec, F. C. Fehsenfeld, J. Meagher, M. J. Newchurch, F. J. Schmidlin, S. Turquety, J. H. Crawford, G. Chen, K. E. Pickering, S. L.
Baughcum, R. C. Cohen, T. H. Bertram, P. Wooldridge, A.
Perring, W. H. Brune, N. Spichtinger and C. C. Brown,
Large upper tropospheric enhancements above mid-latitude
North America during summer: In situ evidence from the
IONS and MOZAIC ozone monitoring networks, J. Geophys.
Res, (2006).
S. Kim, L. G. Huey, R. E. Stickel, D. J. Tanner, J. H.
Crawford, J. R. Olson, G. Chen, W. H. Brune, X. Ren, R.
Lesher, P. J. Wooldridge, T. H. Bertram, A. Perring, R. C.
Cohen, B., B. Lefer, R. E. Shetter, M. Avery, G. Diskin and
I. Sokolik, Measurement of HO2NO2 in the upper troposphere during ICARRT-INTEX-NA, J. Geophys. Res,
(2007).
R. C. Hudman, D. J. Jacob, S. Turquety, E. M. Leibensperger, L. T. Murray, S. Wu, A. B. Gilliland, M. A. Avery, G.
W. Sachse, T. H. Bertram, R. C. Cohen, P. J. Wooldridge, A.
E. Perring, W. H. Brune, X. R. Ren, J. E. Dibb, F. M. Flocke,
A. Fried, J. S. Holloway, A. Newman, T. B. Ryerson, R. Orville and H. B. Singh, Surface and lightning sources of nitrogen oxides in the United States: Magnitudes, chemical evolution and outflow, J. Geophys. Res, (2007).
H. B. Singh, L. Salas, D. Herlth, E. Czech, M. Avery, J. H.
Crawford, R. B. Pierce, G. W. Sachse, D. R. Blake, R. C. Cohen, T. H. Bertram, A. Perring, P. J. Wooldridge, J. Dibb, G.
Huey, R. C. Hudman, S. Turquety, L. K. Emmons, F. Flocke,
Y. Tang, G. R. Carmichael and L. W. Horowitz, Reactive nitrogen distribution and partitioning in the north american troposphere and lowermost stratosphere, J. Geophys. Res,
(2007).
A. Fried, J. Walega, J. Olson, J. Crawford, G. Chen, P.
Weibring, D. Richter, C. Roller, F. Tittel, M. Porter, H. Fuelberg, J. Halland, T. H. Bertram, R. Cohen, K. Pickering, B.
Heikes, J. Snow, H. Shen, D. O’Sullivan, W. Brune, X. Ren,
D. Blake, N. Blake, G. Sachse, G. Diskin, J. Podolski, S.
Vay, R. Shetter, B. Anderson, L. Thornhill, A. Clarke, C.
McNaughton, H. Singh, M. Avery, G. Huey, D. Millet and D.
Jacob, The role of convection in redistributing formaldehyde
to the upper troposphere over North America and the North
Atlantic during the Summer 2004 INTEX Campaign, J. Geophys. Res, (2007).
T. H. Bertram, A. E. Perring, P. J. Wooldridge, J. D.
Crounse, A. J. Kwan, P. O. Wennberg, E. Scheuer, J. Dibb,
M. Avery, G. Sachse, S. A. Vay, J. H. Crawford, C. S.
McNaughton, A. Clarke, K. E. Pickering, H. Fuelberg, G.
Huey, D. R. Blake, H. B. Singh, S. R. Hall, R. E. Shetter, A.
Fried, B. G. Heikes and R. C. Cohen, Direct measurement of
the convective recycling of the upper troposphere, Science,
(2007).
2
CALIFORNIA, SAN DIEGO
K. F. Boersma, D. J. Jacob, E. J. Buscela, A. E. Perring, R.
Dirsken, R. J. can der, A. R. M. Yantosca, R. J. Park, M. O.
Wenig, T. H. Bertram and R. C. Cohen, Validation of OMI
Tropospheric NO2 observations during INTEX-B and application to constrain NOx emissions over the Eastern United
States and Mexico, Atmos. Environment, (2008).
O. R. Cooper, S. Eckhardt, J. H. Crawford, C. C. Brown,
R. C. Cohen, T. H. Bertram, P. Wooldridge, A. Perring, W.
H. Brune, X. Ren, D. Brunner and S. Baughcum, The summertime buildup and decay of lightning NOx and aged thunderstorm outflow above North America, J. Geophys. Res,
(2008).
BOND, F. THOMAS
No publication information submitted for this edition.
BRYDGES, STACEY (b.1972) Lecturer, Potential Security of Employment (LPSOE). B.Sc, 1996, McMaster
University; Ph.D, 2003, McMaster University. Chemistry
Education. TEL: (858) 246-0993 FAX: (858) 534-7042
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C22509
Email: sbrydges@ucsd.edu
No publication information submitted for this edition.
BURKART, MICHAEL D. (b.1972) Associate Professor. B.A, 1994, Rice University; Ph.D, 1999, The
Scripps Research Institute. NIH Postdoctoral Fellow,
1999-2002, Harvard Medical School. Bioorganic Chemistry. Bioorganic chemistry; natural product biosynthesis;
natural product synthesis; molecular diagnostics. TEL:
(858) 534-5673 FAX: (858) 822-2182
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C04373
Email: mburkart@ucsd.edu
K. M. Clarke, A. C. Mercer, J. J. La Clair and M. D. Burkart, In vivo reporter labeling of proteins via metabolic delivery of Coenzyme A Analogues, J. Am. Chem. Soc, 127,
11234-11235 (2005).
M. D. Alexander, S. D. Fontaine, J. J. La Clair, A. G. DiPasquale, A. L. Rheingold and M. D. Burkart, Synthesis of
the mycolactone core by ring-closing metathesis, Chem.
Comm, 44, 4602-4604 (2006).
Andrew S. Worthington and Michael D. Burkart, The old
is new again: Asparagine oxidation in calcium-dependent antibiotic biosynthesis, ACS Chem. Biol, 2, 152-154 (2007).
Alexander L. Mandel, Brian D. Jones, James J. La Clair
and Michael D. Burkart, A synthetic entry to pladienolide B
and FD-895, Bioorg. Med. Chem. Lett, 17, 5159-5164
(2007).
Timothy L. Foley and Michael D. Burkart, Site-specific
protein modification: Advances and applications, Curr. Opin.
Chem. Biol, 11, 12-19 (2007).
Andrew C. Mercer and Michael D. Burkart, The ubiquitous
carrier protein-a window to metabolite biosynthesis, Nat.
Prod. Rep, 24, 750-773 (2007).
Peyman Najmabadi, James J. La Clair and Michael D. Burkart, A systems perspective to digital structures in molecular
analysis, Org. Biomol. Chem, 5, 214-222 (2007).
A. C. Mercer, J. L. Meier, G. H. Hur, A. R. Smith and M.
D. Burkart, Antibiotic evaluation and in vivo analysis of alkynyl Coenzyme A antimetabolites in Escherichia coli, Bioorg
Med Chem Lett, 18, 5991-5994 (2008).
Shiven Kapur, Andrew Worthington, Yinyan Tang, David
E. Cane, Michael D. Burkart and Chaitan Khosla, Mechanism based protein crosslinking of domains from the 6-deoxyerythronolide B synthase, Bioorg. Med. Chem. Lett, 18,
3034-3038 (2008).
Robert W. Haushalter, Andrew S. Worthington, Gene H.
Hur and Michael D. Burkart, An orthogonal purification
strategy for isolating crosslinked domains of modular synthases, Bioorg. Med. Chem. Lett, 18, 3039-3042 (2008).
A. S. Worthington, G. H. Hur, J. L. Meier, Q. Cheng, B. S.
Moore and M. D. Burkart, Probing the compatibility of type
II ketosynthase-carrier protein partners, Chembiochem, 9,
2096-2103 (2008).
Jordan L. Meier, Andrew C. Mercer and Michael D. Burkart, Fluorescent Profiling of Modular Biosynthetic Enzymes
by Complementary Metabolic and Activity Based Probes, J.
Am. Chem. Soc, 130, 5443-5445 (2008).
J. L. Meier, T. Barrows-Yano, T. L. Foley, C. L. Wike and
M. D. Burkart, The unusual macrocycle forming thioesterase
of mycolactone, Mol Biosyst, 4, 663-671 (2008).
Alexander Mandel, Synthetic studies applied to polyketide
natural products. (D)
Andrew Mercer, Co-opting CoA biosynthesis for the in
vivo modification of carrier proteins. (D)
Andrew Worthington, Chemoenzymatic investigations of
protein-protein interactions in carrier protein-mediated biosynthesis. (D)
Jordan Meier, Synthetic active site probes for PKS and
NRPS biosynthetic enzymes. (D)
CASERIO, MARJORIE C. (b.1929) Professor Emeritus. B.Sc, 1950, Chelsea College, University of London;
M.A, 1951, Bryn Mawr College, Pennsylvania; Ph.D,
1956, Bryn Mawr College, Pennsylvania. Postdoctoral
Fellowship, 1956, California Institute of Technology; Se-
nior Research Fellow, 1958, California Institute of Technology. Ion-molecule reactions in the gas phase; organosulfur chemistry; reaction mechanisms. TEL: (619) 5343130 FAX: (619) 534-5211
Email: mcaserio@ucsd.edu
No publication information submitted for this edition.
CLARK, LEIGH B. (b.1934) Professor Emeritus. B.S,
1957, University of California, Berkeley; Ph.D, 1963,
University of Washington. Research Fellowship, 1963,
University of California, Berkeley. Electronic states of
molecules; exciton states of crystals; reflection spectroscopy; optical properties of polynucleotides; optical properties of liquids. TEL: (619) 534-2156
Email: lclark@ucsd.edu
No publication information submitted for this edition.
COHEN, SETH M. (b.1972) Associate Professor. B.S,
1994, Stanford University; B.A, 1994, Stanford University; Ph.D, 1998, University of California, Berkeley. NIH
Postdoctoral Fellow, 1999-2001, M. I. T. Bioinorganic
Chemistry; Inorganic Chemistry. Metalloenzyme inhibitor design, metal-organic frameworks. TEL: (858) 8225596 FAX: (858) 822-5598
Web: www.checohen0.ucsd.edu/
Email: scohen@ucsd.edu
Publication list has not been verified by the department.
Sergio J. Garibay, Jay R. Stork, Zhenqiang Wang, Seth M.
Cohen and Shane G. Telfer, Enantiopure vs. racemic metalloligands: impact on metal-organic framework structure and
synthesis, Chem. Commun. (Cambridge, U. K.), 4881-4883
(2007).
Faith E. Jacobsen, Jana A. Lewis and Seth M. Cohen, The
design of inhibitors for medicinally relevant metalloproteins,
ChemMedChem, 2, 152-171 (2007).
Seth M. Cohen, New approaches for medicinal applications of bioinorganic chemistry, Curr. Opin. Chem. Biol, 11,
115-120 (2007).
Sara R. Halper, Jay R. Stork and Seth M. Cohen, Preparation and characterization of asymmetric ␣-alkoxy dipyrrin ligands and their metal complexes, Dalton Trans, 1067-1074
(2007).
Jay R. Stork, Van S. Thoi and Seth M. Cohen, Rare Examples of Transition-Metal-Main-Group Metal Heterometallic
Metal-Organic Frameworks from Gallium and Indium Dipyrrinato Complexes and Silver Salts: Synthesis and Framework
Variability, Inorg. Chem. (Washington, DC, U. S.), 46,
11213-11223 (2007).
Faith E. Jacobsen, Jana A. Lewis, Katie J. Heroux and Seth
M. Cohen, Characterization and evaluation of pyrone and
tropolone chelators for use in metalloprotein inhibitors,
Inorg. Chim. Acta, 360, 264-272 (2007).
Zhenqiang Wang and Seth M. Cohen, Postsynthetic Covalent Modification of a Neutral Metal-Organic Framework, J.
Am. Chem. Soc, 129, 12368-12369 (2007).
Stephane Petoud, Gilles Muller, Evan G. Moore, Jide Xu,
Jurek Sokolnicki, James P. Riehl, Uyen N. Le, Seth M. Cohen and Kenneth N. Raymond, Brilliant Sm, Eu, Tb, and Dy
Chiral Lanthanide Complexes with Strong Circularly Polarized Luminescence, J. Am. Chem. Soc, 129, 77-83 (2007).
Misha Golynskiy, Sheng Li, Virgil L. Woods, Jr. and Seth
M. Cohen, Conformational studies of the manganese transport regulator (MntR) from Bacillus subtilis using deuterium
exchange mass spectrometry, JBIC, J. Biol. Inorg. Chem, 12,
699-709 (2007).
Yi-Long Yan and Seth M. Cohen, Efficient Synthesis of 5Amido-3-hydroxy-4-pyrones as Inhibitors of Matrix Metalloproteinases, Org. Lett, 9, 2517-2520 (2007).
Zhenqiang Wang and Seth M. Cohen, Tandem modification of metal-organic frameworks by a postsynthetic approach, Angew. Chem., Int. Ed, 47, 4699-4702 (2008).
Emily Dugan, Zhenqiang Wang, Marilyn Okamura, Annette Medina and Seth M. Cohen, Covalent modification of a
metal-organic framework with isocyanates: probing substrate
scope and reactivity, Chem. Commun. (Cambridge, U. K.),
3366-3368 (2008).
Arpita Agrawal, Diego Romero-Perez, Jennifer A. Jacobsen, Francisco J. Villarreal and Seth M. Cohen, Zinc-binding
groups modulate selective inhibition of MMPs, ChemMedChem, 3, 812-820 (2008).
Van S. Thoi, Jay R. Stork, Edwards T. Niles, Ezra C. Depperman, David L. Tierney and Seth M. Cohen, Diamidodipyrrins: Versatile Bipyrrolic Ligands with Multiple Metal
Binding Modes, Inorg. Chem. (Washington, DC, U. S.), 47,
10533-10541 (2008).
Kristine K. Tanabe, Zhenqiang Wang and Seth M. Cohen,
Systematic Functionalization of a Metal-Organic Framework
via a Postsynthetic Modification Approach, J. Am. Chem.
Soc, 130, 8508-8517 (2008).
CONTINETTI, ROBERT E. (b.1962) Professor.
B.A, 1983, John Hopkins University; Ph.D, 1989, University of California, Berkeley. Postdoctoral Fellowship,
1989-1992, University of California, Berkeley. Chemical
Physics; Physical Chemistry. Energetics and dissociation
dynamics of reactive intermediates; photodissociation
and photodetachment dynamics; photoelectron-photofragment coincidence spectroscopy; three-body reaction
dynamics. Charge exchange and dissociative recombination dynamics of molecular and cluster cations. TEL:
(858) 534-5559 FAX: (858) 534-9856
Web: checont6.ucsd.edu
Email: rcontinetti@ucsd.edu
Zhou Lu, Qichi Hu, Jonathan E. Oakman and Robert E.
Continetti, Dynamics on the HOCO potential energy surface
studied by dissociative photodetachment of HOCO- and
DOCO-, J. Chem. Phys, 126, 194305/1-194305/11 (2007).
Silvia De Dea, Dominic Graziani, David R. Miller and
Robert E. Continetti, Growth of magnetic thin films using
CO2 RESS expansions, J. Supercrit. Fluids, 42, 410-418
(2007).
Zhou Lu and Robert E. Continetti, Alignment of a Molecular Anion via a Shape Resonance in Near-Threshold Photodetachment, Phys. Rev. Lett, 99, 113005/1-113005/4 (2007).
Jennifer E. Mann, Zhen Xie, John D. Savee, Bastiaan J.
Braams, Joel M. Bowman and Robert E. Continetti, Probing
the Structure of CH5+ by Dissociative Charge Exchange, J.
Am. Chem. Soc, 130, 3730-3731 (2008).
Vadim A. Mozhayskiy, John D. Savee, Jennifer E. Mann,
Robert E. Continetti and Anna I. Krylov, Conical for Stepwise, Glancing for Concerted: The Role of the Excited-State
Topology in the Three-Body Dissociation of sym-Triazine, J.
Phys. Chem. A, 112, 12345-12354 (2008).
Silvia De Dea, David R. Miller and Robert E. Continetti,
Growth of Nanoscale Magnetic Films Using a Supercritical
CO2/Ferric Acetylacetonate Batch Process Near Room Temperature, J. Phys. Chem. C, 112, 17102-17108 (2008).
Zhou Lu, Jonathan E. Oakman, Qichi Hu and Robert E.
Continetti, Photoelectron-photofragment angular correlations
in the dissociative photodetachment of HOCO-, Mol. Phys,
106, 595-606 (2008).
John D. Savee, Vadim A. Mozhayskiy, Jennifer E. Mann,
Anna I. Krylov and Robert E. Continetti, The Role of Excited-State Topology in Three-Body Dissociation of sym-Triazine, Science (Washington, DC, U. S.), 321, 826-830 (2008).
J. E. Mann, Probing the potential energy surface of elementary neutral reactions using dissociative charge exchange. (D)
S. De Dea, Nano-scale magnetic film formation by decompression of supercritical CO2/ferric acetylacetonate solutions.
(D)
Z. Lu, Dynamics of gas phase transient species studied by
dissociative photodetachment of molecular anions. (D)
CROWELL, JOHN E. (b.1956) Professor. B.S, 1979,
University of Illinois, Urbana; Ph.D, 1984, University of
California, Berkeley. Postdoctoral Research Associate,
1984-1986, University of Pittsburgh. Bioanalytical
Chemistry; Physical Chemistry. Spectroscopic studies of
surface chemistry at well-defined interfaces and surfaces;
kinetic and mechanistic studies of elementary surface
processes, thin film growth by atomic layer deposition,
chemical vapor deposition, and photo-induced surface
chemistry; development of in-situ spectroscopic probes
of surface reactions; surface infrared spectroscopy; desorption / ionization mass spectrometry; nanofunctionalization and patterning for bioanalysis; microfluidics, proteomics and microanalysis. TEL: (858) 534-5441 FAX:
(858) 534-7244
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C00906
Email: jcrowell@ucsd.edu
No publication information submitted for this edition.
CZWORKOWSKI, JOHN (b.1963) Lecturer PSOE.
B.A, 1985, University of Pennsylvania; Ph.D, 1991, University of Texas at Austin. Postdoctoral Associate, 19911996, Yale University; Associate Research Scientist,
1996-1998, Yale University. Chemistry Education. TEL:
(858) 822-6665 FAX: (858) 534-7687
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C20691
Email: jczworkowski@ucsd.edu
No publication information submitted for this edition.
DENNIS, EDWARD A. (b.1941) Professor. B.A,
1963, Yale University; M.A, 1965, Harvard University;
Ph.D, 1968, Harvard University; Ph.D.(Hon.), 2008,
Goethe University of Frankfurt Germany. Research Fellowship, 1967-1969, Harvard Medical School. Biochemistry; Pharmacology. Phospholipases-catalytic mechanism, regulation function and mutagenesis; prostaglandin
control in macrophage cell cultures; phospholipid metabolism and enzyme mechanism; NMR of phospholipids;
membrane and micelle structure and function; signal
transduction; LIPID MAPS; mass spec of lipids and proteins. TEL: (858) 534-3055 FAX: (858) 534-7390
Web: www.cobra.uscd.edu
Email: edennis@ucsd.edu
Matthew W. Buczynski, Daren L. Stephens, Rebecca C.
Bowers-Gentry, Andrej Grkovich, Raymond A. Deems and
Edward A. Dennis, TLR-4 and Sustained Calcium Agonists
Synergistically Produce Eicosanoids Independent of Protein
CALIFORNIA, SAN DIEGO
Synthesis in RAW264.7 Cells, J. Biol. Chem, 282, 2283422847 (2007).
Richard Harkewicz, Eoin Fahy, Alexander Andreyev and
Edward A. Dennis, Arachidonate-derived Dihomoprostaglandin Production Observed in Endotoxin-stimulated Macrophage-like Cells, J. Biol. Chem, 282, 2899-2910 (2007).
Richard Harkewicz, Eoin Fahy, Alexander Andreyev and
Edward A. Dennis, Arachidonate-derived dihomoprostaglandin production observed in endotoxin-stimulated macrophage-like cells. [Erratum to document cited in CA146:
314968], J. Biol. Chem, 282, 29068 (2007).
David A. Six, Efrosini Barbayianni, Vassilios Loukas,
Violetta Constantinou-Kokotou, Dimitra Hadjipavlou-Litina,
Daren Stephens, Alan C. Wong, Victoria Magrioti, Panagiota
Moutevelis-Minakakis, Sharon F. Baker, Edward A. Dennis
and George Kokotos, Structure-Activity Relationship of 2Oxoamide Inhibition of Group IVA Cytosolic Phospholipase
A2 and Group V Secreted Phospholipase A2, J. Med. Chem,
50, 4222-4235 (2007).
Panagiota Moutevelis-Minakakis, Afroditi Neokosmidi,
Maria Filippakou, Daren Stephens, Edward A. Dennis and
George Kokotos, Synthesis of lipophilic 2-oxoamides based
on ␥-aminobutyric and ␦-aminovaleric analogues and their
activity against phospholipase A2, J. Pept. Sci, 13, 634-641
(2007).
Kara Schmelzer, Eoin Fahy, Shankar Subramaniam and
Edward A. Dennis, The lipid maps initiative in lipidomics,
Methods Enzymol, 432, 171-183 (2007).
Raymond Deems, Matthew W. Buczynski, Rebecca Bowers-Gentry, Richard Harkewicz and Edward A. Dennis, Detection and quantitation of eicosanoids via high performance
liquid chromatography-electrospray ionization-mass spectrometry, Methods Enzymol, 432, 59-82 (2007).
Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward A. Dennis, Christopher K. Glass, Alfred H. Merrill, Jr.,
Robert C. Murphy, Christian R. H. Raetz, David W. Russell
and Shankar Subramaniam, LMSD: LIPID MAPS structure
database, Nucleic Acids Res, 35, D527-D532 (2007).
John E. Burke, Mark J. Karbarz, Raymond A. Deems,
Sheng Li, Virgil L. Woods, Jr. and Edward A. Dennis, Interaction of Group IA Phospholipase A2 with Metal Ions and
Phospholipid Vesicles Probed with Deuterium Exchange
Mass Spectrometry, Biochemistry, 47, 6451-6459 (2008).
Georgia Antonopoulou, Efrosini Barbayianni, Victoria
Magrioti, Naomi Cotton, Daren L. Stephens, Violetta Constantinou-Kokotou, Edward A. Dennis and George Kokotos,
Structure-activity relationships of natural and non-natural
amino acid-based Amide and 2-oxoamide inhibitors of human Phospholipase A2 enzymes, Bioorg.Med.Chem, 16,
10257-10269 (2008).
Ruben Lopez-Vales, Xavier Navarro, Takao Shimizu, Constantinos Baskakis, George Kokotos, Violetta ConstantinouKokotou, Daren L. Stephens, Edward A. Dennis and Sameul
David, Intracellular Phospholipase A2 group IVA and group
VIA play important roles in wallerian degeneration and axon
regeneration after peripheral nerve injury, Brain, 131, 26202631 (2008).
Faith E. Jacobsen, Mathew W. Buczynski, Edward A. Dennis and Seth M. Cohen, A macrophage cell model for selective metalloprotein inhibitor design, Chem.Bio.Chem, 9,
2087-2095 (2008).
Georgia Antonopoulou, Victoria Magrioti, Daren L. Stephens, Violetta Constantinou-Kokotou, Edward A. Dennis and
George Kokotos, Synthesis of 2-oxoamides based on sulfonamide analogues of gamma-amino acids and their activity on
Phospholipase A2, J Pept Sci, 10, 1111-1120 (2008).
John E. Burke, Yuan-Hao Hsu, Raymond A. Deems,
Sheng Li, Virgil L. Woods Jr. and Edward A. Dennis, A
phospholipid substrate molecule residing in the membrane
surface mediates opening of the lid region in group IVA cytosolic Phospholipase A2, J. Biol Chem, 283, 31227-31236
(2008).
Yuan-Hao Hsu, John E. Burke, Daren L. Stephens, Raymond A. Deems, Sheng Li, Kyle M. Asmus, Virgil L. Woods
Jr. and Edward A. Dennis, Calcium binding rigidifies the C2
domain of GIVA Phospholipase A2 as revealed by hydrogen/
deuterium exchange mass spectrometry, J. Biol Chem, 283,
9820-9827 (2008).
Richard Harkewicz, Karsten Hartvigsen, Felicidad Almazan, Edward A. Dennis, Joseph L. Witztum and Yury I. Miller, Cholesteryl Ester Hydroperoxides Are Biologically Active Components of Minimally Oxidized Low Density Lipoprotein, J. Biol. Chem, 283, 10241-10251 (2008).
John E. Burke, Yuan-Hao Hsu, Raymond A. Deems,
Sheng Li, Virgil L. Woods, Jr. and Edward A. Dennis, A
Phospholipid Substrate Molecule Residing in the Membrane
Surface Mediates Opening of the Lid Region in Group IVA
Cytosolic Phospholipase A2, J. Biol. Chem, 283, 3122731236 (2008).
Yuan-Hao Hsu, John E. Burke, Daren L. Stephens, Raymond A. Deems, Sheng Li, Kyle M. Asmus, Virgil L.
Woods, Jr. and Edward A. Dennis, Calcium Binding Rigidifies the C2 Domain and the Intradomain Interaction of GIVA
Phospholipase A2 as Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry, J. Biol. Chem, 283, 9820-9827
(2008).
Constantinos Baskakis, Victoria Magrioti, Naomi Cotton,
Daren L. Stephens, Violetta Constantinou-Kokotou, Edward
A. Dennis and George Kokotos, Synthesis of Polyfluoro Ketones for selective inhibition of human Phospholipase A2 enzymes, J. Med. Chem, 51, 8027-8037 (2008).
Oswald Quehenberger, Aaron Armando, Darren Dumlao,
Daren Stephens and Edward A. Dennis, Lipidomics analysis
of essential fatty acids in macrophages, Prostaglandins Leukotrienses and Essential Fatty Acids, 79, 123-129 (2008).
Andrej Grkovich, The function, activation and inhibition of
phosphatidic acid phosphohydrolase-1 and group IVA phospholipase A2 in toll-like receptor activated macrophages. (D)
John E. Burke, Deuterium exchange mass spectrometry
studies of the phospholipase A2 superfamily. (D)
Matthew W. Buczynski, Lipidomic analysis of eicosanoid
synamics in inflammation and disease. (D)
DIXON, JACK E. (b.1943) Professor. B.A, 1966, University of California, Los Angeles; Ph.D, 1971, University of California, Santa Barbara. TEL: (858) 822-3522
FAX: (858) 822-0084
Email: jedixon@ucsd.edu
Publication list has not been verified by the department.
Seema Mattoo, Yvonne M. Lee and Jack E. Dixon, Interactions of bacterial effector proteins with host proteins, Curr.
Opin. Immunol, 19, 392-401 (2007).
Alan Cheng, Mei Zhang, Matthew S. Gentry, Carolyn A.
Worby, Jack E. Dixon and Alan R. Saltiel, A role for AGL
ubiquitination in the glycogen storage disorders of Lafora
and Cori’s disease, Genes Dev, 21, 2399-2409 (2007).
Sandra E. Wiley, Mark L. Paddock, Edward C. Abresch,
Larry Gross, Peter van der Geer, Rachel Nechushtai, Anne N.
Murphy, Patricia A. Jennings and Jack E. Dixon, The outer
mitochondrial membrane protein mitoNEET contains a novel
redox-active 2Fe-2S cluster, J. Biol. Chem, 282, 2374523749 (2007).
Neal M. Alto, Andrew W. Weflen, Matthew J. Rardin,
Defne Yarar, Cheri S. Lazar, Raffi Tonikian, Antonius Koller, Susan S. Taylor, Charles Boone, Sachdev S. Sidhu, Sandra L. Schmid, Gail A. Hecht and Jack E. Dixon, The type III
effector EspF coordinates membrane trafficking by the spatiotemporal activation of two eukaryotic signaling pathways,
J. Cell Biol, 178, 1265-1278 (2007).
Matthew S. Gentry, Robert H. Dowen, III, Carolyn A.
Worby, Seema Mattoo, Joseph R. Ecker and Jack E. Dixon,
The phosphatase laforin crosses evolutionary boundaries and
links carbohydrate metabolism to neuronal disease, J. Cell
Biol, 178, 477-488 (2007).
Lorena Navarro, Antonius Koller, Roland Nordfelth, Hans
Wolf-Watz, Susan Taylor and Jack E. Dixon, Identification
of a molecular target for the Yersinia protein kinase A, Mol.
Cell, 26, 465-477 (2007).
Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron
L. Halpern, Shannon J. Williamson, Karin Remington, Jonathan A. Eisen, Karla B. Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S.
Miller, Huiying Li, Susan T. Mashiyama, Marcin P. Joachimiak, Christopher van Belle, John-Marc Chandonia, David A.
Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benjamin J. Raphael, Vineet Bafna, Robert Friedman, Steven E.
Brenner, Adam Godzik, David Eisenberg, Jack E. Dixon, Susan S. Taylor, Robert L. Strausberg, Marvin Frazier and J.
Craig Venter, The Sorcerer II global ocean sampling expedition: expanding the universe of protein families, PLoS Biol,
5, 432-466 (2007).
Mark L. Paddock, Sandra E. Wiley, Herbert L. Axelrod,
Aina E. Cohen, Melinda Roy, Edward C. Abresch, Dominique Capraro, Anne N. Murphy, Rachel Nechushtai, Jack E.
Dixon and Patricia A. Jennings, MitoNEET is a uniquely
folded 2Fe-2S outer mitochondrial membrane protein stabilized by pioglitazone, Proc. Natl. Acad. Sci. U. S. A, 104,
14342-14347 (2007).
Sandra E. Wiley, Anne N. Murphy, Stuart A. Ross, Peter
van der Geer and Jack E. Dixon, MitoNEET is an iron-containing outer mitochondrial membrane protein that regulates
oxidative capacity, Proc. Natl. Acad. Sci. U. S. A, 104, 53185323 (2007).
Youngjun Kim, Matthew S. Gentry, Thurl E. Harris, Sandra E. Wiley, John C. Lawrence, Jr. and Jack E. Dixon, A
conserved phosphatase cascade that regulates nuclear membrane biogenesis, Proc. Natl. Acad. Sci. U. S. A, 104, 65966601 (2007).
Seema Mattoo, Neal M. Alto and Jack E. Dixon, Subversion of myosin function by E. coli, Dev. Cell, 14, 8-10
(2008).
Stephen J. Juris, Kavita Shah, Kevan Shokat, Jack E. Dixon and Panayiotis O. Vacratsis, Identification of otubain 1 as
a novel substrate for the Yersinia protein kinase using chemical genetics and mass spectrometry. [Erratum to document
cited in CA144:145397], FEBS Lett, 582, 3159 (2008).
Matthew J. Rardin, Sandra E. Wiley, Anne N. Murphy,
David J. Pagliarini and Jack E. Dixon, Dual Specificity Phosphatases 18 and 21 Target to Opposing Sides of the Mitochondrial Inner Membrane, J. Biol. Chem, 283, 15440-15450
(2008).
Carolyn A. Worby, Matthew S. Gentry and Jack E. Dixon,
Malin Decreases Glycogen Accumulation by Promoting the
Degradation of Protein Targeting to Glycogen (PTG), J. Biol.
Chem, 283, 4069-4076 (2008).
Neal M. Alto and Jack E. Dixon, Analysis of Rho-GTPase
mimicry by a family of bacterial type III effector proteins,
Methods Enzymol, 439, 131-143 (2008).
Fred L. Robinson, Ingrid R. Niesman, Kristina K. Beiswenger and Jack E. Dixon, Loss of the inactive myotubula-
3
rin-related phosphatase Mtmr13 leads to a Charcot-MarieTooth 4B2-like peripheral neuropathy in mice, Proc. Natl.
Acad. Sci. U. S. A, 105, 4916-4921 (2008).
Shaun W. Lee, Douglas A. Mitchell, Andrew L. Markley,
Mary E. Hensler, David Gonzalez, Aaron Wohlrab, Pieter C.
Dorrestein, Victor Nizet and Jack E. Dixon, Discovery of a
widely distributed toxin biosynthetic gene cluster, Proc. Natl.
Acad. Sci. U. S. A, 105, 5879-5884 (2008).
Hirohide Iwasaki, Yoshimichi Murata, Youngjun Kim, Israil Hossain, Carolyn A. Worby, Jack E. Dixon, Thomas
McCormack, Takehiko Sasaki and Yasushi Okamura, A voltage-sensing phosphatase, Ci-VSP, which shares sequence
identity with PTEN, dephosphorylates phosphatidylinositol
4,5-bisphosphate, Proc. Natl. Acad. Sci. U. S. A, 105, 79707975 (2008).
DONOGHUE, DANIEL J. (b.1952) Professor. B.Sc,
1974, University of Wisconsin; Ph.D, 1979, M.I.T. Postdoctoral Fellowship, 1980-1982, Salk Institute. Molecular Biology. FGFR2 signaling and FGFR3 activation of
MCF-7 in breast cancer. Nordihydroguaiaretic acid
(NDGA) and FGFR3 in multiple myeloma cells FGFR4
signaling and NF-kappaB regulation in prostate cancer.
Androgen-Independence (AI) cell proliferation, and acquisition of invasiveness and metastatic properties in
prostate cancer cells. Spy1 interaction with p27 and
CDK2 in cell cycle progression, DNA damage, apoptosis, and checkpoint activation. TEL: (858) 534-2463
FAX: (858) 534-7481
Web: cancer.ucsd.edu/summaries/ddonoghue.asp
Email: ddonoghue@ucsd.edu
Randy F. Gastwirt, Christopher W. McAndrew and Daniel
J. Donoghue, Speedy/RINGO regulation of CDKs in cell cycle, checkpoint activation and apoptosis, Cell Cycle, 6, 11881193 (2007).
Christopher W. McAndrew, Randy F. Gastwirt, April N.
Meyer, Lisa A. Porter and Daniel J. Donoghue, Spy1 enhances phosphorylation and degradation of the cell cycle inhibitor p27, Cell Cycle, 6, 1937-1945 (2007).
Azadeh Golipour, Dorothy Myers, Tiffany Seagroves,
Daniel Murphy, Gerard I. Evan, Daniel J. Donoghue, Roger
A. Moorehead and Lisa A. Porter, The Spy1/RINGO Family
Represents a Novel Mechanism Regulating Mammary
Growth and Tumorigenesis, Cancer Res, 68, 3591-3600
(2008).
April N. Meyer, Christopher W. McAndrew and Daniel J.
Donoghue, Nordihydroguaiaretic Acid Inhibits an Activated
Fibroblast Growth Factor Receptor 3 Mutant and Blocks
Downstream Signaling in Multiple Myeloma Cells, Cancer
Res, 68, 7362-7370 (2008).
Randy Francis Gastwirt, Spy1 regulation of the cell cycle,
checkpoint activation and apoptosis. (D)
DOOLITTLE, RUSSELL F. (b.1931) Research Professor. B.A, 1952, Wesleyan University; M.A, 1957,
Trinity College; Ph.D, 1961, Harvard University. Postdoctoral Fellowship, 1962-1964, Karolinska Institute.
Structure and function of fibrinogen; fibrin formation.
Evolution of proteins; peptide synthesis; x-ray crystallography. TEL: (858) 534-4417
Email: rdoolittle@ucsd.edu
Publication list has not been verified by the department.
Russell F. Doolittle and Leela Pandi, Probing the ␤-Chain
Hole of Fibrinogen with Synthetic Peptides That Differ at
Their Amino Termini, Biochemistry, 46, 10033-10038
(2007).
Russell F. Doolittle, Searching for differences between fibrinogen and fibrin that affect the initiation of fibrinolysis,
Cardiovasc. Hematol. Agents Med. Chem, 6, 181-189 (2008).
Russell F. Doolittle, Yong Jiang and Justin Nand, Genomic
Evidence for a Simpler Clotting Scheme in Jawless Vertebrates, J. Mol. Evol, 66, 185-196 (2008).
DORRESTEIN, PIETER C. B.S, 1998, Northern
Arizona University; Ph.D, 2004, Cornell University. NIH
NRSA Fellow, 2004-2006, University of Illinois. Chemical Biology; Mass Spectrometry. TEL: (858) 534-6607
Web: chem-faculty.ucsd.edu/dorrestein/
Email: pdorrestein@ucsd.edu
Jun Yin, Paul D. Straight, Sinisa Hrvatin, Pieter C. Dorrestein, Stefanie B. Bumpus, Cindy Jao, Neil L. Kelleher, Roberto Kolter and Christopher T. Walsh, Genome-wide highthroughput mining of natural-product biosynthetic gene clusters by phage display, Chem. Biol. (Cambridge, MA, U. S.),
14, 303-312 (2007).
Christopher T. Calderone, David F. Iwig, Pieter C. Dorrestein, Neil L. Kelleher and Christopher T. Walsh, Incorporation of Nonmethyl Branches by Isoprenoid-like Logic: Multiple ␤-Alkylation Events in the Biosynthesis of Myxovirescin
A1, Chem. Biol. (Cambridge, MA, U. S.), 14, 835-846
(2007).
Jaclyn M. Winter, Michelle C. Moffitt, Emmanuel Zazopoulos, James B. McAlpine, Pieter C. Dorrestein and Bradley
S. Moore, Molecular Basis for Chloronium-mediated Meroterpene Cyclization: Cloning, sequencing, and the heterologous expression of the napyradiomycin biosynthetic gene
cluster, J. Biol. Chem, 282, 16362-16368 (2007).
4
CALIFORNIA, SAN DIEGO
Lauren J. Pouwels, Liping Zhang, Nam H. Chan, Pieter C.
Dorrestein and Rebekka M. Wachter, Kinetic Isotope Effect
Studies on the de Novo Rate of Chromophore Formation in
Fast- and Slow-Maturing GFP Variants, Biochemistry, 47,
10111-10122 (2008).
Dario Meluzzi, Wei Hao Zheng, Mary Hensler, Victor Nizet and Pieter C. Dorrestein, Top-down mass spectrometry on
low-resolution instruments: Characterization of phosphopantetheinylated carrier domains in polyketide and non-ribosomal biosynthetic pathways, Bioorg. Med. Chem. Lett, 18,
3107-3111 (2008).
Jeremiah W. Hanes, Kristin E. Burns, David G. Hilmey,
Abhishek Chatterjee, Pieter C. Dorrestein and Tadhg P. Begley, Mechanistic Studies on Pyridoxal Phosphate Synthase:
The Reaction Pathway Leading to a Chromophoric Intermediate, J. Am. Chem. Soc, 130, 3043-3052 (2008).
Eduardo Esquenazi, Cameron Coates, Luke Simmons, David Gonzalez, William H. Gerwick and Pieter C. Dorrestein,
Visualizing the spatial distribution of secondary metabolites
produced by marine cyanobacteria and sponges via MALDITOF imaging, Mol. BioSyst, 4, 562-570 (2008).
Jacky Chi Ki Ngo, Kayla Giang, Sutapa Chakrabarti,
Chen-Ting Ma, Nhat Huynh, Jonathan C. Hagopian, Pieter C.
Dorrestein, Xiang-Dong Fu, Joseph A. Adams and Gourisankar Ghosh, A sliding docking interaction is essential for sequential and processive phosphorylation of an SR protein by
SRPK1, Mol. Cell, 29, 563-576 (2008).
Jian Zhang, Steven G. Van Lanen, Jianhua Ju, Wen Liu,
Pieter C. Dorrestein, Wenli Li, Neil L. Kelleher and Ben
Shen, A phosphopantetheinylating polyketide synthase producing a linear polyene to initiate enediyne antitumor antibiotic biosynthesis, Proc. Natl. Acad. Sci. U. S. A, 105, 14601465 (2008).
T. Luke Simmons, R. Cameron Coates, Benjamin R. Clark,
Niclas Engene, David Gonzalez, Eduardo Esquenazi, Pieter
C. Dorrestein and William H. Gerwick, Biosynthetic origin
of natural products isolated from marine microorganism-invertebrate assemblages, Proc. Natl. Acad. Sci. U. S. A, 105,
4587-4594 (2008).
Shaun W. Lee, Douglas A. Mitchell, Andrew L. Markley,
Mary E. Hensler, David Gonzalez, Aaron Wohlrab, Pieter C.
Dorrestein, Victor Nizet and Jack E. Dixon, Discovery of a
widely distributed toxin biosynthetic gene cluster, Proc. Natl.
Acad. Sci. U. S. A, 105, 5879-5884 (2008).
ELLIS, ARTHUR B. (b.1951) Professor. B.Sc, 1973,
Caltech; Ph.D, 1977, MIT. Materials Chemistry. TEL:
(858) 534-3526 FAX: (858) 534-3868
Email: abellis@ucsd.edu
Arthur B. Ellis, Integrating research and education to
create a dynamic physical chemistry curriculum, ACS Symp.
Ser, 973, 40-43 (2007).
FAHEY, ROBERT C. (b.1936) Professor Emeritus.
B.S, 1957, University of California, Berkeley; Ph.D,
1963, University of Chicago. Guggenheim Foundation
Fellowship, 1970-1971, Laboratory Molecular Biology,
Medical Research Council, Cambridge, England; American Cancer Society, Cancer Scholar, 1988-1989, Cancer
Research Campaign Gray Laboratory, Northwood, England. Biochemistry. Thiol biochemistry; current emphasis is on the biosynthesis and metabolism of mycothiol in
Mycobacterium tuberculosis and of bacillithiol in Staphylococcus aureus as targets for new antibiotics. TEL:
(858) 534-2163 FAX: (858) 534-4864
Email: rcfahey@ucsd.edu
Nathan I. Nicely, Derek Parsonage, Carleitta Paige, Gerald
L. Newton, Robert C. Fahey, Roberta Leonardi, Suzanne
Jackowski, T. Conn Mallett and Al Claiborne, Structure of
the Type III Pantothenate Kinase from Bacillus anthracis at
2.0 Å Resolution: Implications for Coenzyme A-Dependent
Redox Biology, Biochemistry, 46, 3234-3245 (2007).
Krzysztof P. Bzymek, Gerald L. Newton, Philong Ta and
Robert C. Fahey, Mycothiol import by Mycobacterium smegmatis and function as a resource for metabolic precursors and
energy production, J. Bacteriol, 189, 6796-6805 (2007).
Gerald L. Newton, Paul R. Jensen, John B. MacMillan,
William Fenical and Robert C. Fahey, An N-acyl homolog of
mycothiol is produced in marine actinomycetes, , 190, 547557 (2008).
Todd Johnson, Gerald L. Newton, Robert C. Fahey and
Mamta Rawat, Unusual production of glutathione in Actinobacteria, Arch. Microbiol, 191, 89-93 (2008).
Gerald L. Newton, Nancy Buchmeier and Robert C. Fahey,
Biosynthesis and functions of mycothiol, the unique protective thiol of Actinobacteria, Microbiol. Mol. Biol. Rev, 72,
471-494 (2008).
Gerald L. Newton and Robert C. Fahey, Regulation of mycothiol metabolism by ␴R and the thiol redox sensor anti-sigma factor RsrA, Mol. Microbiol, 68, 805-809 (2008).
FIGUEROA, JOSHUA S. (b.1978) Assistant Professor. B.Sc, 2000, University of Delaware; Ph.D, 2005,
M.I.T. NIH Postdoctoral Resarch Fellow, 2005-2007,
Columbia University. Inorganic Chemistry; Organometallic Chemistry. Research in the Figueroa Group broadly
encompasses aspects of synthetic inorganic and organometallic chemistry. Areas of interest include: Design and
implementation of highly tailored ancillary ligands for
the stabilization of reactive transition metal fragments.
Modulation and control of redox equivalents for chemical transformations through the explicit use of redox-active ligands and/or spectator agents. Construction of novel transition metal-stabilized main group species. TEL:
(858) 822-7478 FAX: (858) 822-4222
Web: figueroagroup.ucsd.edu/home.htm
Email: jsfig@ucsd.edu
University; M.S, 1988, Albert Einstein College of Medicine; Ph.D, 1991, Albert Einstein College of Medicine.
Postdoctoral Fellow, 1991-1995, Yale University. Regulation of gene expression; high resolution x-ray crystallography, mutational and biochemical approaches to
study biologically active protein/DNA and protein/RNA
complexes. TEL: (858) 822-0469 FAX: (858) 534-7042
Email: gghosh@ucsd.edu
Brian J. Fox, Queena Y. Sun, Antonio G. DiPasquale,
Alexander R. Fox, Arnold L. Rheingold and Joshua S. Figueroa, Solution Behavior and Structural Properties of Cu(I)
Complexes Featuring m-Terphenyl Isocyanides, Inorg.
Chem. (Washington, DC, U. S.), 47, 9010-9020 (2008).
Publication list has not been verified by the department.
FOX, MARYE ANNE (b.1947) Professor, Chancellor.
B.S, 1969, Notre Dame College; M.S, 1970, Cleveland
State University; Ph.D, 1974, Dartmouth College. Postdoctoral fellow, 1974-1976, University of Maryland. Organic Chemistry; Photochemistry. Physical organic
chemsitry at surfaces; self-assembled monolayers;
photoelectrochemistry; spectroscopy of dendrimers.
TEL: (858) 534-3135 FAX: (858) 534-6523
Web: www.chancellor-ucsd.edu
Email: mafox@ucsd.edu
No publication information submitted for this edition.
GALPERIN, M. (b.1969) Assistant Professor. M.Sc,
1991, Ural State University; Ph.D, 2003, Tel Aviv University. Postdoctoral Fellow, 2002-2003, Duke University; Senior Research Associate, 2003-2007, Northwestern
University; Director’s Postdoctoral Fellow, 2007-2008,
Los Alamos National Laboratory. Chemical Physics;
Theoretical Chemistry. Electron transport in condensed
phases. Dissipation and relaxation processes. Open quantum systems out of equilibrium. Molecular electronics.
TEL: (858) 246-0511 FAX: (858) 534-7244
Web: galperingroup.ucsd.edu/
Email: migalperin@ucsd.edu
M. Galperin and D. N. Beratan, Simulation of scanning
tunneling microscope images of 1,3-cyclohexadiene bound to
a silicon surface, Journal of Physical Chemistry B, 109,
1473-1480 (2005).
M. Galperin, A. Nitzan, M. A. Ratner and D. R. Stewart,
Molecular transport junctions: Asymmetry in inelastic tunneling processes, Journal of Physical Chemistry B, 109,
8519-8522 (2005).
M. Galperin, M. A. Ratner and A. Nitzan, Hysteresis,
switching and negative differential resistance in molecular
junctions: A polaron model, Nano Letters, 5, 125-130 (2005).
M. Galperin and A. Nitzan, Current-induced light emission
and light-induced current in molecular-tunneling junctions,
Physical Review Letters, 95, 206802 (2005).
M. Galperin and A. Nitzan, Optical properties of current
carrying molecular wires, Journal of Chemical Physics, 124,
234709 (2006).
M. Galperin, A. Nitzan and M. A. Ratner, Resonant inelastic tunneling in molecular junctions, Physical Review B, 73,
045314 (2006).
M. Galperin, A. Nitzan and M. A. Ratner, Inelastic tunneling effects on noise properties of molecular junctions, Physical Review B, 74, 075326 (2006).
M. Galperin, A. Nitzan and M. A. Ratner, Molecular transport junctions: Current from electronic excitations in the
leads, Physical Review Letters, 96, 166803 (2006).
S. Yeganeh, M. Galperin and M. A. Ratner, Switching in
molecular transport junctions: Polarization response, Journal
of American Chemical Society, 129, 13313-13320 (2007).
M. Galperin, M. A. Ratner and A. Nitzan, Molecular transport junctions: Vibrational effects, Journal of Physics: Condensed Matter, 19, 103201 (2007).
M. Galperin, A. Nitzan and M. A. Ratner, Inelastic effects
in molecular junctions in the Coulomb and Kondo regimes:
Nonequilibrium equation-of-motion approach, Physical Review B, 76, 035301 (2007).
M. Galperin, A. Nitzan and M. A. Ratner, Heat conduction
in molecular transport junctions, Physical Review B, 75,
155312 (2007).
M. Galperin and S. Tretiak, Linear optical response of current-carrying molecular junction: A NEGF-TDDFT approach, Journal of Chemical Physics, 128, 124705 (2008).
M. Galperin, A. Nitzan and M. A. Ratner, The non-linear
response of molecular junctions: The polaron model revisited, Journal of Physics: Condensed Matter, 20, 374107
(2008).
M. Galperin, A. Nitzan and M. A. Ratner, Inelastic effects
in molecular junction transport: scattering and self-consistent
calculations for the Seebeck coefficient, Molecular Physics,
106, 397-404 (2008).
M. Galperin, A. Nitzan and M. A. Ratner, Inelastic transport in the Coulomb blockade regime within a nonequilibrium atomic limit, Physical Review B, 78, 125320 (2008).
M. Galperin, M. A. Ratner, A. Nitzan and A. Troisi, Nuclear coupling and polarization in molecular transport junctions: Beyond tunneling to function, Science, 319, 1056-1060
(2008).
GHOSH, GOURISANKAR (b.1959) Asst. Professor.
B.Sc, 1983, St. Xaviers’ College; M.Sc, 1985, Calcutta
Devin Drew, Eriko Shimada, Kim Huynh, Simon
Bergqvist, Rashmi Talwar, Michael Karin and Gourisankar
Ghosh, Inhibitor ␬B Kinase ␤ Binding by Inhibitor ␬B Kinase ␥, Biochemistry, 46, 12482-12490 (2007).
Soumen Basak, Hana Kim, Jeffrey D. Kearns, Vinay Tergaonkar, Ellen O’Dea, Shannon L. Werner, Chris A. Benedict, Carl F. Ware, Gourisankar Ghosh, Inder M. Verma and
Alexander Hoffmann, A fourth I␬B protein within the NF-␬B
signaling module, Cell (Cambridge, MA, U. S.), 128, 369381 (2007).
Anu K. Moorthy, Tom Huxford and Gourisankar Ghosh,
Structural aspects of NF-␬B and I␬B proteins, Handb.
Transcr. Factor NF-kappaB, 9-24 (2007).
Randall Lukasiewicz, Adolfo Velazquez-Dones, Nhat
Huynh, Jonathan Hagopian, Xiang-Dong Fu, Joseph Adams
and Gourisankar Ghosh, Structurally Unique Yeast and
Mammalian Serine-Arginine Protein Kinases Catalyze Evolutionarily Conserved Phosphorylation Reactions, J. Biol.
Chem, 282, 23036-23043 (2007).
Randall Lukasiewicz, Bradley Nolen, Joseph A. Adams
and Gourisankar Ghosh, The RGG Domain of Npl3p Recruits Sky1p Through Docking Interactions, J. Mol. Biol,
367, 249-261 (2007).
Anu K. Moorthy, De-Bin Huang, Vivien Ya-Fan Wang,
Don Vu and Gourisankar Ghosh, X-ray Structure of a NF-␬B
p50/RelB/DNA Complex Reveals Assembly of Multiple Dimers on Tandem ␬B Sites, J. Mol. Biol, 373, 723-734 (2007).
Stephanie D. Shaw, Sutapa Chakrabarti, Gourisankar
Ghosh and Adrian R. Krainer, Deletion of the N-terminus of
SF2/ASF permits RS-domain-independent pre-mRNA splicing, PLoS One, 2, No pp. given (2007).
Jacky Chi Ki Ngo, Justin Gullingsrud, Kayla Giang, Melinda Jean Yeh, Xiang-Dong Fu, Joseph A. Adams, J. Andrew McCammon and Gourisankar Ghosh, SR Protein Kinase 1 Is Resilient to Inactivation, Structure (Cambridge,
MA, U. S.), 15, 123-133 (2007).
Erika Mathes, Ellen L. O’Dea, Alexander Hoffmann and
Gourisankar Ghosh, NF-␬B dictates the degradation pathway
of I␬B␣, EMBO J, 27, 1357-1367 (2008).
Erika Mathes, Ellen L. O’Dea, Alexander Hoffmann and
Gourisankar Ghosh, NF-␬B dictates the degradation pathway
of I␬B␣. [Erratum to document cited in CA148:555634],
EMBO J, 27, 1421 (2008).
Eileen J. Kennedy, Gourisankar Ghosh and Lorraine Pillus,
Identification of Functionally Distinct Regions That Mediate
Biological Activity of the Protein Kinase A Homolog Tpk2,
J. Biol. Chem, 283, 1084-1093 (2008).
Amanda J. Fusco, Olga V. Savinova, Rashmi Talwar, Jeffrey D. Kearns, Alexander Hoffmann and Gourisankar
Ghosh, Stabilization of RelB Requires Multidomain Interactions with p100/p52, J. Biol. Chem, 283, 12324-12332
(2008).
Malini Sen and Gourisankar Ghosh, Transcriptional Outcome of Wnt-Frizzled Signal Transduction in Inflammation:
Evolving Concepts, J. Immunol, 181, 4441-4445 (2008).
Chen-Ting Ma, Adolfo Velazquez-Dones, Jonathan C. Hagopian, Gourisankar Ghosh, Xiang-Dong Fu and Joseph A.
Adams, Ordered Multi-site Phosphorylation of the Splicing
Factor ASF/SF2 By SRPK1, J. Mol. Biol, 376, 55-68 (2008).
Stephanie M. E. Truhlar, Erika Mathes, Carla F. Cervantes,
Gourisankar Ghosh and Elizabeth A. Komives, Pre-folding
I␬B␣ Alters Control of NF-␬B Signaling, J. Mol. Biol, 380,
67-82 (2008).
Jonathan C. Hagopian, Chen-Ting Ma, Bryan R. Meade,
Claudio P. Albuquerque, Jacky Chi Ki Ngo, Gourisankar
Ghosh, Patricia A. Jennings, Xiang-Dong Fu and Joseph A.
Adams, Adaptable Molecular Interactions Guide Phosphorylation of the SR Protein ASF/SF2 by SRPK1, J. Mol. Biol,
382, 894-909 (2008).
Jacky Chi Ki Ngo, Kayla Giang, Sutapa Chakrabarti,
Chen-Ting Ma, Nhat Huynh, Jonathan C. Hagopian, Pieter C.
Dorrestein, Xiang-Dong Fu, Joseph A. Adams and Gourisankar Ghosh, A sliding docking interaction is essential for sequential and processive phosphorylation of an SR protein by
SRPK1, Mol. Cell, 29, 563-576 (2008).
GHOSH, PARTHO (b.1962) Professor. B.S, 1985,
Yale University; Ph.D, 1992, University of California,
San Francisco. Irvington Institute for Medical Research,
1993-1997, Harvard University. Biochemistry; Structural
Biology. We are interested in understanding the interactions between microbial pathogens and targets on host
mammalian cells. We are studying these interactions using the tools of biochemistry and structural biology. In
understanding the detailed interaction of pathogen and
host macromolecules, we aim to probe fundamental issues in mammalian cell biology and to provide information for the design of antimicrobial therapeutics. TEL:
(858) 822-1139 FAX: (858) 822-2871
Web: pghosh.ucsd.edu
CALIFORNIA, SAN DIEGO
Email: pghosh@ucsd.edu
Sybil C. Lang Hrtska, Melissa M. Kemp, Eva M. Munoz,
Omaira Azizad, Mani Banerjee, Catarina Raposo, Jyothi Kumaran, Partho Ghosh and Robert J. Linhardt, Investigation of
the Mechanism of Binding between Internalin B and Heparin
Using Surface Plasmon Resonance, Biochemistry, 46, 26972706 (2007).
Loren Rodgers, Alicia Gamez, Roland Riek and Partho
Ghosh, The Type III Secretion Chaperone SycE Promotes a
Localized Disorder-to-Order Transition in the Natively Unfolded Effector YopE, J. Biol. Chem, 283, 20857-20863
(2008).
Jason L. Miller, Johanne Le Coq, Asher Hodes, Roman
Barbalat, Jeff F. Miller and Partho Ghosh, Selective ligand
recognition by a diversity-generating retroelement variable
protein, PLoS Biol, 6, 1195-1207 (2008).
Case McNamara, Annelies S. Zinkernagel, Pauline Macheboeuf, Madeleine W. Cunningham, Victor Nizet and Partho
Ghosh, Coiled-Coil Irregularities and Instabilities in Group A
Streptococcus M1 Are Required for Virulence, Science
(Washington, DC, U. S.), 319, 1405-1408 (2008).
GIANNESCHI, NATHAN CLAUDE Assistant Professor. B.Sc, 1999, University of Adelaide; Ph.D, 2005,
Northwestern University. Dow Chemical Foundation
Fellow, 2005-2008, The Scripps Research Institute.
Biomaterials; Bioorganic Chemistry. TEL: (858) 2460857 FAX: (858) 534-0202
Web: gianneschigroup.ucsd.edu/home.htm
Nathan C. Gianneschi and M. Reza Ghadiri, Design of molecular logic devices based on a programmable DNA-regulated semisynthetic enzyme, Angew. Chem., Int. Ed, 46, 39553958 (2007).
Martin S. Masar, III, Nathan C. Gianneschi, Christopher G.
Oliveri, Charlotte L. Stern, SonBinh T. Nguyen and Chad A.
Mirkin, Allosterically Regulated Supramolecular Catalysis of
Acyl Transfer Reactions for Signal Amplification and Detection of Small Molecules, J. Am. Chem. Soc, 129, 1014910158 (2007).
Nathan C. Gianneschi, Supramolecular allosteric catalysts.
(D)
HARPER, E. (b.1930) Professor Emeritus. B.S, 1952,
City College of New York; M.A, 1961, Brooklyn College; Ph.D, 1966, Albert Einstein College of Medicine.
Postdoctoral Fellowship, 1966-1967, Weizmann Institute
of Science, Rehovot, Israel; Resident Fellow, Medicine,
1967-1968, Harvard Medical School. Collagen metabolism; structure-function aspects of the collagenases.
TEL: (619) 534-4177 TEL: (619) 534-4861
Email: eharper@ucsd
No publication information submitted for this edition.
HAYMET, A. D. J. Vice Chancellor and Dean, Marine
Sciences. B.Sc, 1978, University of Sydney; Ph.D, 1981,
University of Chicago; D.Sc, 1997, University of Sydney. Physical Chemistry. Nucleation, clathrates, freezing,
anti-freeze proteins in fish. TEL: (858) 534-2827 FAX:
(858) 453-0167
Web: sio.ucsd.edu/About/Director/
Email: haymet@ucsd.edu
Publication list has not been verified by the department.
Andrzej Wierzbicki, Pranav Dalal, Thomas E. Cheatham,
III, Jared E. Knickelbein, A. D. J. Haymet and Jeffry D. Madura, Antifreeze proteins at the ice/water interface: Three calculated discriminating properties for orientation of type I
proteins, Biophys. J, 93, 1442-1451 (2007).
E. J. Smith, T. Bryk and A. D. J. Haymet, Reply to “Comment on Molecular dynamics study of solvation of Cl- and
Na+ in the ice/water interface’ [J. Chem. Phys. 123, 034706
(2005)], J. Chem. Phys, 126, 237102/1-237102/2 (2007).
P. W. Wilson and A. D. J. Haymet, Workman-Reynolds
Freezing Potential Measurements between Ice and Dilute Salt
Solutions for Single Ice Crystal Faces, J. Phys. Chem. B,
112, 11750-11755 (2008).
P. W. Wilson and A. D. J. Haymet, Comment on “Workman-Reynolds Freezing Potential Measurements between Ice
and Dilute Salt Solutions for Single Ice Crystal Faces, J.
Phys. Chem. B, 112, 15260 (2008).
HENDRICKSON, DAVID N. (b.1943) Professor.
B.S, 1966, University of California, L.A; Ph.D, 1969,
University of California, Berkeley. Fellowship, 1970,
California Institute of Technology. Inorganic Chemistry;
Nanochemistry. Magnetic bistability in single-molecule
magnets; resonant magnetization quantum tunneling; dynamics in transition metal complexes; optical bistability
in valence tautomeric and spin-crossover complexes;
magnetic exchange in polynuclear complexes. TEL:
(858) 534-5580 FAX: (858) 534-5383
Email: dhendrickson@ucsd.edu
Ai-Ju Zhou, Lian-Jing Qin, Christopher C. Beedle, Shu
Ding, Motohiro Nakano, Ji-Dong Leng, Ming-Liang Tong
and David N. Hendrickson, New Mn12 Clusters with Tunable
Oxidation States via the Use of N,N,N’,N’-Tetrakis(2-hy-
droxyethyl)ethylenediamine, Inorg. Chem. (Washington, DC,
U. S.), 46, 8111-8113 (2007).
Patrick L. Feng, Christopher C. Beedle, Wolfgang Wernsdorfer, Changhyun Koo, Motohiro Nakano, Stephen Hill and
David N. Hendrickson, Heterometallic Cubane Single-Molecule Magnets, Inorg. Chem. (Washington, DC, U. S.), 46,
8126-8128 (2007).
Wen-Guo Wang, Ai-Ju Zhou, Wei-Xiong Zhang, MingLiang Tong, Xiao-Ming Chen, Motohiro Nakano, Christopher C. Beedle and David N. Hendrickson, Giant Heterometallic Cu17Mn28 Cluster with Td Symmetry and High-Spin
Ground State, J. Am. Chem. Soc, 129, 1014-1015 (2007).
G. de Loubens, A. D. Kent, V. Krymov, G. J. Gerfen, C. C.
Beedle and D. N. Hendrickson, High frequency EPR on dilute solutions of the single molecule magnet Ni4, J. Appl.
Phys, 103, 07B910-1-07B910-3 (2007).
G. de Loubens, G. D. Chaves-O’Flynn, A. D. Kent, C.
Ramsey, E. del Barco, C. Beedle and D. N. Hendrickson,
Magnetization and EPR studies of the single molecule magnet Ni4 with integrated sensors, J. Appl. Phys, 101, 09E1041-09E104-3 (2007).
Anthony Wilson, En-Che Yang, David N. Hendrickson
and Stephen Hill, On the validity of the giant spin approximation and its application to single-molecule magnets, Polyhedron, 26, 2065-2068 (2007).
Christopher C. Beedle, Katie J. Heroux, Motohiro Nakano,
Antonio G. DiPasquale, Arnold L. Rheingold and David N.
Hendrickson, Antiferromagnetic tetranuclear manganese
complex: Wheel or dicubane?, Polyhedron, 26, 2200-2206
(2007).
Jon Lawrence, Chris C. Beedle, En-Che Yang, James Ma,
Stephen Hill and David N. Hendrickson, High frequency
electron paramagnetic resonance (HFEPR) study of a high
spin Co(II) complex, Polyhedron, 26, 2299-2303 (2007).
M. Bal, J. R. Friedman, W. Chen, M. T. Tuominen, C. C.
Beedle, E. M. Rumberger and D. N. Hendrickson, Radiationand phonon-bottleneck-induced tunneling in the Fe8 singlemolecule magnet, EPL, 82, 17005 (2008).
G. de Loubens, D. A. Garanin, C. C. Beedle, D. N. Hendrickson and A. D. Kent, Magnetization relaxation in the single-molecule magnet Ni4 under continuous microwave irradiation, EPL, 83, 83, 37006 (2008).
Christopher C. Beedle, Casey J. Stephenson, Katie J. Heroux, Wolfgang Wernsdorfer and David N. Hendrickson, Photoluminescent Mn4 Single-Molecule Magnet, Inorg. Chem.
(Washington, DC, U. S.), 47, 10798-10800 (2008).
Jon Lawrence, En-Che Yang, Rachel Edwards, Marilyn M.
Olmstead, Chris Ramsey, Naresh S. Dalal, Peter K. Gantzel,
Stephen Hill and David N. Hendrickson, Disorder and Intermolecular Interactions in a Family of Tetranuclear Ni(II)
Complexes Probed by High-Frequency Electron Paramagnetic Resonance, Inorg. Chem. (Washington, DC, U. S.), 47,
1965-1974 (2008).
Patrick L. Feng, Christopher C. Beedle, Changhyun Koo,
Wolfgang Wernsdorfer, Motohiro Nakano, Stephen Hill and
David N. Hendrickson, Heterometallic Integer-Spin Analogues of S = 9/2 Mn4 Cubane Single-Molecule Magnets,
Inorg. Chem. (Washington, DC, U. S.), 47, 3188-3204
(2008).
Sonali J. Shah, Christopher M. Ramsey, Katie J. Heroux,
James R. O’Brien, Antonio G. DiPasquale, Arnold L. Rheingold, Enrique del Barco and David N. Hendrickson, WheelShaped Mn16 Single-Molecule Magnets, Inorg. Chem.
(Washington, DC, U. S.), 47, 6245-6253 (2008).
Patrick L. Feng, Changhyun Koo, John J. Henderson, Motohiro Nakano, Stephen Hill, Enrique del Barco and David N.
Hendrickson, Single-Molecule-Magnet Behavior and Spin
Changes Affected by Crystal Packing Effects, Inorg. Chem.
(Washington, DC, U. S.), 47, 8610-8612 (2008).
Sonali J. Shah, Christopher M. Ramsey, Katie J. Heroux,
Antonio G. DiPasquale, Naresh S. Dalal, Arnold L. Rheingold, Enrique del Barco and David N. Hendrickson, Molecular Wheels: New Mn12 Complexes as Single-Molecule Magnets, Inorg. Chem. (Washington, DC, U. S.), 47, 9569-9582
(2008).
Emi Evangelio, David N. Hendrickson and Daniel RuizMolina, Intramolecular electron transfer in the mixed-valence
[Co(3,5-DTBCat)(3,5-DTBSQ)(bpy)] complex: Beyond valence tautomerism, Inorg. Chim. Acta, 361, 3403-3409
(2008).
Patrick L. Feng, Christopher C. Beedle, Changhyun Koo,
Jon Lawrence, Stephen Hill and David N. Hendrickson, Origin of magnetization tunneling in single-molecule magnets as
determined by single-crystal high-frequency EPR, Inorg.
Chim. Acta, 361, 3465-3480 (2008).
Michio Sorai, Ramon Burriel, Edgar F. Westrum, Jr. and
David N. Hendrickson, Mechanochemical Effect in the Iron
(III) Spin Crossover Complex [Fe(3-MeO-salenEt)2]PF6 as
Studied by Heat Capacity Calorimetry, J. Phys. Chem. B,
112, 4344-4350 (2008).
Christopher M. Ramsey, Enrique del Barco, Stephen Hill,
Sonali J. Shah, Christopher C. Beedle and David N. Hendrickson, Quantum interference of tunnel trajectories between states of different spin length in a dimeric molecular
nanomagnet, Nat. Phys, 4, 277-281 (2008).
Sonali J. Shah, Single-molecule magnets: Polynuclear
manganese wheels and clusters. (D)
HERMANN, THOMAS Assistant Professor. B.S,
1988, University of Ulm, Germany; M.S, 1992, Univer-
5
sity of Ulm, Germany; Ph.D, 1996, Max-Planck-Institute
for Biochemistry/Ludwig-Maximilians-University, Munich. Postdoctoral Fellow, 1996-1998, IBMC/CNRS,
Strasbourg, France; Research Associate, 1999-2000, Memorial Sloan-Kettering Cancer Center, New York, NY;
Senior Research Scientist, 2001, Memorial Sloan-Kettering Cancer Center, New York, NY. Bioorganic Chemistry; Crystallography. TEL: (858) 534-4467 FAX: (858)
534-0202
Web: tch.ucsd.edu
Email: tch@ucsd.edu
Sergey M. Dibrov, Hillary Johnston-Cox, Yi-Hsin Weng
and Thomas Hermann, Functional architecture of HCV IRES
domain II stabilized by divalent metal ions in the crystal and
in solution, Angew. Chem., Int. Ed, 46, 226-229 (2007).
Christopher M. Barbieri, Malvika Kaul, Melanie BozzaHingos, Fang Zhao, Yitzhak Tor, Thomas Hermann and Daniel S. Pilch, Defining the molecular forces that determine the
impact of neomycin on bacterial protein synthesis: importance of the 2’-amino functionality, Antimicrob. Agents Chemother, 51, 1760-1769 (2007).
Yuefen Zhou, Vlad E. Gregor, Benjamin K. Ayida, Geoffrey C. Winters, Zhongxiang Sun, Douglas Murphy, Greg
Haley, Dwight Bailey, Jamie M. Froelich, Sarah Fish, Stephen E. Webber, Thomas Hermann and Daniel Wall, Synthesis
and SAR of 3,5-diamino-piperidine derivatives: novel antibacterial translation inhibitors as aminoglycoside mimetics,
Bioorg. Med. Chem. Lett, 17, 1206-1210 (2007).
Thomas Hermann, Valentina Tereshko, Eugene Skripkin
and Dinshaw J. Patel, Apramycin recognition by the human
ribosomal decoding site, Blood Cells, Mol., Dis, 38, 193-198
(2007).
Konstantin H. Dragnev, W. Jeffrey Petty, Sumit J. Shah,
Lionel D. Lewis, Candice C. Black, Vincent Memoli, William C. Nugent, Thomas Hermann, Andres Negro-Vilar,
James R. Rigas and Ethan Dmitrovsky, A Proof-of-Principle
Clinical Trial of Bexarotene in Patients with Non-Small Cell
Lung Cancer, Clin. Cancer Res, 13, 1794-1800 (2007).
Jerod Parsons and Thomas Hermann, Conformational flexibility of ribosomal decoding-site RNA monitored by fluorescent pteridine base analogues, Tetrahedron, 63, 3548-3552
(2007).
Qiang Zhao, Qing Han, Charles R. Kissinger, Thomas Hermann and Peggy A. Thompson, Structure of hepatitis C virus
IRES subdomain IIa, Acta Crystallogr., Sect. D: Biol. Crystallogr, D64, 436-443, S436/1-S436/3 (2008).
Yuefen Zhou, Stephen E. Webber, Douglas E. Murphy,
Lian-Sheng Li, Peter S. Dragovich, Chinh V. Tran, Zhongxiang Sun, Frank Ruebsam, Amit M. Shah, Mei Tsan, Richard
E. Showalter, Rupal Patel, Bin Li, Qiang Zhao, Qing Han,
Thomas Hermann, Charles R. Kissinger, Laurie LeBrun, Maria V. Sergeeva and Leo Kirkovsky, Novel HCV NS5B polymerase inhibitors derived from 4-(1’,1’-dioxo-1’,4’-dihydro1’␭6-benzo[1’,2’,4’]thiadiazin-3’-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 1: Exploration of 7’-substitution of benzothiadiazine, Bioorg. Med. Chem. Lett, 18, 1413-1418 (2008).
Yuefen Zhou, Lian-Sheng Li, Peter S. Dragovich, Douglas
E. Murphy, Chinh V. Tran, Frank Ruebsam, Stephen E.
Webber, Amit M. Shah, Mei Tsan, April Averill, Richard E.
Showalter, Rupal Patel, Qing Han, Qiang Zhao, Thomas Hermann, Charles R. Kissinger, Laurie LeBrun and Maria V.
Sergeeva, Novel HCV NS5B polymerase inhibitors derived
from 4-(1’,1’-dioxo-1’,4’-dihydro-1’␭6-benzo[1’,2’,4’]thiadiazin-3’-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 2: Variation of the 2- and 6-pyridazinone substituents, Bioorg. Med.
Chem. Lett, 18, 1419-1424 (2008).
Yuefen Zhou, Chun Chow, Douglas E. Murphy, Zhongxiang Sun, Thomas Bertolini, Jamie M. Froelich, Stephen E.
Webber, Thomas Hermann and Daniel Wall, Antibacterial
activity in serum of the 3,5-diamino-piperidine translation inhibitors, Bioorg. Med. Chem. Lett, 18, 3369-3375 (2008).
HOFFMANN, ALEXANDER (b.1966) Assistant
Professor. B.A, 1988, Cambridge University; M.Ph,
1991, Cambridge University; Ph.D, 1994, Rockefeller
University. Postdoctoral Associate, 1995-1998, M. I. T;
Postdoctoral Associate, 1998-2003, CalTech. Biochemistry. Eukaryotic gene expression is regulated by a circuitry of signaling pathways. My research is focused on NFkB signaling that controls mammalian immune and stress
responses. Using computational modeling, I aim to connect biochemical results from in vitro studies and from
genetically altered cells and mice. Constructing a computational model of this signaling pathway leads to quantitative understanding, novel hypotheses, and exploration
of novel therapeutic agents for a host of human diseases.
TEL: (858) 822-0212 FAX: (858) 534-6693
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C04518
Email: ahoffmann@ucsd.edu
Alexander Hoffmann, Yifeng Xia and Inder M. Verma, Inflammatory tales of liver cancer, Cancer Cell, 11, 99-101
(2007).
Soumen Basak, Hana Kim, Jeffrey D. Kearns, Vinay Tergaonkar, Ellen O’Dea, Shannon L. Werner, Chris A. Benedict, Carl F. Ware, Gourisankar Ghosh, Inder M. Verma and
Alexander Hoffmann, A fourth I␬B protein within the NF-␬B
signaling module, Cell (Cambridge, MA, U. S.), 128, 369381 (2007).
6
CALIFORNIA, SAN DIEGO
E. L. O’Dea, D. Barken, R. Q. Peralta, K. T. Tran, S. L.
Werner, J. D. Kearns, A. Levchenko and A. Hoffmann, A homeostatic model of IkappaB metabolism to control constitutive activity, Molecular Systems Biology, 3, 111 (2007).
Soumen Basak and Alexander Hoffmann, Crosstalk via the
NF-␬B signaling system, Cytokine Growth Factor Rev, 19,
187-197 (2008).
Erika Mathes, Ellen L. O’Dea, Alexander Hoffmann and
Gourisankar Ghosh, NF-␬B dictates the degradation pathway
of I␬B␣, EMBO J, 27, 1357-1367 (2008).
Tomohisa Kato, Jr., Yusuke Gotoh, Alexander Hoffmann
and Yoshitaka Ono, Negative regulation of constitutive NF␬B and JNK signaling by PKN1-mediated phosphorylation
of TRAF1, Genes Cells, 13, 509-520 (2008).
Christine S. Cheng, Tracy L. Johnson and Alexander Hoffmann, Epigenetic control: slow and global, nimble and local,
Genes Dev, 22, 1110-1114 (2008).
Shannon L. Werner, Jeffrey D. Kearns, Victoria Zadorozhnaya, Candace Lynch, Ellen O’Dea, Mark P. Boldin, Averil
Ma, David Baltimore and Alexander Hoffmann, Encoding
NF-␬B temporal control in response to TNF: distinct roles
for the negative regulators I␬B␣ and A20, Genes Dev, 22,
2093-2101 (2008).
Amanda J. Fusco, Olga V. Savinova, Rashmi Talwar, Jeffrey D. Kearns, Alexander Hoffmann and Gourisankar
Ghosh, Stabilization of RelB Requires Multidomain Interactions with p100/p52, J. Biol. Chem, 283, 12324-12332
(2008).
Irene L. Ch’en, Stephen M. Hedrick and Alexander Hoffmann, NF-␬B as a determinant of distinct cell death pathways, Methods Enzymol, 446, 175-187 (2008).
Ellen L. O’Dea, Jeffrey D. Kearns and Alexander Hoffmann, UV as an amplifier rather than inducer of NF-␬B activity, Mol. Cell, 30, 632-641 (2008).
Soumen Basak, Vincent Feng-Sheng Shih and Alexander
Hoffmann, Generation and activation of multiple dimeric
transcription factors within the NF-␬B signaling system, Mol.
Cell. Biol, 28, 3139-3150 (2008).
Irene L. Ch’en, Daniel R. Beisner, Alexei Degterev, Candace Lynch, Junying Yuan, Alexander Hoffmann and Stephen M. Hedrick, Antigen-mediated T cell expansion regulated
by parallel pathways of death, Proc. Natl. Acad. Sci. U. S. A,
105, 17463-17468 (2008).
James Lee, Regulation of the ISRE by NFkB: A novel role
for the P50 homodimer. (M)
D. Barken, Temporal encoding and homeostatic control in
the IKK-IkB-NFkB signaling system. (D)
JENNINGS, PATRICIA A. (b.1962) Professor. B.S,
1985, Rutgers University; Ph.D, 1991, Pennsylvania
State University. Postdoctoral Research Fellowship,
1991-1993, Scripps Research Institute. Biochemistry;
NMR Spectroscopy. Biophysical chemistry: protein
structure, function, dynamics and folding; multinuclear
(1H, 15N, 13C, 2H)-multidimensional (2, 3 and 4D)
NMR spectroscopy; cloning and site-specific mutagenesis by PCR; equilibrium and kinetic-fluorescence, UVabsorbance. TEL: (858) 534-6417 FAX: (858) 534-7042
Web: www.chem/Faculty/Research_txt/jennings.html
Email: pajennin@ucsd.edu
pajennings@ucsd.edu
Publication list has not been verified by the department.
John M. Finke, Patricia A. Jennings, Jennifer C. Lee, Jose
N. Onuchic and Jay R. Winkler, Equilibrium unfolding of the
poly(glutamic acid)20 helix, Biopolymers, 86, 193-211
(2007).
Sandra E. Wiley, Mark L. Paddock, Edward C. Abresch,
Larry Gross, Peter van der Geer, Rachel Nechushtai, Anne N.
Murphy, Patricia A. Jennings and Jack E. Dixon, The outer
mitochondrial membrane protein mitoNEET contains a novel
redox-active 2Fe-2S cluster, J. Biol. Chem, 282, 2374523749 (2007).
Jamie E. Mills, Paul C. Whitford, Jennifer Shaffer, Jose N.
Onuchic, Joseph A. Adams and Patricia A. Jennings, A Novel Disulfide Bond in the SH2 Domain of the C-terminal Src
Kinase Controls Catalytic Activity, J. Mol. Biol, 365, 14601468 (2007).
Benjamin T. Andrews, Andrea R. Schoenfish, Melinda
Roy, Geoffrey Waldo and Patricia A. Jennings, The Rough
Energy Landscape of Superfolder GFP Is Linked to the Chromophore, J. Mol. Biol, 373, 476-490 (2007).
Mark L. Paddock, Sandra E. Wiley, Herbert L. Axelrod,
Aina E. Cohen, Melinda Roy, Edward C. Abresch, Dominique Capraro, Anne N. Murphy, Rachel Nechushtai, Jack E.
Dixon and Patricia A. Jennings, MitoNEET is a uniquely
folded 2Fe-2S outer mitochondrial membrane protein stabilized by pioglitazone, Proc. Natl. Acad. Sci. U. S. A, 104,
14342-14347 (2007).
Jonathan C. Hagopian, Chen-Ting Ma, Bryan R. Meade,
Claudio P. Albuquerque, Jacky Chi Ki Ngo, Gourisankar
Ghosh, Patricia A. Jennings, Xiang-Dong Fu and Joseph A.
Adams, Adaptable Molecular Interactions Guide Phosphorylation of the SR Protein ASF/SF2 by SRPK1, J. Mol. Biol,
382, 894-909 (2008).
Shachi Gosavi, Paul C. Whitford, Patricia A. Jennings and
Jose N. Onuchic, Extracting function from a ␤-trefoil folding
motif, Proc. Natl. Acad. Sci. U. S. A, 105, 10384-10389
(2008).
Benjamin T. Andrews, Shachi Gosavi, John M. Finke, Jose
N. Onuchic and Patricia A. Jennings, The dual-basin landscape in GFP folding, Proc. Natl. Acad. Sci. U. S. A, 105,
12283-12288 (2008).
Dominique T. Capraro, Melinda Roy, Jose N. Onuchic and
Patricia A. Jennings, Backtracking on the folding landscape
of the ␤-trefoil protein interleukin-1␤?, Proc. Natl. Acad. Sci.
U. S. A, 105, 14844-14848 (2008).
Shachi Gosavi, Paul C. Whitford, Patricia A. Jennings and
Jose N. Onuchic, Extracting function from a ␤-trefoil folding
motif. [Erratum to document cited in CA149:240950], Proc.
Natl. Acad. Sci. U. S. A, 105, 16057 (2008).
JOHNSON, JOHN E. (b.1945) Professor. B.A, 1967,
Carthage College, Kenosha, WI; Ph.D, 1972, Iowa State
University, Ames, Iowa. National Cancer Institute Fellowship, 1974-1976, Purdue University; NATO Travel
Fellowship, 1978, Purdue Unversity; Travel Fellowship,
2000, Japanese Society for the Promotion of Science;
Travel Fellowship, 2001, Taiwan National Science Committee. TEL: (858) 784-9705 FAX: (858) 784-8660
Web: www.noda.scripps.edu
Email: jackj@scripps.edu
Publication list has not been verified by the department.
John E. Johnson and Wah Chiu, DNA packaging and delivery machines in tailed bacteriophages, Curr. Opin. Struct.
Biol, 17, 237-243 (2007).
Blair R. Szymczyna, Lu Gan, John E. Johnson and James
R. Williamson, Solution NMR Studies of the Maturation Intermediates of a 13 MDa Viral Capsid, J. Am. Chem. Soc,
129, 7867-7876 (2007).
Anton Poliakov, Esther van Duijn, Gabriel Lander, Chi-yu
Fu, John E. Johnson, Peter E. Prevelige and Albert J. R.
Heck, Macromolecular mass spectrometry and electron microscopy as complementary tools for investigation of the heterogeneity of bacteriophage portal assemblies, J. Struct. Biol,
157, 371-383 (2007).
Sebyung Kang, Gabriel C. Lander, John E. Johnson and
Peter E. Prevelige, Development of bacteriophage P22 as a
platform for molecular display: genetic and chemical modifications of the procapsid exterior surface, ChemBioChem, 9,
514-518 (2008).
Manidipa Banerjee and John E. Johnson, Activation, exposure and penetration of virally encoded, membrane-active
polypeptides during nonenveloped virus entry, Curr. Protein
Pept. Sci, 9, 16-27 (2008).
Daniel Nemecek, Gabriel C. Lander, John E. Johnson,
Sherwood R. Casjens and George J. Thomas, Assembly Architecture and DNA Binding of the Bacteriophage P22 Terminase Small Subunit, J. Mol. Biol, 383, 494-501 (2008).
Gina E. Sosinsky, John Crum, Ying Z. Jones, Jason Lanman, Benjamin Smarr, Masako Terada, Maryann E. Martone,
Thomas J. Deerinck, John E. Johnson and Mark H. Ellisman,
The combination of chemical fixation procedures with high
pressure freezing and freeze substitution preserves highly labile tissue ultrastructure for electron tomography applications, J. Struct. Biol, 161, 359-371 (2008).
Jason Lanman, John Crum, Thomas J. Deerinck, Guido M.
Gaietta, Anette Schneemann, Gina E. Sosinsky, Mark H. Ellisman and John E. Johnson, Visualizing flock house virus
infection in Drosophila cells with correlated fluorescence and
electron microscopy, J. Struct. Biol, 161, 439-446 (2008).
Lu Gan and John E. Johnson, An optimal exposure strategy
for cryoprotected virus crystals with lattice constants greater
than 1000 Å, J. Synchrotron Radiat, 15, 223-226 (2008).
Hanna E. Walukiewicz, Manidipa Banerjee, Anette
Schneemann and John E. Johnson, Rescue of maturation-defective flock house virus infectivity with noninfectious, mature, viruslike particles, J. Virol, 82, 2025-2027 (2008).
Reed B. Wickner, Jinghua Tang, Nora A. Gardner and
John E. Johnson, The yeast dsRNA virus L-A resembles
mammalian dsRNA virus cores, Segmented Double-Stranded
RNA Viruses, 105-114 (2008).
Gabriel C. Lander, Alex Evilevitch, Meerim Jeembaeva,
Clinton S. Potter, Bridget Carragher and John E. Johnson,
Bacteriophage Lambda Stabilization by Auxiliary Protein
gpD: Timing, Location, and Mechanism of Attachment Determined by Cryo-EM, Structure (Cambridge, MA, U. S.), 16,
1399-1406 (2008).
Kelly K. Lee, Lu Gan, Hiro Tsuruta, Crystal Moyer, James
F. Conway, Robert L. Duda, Roger W. Hendrix, Alasdair C.
Steven and John E. Johnson, Virus Capsid Expansion Driven
by the Capture of Mobile Surface Loops, Structure (Cambridge, MA, U. S.), 16, 1491-1502 (2008).
JOSEPH, SIMPSON (b.1966) Full Professor. Ph.D,
1994, University of Vermont. American Cancer Society
Fellowship, 1994-1998, University of California, Santa
Cruz. Biochemistry; Biophysics/Biophysical Chemistry.
Ribosome structure, function and dynamics; role of
rRNA in translation; mechanism of translocation; interaction of antibiotics with ribosomes. TEL: (858) 8222957 FAX: (858) 534-7042
Email: sjoseph@chem.ucsd.edu
Sean M. Studer and Simpson Joseph, Binding of mRNA to
the bacterial translation initiation complex, Methods Enzymol, 430, 31-44 (2007).
Christine M. Dunham, Maria Selmer, Steven S. Phelps,
Ann C. Kelley, Tsutomu Suzuki, Simpson Joseph and V. Ra-
makrishnan, Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit,
RNA, 13, 817-823 (2007).
Lucia Garcia-Ortega, Jenise Stephen and Simpson Joseph,
Precise alignment of peptidyl tRNA by the decoding center is
essential for EF-G-dependent translocation, Mol. Cell, 32,
292-299 (2008).
J. S. Feinberg, Interactions between the acceptor arm of
tRNA and the large subunit of the bacterial ribosome important for translocation. (D)
S. M. Studer, MRNA interaction with the bacterial ribosome during initiation and translocation. (D)
KEARNS, DAVID R. (b.1935) Professor Emeritus.
B.S, 1956, University of Illinois; Ph.D, 1960, University
of California, Berkeley. NAS Postdoctoral Fellow, 19601961, University of Chicago; NAS Postdoctoral Fellow,
1961-1962, M. I. T; Guggenheim Fellowship, 19691970. Physical chemistry of polynucleotides; dynamics
and structural studies by one-, two-, three-dimensional
NMR; drug-DNA, metal-DNA, protein-DNA interactions, unusual DNA structures, and protein structure.
TEL: (858) 534-2760 FAX: (858) 534-0202
Web: www.chem.ucsd.edu/Faculty/emeritus.html#
kearns
Email: dkearns@ucsd.edu
No publication information submitted for this edition.
KIM, JUDY E. Assistant Professor. M.S, 1994, M.I.T;
Ph.D, 2001, University of California, Berkeley. NIH
Postdoc Fellow, 2003-2005, California Institute of Technology. Biophysics/Biophysical Chemistry; Physical
Chemistry. Integral membrane proteins comprise ~30%
of all cell proteins, and play essential roles in cellular
functions as gates, pumps, receptors, energy transducers,
and enzymes. Despite recent progress towards understanding the structure and function of membrane proteins, a more complex and fundamental question persists:
What are the molecular mechanisms for the folding, insertion, and assembly of integral membrane proteins that
give rise to functional structures? TEL: (858) 534-5598
FAX: (858) 534-7042
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C04912
Email: judyk@ucsd.edu
Arneh Babakhani, Alemayehu A. Gorfe, Justin Gullingsrud, Judy E. Kim and J. Andrew McCammon, Peptide insertion, positioning, and stabilization in a membrane: insight
from an all-atom molecular dynamics simulation, Biopolymers, 85, 490-497 (2007).
Katheryn M. Sanchez, Jonathan E. Gable, Diana E. Schlamadinger and Judy E. Kim, Effects of Tryptophan Microenvironment, Soluble Domain, and Vesicle Size on the Thermodynamics of Membrane Protein Folding: Lessons from the
Transmembrane Protein OmpA, Biochemistry, 47, 1284412852 (2008).
Arneh Babakhani, Alemayehu A. Gorfe, Judy E. Kim and
J. Andrew McCammon, Thermodynamics of Peptide Insertion and Aggregation in a Lipid Bilayer, J. Phys. Chem. B,
112, 10528-10534 (2008).
Katheryn M. Sanchez, Tiffany J. Neary and Judy E. Kim,
Ultraviolet Resonance Raman Spectroscopy of Folded and
Unfolded States of an Integral Membrane Protein, J. Phys.
Chem. B, 112, 9507-9511 (2008).
K. M. Sanchez, D. E. Schlamadinger, J. E. Gable and J. E.
Kim, Forster resonance energy transfer and conformational
stability of proteins: An advanced biophysical module for
physical chemistry students, Journal of Chemical Education,
85, 1253-1256 (2008).
Tiffany J. Neary, Ultraviolet resonance raman spectroscopy of the integral membrane protein OmpA: Elucidating
structure and tryptophan microenvironment of folded and unfolded states. (M)
KOBAYASHI, YOSHIHISA (b.1970) Assistant Professor. B.A, 1994, The University of Tokyo; M.A, 1996,
The University of Tokyo; Ph.D, 1999, The University of
Tokyo. Postdoctoral Fellow, 1999-2002, Harvard University; Research Associate, 2002-2003, Harvard University. Natural Products Chemistry; Synthesis. Total
synthesis of natural products, heterocycles, development
of methodology of synthetic organic chemistry. TEL:
(858) 822-5870 FAX: (858) 822-5870
Web: www.chem-faculty.ucsd.edu/kobayashi/index.html
Email: ykoba@chem.ucsd.edu
Matthew J. Buller, Travis G. Cook and Yoshihisa Kobayashi, Versatile synthesis of 2,2-disubstituted indolinones via
protected indolones generated by one-pot multi-oxidation of
2-substituted indoles, Heterocycles, 72, 163-166 (2007).
Jerry Isaacson, Cynthia B. Gilley and Yoshihisa Kobayashi, Expeditious access to unprotected racemic pyroglutamic
acids, J. Org. Chem, 72, 3913-3916 (2007).
Jerry Isaacson, Cynthia B. Gilley and Yoshihisa Kobayashi, Expeditious access to unprotected racemic pyroglutamic
acids. [Erratum to document cited in CA147:031335], J. Org.
Chem, 72, 5024 (2007).
CALIFORNIA, SAN DIEGO
Cynthia B. Gilley, Matthew J. Buller and Yoshihisa Kobayashi, New Entry to Convertible Isocyanides for the Ugi Reaction and Its Application to the Stereocontrolled Formal Total Synthesis of the Proteasome Inhibitor Omuralide, Org.
Lett, 9, 3631-3634 (2007).
Mitchell Vamos, Kerem Ozboya and Yoshihisa Kobayashi,
Synthesis of bicyclic pyroglutamic acid featuring the Ugi reaction and a unique stereoisomerization at the angular position by Grob fragmentation followed by a transannular ketene [2+2] cycloaddition reaction, Synlett, 1595-1599 (2007).
Mitchell Vamos and Yoshihisa Kobayashi, Scalable Preparation of Both Enantiomers of 2-(1-Hydroxy-2-oxocyclohexyl)acetic Acid, J. Org. Chem, 73, 3938-3941 (2008).
Cynthia B. Gilley and Yoshihisa Kobayashi, 2-Nitrophenyl
Isocyanide as a Versatile Convertible Isocyanide: Rapid Access to a Fused ␥-Lactam ␤-Lactone Bicycle, J. Org. Chem,
73, 4198-4204 (2008).
Thong X. Nguyen and Yoshihisa Kobayashi, Synthesis of
the Common Propellane Core Structure of the Hasubanan Alkaloids, J. Org. Chem, 73, 5536-5541 (2008).
Jerry Isaacson, Mandy Loo and Yoshihisa Kobayashi, Total Synthesis of (±)-Dysibetaine, Org. Lett, 10, 1461-1463
(2008).
M. J. Buller, C. B. Gilley, B. Nguyen, L. Olshansky, B.
Fraga and Y. Kobayashi, Synthesis of functionalized pyroglutamic acids. Part 1: The synthetic utility of N-Acylindole
and the ugi reaction with a chiral levulinic acid, Synlett,
2244-2248 (2008).
C. B. Gilley, M. J. Buller and Y. Kobayashi, Synthesis of
functionalized pyroglutamic acids. Part 2: The stereoselective
condensation of multi-functional groups with chiral levulinic
acids, Synlett, 2249-2252 (2008).
S. Born and Y. Kobayashi, A stable synthetic equivalent of
2,3-Dihydropyridine, Synlett, 2479-2482 (2008).
S. Born, G. Bacani, E. E. Olson and Y. Kobayashi, Microwave-assisted intramolecular diels-alder reaction towards the
total synthesis of symbioimine, Synlett, 2877-2881 (2008).
ments meet theory, Curr. Opin. Struct. Biol, 18, 27-34
(2008).
Gina N. Betts, Peter van der Geer and Elizabeth A. Komives, Structural and Functional Consequences of Tyrosine
Phosphorylation in the LRP1 Cytoplasmic Domain, J. Biol.
Chem, 283, 15656-15664 (2008).
Stephanie M. E. Truhlar, Erika Mathes, Carla F. Cervantes,
Gourisankar Ghosh and Elizabeth A. Komives, Pre-folding
I␬B␣ Alters Control of NF-␬B Signaling, J. Mol. Biol, 380,
67-82 (2008).
Shih-Che Sue, Carla Cervantes, Elizabeth A. Komives and
H. Jane Dyson, Transfer of Flexibility between Ankyrin Repeats in I␬B␣ upon Formation of the NF-␬B Complex, J.
Mol. Biol, 380, 917-931 (2008).
David G. Mendoza-Cozatl, Emerald Butko, Franziska
Springer, Justin W. Torpey, Elizabeth A. Komives, Julia
Kehr and Julian I. Schroeder, Identification of high levels of
phytochelatins, glutathione and cadmium in the phloem sap
of Brassica napus. A role for thiol-peptides in the long-distance transport of cadmium and the effect of cadmium on
iron translocation, Plant J, 54, 249-259 (2008).
Diego U. Ferreiro, Aleksandra M. Walczak, Elizabeth A.
Komives and Peter G. Wolynes, The energy landscapes of repeat-containing proteins: topology, cooperativity, and the
folding funnels of one-dimensional architectures, PLoS Comput. Biol, 4, No pp. given (2008).
Stephanie M. E. Truhlar, Carla F. Cervantes, Justin W.
Torpey, Magnus Kjaergaard and Elizabeth A. Komives, Rapid mass spectrometric analysis of 15N-Leu incorporation fidelity during preparation of specifically labeled NMR samples, Protein Sci, 17, 1636-1639 (2008).
S. Bergqvist, G. Ghosh and E. A. Komives, The IkBa /NFkB complex has two hot-spots, one at either end of the interface, Protein Science, 17, 2051-2058 (2008).
Stephanie M. E. Truhlar and Elizabeth A. Komives, LRR
Domain Folding: Just Put a Cap on It, Structure (Cambridge,
MA, U. S.), 16, 655-657 (2008).
C. B. Gilley, New convertible isocyanides for the ugi reaction; application to the stereoselective synthesis of omuralide. (D)
Muneera Beach, Thermodynamics and the role of allostery
in the thrombin-thrombomodulin interaction. (D)
KRAUT, JOSEPH (b.1926) Research Professor. B.S,
KOMIVES, ELIZABETH A. (b.1960) Professor.
B.S, 1982, M.I.T; M.S, 1982, M.I.T; Ph.D, 1987, University of California, San Francisco. NIH Postdoctoral
Fellowship, 1987-1990, Harvard University. Biochemistry; Biophysics/Biophysical Chemistry. Protein-protein
interactions of multidomain proteins; disulfide bonded
domains; thrombomodulin, LRP, IkappaB; NMR, binding kinetics, binding thermodynamics, H/D exchange,
mass spectrometry. TEL: (858) 534-3058 FAX: (858)
534-6174
Web: www.chem.ucsd.edu/Faculty/bios/komives.html
Email: ekomives@ucsd.edu
Xiaohua Wu, Zhi-fang Li, Randolph Brooks, Elizabeth A.
Komives, Justin W. Torpey, Eva Engvall, Steven L. Gonias
and G. Diane Shelton, Autoantibodies in Canine Masticatory
Muscle Myositis Recognize a Novel Myosin Binding Protein-C Family Member, J. Immunol, 179, 4939-4944 (2007).
Diego U. Ferreiro, Carla F. Cervantes, Stephanie M. E.
Truhlar, Samuel S. Cho, Peter G. Wolynes and Elizabeth A.
Komives, Stabilizing I␬B␣ by “Consensus” Design, J. Mol.
Biol, 365, 1201-1216 (2007).
Joachim Laetzer, Garegin A. Papoian, Michael C. Prentiss,
Elizabeth A. Komives and Peter G. Wolynes, Induced Fit,
Folding, and Recognition of the NF-␬B-Nuclear Localization
Signals by I␬B␣ and I␬B␤, J. Mol. Biol, 367, 262-274
(2007).
Ganesh S. Anand, Matthew Hotchko, Simon H. J. Brown,
Lynn F. Ten Eyck, Elizabeth A. Komives and Susan S. Taylor, R-subunit Isoform Specificity in Protein Kinase A: Distinct Features of Protein Interfaces in PKA Types I and II by
Amide H/2H Exchange Mass Spectrometry, J. Mol. Biol, 374,
487-499 (2007).
Dong-Yul Sung, David Lee, Hugh Harris, Andrea Raab,
Jorg Feldmann, Andrew Meharg, Bryan Kumabe, Elizabeth
A. Komives and Julian I. Schroeder, Identification of an arsenic tolerant double mutant with a thiol-mediated component
and increased arsenic tolerance in phyA mutants, Plant J, 49,
1064-1075 (2007).
Diego U. Ferreiro, Joseph A. Hegler, Elizabeth A. Komives and Peter G. Wolynes, Localizing frustration in native
proteins and protein assemblies, Proc. Natl. Acad. Sci. U. S.
A, 104, 19819-19824 (2007).
Diego U. Ferreiro and Elizabeth A. Komives, The plastic
landscape of repeat proteins, Proc. Natl. Acad. Sci. U. S. A,
104, 7735-7736 (2007).
Chun-Ming Huang, Justin W. Torpey, Yu-Tseung Liu,
Yun-Ru Chen, Katherine E. Williams, Elizabeth A. Komives
and Richard L. Gallo, A peptide with a ProGln C terminus in
the human saliva peptidome exerts bactericidal activity
against Propionibacterium acnes, Antimicrob. Agents Chemother, 52, 1834-1836 (2008).
Julia R. Koeppe, Muneera A. Beach, Abel Baerga-Ortiz, S.
Jordan Kerns and Elizabeth A. Komives, Mutations in the
Fourth EGF-like Domain Affect Thrombomodulin-Induced
Changes in the Active Site of Thrombin, Biochemistry, 47,
10933-10939 (2008).
Doug Barrick, Diego U. Ferreiro and Elizabeth A. Komives, Folding landscapes of ankyrin repeat proteins: Experi-
1950, Bucknell University; Ph.D, 1954, California Institute of Technology. Fellowship, 1955-1956, Howard
Hughes Medical Institute. Molecular structure, function
and evolution of proteins and other biologically important molecules; x-ray diffraction crystallography; site directed mutagenesis. TEL: (626) 794-6352 FAX: (858)
534-4864
Email: jkraut@ucsd.edu
joek@chem.ucsd.edu
No publication information submitted for this edition.
KUBIAK, CLIFFORD P. (b.1953) Harold C. Urey
Professor. B.Sc, 1975, Brown University; Ph.D, 1980,
University of Rochester. Postdoctoral Associate, 19801981, M. I. T. Inorganic Chemistry; Materials Chemistry. Inorganic and materials chemistry. Electron and
atom transfer chemistry. Effects of ultrafast intramolecular reactions on IR spectra. Molecular electronics and nanoscience. Energy conversion. Carbon dioxide conversion. TEL: (858) 822-2665 FAX: (858) 822-4442
Web: kubiak.ucsd.edu
Email: ckubiak@ucsd.edu
Clifford P. Kubiak and Eugenio Simon-Manso, Nickel
complexes with carbonyl, isocyanide and carbene ligands,
Comprehensive Organometallic Chemistry III, 8, 1-26
(2007).
Benjamin J. Lear, Starla D. Glover, J. Catherine Salsman,
Casey H. Londergan and Clifford P. Kubiak, Solvent dynamical control of ultrafast ground state electron transfer: implications for class II-III mixed valency, J. Am. Chem. Soc, 129,
12772-12779 (2007).
Benjamin J. Lear and Clifford P. Kubiak, Origins of cooperative noncovalent host-guest chemistry in mixed valence
complexes, J. Phys. Chem. B, 111, 6766-6771 (2007).
Timi P. Singa, Antonio G. DiPasquale, Arnold L. Rheingold and Clifford P. Kubiak, Bis(2, 6-dimethyphenyl isocyanide) gold (I) tetrafluoridoborate, Acta Cryst, E64, m1221
(2008).
John C. Goeltz and Clifford P. Kubiak, Mixed Valence
Self-Assembled Monolayers: Electrostatic Polarizabilities of
the Mixed Valence States, J. Phys. Chem. C, 112, 8114-8116
(2008).
Starla D. Glover, Benjamin J. Lear, Jennifer C. Salsman,
Casey H. Londergan and Clifford P. Kubiak, Electron transfer at the class II/III borderline of mixed valency: Dependence of rates on solvent dynamics and observation of a localized-to-delocalized transitioin in freezing solvents, Phil.
Trans. Roy. Soc. A, 366, 177-185 (2008).
J. Catherine Salsman and Clifford P. Kubiak, Infrared
spectroelectrochemical investigations of ultrafast electron
transfer in mixed-valence complexes, Spectroelectrochem,
123-144 (2008).
Benjamin J. Lear, The effects of electronic delocalization
in highly coupled mixed valence systems. (D)
John C. Stires IV, Charge transfer complexes in molecular
electronics: Approaching metallic conduction. (D)
7
Jonathan B. Caballero, Chemical sensor development leading to an alternative glucose detection method. (D)
KUMMEL, A. C. (b.1959) Professor. B.S, 1981, Yale
University; M.S, 1984, Stanford University; Ph.D, 1988,
Stanford University. 1988, Cornell University. Deposition of oxides on compound semiconductors to form passive interfaces for use in MOSFETs: STM/STS structure
determination of the oxide/semiconductor interface;
Computational modeling of absorbates, oxides, and defects on compounds semiconductor surfaces; Deposition
of organo-metallic films for use in ChemFET sensors;
Chemical Dynamics of gas-surface reaction. TEL: (858)
534-3368 FAX: (858) 534-2063
Web: www.chem-faculty.ucsd.edu/kummel/
Email: ack@chem.ucsd.edu
akummel@ucsd.edu
Publication list has not been verified by the department.
D. L. Winn, T. J. Grassman and A. C. Kummel, Electronic
properties of adsorbates on In0.37Ga0.63As(001)-(2 × 4), ECS
Trans, 11, 441-449 (2007).
M. J. Hale, S. I. Yi, J. Z. Sexton, A. C. Kummel and M.
Passlack, Scanning tunneling microscopy and spectroscopy
of gallium oxide deposition and oxidation on GaAs(001)-c
(2×8)/(2×4). [Erratum to document cited in CA140:009103],
J. Chem. Phys, 127, 049902/1 (2007).
KYTE, JACK (b.1946) Professor Emeritus. B.A, 1967,
Carleton College; Ph.D, 1972, Harvard University. Postdoctoral Fellowship, 1972-1974, University of California, San Diego. Enzymology, active transport, biomembrane, membrane proteins, pharmacological receptors.
TEL: (858) 534-3281 FAX: (858) 534-4864
Email: jkyte@ucsd.edu
No publication information submitted for this edition.
LINDENBERG, KATJA (b.1941) Distinguished Professor. B.A, 1962, Alfred University; Ph.D, 1967, Cornell University. Postdoctoral Fellowship, 1967-1969,
University of Rochester. Chemical Physics; Theoretical
Chemistry. Stochastic processes and their applications,
nonlinear systems, nonequilibrium statistical mechanics,
pulse propagation in granular materials. TEL: (858) 5343285 FAX: (858) 534-7244
Web: hypatia.ucsd.edu
Email: klindenberg@ucsd.edu
A. H. Romero, A. M. Lacasta, J. M. Sancho and Katja Lindenberg, Numerical study of A + A 씮 0 and A + B 씮 0 reactions with inertia, J. Chem. Phys, 127, 174506/1-174506/7
(2007).
J. M. Sancho, A. H. Romero, A. M. Lacasta and Katja Lindenberg, Langevin dynamics of A + A reactions in one dimension, J. Phys.: Condens. Matter, 19, 065108/1-065108/
12 (2007).
J. J. Ruiz-Lorenzo, Santos B. Yuste and Katja Lindenberg,
Simulations for trapping reactions with subdiffusive traps
and subdiffusive particles, J. Phys.: Condens. Matter, 19,
065120/1-065120/12 (2007).
Kevin Wood, C. Van den Broeck, V. Kawai and Katja Lindenberg, Continuous and discontinuous phase transitions and
partial synchronization in stochastic three-state oscillators,
Los Alamos Natl. Lab., Prepr. Arch., Condens. Matter, 1-10
(2007).
Santos Bravo Yuste, J. Klafter and Katja Lindenberg,
Number of distinct sites visited by a subdiffusive random
walker, Los Alamos Natl. Lab., Prepr. Arch., Condens. Matter, 1-4 (2007).
S. B. Yuste and Katja Lindenberg, The subdiffusive target
problem: Survival probability, Los Alamos Natl. Lab., Prepr.
Arch., Condens. Matter, 1-5 (2007).
Francisco J. Cao, Kevin Wood and Katja Lindenberg,
Noise-induced phase transitions in field-dependent relaxational dynamics: the Gaussian ansatz, Los Alamos Natl. Lab.,
Prepr. Arch., Condens. Matter, 1-9 (2007).
Kevin Wood, C. Van den Broeck, R. Kawai and Katja Lindenberg, Effects of disorder on synchronization of discrete
phase-coupled oscillators, Phys. Rev. E: Stat., Nonlinear, Soft
Matter Phys, 75, 041107/1-041107/11 (2007).
Kevin Wood, C. Van den Broeck, R. Kawai and Katja Lindenberg, Continuous and discontinuous phase transitions and
partial synchronization in stochastic three-state oscillators,
Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys, 76, 041132/
1-041132/9 (2007).
Francisco J. Cao, Kevin Wood and Katja Lindenberg,
Noise-induced phase transitions in field-dependent relaxational dynamics: the Gaussian ansatz, Phys. Rev. E: Stat.,
Nonlinear, Soft Matter Phys, 76, 051111/1-051111/9 (2007).
S. B. Yuste and Katja Lindenberg, Subdiffusive target
problem: survival probability, Phys. Rev. E: Stat., Nonlinear,
Soft Matter Phys, 76, 051114/1-051114/6 (2007).
Kevin Wood, C. Van den Broeck, R. Kawai and Katja Lindenberg, Continuous and discontinuous phase transitions and
partial synchronization in stochastic three-state oscillators.
[Erratum to document cited in CA148:086141], Phys. Rev. E:
Stat., Nonlinear, Soft Matter Phys, 76, 059901/1 (2007).
Kevin Wood, C. Van den Broeck, R. Kawai and Katja Lindenberg, Fluctuation theorem for entropy production during
effusion of an ideal gas with momentum transfer, Phys. Rev.
8
CALIFORNIA, SAN DIEGO
E: Stat., Nonlinear, Soft Matter Phys, 75, 061116/1-061116/8
(2007).
Katja Lindenberg, J. M. Sancho, A. M. Lacasta and I. M.
Sokolov, Dispersionless Transport in a Washboard Potential,
Phys. Rev. Lett, 98, 020602/1-020602/4 (2007).
Alexandre Rosas, Aldo H. Romero, Vitali F. Nesterenko
and Katja Lindenberg, Observation of Two-Wave Structure
in Strongly Nonlinear Dissipative Granular Chains, Phys.
Rev. Lett, 98, 164301/1-164301/4 (2007).
Massimiliano Esposito and Katja Lindenberg, Continuous
time random walk for open systems: fluctuation theorems
and counting statistics, arXiv.org, e-Print Arch., Condens.
Matter, 1-13 (2008).
Alexandre Rosas, Aldo H. Romero, Vitali F. Nesterenko
and Katja Lindenberg, Short pulse dynamics in strongly nonlinear dissipative granular chains, arXiv.org, e-Print Arch.,
Condens. Matter, 1-16 (2008).
I. M. Sokolov, S. B. Yuste, J. J. Ruiz-Lorenzo and Katja
Lindenberg, Mean field model of coagulation and annihilation reactions of a subdiffusive species, arXiv.org, e-Print
Arch., Condens. Matter, 1-9 (2008).
Ramon Reigada, Javier Buceta, Jordi Gomez, Francesc Sagues and Katja Lindenberg, Phase separation in three-component lipid membranes: From Monte Carlo simulations to
Ginzburg-Landau equations, J. Chem. Phys, 128, 025102/1025102/10 (2008).
M. Khoury, A. M. Lacasta, J. M. Sancho, A. H. Romero
and Katja Lindenberg, Charged particle transport in antidot
lattices in the presence of magnetic and electric fields: Langevin approach, Phys. Rev. B, 78, 155433/1-155433/9
(2008).
S. B. Yuste, G. Oshanin, Katja Lindenberg, O. Benichou
and J. Klafter, Survival probability of a particle in a sea of
mobile traps: A tale of tails, Phys. Rev. E, 78, 021105/1021105/7 (2008).
S. B. Yuste, J. Klafter and Katja Lindenberg, Number of
distinct sites visited by a subdiffusive random walker, Phys.
Rev. E, 77, 032101/1-032101/3 (2008).
A. Rosas, A. H. Romero, V. F. Nesterenko and Katja Lindenberg, Short-pulse dynamics in strongly nonlinear dissipative granular chains, Phys. Rev. E, 78, 051303/1-051303/10
(2008).
Massimiliano Esposito and Katja Lindenberg, Continuoustime random walk for open systems: Fluctuation theorems
and counting statistics, Phys. Rev. E: Stat., Nonlinear, Soft
Matter Phys, 77, 051119/1-051119/12 (2008).
Kevin Wood, Nonequilibrium phase transitions in stochastic spatially extended systems. (D)
MAGDE, DOUGLAS (b.1942) Professor. B.S, 1963,
Boston College; M.S, 1968, Cornell University; Ph.D,
1970, Cornell University. Postdoctoral Resident Associate, 1970-1972, Cornell University; Postdoctoral Resident Associate, 1972-1974, Washington State University.
Biophysics/Biophysical Chemistry; Physical Chemistry.
Femtosecond lasers; hemoglobin, guanylatecyclase and
other heme enzymes; inorganic photochemistry, chemical sensors, and general photophysical chemistry. TEL:
(858) 534-3199 FAX: (858) 822-2563
Email: dmagde@ucsd.edu
Edith C. Glazer, Douglas Magde and Yitzhak Tor, Ruthenium Complexes That Break the Rules: Structural Features
Controlling Dual Emission, J. Am. Chem. Soc, 129, 85448551 (2007).
MARTI, K. (b.1936) Professor Emeritus. M.S, 1963,
University of Berne; Ph.D, 1965, University of Berne.
Postgraduate Resident Chemist, 1965-1968, University
of California, San Diego; Guggenheim Fellowship, 1976.
Variations in isotopic compositions and origin of the
chemical elements; extinct elements; nuclear reactions
induced by cosmic rays; history of the moon, history of
Mars, the meteorites and the solar system. TEL: (858)
534-2939 FAX: (858) 534-7441
Email: kmarti@ucsd.edu
Publication list has not been verified by the department.
A. J. T. Jull, D. Lal, S. Taylor, R. Wieler, A. Grimberg, L.
Vacher, L. R. McHargue, S. P. H. T. Freeman, C. Maden, C.
Schnabel, S. Xu, R. C. Finkel, K. J. Kim and K. Marti, 3He,
20,21,22Ne, 14C, 10Be, 26Al, and 36Cl in magnetic fractions of
cosmic dust from Greenland and Antarctica, Meteorit. Planet. Sci, 42, 1831-1840 (2007).
K. V. Ponganis and K. Marti, Nitrogen components in
IAB/IIICD iron meteorites, Meteorit. Planet. Sci, 42, 331346 (2007).
MCCAMMON, J. ANDREW (b.1947) Joseph E.
Mayer Professor of Theoretical Chemistry. A.B, 1969,
Pomona College; A.M, 1970, Harvard University; Ph.D,
1976, Harvard University. NSF Postdoctoral Fellowship,
1976-1977, Harvard University; NIH Postdoctoral Fellowship, 1977-1978, Harvard University. Biophysics/
Biophysical Chemistry; Chemical Physics. We use theoretical and computational methods to study biological
molecules. Most of our work uses methods from statistical mechanics. These methods range from computer simulations of molecular behavior to purely theoretical
work. The studies show, for example, how a substrate
may be attracted to the active site of an enzyme by electrostatic interactions. We also use these methods for
computer-aided drug discovery. TEL: (858) 534-2905
FAX: (858) 534-4974
Web: mccammon.ucsd.edu/
Email: jmccammon@ucsd.edu
Alemayehu A. Gorfe, Arneh Babakhani and J. Andrew
McCammon, Free energy profile of H-ras membrane anchor
upon membrane insertion, Angew. Chem., Int. Ed, 46, 82348237 (2007).
Riccardo Baron and J. Andrew McCammon, Dynamics,
Hydration, and Motional Averaging of a Loop-Gated Artificial Protein Cavity: The W191G Mutant of Cytochrome c
Peroxidase in Water as Revealed by Molecular Dynamics
Simulations, Biochemistry, 46, 10629-10642 (2007).
Yuhui Cheng, Jason K. Suen, Zoran Radic, Stephen D.
Bond, Michael J. Holst and J. Andrew McCammon, Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models, Biophys. Chem, 127, 129-139 (2007).
Xiaolin Cheng, Ivaylo Ivanov, Hailong Wang, Steven M.
Sine and J. Andrew McCammon, Nanosecond-timescale conformational dynamics of the human ␣7 nicotinic acetylcholine receptor, Biophys. J, 93, 2622-2634 (2007).
Yuhui Cheng, Jason K. Suen, Deqiang Zhang, Stephen D.
Bond, Yongjie Zhang, Yuhua Song, Nathan A. Baker, Chandrajit L. Bajaj, Michael J. Holst and J. Andrew McCammon,
Finite element analysis of the time-dependent Smoluchowski
equation for acetylcholinesterase reaction rate calculations,
Biophys. J, 92, 3397-3406 (2007).
Joanna Trylska, Valentina Tozzini, Chia-en A. Chang and
J. Andrew McCammon, HIV-1 protease substrate binding
and product release pathways explored with coarse-grained
molecular dynamics, Biophys. J, 92, 4179-4187 (2007).
Arneh Babakhani, Alemayehu A. Gorfe, Justin Gullingsrud, Judy E. Kim and J. Andrew McCammon, Peptide insertion, positioning, and stabilization in a membrane: insight
from an all-atom molecular dynamics simulation, Biopolymers, 85, 490-497 (2007).
Jesper Soerensen, Donald Hamelberg, Birgit Schioett and
J. Andrew McCammon, Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation
mechanism, Biopolymers, 86, 73-82 (2007).
Chia-En A. Chang, Joanna Trylska, Valentina Tozzini and
J. Andrew McCammon, Binding pathways of ligands to
HIV-1 protease: coarse-grained and atomistic simulations,
Chem. Biol. Drug Des, 69, 5-13 (2007).
Cesar Augusto F. de Oliveira, Maurice Zissen, John Mongon and J. Andrew Mccammon, Molecular dynamics simulations of metalloproteinases types 2 and 3 reveal differences
in the dynamic behavior of the S1’ binding pocket, Curr.
Pharm. Des, 13, 3471-3475 (2007).
Richard H. Henchman and J. Andrew McCammon, Protein
structural flexibility: molecular motions, Handb. Proteins, 1,
166-171 (2007).
Alemayehu A. Gorfe, Arneh Babakhani and J. Andrew
McCammon, H-ras Protein in a Bilayer: Interaction and
Structure Perturbation, J. Am. Chem. Soc, 129, 12280-12286
(2007).
Yuhui Cheng, Xiaolin Cheng, Zoran Radic and J. Andrew
McCammon, Acetylcholinesterase: Mechanisms of Covalent
Inhibition of Wild-Type and H447I Mutant Determined by
Computational Analyses, J. Am. Chem. Soc, 129, 6562-6570
(2007).
Rommie E. Amaro, David D. L. Minh, Lily S. Cheng, William M. Lindstrom, Jr., Arthur J. Olson, Jung-Hsin Lin,
Wilfred W. Li and J. Andrew McCammon, Remarkable Loop
Flexibility in Avian Influenza N1 and Its Implications for
Antiviral Drug Design, J. Am. Chem. Soc, 129, 7764-7765
(2007).
Ivaylo Ivanov, Xiaolin Cheng, Steven M. Sine and J. Andrew McCammon, Barriers to Ion Translocation in Cationic
and Anionic Receptors from the Cys-Loop Family, J. Am.
Chem. Soc, 129, 8217-8224 (2007).
Li-Tien Cheng, Joachim Dzubiella, J. Andrew McCammon
and Bo Li, Application of the level-set method to the implicit
solvation of nonpolar molecules, J. Chem. Phys, 127,
084503/1-084503/10 (2007).
Ilja V. Khavrutskii and J. Andrew McCammon, Generalized gradient-augmented harmonic Fourier beads method
with multiple atomic and/or center-of-mass positional restraints, J. Chem. Phys, 127, 124901/1-124901/12 (2007).
Benzhuo Lu, Y. C. Zhou, Gary A. Huber, Stephen D.
Bond, Michael J. Holst and J. Andrew McCammon, Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution, J. Chem.
Phys, 127, 135102/1-135102/17 (2007).
David D. L. Minh, Donald Hamelberg and J. Andrew
McCammon, Accelerated entropy estimates with accelerated
dynamics, J. Chem. Phys, 127, 154105/1-154105/5 (2007).
David S. Cerutti, Nathan A. Baker and J. Andrew McCammon, Solvent reaction field potential inside an uncharged
globular protein: A bridge between implicit and explicit solvent models?, J. Chem. Phys, 127, 155101/1-155101/12
(2007).
Donald Hamelberg, Cesar Augusto F. de Oliveira and J.
Andrew McCammon, Sampling of slow diffusive conformational transitions with accelerated molecular dynamics, J.
Chem. Phys, 127, 155102/1-155102/9 (2007).
Cesar Augusto F. de Oliveira, Donald Hamelberg and J.
Andrew McCammon, Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in
explicit solvent as a case study, J. Chem. Phys, 127, 175105/
1-175105/8 (2007).
Benzhuo Lu and J. Andrew McCammon, Improved
Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations, J. Chem. Theory
Comput, 3, 1134-1142 (2007).
John Mongan, Carlos Simmerling, J. Andrew McCammon,
David A. Case and Alexey Onufriev, Generalized Born Model with a Simple, Robust Molecular Volume Correction, J.
Chem. Theory Comput, 3, 156-169 (2007).
J. Swanson, J. Wagoner, N. Baker and J. A. McCammon,
Optimizing the poisson dielectric boundary with explicit solvent simulations: lessons learned with atom-centered dielectric functions, J. Chem. Theory Comput, 3, 170-183 (2007).
Benzhuo Lu, Xiaolin Cheng and J. Andrew McCammon,
New-version-fast-multipole-method” accelerated electrostatic calculations in biomolecular systems, J. Comput. Phys,
226, 1348-1366 (2007).
Alemayehu A. Gorfe, Michael Hanzal-Bayer, Daniel
Abankwa, John F. Hancock and J. Andrew McCammon,
Structure and Dynamics of the Full-Length Lipid-Modified
H-Ras Protein in a 1,2-Dimyristoylglycero-3-phosphocholine
Bilayer, J. Med. Chem, 50, 674-684 (2007).
Barry J. Grant, J. Andrew McCammon, Leo S. D. Caves
and Robert A. Cross, Multivariate Analysis of Conserved Sequence-Structure Relationships in Kinesins: Coupling of the
Active Site and a Tubulin-binding Sub-domain, J. Mol. Biol,
368, 1231-1248 (2007).
Valentina Tozzini, Joanna Trylska, Chia-en Chang and J.
Andrew McCammon, Flap opening dynamics in HIV-1 protease explored with a coarse-grained model, J. Struct. Biol,
157, 606-615 (2007).
Philip R. Leduc, Michael S. Wong, Placid M. Ferreira,
Richard E. Groff, Kiryn Haslinger, Michael P. Koonce, Woo
Y. Lee, J. Christopher Love, J. Andrew McCammon, Nancy
A. Monteiro-Riviere, Vincent M. Rotello, Gary W. Rubloff,
Robert Westervelt and Minami Yoda, Towards an in vivo biologically inspired nanofactory, Nat. Nanotechnol, 2, 3-7
(2007).
Rommie E. Amaro, Robert V. Swift and J. Andrew
McCammon, Functional and structural insights revealed by
molecular dynamics simulations of an essential RNA editing
ligase in Trypanosoma brucei, PLoS Neglected Trop. Dis, 1,
No pp. given (2007).
Ivaylo Ivanov, John A. Tainer and J. Andrew McCammon,
Unraveling the three-metal-ion catalytic mechanism of the
DNA repair enzyme endonuclease IV, Proc. Natl. Acad. Sci.
U. S. A, 104, 1465-1470 (2007).
Donald Hamelberg, Tongye Shen and J. Andrew McCammon, A proposed signaling motif for nuclear import in
mRNA processing via the formation of arginine claw, Proc.
Natl. Acad. Sci. U. S. A, 104, 14947-14951 (2007).
Jacky Chi Ki Ngo, Justin Gullingsrud, Kayla Giang, Melinda Jean Yeh, Xiang-Dong Fu, Joseph A. Adams, J. Andrew McCammon and Gourisankar Ghosh, SR Protein Kinase 1 Is Resilient to Inactivation, Structure (Cambridge,
MA, U. S.), 15, 123-133 (2007).
Robert V. Swift and J. Andrew McCammon, Catalytically
Requisite Conformational Dynamics in the mRNA-Capping
Enzyme Probed by Targeted Molecular Dynamics, Biochemistry, 47, 4102-4111 (2008).
Alemayehu A. Gorfe, Chia-en A. Chang, Ivaylo Ivanov
and J. Andrew McCammon, Dynamics of the acetylcholinesterase tetramer, Biophys. J, 94, 1144-1154 (2008).
Alemayehu A. Gorfe, Riccardo Baron and J. Andrew
McCammon, Water-membrane partition thermodynamics of
an amphiphilic lipopeptide: an enthalpy-driven hydrophobic
effect, Biophys. J, 95, 3269-3277 (2008).
Yuhui Cheng, Chia-en A. Chang, Zeyun Yu, Yongjie
Zhang, Meihao Sun, Thomas S. Leyh, Michael J. Holst and J.
Andrew McCammon, Diffusional channeling in the sulfateactivating complex: combined continuum modeling and
coarse-grained Brownian dynamics studies, Biophys. J, 95,
4659-4667 (2008).
Sergio E. Wong, Riccardo Baron and J. Andrew McCammon, Hot-spot residues at the E9/Im9 interface help binding
via different mechanisms, Biopolymers, 89, 916-920 (2008).
Melissa R. Landon, Rommie E. Amaro, Riccardo Baron,
Chi Ho Ngan, David Ozonoff, J. Andrew McCammon and
Sandor Vajda, Novel druggable hot spots in avian influenza
neuraminidase H5N1 revealed by computational solvent
mapping of a reduced and representative receptor ensemble,
Chem. Biol. Drug Des, 71, 106-116 (2008).
Benzhuo Lu and J. Andrew McCammon, Molecular surface-free continuum model for electrodiffusion processes,
Chem. Phys. Lett, 451, 282-286 (2008).
Jennifer M. Bui and J. Andrew McCammon, Intrinsic conformational flexibility of acetylcholinesterase, Chem.-Biol.
Interact, 175, 303-304 (2008).
Riccardo Baron and J. Andrew McCammon, (Thermo)dynamic role of receptor flexibility, entropy, and motional
correlation in protein-ligand binding, ChemPhysChem, 9,
983-988 (2008).
B. Z. Lu, Y. C. Zhou, M. J. Holst and J. A. McCammon,
Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications, Commun. Comp.
Physics, 3, 973-1009 (2008).
Donald Hamelberg and J. Andrew McCammon, Dealing
CALIFORNIA, SAN DIEGO
with bound waters in a site: do they leave or stay?, Comput.
Struct. Approaches Drug Discovery, 95-110 (2008).
Daniel Abankwa, Michael Hanzal-Bayer, Nicolas Ariotti,
Sarah J. Plowman, Alemayehu A. Gorfe, Robert G. Parton, J.
Andrew McCammon and John F. Hancock, A novel switch
region regulates H-ras membrane orientation and signal output, EMBO J, 27, 727-735 (2008).
Z. Yu, M. Holst and J. A. McCammon, High-fidelity geometric modelling for biomedicine and other applications, Finite Elements in Analysis and Design, 44, 715-723 (2008).
Alemayehu A. Gorfe and J. Andrew McCammon, Similar
Membrane Affinity of Mono- and Di-S-acylated Ras Membrane Anchors: A New Twist in the Role of Protein Lipidation, J. Am. Chem. Soc, 130, 12624-12625 (2008).
Ilja V. Khavrutskii, Joachim Dzubiella and J. Andrew
McCammon, Computing accurate potentials of mean force in
electrolyte solutions with the generalized gradient-augmented
harmonic Fourier beads method, J. Chem. Phys, 128,
044106/1-044106/13 (2008).
Cesar Augusto F. de Oliveira, Donald Hamelberg and J.
Andrew McCammon, Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations, J. Chem. Theory Comput, 4, 1516-1525 (2008).
Ilja V. Khavrutskii, Mikolai Fajer and J. Andrew McCammon, Intrinsic Free Energy of the Conformational Transition
of the KcsA Signature Peptide from Conducting to Nonconducting State, J. Chem. Theory Comput, 4, 1541-1554
(2008).
Mikolai Fajer, Donald Hamelberg and J. Andrew McCammon, Replica-Exchange Accelerated Molecular Dynamics
(REXAMD) Applied to Thermodynamic Integration, J.
Chem. Theory Comput, 4, 1565-1569 (2008).
Rommie E. Amaro, Riccardo Baron and J. Andrew
McCammon, An improved relaxed complex scheme for receptor flexibility in computer-aided drug design, J. Comput.Aided Mol. Des, 22, 693-705 (2008).
Y. Zhou, M. Holst and J. A. McCammon, A nonlinear
elasticity model of macromolecular conformational change
induced by electrostatic forces, J. Math. Analysis Applic,
340, 135-164 (2008).
Lily S. Cheng, Rommie E. Amaro, Dong Xu, Wilfred W.
Li, Peter W. Arzberger and J. Andrew McCammon, Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase, J. Med.
Chem, 51, 3878-3894 (2008).
Zeyun Yu, Michael J. Holst, Yuhui Cheng and J. Andrew
McCammon, Feature-preserving adaptive mesh generation
for molecular shape modeling and simulation, J. Mol. Graphics Modell, 26, 1370-1380 (2008).
Arneh Babakhani, Alemayehu A. Gorfe, Judy E. Kim and
J. Andrew McCammon, Thermodynamics of Peptide Insertion and Aggregation in a Lipid Bilayer, J. Phys. Chem. B,
112, 10528-10534 (2008).
Riccardo Baron, Sergio E. Wong, Cesar A. F. de Oliveira
and J. Andrew McCammon, E9-Im9 Colicin DNase-Immunity Protein Biomolecular Association in Water: A MultipleCopy and Accelerated Molecular Dynamics Simulation
Study, J. Phys. Chem. B, 112, 16802-16814 (2008).
Y. C. Zhou, Benzhuo Lu, Gary A. Huber, Michael J. Holst
and J. Andrew McCammon, Continuum Simulations of Acetylcholine Consumption by Acetylcholinesterase: A PoissonNernst-Planck Approach, J. Phys. Chem. B, 112, 270-275
(2008).
Jianwei Che, Joachim Dzubiella, Bo Li and J. Andrew
McCammon, Electrostatic Free Energy and Its Variations in
Implicit Solvent Models, J. Phys. Chem. B, 112, 3058-3069
(2008).
David D. L. Minh and J. Andrew McCammon, Springs and
Speeds in Free Energy Reconstruction from Irreversible Single-Molecule Pulling Experiments, J. Phys. Chem. B, 112,
5892-5897 (2008).
Z. Yu, M. Holst, T. Hayashi, C. L. Bajaj, M. H. Ellisman,
J. A. McCammon and M. Hoshijima, Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: Bridging the gap between microscopic imaging
and mathematical simulation, J. Struct. Biol, 164, 304-313
(2008).
Shamila S. Gunatilleke, Cesar Augusto F. Oliveira, J. Andrew McCammon and Amy M. Barrios, Inhibition of cathepsin B by Au(I) complexes: a kinetic and computational study,
JBIC, J. Biol. Inorg. Chem, 13, 555-561 (2008).
Cameron Mura and J. Andrew McCammon, Molecular dynamics of a ␬B DNA element: base flipping via cross-strand
intercalative stacking in a microsecond-scale simulation,
Nucl. Acids Res, 36, 4941-4955 (2008).
Hai-Long Wang, Xiaolin Cheng, Palmer Taylor, J. Andrew
McCammon and Steven M. Sine, Control of cation permeation through the nicotinic receptor channel, PLoS Comput.
Biol, 4, No pp. given (2008).
Chia-en A. Chang, William A. McLaughlin, Riccardo Baron, Wei Wang and J. Andrew McCammon, Entropic contributions and the influence of the hydrophobic environment in
promiscuous protein-protein association, Proc. Natl. Acad.
Sci. U. S. A, 105, 7456-7461 (2008).
R. Amaro, A. Schnaufer, W. Hol, K. Stuart and J. A.
McCammon, Discovery of drug-like inhibitors of an essential
RNA editing ligase in Trypanosoma brucei, Proc. Natl.
Acad. Sci. USA, 106, 17278–17283 (2008).
Alemayehu A. Gorfe, Barry J. Grant and J. Andrew
McCammon, Mapping the Nucleotide and Isoform-Depen-
dent Structural and Dynamical Features of Ras Proteins,
Structure (Cambridge, MA, U. S.), 16, 885-896 (2008).
David Cerutti, Models for solvated biomolecular structures. (D)
David Minh, Free energy reconstruction from irreversible
single-molecule pulling experiments. (D)
Yuhui Cheng, Multiscale simulations of biochemically reacting systems. (D)
MCMORRIS, TREVOR C. (b.1930) Professor. B.S,
1952, London University; M.Sc, 1955, London University; Ph.D, 1958, London University. Interuniversity Fellow, Organic Chemistry, 1958-1959, London University,
Imperial College; Fellowship, Organic Chemistry, 19591960, University of Western Ontario. Chemistry of steroids and other natural products; isolation, structure elucidation and synthesis of sex hormones and other biologically active substances in fungi and higher plants; illudin analogs as new anticancer drugs. TEL: (858) 5344178 FAX: (858) 534-4864
Email: tmcmorris@ucsd.edu
Publication list has not been verified by the department.
Trevor C. McMorris, Ramesh Chimmani, Mahender Gurram, Michael D. Staake and Michael J. Kelner, Synthesis and
antitumor activity of amine analogs of irofulven, Bioorg.
Med. Chem. Lett, 17, 6770-6772 (2007).
MOLINA, MARIO J. (b.1943) Professor. Nobel
Prize, 1995, University of California, Berkeley. TEL:
(858) 534-1696 FAX: (858) 534-4864
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C04871
Email: mjmolina@ucsd.edu
Publication list has not been verified by the department.
Rainer Volkamer, Federico San Martini, Luisa T. Molina,
Dara Salcedo, Jose L. Jimenez and Mario J. Molina, A missing sink for gas-phase glyoxal in Mexico City: formation of
secondary organic aerosol, Geophys. Res. Lett, 34, L19807/1L19807/5 (2007).
Katja Dzepina, Janet Arey, Linsey C. Marr, Douglas R.
Worsnop, Dara Salcedo, Qi Zhang, Timothy B. Onasch, Luisa T. Molina, Mario J. Molina and Jose L. Jimenez, Detection of particle-phase polycyclic aromatic hydrocarbons in
Mexico City using an aerosol mass spectrometer, Int. J. Mass
Spectrom, 263, 152-170 (2007).
Andrey V. Ivanov, Sofia Trakhtenberg, Allan K. Bertram,
Yulii M. Gershenzon and Mario J. Molina, OH, HO2, and
Ozone Gaseous Diffusion Coefficients, J. Phys. Chem. A,
111, 1632-1637 (2007).
V. Faye McNeill, Franz M. Geiger, Thomas Loerting,
Bernhardt L. Trout, Luisa T. Molina and Mario J. Molina, Interaction of Hydrogen Chloride with Ice Surfaces: The Effects of Grain Size, Surface Roughness, and Surface Disorder, J. Phys. Chem. A, 111, 6274-6284 (2007).
Ryan C. Moffet, Yury Desyaterik, Rebecca J. Hopkins,
Alexei V. Tivanski, Mary K. Gilles, Y. Wang, V. Shutthanandan, Luisa T. Molina, Rodrigo Gonzalez Abraham, Kirsten
S. Johnson, Violeta Mugica, Mario J. Molina, Alexander
Laskin and Kimberly A. Prather, Characterization of Aerosols Containing Zn, Pb, and Cl from an Industrial Region of
Mexico City, Environ. Sci. Technol, 42, 7091-7097 (2008).
Jong-Ho Park, Andrey V. Ivanov and Mario J. Molina, Effect of Relative Humidity on OH Uptake by Surfaces of Atmospheric Importance, J. Phys. Chem. A, 112, 6968-6977
(2008).
MOLINSKI, TADEUSZ F. (b.1957) Professor. B.Sc,
1978, Monash University; Ph.D, 1985, Australian National University. Postdoctoral Fellow, 1984-1987,
Scripps Institution of Oceanography; Postdoctoral Fellow, 1987-1988, University of Utah; Visiting Chemist,
1988, UC San Diego; Assistant Professor, 1989-1995,
UC Davis; Associate Professor, 1995-1997, UC Davis;
Professor, 1997-2005, UC Davis. Natural Products
Chemistry; Organic Chemistry. Structure and synthesis
of marine natural products. Chiroptical methods in organic stereochemistry. NMR. ‘Nanomole-scale’ natural
products. Biological chemistry. Discovery of therapeutics for AIDS-related disease and cancer. TEL: (858)
534-7115 FAX: (858) 822-0386
Web: www-chem.ucsd.edu/Faculty/bios/molinski.html
Email: tmolinski@ucsd.edu
Tianzhong Yang, Eric Esteve, Isaac N. Pessah, Tadeusz F.
Molinski, Paul D. Allen and Jose R. Lopez, Elevated resting
[Ca2+]i in myotubes expressing malignant hyperthermia
RyR1 cDNAs is partially restored by modulation of passive
calcium leak from the SR, Am. J. Physiol, 292, C1591-C1598
(2007).
Anne Schuetz, Jochen Junker, Andrei Leonov, Oliver F.
Lange, Tadeusz F. Molinski and Christian Griesinger,
Stereochemistry of sagittamide A from residual dipolar coupling enhanced NMR, J. Am. Chem. Soc, 129, 15114-15115
(2007).
Colin K. Skepper, John B. MacMillan, Guang-Xiong
Zhou, Makoto N. Masuno and Tadeusz F. Molinski,
Chlorocyclopropane Macrolides from the Marine Sponge
9
Phorbas sp. Assignment of the Configurations of Phorbasides
A and B by Quantitative CD, J. Am. Chem. Soc, 129, 41504151 (2007).
Evan W. Rogers and Tadeusz F. Molinski, Highly Polar
Spiroisoxazolines from the Sponge Aplysina fulva, J. Nat.
Prod, 70, 1191-1194 (2007).
Tatyana N. Makarieva, Pavel S. Dmitrenok, Alexander M.
Zakharenko, Vladimir A. Denisenko, Alla G. Guzii, Ronghua
Li, Colin K. Skepper, Tadeusz F. Molinski and Valentin A.
Stonik, Rhizochalins C and D from the Sponge Rhizochalina
incrustata. A Rare threo-Sphingolipid and a Facile Method
for Determination of the Carbonyl Position in ␣,␻-Bifunctionalized Ketosphingolipids, J. Nat. Prod, 70, 1991-1998
(2007).
Jonel P. Saludes, Sarah C. Lievens and Tadeusz F. Molinski, Occurrence of the ␣-Glucosidase Inhibitor 1,4-Dideoxy1,4-imino-D-arabinitol and Related Iminopentitols in Marine
Sponges, J. Nat. Prod, 70, 436-438 (2007).
Brandon I. Morinaka, Colin K. Skepper and Tadeusz F.
Molinski, Ene-yne Tetrahydrofurans from the Sponge Xestospongia muta. Exploiting a Weak CD Effect for Assignment of Configuration, Org. Lett, 9, 1975-1978 (2007).
Evan W. Rogers and Tadeusz F. Molinski, Asymmetric
Synthesis of Diastereomeric Diaminoheptanetetraols. A Proposal for the Configuration of (+)-Zwittermicin A, Org. Lett,
9, 437-440 (2007).
Brandon I. Morinaka, Makoto N. Masuno, Joseph R. Pawlik and Tadeusz F. Molinski, Amaranzole A, a New N-Imidazolyl Steroid from Phorbas amaranthus, Org. Lett, 9, 52195222 (2007).
Brandon I. Morinaka and Tadeusz F. Molinski, Exciton
coupling circular dichroism of an allylic N-imidazolyl group
in amaranzole A, a marine natural product from Phorbas
amaranthus, Chirality, 20, 1066-1070 (2008).
Sepehr Dadsetan, Liudmila Zakharova, Tadeusz F. Molinski and Alla F. Fomina, Store-operated Ca2+ Influx Causes
Ca2+ Release from the Intracellular Ca2+ Channels That Is
Required for T Cell Activation, J. Biol. Chem, 283, 1251212519 (2008).
Colin K. Skepper and Tadeusz F. Molinski, Long-Chain
2H-Azirines with Heterogeneous Terminal Halogenation
from the Marine Sponge Dysidea fragilis, J. Org. Chem, 73,
2592-2597 (2008).
John B. MacMillan, Xiong-Zhou Guang, Colin K. Skepper
and Tadeusz F. Molinski, Phorbasides A-E, Cytotoxic
Chlorocyclopropane Macrolide Glycosides from the Marine
Sponge Phorbas sp. CD Determination of C-Methyl Sugar
Configurations, J. Org. Chem, 73, 3699-3706 (2008).
Colin K. Skepper, Doralyn S. Dalisay and Tadeusz F. Molinski, Synthesis and Antifungal Activity of (-)-(Z)-Dysidazirine, Org. Lett, 10, 5269-5271 (2008).
Evan W. Rogers, Zwittermicin A: Determination of its
complete configuration and total synthesis of its enantiomer.
(D)
Makoto N. Masuno, Synthesis and biological evaluation of
brominated marine natural product analogs that modulate teh
skeletal muscle FKBP12/calcium channel complex. (D)
MÜLLER, ULRICH F. (b.1969) Assistant Professor.
Ph.D, 2000, Darmstadt University of Technology. Postdoctoral Fellow, 2001-2006, Whitehead Institute. Biochemistry. TEL: (858) 534-6823 FAX: (858) 822-4442
Web: www-chem.ucsd.edu/Faculty/bios/muller.html
Email: ufmuller@ucsd.edu
No publication information submitted for this edition.
NAKAGAWA, TERUNAGA Assistant Professor.
M.D, 1996, University of Tokyo; Ph.D, 2000, University
of Tokyo. HFSP long term fellow, 2000-2001, MGH,
Harvard Medical School; HFSP long term fellow, 20012003, MIT; HHMI post-doctoral fellow, 2003-2005,
MIT. Biochemistry; Neuroscience. Structure and function of glutamate receptors. TEL: (858) 534-2974 FAX:
(858) 534-7042
K. Takao, K. Okamoto, T. Nakagawa, R. L. Neve, T. Nagai, A. Miyawaki, T. Hashikawa, S. Kobayashi and Y. Hayashi, Visualization of synaptic Ca2+ /calmodulin-dependent
protein kinase II activity in living neurons, J. Neurosci, 25,
3107-3112 (2005).
T. Nakagawa, Y. Cheng, E. Ramm, M. Sheng and T. Walz,
Structure and different conformational states of native
AMPA receptor complexes, Nature, 433, 545-549 (2005).
X. Chen, L. Vinade, R. D. Leapman, J. D. Petersen, T.
Nakagawa, T. M. Phillips, M. Sheng and T. S. Reese, Mass
of the post synaptic density and enumeration of three key
molecules, PNAS, 102, 11551-11556 (2005).
T. Nakagawa, Y. Cheng, M. Sheng and T. Walz, Three-dimensional structure of an AMPA receptor without associated
stargazin/TARP proteins, Biol. Chem, 387, 179-187 (2006).
T. Nakagawa, M. I. Feliu-Mojer, P. Wulf, C. Lois, M.
Sheng and C. C. Hoogenraad, Generation of lentiviral transgenic rats expressing glutamate receptor binding protein 1
(GRIP1) in brain, spinal cord, and testis, J. Neurosci. Methods, 152, 1-9 (2006).
D. Cheng, C. C. Hoogenraad, J. Rush, E. Ramm, M. A.
Schlager, D. M. Duong, P. Xu, S. R. Wijayawardana, J. Hanfelt, T. Nakagawa, M. Sheng and J. Peng, Relative and absolute quantification of postsynaptic density proteome isolated
10
CALIFORNIA, SAN DIEGO
from rat forebrain and cerebellum, Mol. Cell. Proteomics,
5(6), 1158-1170 (2006).
Audrey Fischer, Consuelo Garcia-Rodriguez, Isin Geren,
Jianlong Lou, James D. Marks, Terunaga Nakagawa and
Mauricio Montal, Molecular Architecture of Botulinum Neurotoxin E Revealed by Single Particle Electron Microscopy,
J. Biol. Chem, 283, 3997-4003 (2008).
Terunaga Nakagawa, Identification and characterization of
novel kinesin super family (KIF) proteins. (D)
NEWSAM, JOHN M. Adjunct Professor. B.A, 1976,
Oxford University; M.A, 1980, Oxford University;
D.Phil, 1980, Oxford University. Biomaterials; Materials Chemistry. Development and application of high
throughput experimentation for materials applications.
Use of HTE in discovery of catalytic materials. Use of
HTE in development of novel drug and other products
for application to the skin. Innovation. TEL: (858) 6776732 FAX: (858) 677-6737
Email: jnewsam@ucsd,edu
J. M. Newsam, R. D. King-Smith, A. Jain, P. Karande, I.
Feygin, J. Burbaum, T. R. Gowrishankar, M. Sergeeva and S.
Mitragotri, Screening soft materials for their effect on skin
barrier function by high throughput experimentation, J. Materials Chemistry, 15, 3061-3068 (2005).
R. D. King-Smith and J. M. Newsam, Accelerated development of topical and transdermal delivery systems, Skin Delivery Systems: Cosmetics, Dermatologicals, and Transdermals, 297-308 (2006).
NGUYEN-HUU, XUONG (b.1933) Professor Emeritus. B.S, 1955, Marseille EE Sch; M.S, 1958, Paris EE
Sch. and University of Paris; M.A, 1961, University of
California, Berkeley; Ph.D, 1962, University of California, Berkeley. Determination of 3-dimensional structures
of protein using x-ray diffraction method; development
of new instruments. TEL: (858) 534-2501 FAX: (858)
534-7042
Email: nxuong@ucsd.edu
No publication information submitted for this edition.
NICOLAOU, K. C. —See Chemistry Section, The
Scripps Research Institute, Department of Chemistry.
NICOLAOU, KYRIACOS
No publication information submitted for this edition.
NOEL, JOSEPH P. (b.1964) Adjunct Assistant Professor. B.S, 1985, University of Pittsburgh at Johnstown;
Ph.D, 1990, The Ohio State University. NSF Chemistry
Fellowship, 1990-1992, Yale University; NIH Fellowship, 1993-1994, Yale University. Structural and stereochemical analysis of signal transduction cascade and
cyclic terpenoid biosynthesis. TEL: (619) 453-4100 Ext.
1442 FAX: (619) 452-3683
Email: noel@sbl.salk.edu
Publication list has not been verified by the department.
Yan Zhang, Sebastian Daum, Dirk Wildemann, Xiao Zhen
Zhou, Mark A. Verdecia, Marianne E. Bowman, Christian
Lucke, Tony Hunter, Kun-Ping Lu, Gunter Fischer and Joseph P. Noel, Structural basis for high-affinity peptide inhibition of human Pin1, ACS Chem. Biol, 2, 320-328 (2007).
Michael B. Austin and Joseph P. Noel, Mechanisms of
type III polyketide synthase functional diversity: from ‘steric
modulation’ to the ‘reaction partitioning’ model, ACS Symp.
Ser, 955, 185-197 (2007).
Michelle C. Moffitt, Gordon V. Louie, Marianne E. Bowman, Janelle Pence, Joseph P. Noel and Bradley S. Moore,
Discovery of Two Cyanobacterial Phenylalanine Ammonia
Lyases: Kinetic and Structural Characterization, Biochemistry, 46, 1004-1012 (2007).
Shunji Takahashi, Yunsoo Yeo, Bryan T. Greenhagen,
Tom McMullin, Linsheng Song, Julie Maurina-Brunker, Reinhardt Rosson, Joseph P. Noel and Joe Chappell, Metabolic
engineering of sesquiterpene metabolism in yeast, Biotechnol. Bioeng, 97, 170-181 (2007).
Juan A. Faraldos, Yuxin Zhao, Paul E. O’Maille, Joseph P.
Noel and Robert M. Coates, Interception of the enzymatic
conversion of farnesyl diphosphate to 5-epi-aristolochene by
using a fluoro substrate analogue: 1-fluorogermacrene a from
(2E,6Z)-6-fluorofarnesyl diphosphate, ChemBioChem, 8,
1826-1833 (2007).
Yvonne Haagen, Inge Unsoeld, Lucia Westrich, Bertolt
Gust, Stephane B. Richard, Joseph P. Noel and Lutz Heide,
A soluble, magnesium-independent prenyltransferase catalyzes reverse and regular C-prenylations and O-prenylations
of aromatic substrates, FEBS Lett, 581, 2889-2893 (2007).
Shunji Takahashi, Yun-Soo Yeo, Yuxin Zhao, Paul E.
O’Maille, Bryan T. Greenhagen, Joseph P. Noel, Robert M.
Coates and Joe Chappell, Functional Characterization of
Premnaspirodiene Oxygenase, a Cytochrome P450 Catalyzing Regio- and Stereo-specific Hydroxylations of Diverse
Sesquiterpene Substrates, J. Biol. Chem, 282, 31744-31754
(2007).
Joseph P. Noel, Digging for answers, smelling a hint of
success and tasting triumph, Nat. Chem. Biol, 3, 690-691
(2007).
Wenyuan Wang, Jeffrey K. Takimoto, Gordon V. Louie,
Thomas J. Baiga, Joseph P. Noel, Kuo-Fen Lee, Paul A. Slesinger and Lei Wang, Genetically encoding unnatural amino
acids for cellular and neuronal studies, Nat. Neurosci, 10,
1063-1072 (2007).
Marina Varbanova, Shinjiro Yamaguchi, Yue Yang,
Katherine McKelvey, Atsushi Hanada, Roy Borochov, Fei
Yu, Yusuke Jikumaru, Jeannine Ross, Diego Cortes, Choong
Je Ma, Joseph P. Noel, Lew Mander, Vladimir Shulaev, Yuji
Kamiya, Steve Rodermel, David Weiss and Eran Pichersky,
Methylation of gibberellins by Arabidopsis GAMT1 and
GAMT2, Plant Cell, 19, 32-45 (2007).
Gordon V. Louie, Thomas J. Baiga, Marianne E. Bowman,
Takao Koeduka, John H. Taylor, Snejina M. Spassova, Eran
Pichersky and Joseph P. Noel, Structure and reaction mechanism of basil eugenol synthase, PLoS One, 2, No pp. given
(2007).
Thomas J. Baiga, Haibing Guo, Yalan Xing, George A.
O’Doherty, Andrew Dillin, Michael B. Austin, Joseph P.
Noel and James J. La Clair, Metabolite Induction of Caenorhabditis elegans Dauer Larvae Arises via Transport in the
Pharynx, ACS Chem. Biol, 3, 294-304 (2008).
Takuto Kumano, Stephane B. Richard, Joseph P. Noel,
Makoto Nishiyama and Tomohisa Kuzuyama, Chemoenzymatic syntheses of prenylated aromatic small molecules using Streptomyces prenyltransferases with relaxed substrate
specificities, Bioorg. Med. Chem, 16, 8117-8126 (2008).
Yi Tao, Jean-Luc Ferrer, Karin Ljung, Florence Pojer,
Fangxin Hong, Jeff A. Long, Lin Li, Javier E. Moreno, Marianne E. Bowman, Lauren J. Ivans, Youfa Cheng, Jason Lim,
Yunde Zhao, Carlos L. Ballare, Goran Sandberg, Joseph P.
Noel and Joanne Chory, Rapid synthesis of auxin via a new
tryptophan-dependent pathway is required for shade avoidance in plants, Cell (Cambridge, MA, U. S.), 133, 164-176
(2008).
Alessandra S. Eustaquio, Johannes Harle, Joseph P. Noel
and Bradley S. Moore, S-adenosyl-L-methionine hydrolase
(adenosine-forming), a conserved bacterial and archeal protein related to SAM-dependent halogenases, ChemBioChem,
9, 2215-2219 (2008).
Michael B. Austin, Paul E. O’Maille and Joseph P. Noel,
Evolving biosynthetic tangos negotiate mechanistic landscapes, Nat. Chem. Biol, 4, 217-222 (2008).
Paul E. O’Maille, Arthur Malone, Nikki Dellas, B. Andes
Hess, Jr., Lidia Smentek, Iseult Sheehan, Bryan T. Greenhagen, Joe Chappell, Gerard Manning and Joseph P. Noel,
Quantitative exploration of the catalytic landscape separating
divergent plant sesquiterpene synthases, Nat. Chem. Biol, 4,
617-623 (2008).
Alessandra S. Eustaquio, Florence Pojer, Joseph P. Noel
and Bradley S. Moore, Discovery and characterization of a
marine bacterial SAM-dependent chlorinase, Nat. Chem.
Biol, 4, 69-74 (2008).
Takao Koeduka, Gordon V. Louie, Irina Orlova, Christine
M. Kish, Mwafaq Ibdah, Curtis G. Wilkerson, Marianne E.
Bowman, Thomas J. Baiga, Joseph P. Noel, Natalia Dudareva and Eran Pichersky, The multiple phenylpropene synthases in both Clarkia breweri and Petunia hybrida represent
two distinct protein lineages, Plant J, 54, 362-374 (2008).
Nan Zhao, Jean-Luc Ferrer, Jeannine Ross, Ju Guan, Yue
Yang, Eran Pichersky, Joseph P. Noel and Feng Chen, Structural, biochemical, and phylogenetic analyses suggest that indole-3-acetic acid methyltransferase is an evolutionarily ancient member of the SABATH family, Plant Physiol, 146,
455-467 (2008).
Sigal Savaldi-Goldstein, Thomas J. Baiga, Florence Pojer,
Tsegeye Dabi, Cristina Butterfield, Geraint Parry, Aaron
Santner, Nihal Dharmasiri, Yi Tao, Mark Estelle, Joseph P.
Noel and Joanne Chory, New auxin analogs with growth-promoting effects in intact plants reveal a chemical strategy to
improve hormone delivery, Proc. Natl. Acad. Sci. U. S. A,
105, 15190-15195 (2008).
O’CONNOR, JOSEPH M. Professor. Ph.D, 1984,
University of Wisconsin, Madison. Postdoctoral Fellowship, 1984, University of California, Berkeley. Organic
Chemistry; Organometallic Chemistry. Bioorganometallic chemistry; transition metal catalysts; alkyne and metallacycle chemistry; mechanistic and synthetic organometallic chemistry; metal-mediated organic trasformations. TEL: (858) 534-5836 FAX: (858) 534-5383
Email: jmoconno@ucsd.edu
Charles L. Perrin, Betsy L. Rodgers and Joseph M.
O’Connor, Nucleophilic Addition to a p-Benzyne Derived
from an Enediyne: A New Mechanism for Halide Incorporation into Biomolecules, J. Am. Chem. Soc, 129, 4795-4799
(2007).
Joseph M. O’Connor, Anna G. Wenzel and Kristin Hiibner, Iridium(III)-vinylidene chemistry: conversion of an
iridacyclopentadiene-chlorido complex and terminal alkynes
to iridacyclopentadiene-vinyl complexes, Inorg. Chim. Acta,
361, 3033-3041 (2008).
Ryan L. Holland, Kevin D. Bunker, Christopher H. Chen,
Antonio G. Di Pasquale, Arnold L. Rheingold, Kim K. Baldridge and Joseph M. O’Connor, Reactions of a Metallacyclobutene Complex with Alkenes, J. Am. Chem. Soc, 130,
10093-10095 (2008).
Oanh P. Lam, Patrick L. Feng, Frank W. Heinemann, Joseph M. O’Connor and Karsten Meyer, Charge-Separation in
Uranium Diazomethane Complexes Leading to C-H Activa-
tion and Chemical Transformation, J. Am. Chem. Soc, 130,
2806-2816 (2008).
Oanh P. Lam, Christian Anthon, Frank W. Heinemann, Joseph M. O’Connor and Karsten Meyer, Structural and Spectroscopic Characterization of a Charge-Separated Uranium
Benzophenone Ketyl Radical Complex, J. Am. Chem. Soc,
130, 6567-6576 (2008).
Joseph M. O’Connor and Seth J. Friese, Transition-Metal
Hydrides as Hydrogen Atom Donors: Stronger Metal-Hydrogen Bonds Can Be Advantageous, Organometallics, 27,
4280-4281 (2008).
OESTERREICHER, H. (b.1939) Professor. Ph.D,
1965, University of Vienna. Resident Associate, 19651966, University of Pittsburgh; Resident Associate,
1966-1967, Brookhaven National Laboratory; Resident
Associate, 1967, Cornell University. Structural, magnetic
and superconducting properties of metallic and semiconducting systems. TEL: (858) 534-4179 FAX: (858) 5344864
Email: joesterreicher@ucsd.edu
Publication list has not been verified by the department.
H. Oesterreicher, Superconductivity and Structure, J. Supercond. Novel Magn, 20, 201-213 (2007).
H. Oesterreicher, Phenomenological laws and charge order
concepts in high Tc superconductors, Phys. C (Amsterdam,
Neth.), 460, 362-363 (2007).
H. Oesterreicher, Plane isolation model for superconducting Tc prediction using an parent-calibration’ obtained for
YBa2CuCu2Oy and applied to other model systems, Solid
State Commun, 142, 583-586 (2007).
OPELLA, STANLEY J. (b.1947) Professor. B.S,
1969, University of Kentucky; Ph.D, 1974, Stanford
University. Postdoctoral Fellow, 1975-1976, M. I. T.
NMR Spectroscopy; Structural Biology. Development
and application of NMR spectroscopy for the study of
proteins. TEL: (858) 822-4820 FAX: (858) 822-4821
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C03864
Email: sopella@ucsd.edu
Publication list has not been verified by the department.
Sonja D. Mueller, Anna A. De Angelis, Torsten H. Walther, Stephan L. Grage, Christian Lange, Stanley J. Opella and
Anne S. Ulrich, Structural characterization of the pore forming protein TatAd of the twin-arginine translocase in membranes by solid-state 15N-NMR, Biochim. Biophys. Acta,
Biomembr, 1768, 3071-3079 (2007).
Sangwon Lee, Stephen B. Howell and Stanley J. Opella,
NMR and mutagenesis of human copper transporter 1
(hCtr1) show that Cys-189 is required for correct folding and
dimerization, Biochim. Biophys. Acta, Biomembr, 1768,
3127-3134 (2007).
Stanley J. Opella and Francesca M. Marassi, Nuclear magnetic resonance (NMR): solid state, Handb. Proteins, 2,
1129-1133 (2007).
Min-Ju Kim, Sang Ho Park, Stanley J. Opella, Thomas H.
Marsilje, Pierre-Yves Michellys, H. Martin Seidel and ShinShay Tian, NMR Structural Studies of Interactions of a
Small, Nonpeptidyl Tpo Mimic with the Thrombopoietin Receptor Extracellular Juxtamembrane and Transmembrane
Domains, J. Biol. Chem, 282, 14253-14261 (2007).
Alexander A. Nevzorov, Sang Ho Park and Stanley J.
Opella, Three-dimensional experiment for solid-state NMR
of aligned protein samples in high field magnets, J. Biomol.
NMR, 37, 113-116 (2007).
Christopher V. Grant, Siu-Ling Sit, Anna A. De Angelis,
Kelli S. Khuong, Chin H. Wu, Leigh A. Plesniak and Stanley
J. Opella, An efficient 1H/31P double-resonance solid-state
NMR probe that utilizes a scroll coil, J. Magn. Reson, 188,
279-284 (2007).
Bibhuti B. Das, T. G. Ajithkumar, Neeraj Sinha, Stanley J.
Opella and K. V. Ramanathan, Cross- and axial-peak intensities in 2D-SLF experiments based on cross-polarization-The
role of the initial density matrix, J. Magn. Reson, 185, 308317 (2007).
Neeraj Sinha, Christopher V. Grant, Sang Ho Park, Jonathan Miles Brown and Stanley J. Opella, Triple resonance experiments for aligned sample solid-state NMR of 13C and 15N
labeled proteins, J. Magn. Reson, 186, 51-64 (2007).
Alexander A. Nevzorov and Stanley J. Opella, Selective
averaging for high-resolution solid-state NMR spectroscopy
of aligned samples, J. Magn. Reson, 185, 59-70 (2007).
Neeraj Sinha, Fabian V. Filipp, Lena Jairam, Sang Ho
Park, Joel Bradley and Stanley J. Opella, Tailoring 13C labeling for triple-resonance solid-state NMR experiments on
aligned samples of proteins, Magn. Reson. Chem, 45, S107S115 (2007).
Anna A. De Angelis and Stanley J. Opella, Bicelle samples
for solid-state NMR of membrane proteins, Nat. Protoc, 2,
2332-2338 (2007).
Sang Ho Park and Stanley J. Opella, Conformational
changes induced by a single amino acid substitution in the
trans-membrane domain of Vpu: implications for HIV-1 susceptibility to channel blocking drugs, Protein Sci, 16, 22052215 (2007).
Stanley J. Opella, Ana Carolina Zeri and Sang Ho Park,
Structure, dynamics, and assembly of filamentous bacterio-
CALIFORNIA, SAN DIEGO
phages by nuclear magnetic resonance spectroscopy, Annu.
Rev. Phys. Chem, 59, 635-657 (2008).
Vitaly V. Vostrikov, Christopher V. Grant, Anna E. Daily,
Stanley J. Opella and Roger E. Koeppe, II, Comparison of
“Polarization Inversion with Spin Exchange at Magic Angle”
and “Geometric Analysis of Labeled Alanines” Methods for
Transmembrane Helix Alignment, J. Am. Chem. Soc, 130,
12584-12585 (2008).
Chin H. Wu and Stanley J. Opella, Shiftless nuclear magnetic resonance spectroscopy, J. Chem. Phys, 128, 052312/1052312/5 (2008).
Chin H. Wu and Stanley J. Opella, Proton-detected separated local field spectroscopy, J. Magn. Reson, 190, 165-170
(2008).
PAESANI, FRANCESCO (b.1971) Assistant Professor. Ph.D, 2000, University of Rome “La Sapienza”.
Postdoctoral Fellow, 2002-2005, University of California, Berkeley; Postdoctoral Researcher, 2005-2009, University of Utah. Physical Chemistry; Theoretical Chemistry. TEL: (858) 534-5658 FAX: (858) 534-7244
Web: paesanigroup.ucsd.edu
Email: fpaesani@ucsd.edu
R. E. Zillich, F. Paesani, Y. Kwon and K. B. Whaley, Path
integral methods for rotating molecules in superfluids, J.
Chem. Phys, 123, 114301 (2005).
F. Paesani, R. E. Zillich, Y. Kown and K. B. Whaley, OCS
in para-hydrogen clusters: Rotational dynamics and superfluidity, J. Chem. Phys, 122, 181106 (2005).
F. Paesani, Y. Kwon and K. B. Whaley, Onset of superfluidity in small CO2(4He)N clusters, Phys. Rev. Lett, 94,
153401 (2005).
F. Paesani, W. Zhang, T. E. Cheatham III, D. A. Case and
G. A. Voth, An accurate and simple quantum model for liquid water, J. Chem. Phys, 125, 184507 (2006).
F. Paesani and K. B. Whaley, Vibrational shifts of OCS in
mixed clusters of parahydrogen and helium, J. Chem. Phys,
124, 234310 (2006).
F. Paesani and K. B. Whaley, Potential energy surface and
infrared spectra of OCS hydrogen complexes, Mol. Phys,
104, 61 (2006).
Y. Kwon, F. Paesani and K. B. Whaley, Local superfluidity in inhomogeneous systems, Phys. Rev. B, 74, 174522
(2006).
F. Paesani, S. Iuchi and G. A. Voth, Quantum effects in
liquid water from an ab initio-based polarizable force field, J.
Chem. Phys, 127, 074506 (2007).
F. Paesani, K. B. Whaley, G. E. Douberly and R. E. Miller,
Rovibrational spectra for the HCCCN•HCN and
HCN•HCCCN binary complexes in 4He droplets, J. Phys.
Chem. A, 111, 7516 (2007).
F. Paesani and G. A. Voth, Nonlinear quantum time correlation functions from centroid molecular dynamics and the
maximum entropy method, J. Chem. Phys, 129, 194113
(2008).
Y. Wu, H. Chen, F. Wang, F. Paesani and G. A. Voth, An
improved multistate empirical valence bond model for aqueous proton transport, J. Phys. Chem. B, 112, 467 (2008).
O. Markovitch, H. Chen, S. Izvekov, F. Paesani, G. A.
Voth and N. Agmon, Statistical validation of the mechanism
of proton mobility, J. Phys. Chem. B, 112, 9456 (2008).
F. Paesani and G. A. Voth, Quantum effects strongly influence the surface premelting of ice, J. Phys. Chem. C, 112,
324 (2008).
PERRIN, CHARLES L. (b.1938) Professor. A.B,
1959, Harvard University; Ph.D, 1963, Harvard University. NSF Postdoctoral Fellowship, 1963, University of
California, Berkeley. Organic Chemistry; Physical Organic Chemistry. Physical-Organic Chemistry (Molecular Structure, and Mechanisms of Organic Reactions):
Substituent effects, proton exchange, dynamic NMR,
anomeric effects, isotope effects, stereoelectronic control, hydrogen bonding, conformational analysis, steric
hindrance to ionic solvation, malonic anhydrides, nonradical reactions of para-benzynes. TEL: (858) 534-2164
FAX: (858) 822-0386
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C00389
Email: cperrin@ucsd.edu
Charles L. Perrin and Yanmei Dong, Secondary Deuterium
Isotope Effects on the Acidity of Carboxylic Acids and Phenols, J. Am. Chem. Soc, 129, 4490-4497 (2007).
Charles L. Perrin, Betsy L. Rodgers and Joseph M.
O’Connor, Nucleophilic Addition to a p-Benzyne Derived
from an Enediyne: A New Mechanism for Halide Incorporation into Biomolecules, J. Am. Chem. Soc, 129, 4795-4799
(2007).
Charles L. Perrin and Yanmei Dong, Nonadditivity of Secondary Deuterium Isotope Effects on Basicity of Trimethylamine, J. Am. Chem. Soc, 130, 11143-11148 (2008).
Charles L. Perrin and Chen Zhao, Intramolecular kinetic
isotope effect in hydride transfer from dihydroacridine to a
quinolinium ion. Rejection of a proposed two-step mechanism with a kinetically significant intermediate, Org. Biomol.
Chem, 6, 3349-3353 (2008).
POMEROY, ROBERT S. (b.1958) LPSOE. Ph.D,
1990, University of Arizona. Post-doctoral Researcher,
1990-1992, Scripps Institution of Oceanography. Analytical Chemistry. Forensic science. I interact with a group
of colleagues interested in the application of Real Time
PCR to forensic analyses. Determining SNP genotype
frequencies in different ethnic groups, and most recently
the use of the BioTrove Open Array Platform for the
analysis of a SNP panel for use in human identification.
TEL: (858) 822-5736 FAX: (858) 534-7687
Email: rpomeroy@ucsd.edu
No publication information submitted for this edition.
PRATHER, KIMBERLY A. (b.1962) Professor.
B.Sc, 1985, University of California, Davis; Ph.D, 1990,
University of California, Davis. Postdoctoral Fellow,
1990-1992, University of California, Berkeley. Analytical Chemistry; Atmospheric Chemistry. Atmospheric,
physical, analytical chemistry: Field and laboratory investigations of gas/particle (heterogeneous) reaction processes of tropospheric significance using mass spectrometry and laser-based techniques. Understanding the role
of aerosols and their impacts on climate, regional weather and water supply, and human health. TEL: (858) 8225312 FAX: (858) 534-7042
Web: www.chem.ucsd.edu/Faculty/bios/prather.html
Email: kprather@ucsd.edu
Thomas P. Rebotier and Kimberly A. Prather, Aerosol
time-of-flight mass spectrometry data analysis: A benchmark
of clustering algorithms, Anal. Chim. Acta, 585, 38-54
(2007).
R. C. Sullivan, S. A. Guazzotti, D. A. Sodeman and K. A.
Prather, Direct observations of the atmospheric processing of
Asian mineral dust, Atmos. Chem. Phys, 7, 1213-1236
(2007).
Laura G. Shields, David T. Suess and Kimberly A. Prather,
Determination of single particle mass spectral signatures
from heavy-duty diesel vehicle emissions for PM2.5 source
apportionment, Atmos. Environ, 41, 3841-3852 (2007).
Ryan C. Sullivan, Sergio A. Guazzotti, David A. Sodeman,
Youhua Tang, Gregory R. Carmichael and Kimberly A.
Prather, Mineral dust is a sink for chlorine in the marine
boundary layer, Atmos. Environ, 41, 7166-7179 (2007).
Matthew T. Spencer, Laura G. Shields and Kimberly A.
Prather, Simultaneous Measurement of the Effective Density
and Chemical Composition of Ambient Aerosol Particles,
Environ. Sci. Technol, 41, 1303-1309 (2007).
Kerri A. Denkenberger, Ryan C. Moffet, John C. Holecek,
Thomas P. Rebotier and Kimberly A. Prather, Real-Time,
Single-Particle Measurements of Oligomers in Aged Ambient Aerosol Particles, Environ. Sci. Technol, 41, 5439-5446
(2007).
Ryan C. Sullivan and Kimberly A. Prather, Investigations
of the Diurnal Cycle and Mixing State of Oxalic Acid in Individual Particles in Asian Aerosol Outflow, Environ. Sci.
Technol, 41, 8062-8069 (2007).
J. Muhle, T. J. Lueker, Y. Su, B. R. Miller, K. A. Prather
and R. F. Weiss, Trace gas and particulate emissions from
the 2003 southern California wildfires, J. Geophy. Res, 112
(2007).
J. C. Holecek, M. T. Spencer and K. A. Prather, Analysis
of rainwater samples: Comparison of single particle residues
with ambient particle chemistry from the northeast Pacific
and Indian Oceans, J. Geophy. Res, 112 (2007).
L. G. Shields, X. Y. Qin, S. M. Toner and K. A. Prather,
Detection of ambient ultrafine aerosols by single particle
techniques during the SOAR 2005 campaign, Aer. Sci. Technol, 42, 674-684 (2008).
K. A. Prather, C. D. Hatch and V. H. Grassian, Analysis of
atmospheric aerosols, Annual Review of Analytical Chemistry, 1, 485-514 (2008).
R. C. Moffet, B. de Foy, L. T. Molina, M. J. Molina and K.
A. Prather, Measurement of ambient aerosols in northern
Mexico City by single particle mass spectrometry, Atmos.
Chem. Phys, 8, 4499-4516 (2008).
M. J. Cubison, B. Ervens, G. Feingold, K. S. Docherty, I.
M. Ulbrich, L. Shields, K. Prather, S. Hering and J. L. Jimenez, The influence of chemical composition and mixing state
of Los Angeles urban aerosol on CCN number and cloud
properties, Atmos. Chem. Phys, 8, 5649-5667 (2008).
H. Furutani, M. Dall’osto, G. C. Roberts and K. A. Prather,
Assessment of the relative importance of atmospheric aging
on CCN activity derived from field observations, Atmos. Environ, 42, 3130-3142 (2008).
Stephen M. Toner, Laura G. Shields, David A. Sodeman
and Kimberly A. Prather, Using mass spectral source signatures to apportion exhaust particles from gasoline and diesel
powered vehicles in a freeway study using UF-ATOFMS,
Atmos. Environ, 42, 568-581 (2008).
Weixiang Zhao, Philip K. Hopke and Kimberly A. Prather,
Comparison of two cluster analysis methods using single particle mass spectra, Atmos. Environ, 42, 881-892 (2008).
Ryan C. Moffet, Yury Desyaterik, Rebecca J. Hopkins,
Alexei V. Tivanski, Mary K. Gilles, Y. Wang, V. Shutthanandan, Luisa T. Molina, Rodrigo Gonzalez Abraham, Kirsten
S. Johnson, Violeta Mugica, Mario J. Molina, Alexander
Laskin and Kimberly A. Prather, Characterization of Aerosols Containing Zn, Pb, and Cl from an Industrial Region of
Mexico City, Environ. Sci. Technol, 42, 7091-7097 (2008).
M. T. Spencer, J. C. Holecek, C. E. Corrigan, V. Ramanathan and K. A. Prather, Size-resolved chemical composition
11
of aerosol particles during a monsoonal transition period over
the Indian Ocean, J. Geophy. Res, 113 (2008).
R. C. Moffet, X. Y. Qin, T. Rebotier, H. Furutani and K.
A. Prather, Chemically segregated optical and microphysical
properties of ambient aerosols measured in a single-particle
mass spectrometer, J. Geophy. Res, 113 (2008).
Matthew T. Spencer, Hiroshi Furutani, Steven J. Oldenburg, Thomas K. Darlington and Kimberly A. Prather, Gold
Nanoparticles as a Matrix for Visible-Wavelength SingleParticle Matrix-Assisted Laser Desorption/Ionization Mass
Spectrometry of Small Biomolecules, J. Phys. Chem. C, 112,
4083-4090 (2008).
Laura Shields, Single particle characterization, source apportionment, and aging effects of ambient aerosols in Southern California. (D)
Matthew Spencer, Approaches for the chemical and physical characterization of aerosols using a single particle mass
spectrometry based technique. (D)
Ryan Moffet, Measurements of the chemical, physical, and
optical properties of single aerosol particles. (D)
Ryan Sullivan, Heterogeneous chemistry of atmospheric
mineral dust particles and their resulting cloud-nucleation
properties. (D)
Stephen Toner, Anthropogenic particulate source characterization and source apportionment using aerosol time-offlight mass spectrometry. (D)
Xueying (Sharon) Qin, Characterization of ambient aerosol
composition and formation mechanisms and development of
quantification methodologies utilizing ATOFMS. (D)
RHEINGOLD, ARNOLD L. (b.1940) Professor.
A.B, 1962, Western Reserve University; M.S, 1963,
Western Reserve University; Ph.D, 1969, University of
Maryland. Research Associate, 1970, Virginia Polytechnic Institute. Inorganic Chemistry. Main-group organometallic chemistry; metal/main-group clusters; smallmolecule crystallography; polymorphism; thermoelectric
materials. TEL: (858) 822-3870 FAX: (858) 822-3872
Web: www-chem.ucsd.edu/Faculty/bios/rheingold.html
Email: arheingold@ucsd.edu
Christina S. Angle, Kathryn J. Woolard, Michael I. Kahn,
James A. Golen, Arnold L. Rheingold and Linda H. Doerrer,
Metallophilic interactions in iodido(2,2’:6’,2’’-terpyridine)
platinum(II) diiodidoaurate(I), Acta Crystallogr., Sect. C:
Cryst. Struct. Commun, C63, m231-m234 (2007).
Jason C. Sanchez, Antonio G. DiPasquale, Arnold L.
Rheingold and William C. Trogler, Synthesis, Luminescence
Properties, and Explosives Sensing with 1,1-Tetraphenylsilole- and 1,1-Silafluorene-vinylene Polymers, Chem. Mater, 19, 6459-6470 (2007).
Pirmin A. Ulmann, Aaron M. Brown, Maxim V. Ovchinnikov, Chad A. Mirkin, Antonio G. DiPasquale and Arnold L.
Rheingold, Spontaneous formation of heteroligated PtII complexes with chelating hemilabile ligands, Chem.—Eur. J, 13,
4529-4534 (2007).
Katie J. Heroux, Katrina S. Woodin, David J. Tranchemontagne, Peter C. B. Widger, Evan Southwick, Edward H.
Wong, Gary R. Weisman, Sterling A. Tomellini, Thaddeus J.
Wadas, Carolyn J. Anderson, Scott Kassel, James A. Golen
and Arnold L. Rheingold, The long and short of it: the influence of N-carboxyethyl versus N-carboxymethyl pendant
arms on in vitro and in vivo behavior of copper complexes of
cross-bridged tetraamine macrocycles, Dalton Trans, 21502162 (2007).
Jacky Chen, Robert Russo, Wilson Chao, Lawrence D.
Margerum, Mitchell R. Malachowski, Ryan White, Zachary
Thawley, Angelina Thayer, Arnold L. Rheingold and Lev N.
Zakharov, Synthesis, structure, redox properties and azide
binding for a series of biphenyl-based Cu(II) complexes,
Dalton Trans, 2571-2579 (2007).
John J. Eisch, Yun Qian and Arnold L. Rheingold, Nickel
(II)-carbene intermediates in reactions of geminal dihaloalkanes with nickel(0) reagents and the corresponding carbene
capture as the phosphonium ylide, Eur. J. Inorg. Chem,
1576-1584 (2007).
Jian Yuan, Russell P. Hughes and Arnold L. Rheingold,
The first example of a bis(trifluoromethyl)carbene transitionmetal complex and its reduction to a perfluoroallene complex, Eur. J. Inorg. Chem, 4723-4725 (2007).
Kil Sik Min, Antonio DiPasquale, Arnold L. Rheingold
and Joel S. Miller, Room-Temperature Spin Crossover Observed for [(TPyA)FeII(DBQ2-)FeII(TPyA)]2+ [TPyA = Tris
(2-pyridylmethyl)amine; DBQ2- = 2,5-Di-tert-butyl-3,6-dihydroxy-1,4-benzoquinonate], Inorg. Chem, 46, 1048-1050
(2007).
Konstantin I. Pokhodnya, Michael Bonner, Antonio G. DiPasquale, Arnold L. Rheingold, Jae-Hyuk Her, Peter W.
Stephens, Jong-Won Park, Bretni S. Kennon, Atta M. Arif
and Joel S. Miller, Structural and Magnetic Properties of
MCl2 (M = Fe, Mn, Co): Acetonitrile Solvates, Inorg. Chem.
(Washington, DC, U. S.), 46, 2471-2477 (2007).
Eduardo E. Chufan, Claudio N. Verani, Simona C. Puiu,
Eva Rentschler, Ulrich Schatzschneider, Christopher Incarvito, Arnold L. Rheingold and Kenneth D. Karlin, Generation
and Characterization of [(P)M-(X)-Co(TMPA)]n+ Assemblies; P = Porphyrinate, M = FeIII and CoIII, X = O2-, OH-,
O22-, and TMPA = Tris(2-pyridylmethyl)amine, Inorg. Chem.
(Washington, DC, U. S.), 46, 3017-3026 (2007).
Sonia Nieto, Julio Perez, Lucia Riera, Victor Riera, Daniel
12
CALIFORNIA, SAN DIEGO
Miguel, James A. Golen and Arnold L. Rheingold, Pyrazole
Complexes as Anion Receptors: Effects of Changing the
Metal, the Pyrazole Substitution Pattern, and the Number of
Pyrazole Ligands, Inorg. Chem. (Washington, DC, U. S.), 46,
3407-3418 (2007).
Helen W. Richter, Gerald F. Koser, Christopher D. Incarvito and Arnold L. Rheingold, Preparation and Structure of a
Solid-State Hypervalent-Iodine Polymer Containing Iodine
and Oxygen Atoms in Fused 12-Atom Hexagonal Rings,
Inorg. Chem. (Washington, DC, U. S.), 46, 5555-5561
(2007).
Dong-Heon Lee, Lanying Q. Hatcher, Michael A. Vance,
Ritimukta Sarangi, Ashley E. Milligan, Amy A. Narducci
Sarjeant, Christopher D. Incarvito, Arnold L. Rheingold,
Keith O. Hodgson, Britt Hedman, Edward I. Solomon and
Kenneth D. Karlin, Copper(I) Complex O2-Reactivity with a
N3S Thioether Ligand: a Copper-Dioxygen Adduct Including
Sulfur Ligation, Ligand Oxygenation, and Comparisons with
All Nitrogen Ligand Analogues, Inorg. Chem. (Washington,
DC, U. S.), 46, 6056-6068 (2007).
Anthony E. Wetherby, Jr., Lindy R. Goeller, Antonio G.
DiPasquale, Arnold L. Rheingold and Charles S. Weinert,
Synthesis and Structures of an Unusual Germanium(II) Calix
[4]arene Complex and the First Germanium(II) Calix[8]arene
Complex and Their Reactivity with Diiron Nonacarbonyl,
Inorg. Chem. (Washington, DC, U. S.), 46, 7579-7586
(2007).
Julie A. Cissell, Thomas P. Vaid, Antonio G. DiPasquale
and Arnold L. Rheingold, Germanium Phthalocyanine, GePc,
and the Reduced Complexes SiPc(pyridine)2 and GePc(pyridine)2 Containing Antiaromatic ␲-Electron Circuits, Inorg.
Chem. (Washington, DC, U. S.), 46, 7713-7715 (2007).
Yonglian Zhang, Hong-Chang Liang, Lev N. Zakharov,
Sanjib K. Das, Marcel M. Hetu and Arnold L. Rheingold,
Carboxyester hydrolysis promoted by Cu(II) complexes of
pyridyl-amine carboxylate-pendant ligands, Inorg. Chim.
Acta, 360, 1691-1701 (2007).
Jose L. Lamboy, Antonio Pasquale, Arnold L. Rheingold
and Enrique Melendez, Synthesis, solution and solid state
structure of titanium-maltol complex, Inorganica Chimica
Acta, 360, 2115-2120 (2007).
Kil Sik Min, Antonio G. DiPasquale, James A. Golen, Arnold L. Rheingold and Joel S. Miller, Synthesis, Structure,
and Magnetic Properties of Valence Ambiguous Dinuclear
Antiferromagnetically Coupled Cobalt and Ferromagnetically Coupled Iron Complexes Containing the Chloranilate(2-)
and the Significantly Stronger Coupling Chloranilate(•3-)
Radical Trianion, J. Am. Chem. Soc, 129, 2360-2368 (2007).
Kil Sik Min, Antonio G. DiPasqual, James A. Golen, Arnold L. Rheingold, Atta M. Arif and Joel S. Miller, Synthesis, structure, and magnetic properties of valence ambiguous
dinuclear antiferromagnetically coupled cobalt and ferromagnetically coupled iron complexes containing the chloranilate
(2-) and the significantly stronger coupling chloranilate(•3-)
radical trianion. [Erratum to document cited in CA146:
393663], J. Am. Chem. Soc, 129, 6056 (2007).
Natalia F. Blank, Jillian R. Moncarz, Tim J. Brunker, Corina Scriban, Brian J. Anderson, Omar Amir, David S. Glueck,
Lev N. Zakharov, James A. Golen, Christopher D. Incarvito
and Arnold L. Rheingold, Palladium-Catalyzed Asymmetric
Phosphination. Scope, Mechanism, and Origin of Enantioselectivity, J. Am. Chem. Soc, 129, 6847-6858 (2007).
Jennifer E. Sprague, Yijie Peng, Ashley L. Fiamengo, Katrina S. Woodin, Evan A. Southwick, Gary R. Weisman, Edward H. Wong, James A. Golen, Arnold L. Rheingold and
Carolyn J. Anderson, Synthesis, Characterization and In
Vivo Studies of Cu(II)-64-Labeled Cross-Bridged Tetraazamacrocycle-amide Complexes as Models of Peptide Conjugate Imaging Agents, J. Med. Chem, 50, 2527-2535 (2007).
Harry W. Gibson, Hong Wang, Carla Slebodnick, Joseph
Merola, W. Scott Kassel and Arnold L. Rheingold, Isomeric
2,6-Pyridino-Cryptands Based on Dibenzo-24-crown-8, J.
Org. Chem, 72, 3381-3393 (2007).
Jinqiang Zhang, Feihe Huang, Ning Li, Hong Wang, Harry
W. Gibson, Peter Gantzel and Arnold L. Rheingold, Paraquat
Substituent Effect on Complexation with a Dibenzo-24crown-8-Based Cryptand, J. Org. Chem, 72, 8935-8938
(2007).
Brenna L. Ghent, Sarah L. Martinak, Lauren A. Sites,
James A. Golen, Arnold L. Rheingold and Chip Nataro, Electrochemistry and complexation of Josiphos ligands, J. Organomet. Chem, 692, 2365-2374 (2007).
Tim J. Brunker, Brian J. Anderson, Natalia F. Blank, David S. Glueck and Arnold L. Rheingold, Enantioselective
Synthesis of P-Stereogenic Benzophospholanes via Palladium-Catalyzed Intramolecular Cyclization, Org. Lett, 9, 11091112 (2007).
Cameron K. Gren, Timothy P. Hanusa and Arnold L.
Rheingold, Threefold Cation-␲ Bonding in Trimethylsilylated Allyl Complexes, Organometallics, 26, 1643-1649
(2007).
Corina Scriban, David S. Glueck, James A. Golen and Arnold L. Rheingold, Platinum-Catalyzed Asymmetric Alkylation of a Secondary Phosphine: Mechanism and Origin of
Enantioselectivity, Organometallics, 26, 1788-1800 (2007).
Cheryl J. Bourgeois, Hui Huang, Roman B. Larichev, Lev
N. Zakharov, Arnold L. Rheingold and Russell P. Hughes,
Variable-Temperature NMR Determination of the Barriers to
Rotation about the Ir-C ␴-Bond in a Series of Primary Perfluoroalkyl Iridium Complexes [IrCp*{(CF2)nCF3}(PMe3)2]+
X- [n = 1, 2, 3, 5, 7, 9, 11; X = I, OTf], Organometallics, 26,
264-271 (2007).
Douglas B. Grotjahn, Xi Zeng, Andrew L. Cooksy, W.
Scott Kassel, Antonio G. DiPasquale, Lev. N. Zakharov and
Arnold L. Rheingold, Experimental and Computational
Study of the Transformation of Terminal Alkynes to Vinylidene Ligands on trans-(Chloro)bis(phosphine)Rh Fragments
and Effects of Phosphine Substituents, Organometallics, 26,
3385-3402 (2007).
William J. Evans, Kevin A. Miller, Stosh A. Kozimor, Joseph W. Ziller, Antonio G. DiPasquale and Arnold L. Rheingold, Actinide Hydride Complexes as Multielectron Reductants: Analogous Reduction Chemistry from [(C5Me5)2UH]2,
[(C5Me5)2UH2]2, and [(C5Me5)2ThH2]2, Organometallics, 26,
3568-3576 (2007).
William J. Evans, Kevin A. Miller, Joseph W. Ziller, Antonio G. DiPasquale, Katie J. Heroux and Arnold L. Rheingold,
Formation of (C5Me5)2U(EPh)Me, (C5Me5)2U(EPh)2, and
(C5Me5)2U(␩2-TeC6H4) from (C5Me5)2UMe2 and PhEEPh (E
= S, Se, Te), Organometallics, 26, 4287-4293 (2007).
William J. Evans, Daniel B. Rego, Joseph W. Ziller, Antonio G. DiPasquale and Arnold L. Rheingold, Facile Insertion
of CO2 into Tetra- and Pentamethylcyclopentadienyl Lanthanide Moieties To Form (C5Me4RCO2)- Carboxylate Ligands (R = H, Me), Organometallics, 26, 4737-4745 (2007).
K. Brian Davis, T. David Harris, Michael P. Castellani,
James A. Golen and Arnold L. Rheingold, Synthesis and xray Crystal Structure of [(C5Ph5)CrCl(␮-Cl)2Tl]2: An Example of the Rare M-X-TlI Linkage (X = Halide), Organometallics, 26, 4843-4845 (2007).
Corina Scriban, David S. Glueck, James A. Golen and Arnold L. Rheingold, Platinum-catalyzed asymmetric alkylation
of a secondary phosphine: Mechanism and origin of enantioselectivity. [Erratum to document cited in CA146:
422111], Organometallics, 26, 5124 (2007).
Nicole A. Ketterer, Joseph W. Ziller, Arnold L. Rheingold
and Alan F. Heyduk, Imido and Organometallic-Amido Titanium(IV) Complexes of a Chelating Phenanthrenediamide
Ligand, Organometallics, 26, 5330-5338 (2007).
Gerd W. Rabe, Florian A. Riederer, Mei Zhang-Presse and
Arnold L. Rheingold, A Partially Demethylated Donor-Functionalized Terphenyl Lanthanide Compound, Organometallics, 26, 5724-5726 (2007).
Lyudmila Leontyeva, Russell P. Hughes and Arnold L.
Rheingold, An Unusual Migratory Insertion of CO into a
Pentamethylcyclopentadienyl-Platinum Bond, Organometallics, 26, 5735-5736 (2007).
Anand Sundararaman, Resmi Varughese, Haiyan Li, Lev
N. Zakharov, Arnold L. Rheingold and Frieder Jaekle, A Donor-Acceptor Dyad with a Highly Lewis Acidic Boryl Group,
Organometallics, 26, 6126-6131 (2007).
Julie A. DuPont, Michael B. Coxey, Peter J. Schebler,
Christopher D. Incarvito, William B. Dougherty, Glenn P. A.
Yap, Arnold L. Rheingold and Charles G. Riordan, HighSpin Organocobalt(II) Complexes in a Thioether Coordination Environment, Organometallics, 26, 971-979 (2007).
Daniel P. Kennedy, Antonio G. DiPasquale, Arnold L.
Rheingold and Roy P. Planalp, Ni(II)-mediated synthesis of
the novel tripodal aminopyridyl ligand tamepyr: Coordination geometry and rigidity of complexes with the divalent 3d
metals Fe-Zn and with In(III), Polyhedron, 26, 197-203
(2007).
Christopher C. Beedle, Katie J. Heroux, Motohiro Nakano,
Antonio G. DiPasquale, Arnold L. Rheingold and David N.
Hendrickson, Antiferromagnetic tetranuclear manganese
complex: Wheel or dicubane?, Polyhedron, 26, 2200-2206
(2007).
Timi P. Singa, Antonio G. DiPasquale, Arnold L. Rheingold and Clifford P. Kubiak, Bis(2,6-dimethylphenyl isocyanide-.kappa.C)gold(I) tetrafluoridoborate, Acta Crystallographica, Section E: Structure Reports Online, E64, m1221/1m1221/7 (2008).
William J. Evans, Kevin A. Miller, Antonio G. DiPasquale, Arnold L. Rheingold, Timothy J. Stewart and Robert
Bau, A crystallizable f-element tuck-in complex: the tuck-in
tuck-over uranium metallocene [(C5Me5)U{␮-␩5:␩1:␩1C5Me3(CH2)2}(␮-H)2U(C5Me5)2], Angew. Chem., Int. Ed, 47,
5075-5078 (2008).
Kil Sik Min, Krzysztof Swierczek, Antonio G. DiPasquale,
Arnold L. Rheingold, William M. Reiff, Atta M. Arif and
Joel S. Miller, A dinuclear iron(ii) complex, [(TPyA)FeII
(THBQ2-)FeII(TPyA)](BF4)2 [TPyA = tris(2-pyridylmethyl)
amine; THBQ2- = 2,3,5,6-tetrahydroxy-1,4-benzoquinonate]
exhibiting both spin crossover with hysteresis and ferromagnetic exchange, Chem. Commun. (Cambridge, U. K.), 317319 (2008).
Ami Doshi, Krishnan Venkatasubbaiah, Arnold L. Rheingold and Frieder Jaekle, Binary stacks of [CuC6F5]4 with arenes, Chem. Commun. (Cambridge, U. K.), 4264-4266
(2008).
Arnold L. Rheingold, Antonio G. DiPasquale and Peter A.
Beckmann, The relationship between crystal structure and
NMR relaxation in molecular solids with tert-butyl groups,
Chem. Phys, 345, 116-118 (2008).
Krishnan Venkatasubbaiah, Ami Doshi, Israel Nowik,
Rolfe H. Herber, Arnold L. Rheingold and Frieder Jakle, Examination of the mixed-valence state of the doubly boronbridged diferrocene cation [(FeCp)2{␮-C10H6(BPh)2}]+,
Chem.—Eur. J, 14, 444-458 (2008).
Konstantin I. Pokhodnya, Michael Bonner, Antonio G. DiPasquale, Arnold L. Rheingold and Joel S. Miller, Acetoni-
trile-facilitated reductive dimerization of TCNE to octacyanobutanediide, [C4(CN)8]2-, by iron(II) chloride, Chem.—Eur.
J, 14, 714-720 (2008).
Peter M. Iovine, Charles R. Gyselbrecht, Emily K. Perttu,
Cole Klick, Alexander Neuwelt, Jason Loera, Antonio G. Di
Pasquale, Arnold L. Rheingold and Jeremy Kua, Hetero-arylboroxines: the first rational synthesis, X-ray crystallographic
and computational analysis, Dalton Trans, 3791-3794
(2008).
Roman Dembinski, Pablo Espinet, Sergio Lentijo, Marcin
W. Makowicz, Jose M. Martin-Alvarez, Arnold L. Rheingold, Daniel J. Schmidt and Adam Sniady, Fluorophobic effect in metallomesogens the synthesis and mesomorphism of
Ag, Au, Cu, Fe, Pd, and Pt fluorous isocyanide complexes,
European Journal of Inorganic Chemistry, 1565-1572
(2008).
Harry W. Gibson, Hong Wang, Chin P. Chng, Thomas E.
Glass, Daniel Schoonover, Lev N. Zakharov and Arnold L.
Rheingold, Synthesis and conformational analysis of a small
meta-cyclophane,
bis(5-carbomethoxy-1,3-phenylene)-14crown-4, Heteroatom Chemistry, 19, 48-54 (2008).
William J. Evans, Justin R. Walensky, Filipp Furche, Joseph W. Ziller, Antonio G. DiPasquale and Arnold L. Rheingold, Synthesis of (C5Me5)2(C5Me4H)UMe, (C5Me5)2(C5H5)
UMe, and (C5Me5)2UMe[CH(SiMe3)2] from Cationic Metallocenes for the Evaluation of Sterically Induced Reduction,
Inorg. Chem. (Washington, DC, U. S.), 47, 10169-10176
(2008).
Lihua Liu, Lev N. Zakharov, James A. Golen, Arnold L.
Rheingold and Tracy A. Hanna, Synthesis and Characterization of Bismuth(III) and Antimony(III) Calixarene Complexes, Inorg. Chem. (Washington, DC, U. S.), 47, 1114311153 (2008).
William J. Evans, Elizabeth Montalvo, Dustin J. Dixon, Joseph W. Ziller, Antonio G. DiPasquale and Arnold L. Rheingold, Lanthanide metallocene complexes of the 1,3,4,6,7,8Hexahydro-2H-pyrimido[1,2-a]pyrimidinato ligand, (hpp)1-,
Inorg. Chem. (Washington, DC, U. S.), 47, 11376-11381
(2008).
Anthony E. Wetherby, Jr., Lindy R. Goeller, Antonio G.
DiPasquale, Arnold L. Rheingold and Charles S. Weinert,
Metal-dependent reactions of bulky metal(II) amides M[N
with
3,3’-disubstituted
binaphthols
(SiMe3)2]2
(HO)2C20H10(SiR3)2-3,3’: selective conversion of one equivalent -OH group to a silyl ether -OSiMe3, Inorg. Chem.
(Washington, DC, U. S.), 47, 2162-2170 (2008).
Sonali J. Shah, Christopher M. Ramsey, Katie J. Heroux,
James R. O’Brien, Antonio G. DiPasquale, Arnold L. Rheingold, Enrique del Barco and David N. Hendrickson, WheelShaped Mn16 Single-Molecule Magnets, Inorg. Chem.
(Washington, DC, U. S.), 47, 6245-6253 (2008).
Kendric J. Nelson, Antonio G. DiPasquale, Arnold L.
Rheingold, Matthew C. Daniels and Joel S. Miller, Structure
and Properties of [CrIIIF(NCMe)5](BF4)2·MeCN: A Nonaqueous Source of CrIIIF2+ and a Building Block for New Prussian-Blue-Like Magnetic Materials, Inorg. Chem. (Washington, DC, U. S.), 47, 7768-7774 (2008).
Brian J. Fox, Queena Y. Sun, Antonio G. DiPasquale,
Alexander R. Fox, Arnold L. Rheingold and Joshua S. Figueroa, Solution Behavior and Structural Properties of Cu(I)
Complexes Featuring m-Terphenyl Isocyanides, Inorg.
Chem. (Washington, DC, U. S.), 47, 9010-9020 (2008).
Sonali J. Shah, Christopher M. Ramsey, Katie J. Heroux,
Antonio G. DiPasquale, Naresh S. Dalal, Arnold L. Rheingold, Enrique del Barco and David N. Hendrickson, Molecular Wheels: New Mn12 Complexes as Single-Molecule Magnets, Inorg. Chem. (Washington, DC, U. S.), 47, 9569-9582
(2008).
Hyojong Yoo, Chad A. Mirkin, Antonio G. DiPasquale,
Arnold L. Rheingold and Charlotte L. Stern, Reversible COInduced Chloride Shuttling in RhI Tweezer Complexes Containing Urea-Functionalized Hemilabile Ligands, Inorg.
Chem. (Washington, DC, U. S.), 47, 9727-9729 (2008).
H. Christopher Fry, Heather R. Lucas, Lev N. Zakharov,
Arnold L. Rheingold, Gerald J. Meyer and Kenneth D. Karlin, Intermolecular versus intramolecular electron-/atom- (Cl)
transfer in heme-iron and copper pyridylalkylamine complexes, Inorg. Chim. Acta, 361, 1100-1115 (2008).
Annalese F. Maddox, Arnold L. Rheingold, James A. Golen, W. Scott Kassel and Chip Nataro, Taniaphos and Walphos ligands: Oxidative electrochemistry and complexation.
Synthesis, characterization, oxidative electrochemistry and
X-ray structures of [(Taniaphos/Walphos)MCl2] (M = Pd or
Pt), Inorg. Chim. Acta, 361, 3283-3293 (2008).
Phillip Moheno, Wolfgang Pfleiderer, Antonio G. DiPasquale, Arnold L. Rheingold and Dietmar Fuchs, Cytokine and
IDO metabolite changes effected by calcium pterin during inhibition of MDA-MB-231 xenograph tumors in nude mice,
Int. J. Pharm, 355, 238-248 (2008).
Ryan L. Holland, Kevin D. Bunker, Christopher H. Chen,
Antonio G. Di Pasquale, Arnold L. Rheingold, Kim K. Baldridge and Joseph M. O’Connor, Reactions of a Metallacyclobutene Complex with Alkenes, J. Am. Chem. Soc, 130,
10093-10095 (2008).
Valentin Miranda-Soto, Douglas B. Grotjahn, Antonio G.
DiPasquale and Arnold L. Rheingold, Imidazol-2-yl Complexes of Cp*Ir as Bifunctional Ambident Reactants, J. Am.
Chem. Soc, 130, 13200-13201 (2008).
Dayna L. Turner, Thomas P. Vaid, Peter W. Stephens,
Kevin H. Stone, Antonio G. DiPasquale and Arnold L.
CALIFORNIA, SAN DIEGO
Rheingold, Semiconducting Lead-Sulfur-Organic Network
Solids, J. Am. Chem. Soc, 130, 14-15 (2008).
William J. Evans, Elizabeth Montalvo, Timothy M. Champagne, Joseph W. Ziller, Antonio G. DiPasquale and Arnold
L. Rheingold, Organolanthanide-Based Synthesis of 1,2,3Triazoles from Nitriles and Diazo Compounds, J. Am. Chem.
Soc, 130, 16-17 (2008).
Daesung Chong, Derek R. Laws, Ayman Nafady, Paulo
Jorge Costa, Arnold L. Rheingold, Maria Jose Calhorda and
William E. Geiger, [Re(␩5-C5H5)(CO)3]+ Family of 17-Electron Compounds: Monomer/Dimer Equilibria and Other Reactions, J. Am. Chem. Soc, 130, 2692-2703 (2008).
William J. Evans, Benjamin M. Schmiege, Sara E. Lorenz,
Kevin A. Miller, Timothy M. Champagne, Joseph W. Ziller,
Antonio G. Di Pasquale and Arnold L. Rheingold, Reductive
Reactivity of the Organolanthanide Hydrides, [
(C5Me5)2LnH]x, Leads to ansa-Allyl Cyclopentadienyl (␩5C5Me4CH2-C5Me4CH2-␩3)2- and Trianionic Cyclooctatetraenyl (C8H7)3- Ligands, J. Am. Chem. Soc, 130, 8555-8563
(2008).
Derek R. Laws, Daesung Chong, Karen Nash, Arnold L.
Rheingold and William E. Geiger, Cymantrene radical cation
family: spectral and structural characterization of the halfsandwich analogues of ferrocenium ion, J. Am. Chem. Soc,
130, 9859-9870 (2008).
Xianlong Wang, Arnold L. Rheingold, Antonio G. DiPasquale, Frank B. Mallory, Clelia W. Mallory and Peter A.
Beckmann, The quenching of isopropyl group rotation in van
der Waals molecular solids, J. Chem. Phys, 128, 124502/1124502/3 (2008).
Matt L. Childers, Joonhyung Cho, Celeste A. S. Regino,
Martin W. Brechbiel, Antonio G. DiPasquale, Arnold L.
Rheingold, Suzy V. Torti, Frank M. Torti and Roy P. Planalp, Influence of ligand structure on Fe(II) spin-state and redox rate in cytotoxic tripodal chelators, J. Inorg. Biochem,
102, 150-156 (2008).
Zhenfu Han, Thomas P. Vaid and Arnold L. Rheingold,
Hexakis(4-(N-butylpyridylium))benzene: A Six-Electron Organic Redox System, J. Org. Chem, 73, 445-450 (2008).
Monika L. Amadoruge, Antonio G. DiPasquale, Arnold L.
Rheingold and Charles S. Weinert, Hydrogermolysis reactions involving the ␣-germylated nitriles R3GeCH2CN (R =
Ph, Pri, But) and germanium amides R3GeNMe2 (R = Pri, But
) with Ph3GeH: Substituent-dependent reactivity and crystal
structures of Pri3GeGePh3 and But3Ge[NHC(CH3)CHCN], J.
Organomet. Chem, 693, 1771-1778 (2008).
Katherine A. McArthur, Scott S. Mitchell, Ginger Tsueng,
Arnold Rheingold, Donald J. White, Jennifer Grodberg, Kin
S. Lam and Barbara C. M. Potts, Lynamicins A-E, chlorinated bisindole pyrrole antibiotics from a novel marine actinomycete, Journal of Natural Products, 71, 1732-1737 (2008).
Jason C. Sanchez, Sara A. Urbas, Sarah J. Toal, Antonio
G. DiPasquale, Arnold L. Rheingold and William C. Trogler,
Catalytic Hydrosilylation Routes to Divinylbenzene Bridged
Silole and Silafluorene Polymers. Applications to Surface
Imaging of Explosive Particulates, Macromolecules (Washington, DC, U. S.), 41, 1237-1245 (2008).
Craig D. Sergeant, Ingo Ott, Adam Sniady, Srinivasarao
Meneni, Ronald Gust, Arnold L. Rheingold and Roman
Dembinski, Metallo-nucleosides: synthesis and biological
evaluation of hexacarbonyl dicobalt 5-alkynyl-2’-deoxyuridines, Org. Biomol. Chem, 6, 73-80 (2008).
Brian J. Anderson, Marites A. Guino-o, David S. Glueck,
James A. Golen, Antonio G. DiPasquale, Louise M. LiableSands and Arnold L. Rheingold, Platinum-Catalyzed Enantioselective Tandem Alkylation/Arylation of Primary Phosphines. Asymmetric Synthesis of P-Stereogenic 1-Phosphaacenaphthenes, Org. Lett, 10, 4425-4428 (2008).
Thomas M. Cameron, Chongying Xu, Antonio G. Dipasquale and Arnold L. Rheingold, Synthesis and Structure of
Strontium and Barium Guanidinates and Mixed-Ligand
Guanidinate Pentamethylcyclopentadienyl Complexes, Organometallics, 27, 1596-1604 (2008).
Monika L. Amadoruge, James A. Golen, Arnold L. Rheingold and Charles S. Weinert, Preparation, Structure, and Reactivity of Discrete Branched Oligogermanes, Organometallics, 27, 1979-1984 (2008).
Thilagar Pakkirisamy, Krishnan Venkatasubbaiah, W.
Scott Kassel, Arnold L. Rheingold and Frieder Jakle, Examination of the Pyridine Binding to the Bifunctional Lewis
Acid B,B’-Diphenyldiboradiferrocene, Organometallics, 27,
3056-3064 (2008).
William J. Evans, Elizabeth Montalvo, Timothy M. Champagne, Joseph W. Ziller, Antonio G. DiPasquale and Arnold
L. Rheingold, Diazomethane Insertion into Lanthanide- and
Yttrium-C(allyl) Bonds To Form the ␩2-Hydrazonato Complexes (C5Me5)2Ln[␩2(N,N’)-RNN=CHSiMe3] (R = C3H5),
Organometallics, 27, 3582-3586 (2008).
Douglas B. Grotjahn, Xi Zeng, Andrew L. Cooksy, W.
Scott Kassel, Antonio G. DiPasquale, Lev N. Zakharov and
Arnold L. Rheingold, Experimental and Computational
Study of the Transformation of Terminal Alkynes to Vinylidene Ligands on trans-(Chloro)bis(phosphine)Rh Fragments
and Effects of Phosphine Substituents. [Erratum to document
cited in CA147:212016], Organometallics, 27, 3626 (2008).
Brian J. Anderson, David S. Glueck, Antonio G. DiPasquale and Arnold L. Rheingold, Substrate and Catalyst
Screening in Platinum-Catalyzed Asymmetric Alkylation of
Bis(secondary) Phosphines. Synthesis of an Enantiomerically
Pure C2-Symmetric Diphosphine, Organometallics, 27,
4992-5001 (2008).
Theodor Agapie, Lawrence M. Henling, Antonio G. DiPasquale, Arnold L. Rheingold and John E. Bercaw, Zirconium and Titanium Complexes supported by tridentate LX2 ligands having two phenolates linked to Furan, Thiophene, and
Pyridine donors: Precatalysts for propylene polymerization
and oligomerization, Organometallics, 27, 6245-6256
(2008).
Joerg Eppinger, Katharina R. Nikolaides, Mei ZhangPresse, Florian A. Riederer, Gerd W. Rabe and Arnold L.
Rheingold, Alkyl Complexes of Rare-Earth Metal Centers
Supported by Chelating 1,1’-Diamidoferrocene Ligands:
Synthesis, Structure, and Application in Methacrylate Polymerization, Organometallics, 27, 736-740 (2008).
Anthony E. Wetherby, Arnold L. Rheingold, Christa L.
Feasley and Charles S. Weinert, Synthesis and crystal structure of a germanium(II) calix[6]arene containing unusual
diamidosilyl ether groups, Polyhedron, 27, 1841-1847
(2008).
Hui Huang, Russell P. Hughes and Arnold L. Rheingold,
Synthesis and structural characterization of a coordinatively
unsaturated ruthenium complex, Cp*Ru(Ph2nacnac), and its
CO adduct, Polyhedron, 27, 734-738 (2008).
You-Moon Jeon, Dongwoo Kim, Chad A. Mirkin, James
A. Golen and Arnold L. Rheingold, Pyrene-appended fluorescent tweezers generated via the Weak-Link Approach and
their halide recognition properties, Tetrahedron, 64, 84288434 (2008).
SAILOR, MICHAEL J. (b.1961) Professor. B.S,
1983, Harvey Mudd College; Ph.D, 1988, Northwestern
University. Postdoctoral Associate, 1988, Stanford University; Postdoctoral Associate, 1988-1990, California
Institute of Technology. Bioengineering; Materials Science. Synthesis and study of nanophase materials with
unusual optical, magnetic, or electronic properties, with
emphasis on silicon-based systems. Current projects are
directed at problems in nanoparticle-based diagnosis and
treatment of disease, remote sensing of toxins and pollutants, high-throughput screening of biomarkers, point detectors for chemical or biological warfare agents, and microfluidic technologies. TEL: (858) 534-8188 FAX:
(858) 534-5383
Web: www.chem-faculty.ucsd.edu/sailor/
Email: msailor@ucsd.edu
Michael J. Sailor, Color Me Sensitive: Amplification and
Discrimination in Photonic Silicon Nanostructures, ACS
Nano, 1, 248-252 (2007).
Ester Segal, Loren A. Perelman, Frederique Cunin, Francesco Di Renzo, Jean-Marie Devoisselle, Yang Yang Li and
Michael J. Sailor, Confinement of thermoresponsive hydrogels in nanostructured porous silicon dioxide templates, Adv.
Funct. Mater, 17, 1153-1162 (2007).
B. H. King, A. M. Ruminski, J. L. Snyder and M. J. Sailor,
Optical fiber-mounted porous silicon photonic crystals for
sensing of organic vapor breakthrough in activated carbon,
Adv. Mater, 19, (24), 4530—4534 (2007).
Brian H. King, Andrei Gramada, Jamie R. Link and Michael J. Sailor, Internally referenced ammonia sensor based
on an electrochemically prepared porous SiO2 photonic crystal, Adv. Mater. (Weinheim, Ger.), 19, 4044-4048 (2007).
Brian H. King, Anne M. Ruminski, Jay L. Synder and Michael J. Sailor, Optical-fiber-mounted porous silicon photonic crystals for sensing organic vapor breakthrough in activated carbon, Adv. Mater. (Weinheim, Ger.), 19, 4530-4534
(2007).
Michael P. Schwartz, Sara D. Alvarez and Michael J. Sailor, Porous SiO2 Interferometric Biosensor for Quantitative
Determination of Protein Interactions: Binding of Protein A
to Immunoglobulins Derived from Different Species, Anal.
Chem, 79, 327-334 (2007).
Geoffrey Von Maltzahn, Todd J. Harris, Ji-Ho Park, DalHee Min, Alexander J. Schmidt, Michael J. Sailor and Sangeeta N. Bhatia, Nanoparticle Self-Assembly Gated by Logical Proteolytic Triggers, J. Am. Chem. Soc, 129, 6064-6065
(2007).
Jennifer S. Park, Shawn O. Meade, Ester Segal and Michael J. Sailor, Porous silicon-based polymer replicas formed
by bead patterning, Phys. Status Solidi A, 204, 1383-1387
(2007).
Loren A. Perelman, Michael P. Schwartz, Aaron M. Wohlrab, Michael S. VanNieuwenhze and Michael J. Sailor, A
simplified biomolecule attachment strategy for biosensing
using a porous Si oxide interferometer, Phys. Status Solidi A,
204, 1394-1398 (2007).
Sara D. Alvarez, Michael P. Schwartz, Ben Migliori, Camilla U. Rang, Lin Chao and Michael J. Sailor, Using a porous
silicon photonic crystal for bacterial cell-based biosensing,
Phys. Status Solidi A, 204, 1439-1443 (2007).
Michael P. Schwartz, Christine Yu, Sara D. Alvarez, Benjamin Migliori, Denis Godin, Lin Chao and Michael J. Sailor,
Using an oxidized porous silicon interferometer for determination of relative protein binding affinity through non-covalent capture probe immobilization, Phys. Status Solidi A, 204,
1444-1448 (2007).
Claudia Pacholski and Michael J. Sailor, Sensing with porous silicon double layers: a general approach for background suppression, Phys. Status Solidi C, 4, 2088-2092
(2007).
Shawn O. Meade and Michael J. Sailor, Microfabrication
13
of freestanding porous silicon particles containing spectral
barcodes, Phys. Status Solidi RRL, 1, R71-R73 (2007).
Dmitri Simberga, Tasmia Duza, Ji Ho Park, Markus Essler,
Jan Pilch, Lianglin Zhang, Austin M. Derfus, Meng Yang,
Robert M. Hoffman, Sangeeta Bhatia, Michael J. Sailor and
Erkki Ruoslahti, Biomimetic amplification of nanoparticle
homing to tumors, Proc. Natl. Acad. Sci. U. S. A, 104, 932936 (2007).
Frederique Cunin, Pierre-Emmanuel Milhiet, Emily Anglin, Michael J. Sailor, Cedric Espenel, Christian Le Grimellec, Daniel Brunel and Jean-Marie Devoisselle, Continuous
planar phospholipid bilayer supported on porous silicon thin
film reflector, Ultramicroscopy, 107, 1048-1052 (2007).
Emily J. Anglin, Lingyun Cheng, William R. Freeman and
Michael J. Sailor, Porous silicon in drug delivery devices and
materials, Adv. Drug Delivery Rev, 60, 1266-1277 (2008).
J.-H. Park, G. A. V. Maltzahn, L. Zhang, M. P. Schwartz,
S. N. Bhatia, E. Ruoslahti and M. J. Sailor, Magnetic iron oxide nanoworms for tumor targeting and imaging, Adv. Mater,
20, (9), 1630-1635 (2008).
Ji-Ho Park, Geoffrey von Maltzahn, Lianglin Zhang, Michael P. Schwartz, Erkki Ruoslahti, Sangeeta N. Bhatia and
Michael J. Sailor, Magnetic iron oxide nanoworms for tumor
targeting and imaging, Adv. Mater. (Weinheim, Ger.), 20,
1630-1635 (2008).
Ji-Ho Park, Geoffrey von Maltzahn, Erkki Ruoslahti, Sangeeta N. Bhatia and Michael J. Sailor, Micellar hybrid nanoparticles for simultaneous magnetofluorescent imaging and
drug delivery, Angew. Chem., Int. Ed, 47, 7284-7288 (2008).
Geoffrey von Maltzahn, Yin Ren, Ji-Ho Park, Dal-Hee
Min, Venkata Ramana Kotamraju, Jayanthi Jayakumar, Valentina Fogal, Michael J. Sailor, Erkki Ruoslahti and Sangeeta N. Bhatia, In Vivo Tumor Cell Targeting with “Click” Nanoparticles, Bioconjugate Chem, 19, 1570-1578 (2008).
Jason R. Dorvee, Michael J. Sailor and Gordon M. Miskelly, Digital microfluidics and delivery of molecular payloads
with magnetic porous silicon chaperones, Dalton Trans, 721730 (2008).
Loren A. Perelman, Claudia Pacholski, Yang Yang Li, Michael S. VanNiewenhze and Michael J. Sailor, pH-triggered
release of vancomycin from protein-capped porous silicon
films, Nanomedicine (London, U. K.), 3, 31-43 (2008).
Felix Casanova, Casey E. Chiang, Chang-Peng Li, Igor V.
Roshchin, Anne M. Ruminski, Michael J. Sailor and Ivan K.
Schuller, Gas adsorption and capillary condensation in nanoporous alumina films, Nanotechnology, 19, 315709/1315709/6 (2008).
SAWREY, B. A. (b.1951) Associate Vice Chancellor/
Undergraduate Education. B.S, 1973, Baldwin-Wallace
College; M.A, 1982, San Diego State University; Ph.D,
1983, University of California, San Diego. Chemistry
Education. Cognition and understanding in college-level
chemistry courses. TEL: (858) 822-4358 FAX: (858)
822-3044
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C00298
Email: bsawrey@ucsd.edu
No publication information submitted for this edition.
SCHRAUZER, G. N.
Publication list has not been verified by the department.
G. N. Schrauzer, Interactive Effects of Selenium and Cadmium on Mammary Tumor Development and Growth in
MMTV-Infected Female Mice. A Model Study on the Roles
of Cadmium and Selenium in Human Breast Cancer, Biol.
Trace Elem. Res, 123, 27-34 (2008).
G. N. Schrauzer, Antioxidant supplementation increases
skin cancer risk, or, why zinc should not be considered an antioxidant. Comments, J. Nutr, 138, 820 (2008).
SHULER, K. E. (b.1922) Professor Emeritus. B.S,
1942, Georgia Institute of Technology; Ph.D, 1949,
Catholic University of America. AEC Postdoctoral Fellow, 1949-1951, Johns Hopkins University, Applied
Physics Laboratory. Non-equilibrium statistical mechanics, relaxation phenomena, stochastic processes, theory
of random walks. Transport in inhomogeneous media.
TEL: (858) 822-4136 FAX: (858) 756-2359
Email: kshuler@ucsd
No publication information submitted for this edition.
SINHA, AMITABHA (b.1956) Professor. B.S, 1978,
Case Western Reserve University; Ph.D, 1985, M.I.T.
Postdoctoral Fellowship, 1985-1987, National Oceanic
and Atmospheric Administration Boulder, CO; Postdoctoral Fellowship, 1987-1992, University of Wisconsin,
Madison. Physical Chemistry. Laser spectroscopy, reaction dynamics and photochemistry of vibrationally excited molecules, laser control of chemical reactions, kinetics and photochemistry of free radicals and transient
molecules occurring in atmospheric and combustion
chemistry. TEL: (858) 534-5593 FAX: (858) 534-7042
Email: asinha@ucsd.edu
Jamie Matthews, Monica Martinez-Aviles, Joseph S. Francisco and Amitabha Sinha, Probing OH stretching overtones
of CH3OOH through action spectroscopy: Influence of dipole
14
CALIFORNIA, SAN DIEGO
moment dependence on HOOC torsion, J. Chem. Phys, 129,
074316/1-074316/16 (2008).
Jamie Matthews, Juliane L. Fry, Coleen M. Roehl, Paul O.
Wennberg and Amitabha Sinha, Vibrational overtone initiated unimolecular dissociation of HOCH2OOH and
HOCD2OOH: Evidence for mode selective behavior, J.
Chem. Phys, 128, 184306/1-184306/12 (2008).
Shuping Li, Jamie Matthews and Amitabha Sinha, Atmospheric Hydroxyl Radical Production from Electronically Excited NO2 and H2O, Science (Washington, DC, U. S.), 319,
1657-1660 (2008).
Jamie Matthews, State-resolved photochemistry and spectroscopic charecterization of atmospherically relevant hydroperoxides. (D)
SUBRAMANIAM, SHANKAR (b.1953) Professor.
B.Sc, 1972, Osmania University; M.A.Sc, 1974, Osmania University; Ph.D, 1982, Indian Institute of Technology Kanpur. His present research focuses several important aspects of computational biology. These include
web-based approaches to bioinformatics, going from
protein sequence to structure and function and studying
protein recognition and function. TEL: (858) 822-0986
FAX: (858) 534-5722
Web: www.chem.ucsd.edu/Faculty/bios/subramaniam.
html
Email: shsubramaniam@ucsd.edu
Publication list has not been verified by the department.
Jayesh Pandey, Mehmet Koyutuerk, Yohan Kim, Wojciech
Szpankowski, Shankar Subramaniam and Ananth Grama,
Functional
annotation
of
regulatory
pathways,
Bioinformatics, 23, i377-i386 (2007).
Mano Ram Maurya and Shankar Subramaniam, A kinetic
model for calcium dynamics in RAW 264.7 cells: 1. Mechanisms, parameters, and subpopulational variability, Biophys.
J, 93, 709-728 (2007).
Mano Ram Maurya and Shankar Subramaniam, A kinetic
model for calcium dynamics in RAW 264.7 cells: 2. Knockdown response and long-term response, Biophys. J, 93, 729740 (2007).
Andrea L. Hevener, Jerrold M. Olefsky, Donna Reichart,
M. T. Audrey Nguyen, Gautam Bandyopadyhay, Ho-Yin
Leung, Matthew J. Watt, Chris Benner, Mark A. Febbraio,
Anh-Khoi Nguyen, Brian Folian, Shankar Subramaniam,
Frank J. Gonzalez, Christopher K. Glass and Mercedes Ricote, Macrophage PPAR␥ is required for normal skeletal
muscle and hepatic insulin sensitivity and full antidiabetic effects of thiazolidinediones, J. Clin. Invest, 117, 1658-1669
(2007).
Jin Sun, Francine Battaglia and Shankar Subramaniam,
Hybrid two-fluid DEM simulation of gas-solid fluidized
beds, J. Fluids Eng, 129, 1394-1403 (2007).
Robert W. Byrnes, Eoin Fahy and Shankar Subramaniam,
A laboratory information management system for highthroughput experimental lipidomics: Minimal information required for the analysis of lipidomics experiments (MIALE),
JALA, 12, 230-238 (2007).
Kara Schmelzer, Eoin Fahy, Shankar Subramaniam and
Edward A. Dennis, The lipid maps initiative in lipidomics,
Methods Enzymol, 432, 171-183 (2007).
Eoin Fahy, Dawn Cotter, Robert Byrnes, Manish Sud, Andrea Maer, Joshua Li, David Nadeau, Yihua Zhau and Shankar Subramaniam, Bioinformatics for lipidomics, Methods
Enzymol, 432, 247-273 (2007).
Purnima Guda, Shankar Subramaniam and Chittibabu
Guda, Mitoproteome: human heart mitochondrial protein sequence database, Methods Mol. Biol. (Totowa, NJ, U. S.),
357, 375-383 (2007).
Joelle R. Zavzavadjian, Sam Couture, Wei Sun Park,
James Whalen, Stephen Lyon, Genie Lee, Eileen Fung,
Qingli Mi, Jamie Liu, Estelle Wall, Leah Santat, Kavitha
Dhandapani, Christine Kivork, Adrienne Driver, Xiaocui
Zhu, Mi Sook Chang, Baljinder Randhawa, Elizabeth Gehrig,
Heather Bryan, Mary Verghese, Andreia Maer, Brian Saunders, Yuhong Ning, Shankar Subramaniam, Tobias Meyer,
Melvin I. Simon, Nancy O’Rourke, Grischa Chandy and Iain
D. C. Fraser, The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies
and signaling pathway analysis, Mol. Cell. Proteomics, 6,
413-424 (2007).
Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward A. Dennis, Christopher K. Glass, Alfred H. Merrill, Jr.,
Robert C. Murphy, Christian R. H. Raetz, David W. Russell
and Shankar Subramaniam, LMSD: LIPID MAPS structure
database, Nucleic Acids Res, 35, D527-D532 (2007).
Ying Xu and Shankar Subramaniam, Consistent modeling
of interphase turbulent kinetic energy transfer in particle-laden turbulent flows, Phys. Fluids, 19, 085101/1-085101/9
(2007).
Srinivasan Ramachandran, Lai-Hua Xie, Scott A. John,
Shankar Subramaniam and Ratnesh Lal, A novel role for
connexin hemichannel in oxidative stress and smoking-induced cell injury, PLoS One, 2, No pp. given (2007).
Colin T. Walsh, Julie Radeff-Huang, Rosalia Matteo, Albert Hsiao, Shankar Subramaniam, Dwayne Stupack and
Joan Heller Brown, Thrombin receptor and RhoA mediate
cell proliferation through integrins and cysteine-rich protein
61, FASEB J, 22, 4011-4021 (2008).
Sergiy Markutsya, Shankar Subramaniam, R. Dennis Vigil
and Rodney O. Fox, On Brownian Dynamics Simulation of
Nanoparticle Aggregation, Ind. Eng. Chem. Res, 47, 33383345 (2008).
Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette and Shankar Subramaniam, The Molecule Pages database, Nucleic Acids Res, 36, D700-D706
(2008).
TAUBER, MICHAEL J. Assistant Professor. B.A,
1992, Cornell University; Ph.D, 2002, University of California, Berkeley. Postdoctoral researcher, 2002-2003,
University of California, Berkeley; ACS-PRF Research
Associate, 2003-2006, Northwestern University. Physical Chemistry. Our group investigates charge sharing and
excited state dynamics in organic molecular assemblies,
including self-assembled systems, by a variety of spectroscopic techniques including pump-probe Raman &
resonance Raman, EPR, and transient absorption. Other
topics of current research are new 3-dimensional architectures for dye-sensitized solar cells, and solvation
structure/dynamics. TEL: (858) 534-7334 FAX: (858)
000-0000
Email: mtauber@ucsd.edu
E. A. Weiss, M. J. Tauber, R. F. Kelley, M. J. Ahrens, M.
A. Ratner and M. R. Wasielewski, Conformationally gated
switching between superexchange and hopping within oligop-phenylene-based molecular wires, J. Am. Chem. Soc, 127,
11842-11850 (2005).
E. A. Weiss, M. J. Tauber, M. A. Ratner and M. R. Wasielewski, Electron spin dynamics as a probe of molecular dynamics: Temperature-dependent magnetic field effects on
charge recombination within a covalent radical ion pair, J.
Am. Chem. Soc, 127, 6052-6061 (2005).
R. F. Kelley, M. J. Tauber and M. R. Wasielewski, Linkercontrolled energy and charge transfer within chlorophyll trefoils, Angew. Chem. Int. Ed, 45, 7979-7982 (2006).
M. J. Tauber, R. F. Kelley, J. M. Giaimo, B. Rybtchinski
and M. R. Wasielewski, Electron hopping in pi-stacked covalent and self-assembled perylene diimides observed by ENDOR spectroscopy, J. Am. Chem. Soc, 128, 1782-1783
(2006).
R. F. Kelley, M. J. Tauber and M. R. Wasielewski, Intramolecular electron transfer through the 20-position of a
chlorophyll-a derivative: An unexpectedly efficient conduit
for charge transport, J. Am. Chem. Soc, 128, 4779-4791
(2006).
M. J. Ahrens, M. J. Tauber and M. R. Wasielewski, Bis(noctylamino)perylene-3,4:9,10-bis(dicarboximide)s and their
radical cations: Synthesis, electrochemistry, and ENDOR
spectroscopy, J. Org. Chem, 71, 2107-2114 (2006).
Richard F. Kelley, Michael J. Tauber, Thea M. Wilson and
Michael R. Wasielewski, Controlling energy and charge
transfer in linear chlorophyll dimers, Chem. Commun. (Cambridge, U. K.), 42, 4407-4409 (2007).
Christina M. Stuart, Michael J. Tauber and Richard A. Mathies, Structure and Dynamics of the Solvated Electron in Alcohols from Resonance Raman Spectroscopy, J. Phys. Chem.
A, 111, 8390-8400 (2007).
TAYLOR, SUSAN S. (b.1942) Professor. B.A, 1964,
University of Wisconsin; Ph.D, 1968, The Johns Hopkins University. Postdoctoral Fellowship, 1969-1971,
Laboratory of Molecular Biology, Cambridge, England;
Postdoctoral Fellowship, 1971-1972, University of California, San Diego. Biochemistry; Crystallography.
CAMP-dependent Protein Kinase: Dynamics of Structures and Localization cAMP-dependent protein kinase
(cAPK) serves as a prototype for the entire protein kinase superfamily. Crystal structures of the RIa and RIIb
cAMP binding domains of the R subunits show clear isoform differences. From these structures we can more fully appreciate the conformational versatility of this ancient signaling module that binds cAMP and mediates a
biological response. This stable module binds with high
affinity to scaffold proteins. The molecular basis for targeting has been elucidated by solving high-resolution
structures of two D/D domains by hetero nuclear NMR
in collaboration with Dr. Patricia Jennings. Isoform differences in PKA targeting are being explored. We have
identified two novel AKAPs that bind to both RIa and
RIIb. Both target cAPK to mitochondria. We are beginning to elucidate the molecular basis for this targeting.
TEL: (858) 534-3677 FAX: (858) 534-8193
Web: susantaylorlab.ucsd.edu/
Email: staylor@ucsd.edu
Publication list has not been verified by the department.
Ganesh Anand, Susan S. Taylor and David A. Johnson,
Cyclic-AMP and Pseudosubstrate Effects on Type-I A-Kinase Regulatory and Catalytic Subunit Binding Kinetics, Biochemistry, 46, 9283-9291 (2007).
Choel Kim, Cecilia Y. Cheng, S. Adrian Saldanha and Susan S. Taylor, PKA-I holoenzyme structure reveals a mechanism for cAMP-dependent activation, Cell (Cambridge, MA,
U. S.), 130, 1032-1043 (2007).
Brent R. Martin, Thomas J. Deerinck, Mark H. Ellisman,
Susan S. Taylor and Roger Y. Tsien, Isoform-Specific PKA
Dynamics Revealed by Dye-Triggered Aggregation and DAKAP1␣-Mediated Localization in Living Cells, Chem. Biol.
(Cambridge, MA, U. S.), 14, 1031-1042 (2007).
Natarajan Kannan, Jian Wu, Ganesh S. Anand, Shibu Yooseph, Andrew F. Neuwald, J. Craig Venter and Susan S. Taylor, Evolution of allostery in the cyclic nucleotide binding
module, GenomeBiology, 8, No pp. given (2007).
Sharmin Schauble, Charles C. King, Manjula Darshi, Antonius Koller, Kavita Shah and Susan S. Taylor, Identification of ChChd3 as a Novel Substrate of the cAMP-dependent
Protein Kinase (PKA) Using an Analog-sensitive Catalytic
Subunit, J. Biol. Chem, 282, 14952-14959 (2007).
Kenneth M. Humphries, Juniper K. Pennypacker and Susan S. Taylor, Redox Regulation of cAMP-dependent Protein
Kinase Signaling: kinase versus phosphatase inactivation, J.
Biol. Chem, 282, 22072-22079 (2007).
Neal M. Alto, Andrew W. Weflen, Matthew J. Rardin,
Defne Yarar, Cheri S. Lazar, Raffi Tonikian, Antonius Koller, Susan S. Taylor, Charles Boone, Sachdev S. Sidhu, Sandra L. Schmid, Gail A. Hecht and Jack E. Dixon, The type III
effector EspF coordinates membrane trafficking by the spatiotemporal activation of two eukaryotic signaling pathways,
J. Cell Biol, 178, 1265-1278 (2007).
Ganesh S. Anand, Matthew Hotchko, Simon H. J. Brown,
Lynn F. Ten Eyck, Elizabeth A. Komives and Susan S. Taylor, R-subunit Isoform Specificity in Protein Kinase A: Distinct Features of Protein Interfaces in PKA Types I and II by
Amide H/2H Exchange Mass Spectrometry, J. Mol. Biol, 374,
487-499 (2007).
Marat Valiev, Jie Yang, Joseph A. Adams, Susan S. Taylor
and John H. Weare, Phosphorylation Reaction in cAPK Protein Kinase-Free Energy Quantum Mechanical/Molecular
Mechanics Simulations, J. Phys. Chem. B, 111, 13455-13464
(2007).
Chinten James Lim, Jaewon Han, Nima Yousefi, Yuliang
Ma, Paul S. Amieux, G. Stanley McKnight, Susan S. Taylor
and Mark H. Ginsberg, ␣4 Integrins are type I cAMP-dependent protein kinase-anchoring proteins, Nat. Cell Biol, 9,
415-421 (2007).
Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron
L. Halpern, Shannon J. Williamson, Karin Remington, Jonathan A. Eisen, Karla B. Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S.
Miller, Huiying Li, Susan T. Mashiyama, Marcin P. Joachimiak, Christopher van Belle, John-Marc Chandonia, David A.
Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benjamin J. Raphael, Vineet Bafna, Robert Friedman, Steven E.
Brenner, Adam Godzik, David Eisenberg, Jack E. Dixon, Susan S. Taylor, Robert L. Strausberg, Marvin Frazier and J.
Craig Venter, The Sorcerer II global ocean sampling expedition: expanding the universe of protein families, PLoS Biol,
5, 432-466 (2007).
Natarajan Kannan, Susan S. Taylor, Yufeng Zhai, J. Craig
Venter and Gerard Manning, Structural and functional diversity of the microbial kinome, PLoS Biol, 5, 467-478 (2007).
Natarajan Kannan, Nina Haste, Susan S. Taylor and Andrew F. Neuwald, The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module, Proc. Natl. Acad. Sci. U. S. A, 104, 1272-1277 (2007).
Rahul Das, Veronica Esposito, Mona Abu-Abed, Ganesh
S. Anand, Susan S. Taylor and Giuseppe Melacini, cAMP activation of PKA defines an ancient signaling mechanism,
Proc. Natl. Acad. Sci. U. S. A, 104, 93-98 (2007).
Jian Wu, Simon H. J. Brown, Sventja von Daake and Susan S. Taylor, PKA Type II␣ Holoenzyme Reveals a Combinatorial Strategy for Isoform Diversity, Science (Washington,
DC, U. S.), 318, 274-279 (2007).
Susan S. Taylor, Choel Kim, Cecilia Y. Cheng, Simon H.
J. Brown, Jian Wu and Natarajan Kannan, Signaling through
cAMP and cAMP-dependent protein kinase: Diverse strategies for drug design, Biochim. Biophys. Acta, Proteins Proteomics, 1784, 16-26 (2008).
Lynn F. Ten Eyck, Susan S. Taylor and Alexandr P. Kornev, Conserved spatial patterns across the protein kinase
family, Biochim. Biophys. Acta, Proteins Proteomics, 1784,
238-243 (2008).
Natarajan Kannan, Andrew F. Neuwald and Susan S. Taylor, Analogous regulatory sites within the ␣C-␤4 loop regions of ZAP-70 tyrosine kinase and AGC kinases, Biochim.
Biophys. Acta, Proteins Proteomics, 1784, 27-32 (2008).
Natarajan Kannan and Susan S. Taylor, Rethinking pseudokinases, Cell (Cambridge, MA, U. S.), 133, 204-205
(2008).
Yuliang Ma and Susan S. Taylor, A Molecular Switch for
Targeting between Endoplasmic Reticulum (ER) and Mitochondria: Conversion of a mitochondria-targeting element
into an er-targeting signal in DAKAP1, J. Biol. Chem, 283,
11743-11751 (2008).
Alexandr P. Kornev, Susan S. Taylor and Lynn F. Ten
Eyck, A generalized allosteric mechanism for cis-regulated
cyclic nucleotide binding domains, PLoS Comput. Biol, 4,
No pp. given (2008).
Alexandr P. Kornev, Susan S. Taylor and Lynn F. Ten
Eyck, A helix scaffold for the assembly of active protein kinases, Proc. Natl. Acad. Sci. U. S. A, 105, 14377-14382
(2008).
Larry R. Masterson, Alessandro Mascioni, Nathaniel J.
Traaseth, Susan S. Taylor and Gianluigi Veglia, Allosteric
cooperativity in protein kinase A, Proc. Natl. Acad. Sci. U. S.
A, 105, 506-511 (2008).
Ali Torkamani, Natarajan Kannan, Susan S. Taylor and
CALIFORNIA, SAN DIEGO
Nicholas J. Schork, Congenital disease SNPs target lineage
specific structural elements in protein kinases, Proc. Natl.
Acad. Sci. U. S. A, 105, 9011-9016 (2008).
Natarajan Kannan, Nina Haste, Susan S. Taylor and Andrew F. Neuwald, The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module. [Erratum to document cited in CA146:333062], Proc.
Natl. Acad. Sci. U. S. A, 105, 9130 (2008).
TEZCAN, F. AKIF (b.1972) Assistant Professor. A.B,
1995, Macalester College; Ph.D, 2001, Caltech. Research Fellow, 2001-2005, Caltech. Bioinorganic Chemistry. Metal-Protein and Protein-Protein Interactions
Metal-Directed Protein Self-Assembly Biological Nitrogen Fixation. TEL: (858) 534-4862 FAX: (858) 5346157
Web: tezcan.ucsd.edu
Email: tezcan@ucsd.edu
Eric N. Salgado, Jasmin Faraone-Mennella and F. Akif
Tezcan, Controlling Protein-Protein Interactions through
Metal Coordination: Assembly of a 16-Helix Bundle Protein,
J. Am. Chem. Soc, 129, 13374-13375 (2007).
Eric N. Salgado, Richard A. Lewis, Jasmin Faraone-Mennella and F. Akif Tezcan, Metal-Mediated Self-Assembly of
Protein Superstructures: Influence of Secondary Interactions
on Protein Oligomerization and Aggregation, J. Am. Chem.
Soc, 130, 6082-6084 (2008).
THEODORAKIS, EMMANUEL A. (b.1964) Professor. B.S, 1987, University of Athens, Greece; M.S,
1989, University of Paris XI, France; Ph.D, 1993, University of Paris XI, France. Postdoctoral, 1993-1995,
Scripps Research Institute. Bioorganic Chemistry; Organic Chemistry. Synthesis of natural products; development of synthetic methodology; and interaction of organic molecules with biomolecules. TEL: (858) 822-0456
FAX: (858) 822-0386
Web: www.chem-faculty.ucsd.edu/Theodorakis/index.
html
Email: etheodor@ucsd.edu
Gianni Guizzunti, Thomas P. Brady, Vivek Malhotra and
Emmanuel A. Theodorakis, Trifunctional norrisolide probes
for the study of Golgi vesiculation, Bioorg. Med. Chem. Lett,
17, 320-325 (2007).
Derek Fischer and Emmanuel A. Theodorakis, Studies on
the synthesis of Schisandraceae natural products: exploring a
cyclopropylcarbinol ring expansion strategy, Eur. J. Org.
Chem, 4193-4196 (2007).
Paqui G. Traves, Sonsoles Hortelano, Miriam Zeini, TaHsiang Chao, Thanh Lam, Saskia T. Neuteboom, Emmanuel
A. Theodorakis, Michael A. Palladino, Antonio Castrillo and
Lisardo Bosca, Selective activation of liver X receptors by
acanthoic acid-related diterpenes, Mol. Pharmacol, 71, 15451553 (2007).
Derek Fischer, Emmanuel A. Theodorakis and Mark A.
Haidekker, Synthesis and use of an in-solution ratiometric
fluorescent viscosity sensor, Nat. Protoc, 2, 227-236 (2007).
Mark A. Haidekker and Emmanuel A. Theodorakis, Molecular rotors-fluorescent biosensors for viscosity and flow,
Org. Biomol. Chem, 5, 1669-1678 (2007).
Ayse Batova, Thanh Lam, Veit Wascholowski, Alice L.
Yu, Athanassios Giannis and Emmanuel A. Theodorakis,
Synthesis and evaluation of caged Garcinia xanthones, Org.
Biomol. Chem, 5, 494-500 (2007).
Matthew E. Nipper, Sheereen Majd, Michael Mayer, James
C.-M. Lee, Emmanuel A. Theodorakis and Mark A. Haidekker, Characterization of changes in the viscosity of lipid
membranes with the molecular rotor FCVJ, Biochim. Biophys. Acta, Biomembr, 1778, 1148-1153 (2008).
Alba Diaz-Rodriguez, Susana Fernandez, Yogesh S.
Sanghvi, Emmanuel A. Theodorakis, Vicente Gotor and Miguel Ferrero, Synthesis of 2’,3’-cyclohexene bicyclic nucleoside analogues as antiviral compounds, Nucleic Acids Symp.
Ser, 52, 99-100 (2008).
Derek A. Fischer, Synthetic studies toward complex natural products. (D)
Fatima R. Rivas, Synthetic studies towards the total synthesis of norzoanthamine. (D)
Thanh T. Lam, synthetic studies towards diterpenes; synthetic studies towards the caged garcinia xanthones. (D)
Thomas Patrick Brady, Total synthesis of norrisolide, synthesis of norrisolide analogues, and biological evaluation of
norrisolide probes. (D)
THIEMENS, MARK H. (b.1950) Professor and
Dean. B.S, 1972, University of Miami; M.S, 1974, Old
Dominion University; Ph.D, 1977, Florida State University. Postdoctoral Fellowship, 1977-1980, University of
Chicago. Atmospheric Chemistry; Physical Chemistry.
Measurement of isotope ratios in atmospheric species;
application of high precision stable isotope ratio measurement to resolve quantum chemical astrophysical and
atmospheric processes; studies on the evolution of the
solar system and nucleosynthesis. Paleoclimatology and
ice core studies. Investigations of the origin and evolution of planets and life. TEL: (858) 534-6882 FAX:
(858) 822-0389
Email: mht@chem.ucsd.edu
mthiemens@ucsd.edu
S. A. Aireau, J. Farquhar, M. H. Thiemens, L. A. Leshin,
H. Bao and E. Young, Planetesimal sulfate and aqueous alteration in CM and CI carbonaceous chondrites, Geochinica
Cosmochimica Acta, 69, 4166-4171 (2005).
R. Jost, G. Michalski and M. H. Thiemens, Comparison of
rovibronic density of symmetric versus symmetric NO2 isotopologues at dissociation threshold: Broken symmetry effects, J. (Chemistry). Physics, 123, 054230 (2005).
J. R. McCabe, C. S. Boxe, A. J. Colussi, M. R. Hoffmann
and M. H. Thiemens, Oxygen isotopic fractionation in the
photochemistry of nitrate and ice, J. Geophys. Res, 110, D15D15310 (2005).
B. Alexander, R. J. Park, D. J. Jacob, Q. B. Li, R. M. Yantosca, J. Savarino, C. C. W. Lee and M. H. Thiemens, Sulfate
formation in sea-salt aerosols: Constraints from oxygen isotopes, J. Geophys. Res. Atmospheres). J. Geophys. Res, 110,
D10307 (2005).
V. K. Rai, T. L. Jackson and M. H. Thiemens, Photochemical mass independent sulfur isotopes in achondritic meteorites, Science, 309, 1062-1065 (2005).
Mark H. Thiemens, History and applications of mass independent isotope effects, Annual Reviews of Earth and Planetary Sciences, 34, 217-262 (2006).
T. A. Mather, J. R. McCabe, V. K. Rai, M. K. Thiemens,
D. M. Pyle, T. H. E. Heaton, H. J. Sloane and G. Fern, Oxygen and sulfur isotopic composition of volcanic sulfate aerosol at the point of emission, J. Geophys. Res, 111, D18205
(2006).
J. Savarino, J. Kaiser, S. Morin, D. M. Sigman and M. H.
Thiemens, Nitrogen and oxygen isotopic constraints on the
origin of atmospheric nitrate in coastal Antarctica, Atmos.
Chem. Phys, 7, 1925-1945 (2007).
M. De Angelis, M. H. Thiemens, J. Savarino and J. R. Petit, Contributions of an ancient evaporitic-type reservoir to
Lake Vostok chemistry, Earth and Planetary Science Letters,
222, 751-765 (2007).
Tetsuya Yokoyama, Vinai K. Rai, Conel M. O’D. Alexander, Roy S. Lewis, Richard W. Carlson, Steven B. Shirey,
Mark H. Thiemens and Richard J. Walker, Osmium isotope
evidence for uniform distribution of s- and r-process components in the early Solar system, Earth Planet. Sci. Lett, 259,
567-580 (2007).
Vinai K. Rai and Mark H. Thiemens, Mass independently
fractionated sulfur components in chondrites, Geochim. Cosmochim. Acta, 71, 1341-1354 (2007).
M. A. Tyra, J. Farquhar, B. A. Wing, G. K. Benedix, A. J.
T. Jull, T. Jackson and M. H. Thiemens, Terrestrial alteration
of Antarctic CM chondrite meteorites in a suite of Antarctic
CM chondrites: Evidence from oxygen and carbon isotopes,
Geochimica Cosmochimica Acta, 71, 782-795 (2007).
S. A. Ewing, G. Michalski, M. Thiemens, R. C. Quinn, J.
L. Macalady, S. Kohl, S. D. Wankel, C. Kendall, C. P.
McKay and R. Amundson, Rainfall limit of the N cycle on
Earth, Global Biogeochemical Cycles, 21, GB3009 (2007).
Justin R. McCabe, Mark H. Thiemens and Joel Savarino, A
record of ozone variability in South Pole Antarctic snow: role
of nitrate oxygen isotopes, J. Geophys. Res., [Atmos.], 112,
D12303/1-D12303/9 (2007).
N. Patris, S. S. Cliff, P. K. Quinn, M. Kasem and M. H.
Thiemens, Isotopic analysis of aerosol sulfate and nitrate during ICT-2k2: Determination of different formation pathways
as a function of particle size, J. Geophysical Research, 112,
D23301 (2007).
Yuki Kimura, Joseph A. Nuth, III, Subrata Chakraborty
and Mark H. Thiemens, Non-mass-dependent oxygen isotopic fractionation in smokes produced in an electrical discharge, Meteorit. Planet. Sci, 42, 1429-1439 (2007).
Melanie Baroni, Mark H. Thiemens, Robert J. Delmas and
Joel Savarino, Mass-independent sulfur isotopic compositions in stratospheric volcanic eruptions, Science (Washington, DC, U. S.), 315, 84-87 (2007).
Gerardo Dominguez, Terri Jackson, Burton Brothers,
Bryan Nguyen and Mark H. Thiemens, Discovery and measurement of an isotopically distinct source of sulfate in
Earth’s atmosphere, Proc. Natl. Acad. Sci. U. S. A, 105,
12769-12773 (2008).
Subrata Chakraborty, Musahid Ahmed, Teresa L. Jackson
and Mark H. Thiemens, Experimental Test of Self-Shielding
in Vacuum Ultraviolet Photodissociation of CO, Science
(Washington, DC, U. S.), 321, 1328-1331 (2008).
TOOR, NAVTEJ SINGH (b.1973) Assistant Professor. B.Sc, 1996, University of Calgary; Ph.D, 2004, University of Calgary. Howard Hughes Medical Institute
Postdoctoral Fellow, 2004-2009, Yale University. Biochemistry; Structural Biology. Group II introns are selfsplicing RNAs which are thought to be the ancestors of
both retrotransposons and spliceosomal introns, which
together make up more than 50% of the human genome.
My research interests include studying the structure and
function of group II introns, as well as the spliceosome,
using a combination of x-ray crystallography and
biochemistry. TEL: (858) 534-3211 FAX: (858) 5346255
Email: ntoor@ucsd.edu
N. Toor, A. R. Robart, J. Christianson and S. Zimmerly,
Self-splicing of a group IIC intron: 5’ exon recognition and
alternative 5’ splicing events implicate the stem-loop motif
15
of a transcriptional terminator, Nucleic Acids Research, 34,
6461-6471 (2006).
K. S. Keating, N. Toor and A. M. Pyle, The GANC tetraloop receptor interaction, Journal of Molecular Biology, 383,
475-481 (2008).
N. Toor, K. Rajashankar, K. S. Keating and A. M. Pyle,
Structural basis of exon recognition by a group II intron, Nature Structural and Molecular Biology, 15, 1221-1222
(2008).
N. Toor, K. S. Keating, S. D. Taylor and A. M. Pyle, Crystal structure of a self-spliced group II intron, Science, 320,
77-82 (2008).
TOR, YITZHAK (b.1960) Professor. B.Sc, 1982, TelAviv University, Israel; Ph.D, 1990, The Weizmann Institute of Science, Israel. Weizmann Postdoctoral Fellowship, 1990-1993, California Institute of Technology.
Bioorganic Chemistry; Organic Chemistry. RNA–small
molecule interactions; antiviral and antibacterial agents;
new emissive nucleosides and oligonucleotides; novel
cellular delivery agents. TEL: (858) 534-6401 FAX:
(858) 534-0202
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C02218
Email: ytor@ucsd.edu
Lev Elson-Schwab and Yitzhak Tor, Targeting HIV-1
RNA with aminoglycoside antibiotics and their derivatives,
Aminoglycoside Antibiot, 267-287, 2 plates (2007).
Christopher M. Barbieri, Malvika Kaul, Melanie BozzaHingos, Fang Zhao, Yitzhak Tor, Thomas Hermann and Daniel S. Pilch, Defining the molecular forces that determine the
impact of neomycin on bacterial protein synthesis: importance of the 2’-amino functionality, Antimicrob. Agents Chemother, 51, 1760-1769 (2007).
Seergazhi G. Srivatsan and Yitzhak Tor, Fluorescent Pyrimidine Ribonucleotide: Synthesis, Enzymatic Incorporation, and Utilization, J. Am. Chem. Soc, 129, 2044-2053
(2007).
Victor K. Tam, Denise Kwong and Yitzhak Tor, Fluorescent HIV-1 Dimerization Initiation Site: Design, Properties,
and Use for Ligand Discovery, J. Am. Chem. Soc, 129, 32573266 (2007).
Edith C. Glazer, Douglas Magde and Yitzhak Tor, Ruthenium Complexes That Break the Rules: Structural Features
Controlling Dual Emission, J. Am. Chem. Soc, 129, 85448551 (2007).
Lev Elson-Schwab, Omai B. Garner, Manuela Schuksz,
Brett E. Crawford, Jeffrey D. Esko and Yitzhak Tor, Guanidinylated Neomycin Delivers Large, Bioactive Cargo into
Cells through a Heparan Sulfate-dependent Pathway, J. Biol.
Chem, 282, 13585-13591 (2007).
Seergazhi G. Srivatsan and Yitzhak Tor, Synthesis and enzymatic incorporation of a fluorescent pyrimidine ribonucleotide, Nat. Protoc, 2, 1547-1555 (2007).
Nicholas J. Greco and Yitzhak Tor, Synthesis and site-specific incorporation of a simple fluorescent pyrimidine, Nat.
Protoc, 2, 305-316 (2007).
Renatus W. Sinkeldam and Yitzhak Tor, To D or not to D?
On estimating the microenvironment polarity of biomolecular cavities, Org. Biomol. Chem, 5, 2523-2528 (2007).
Nicholas J. Greco and Yitzhak Tor, Furan decorated nucleoside analogues as fluorescent probes: synthesis, photophysical evaluation, and site-specific incorporation, Tetrahedron,
63, 3515-3527 (2007).
Seergazhi G. Srivatsan and Yitzhak Tor, Using an emissive
uridine analogue for assembling fluorescent HIV-1 TAR constructs, Tetrahedron, 63, 3601-3607 (2007).
Yitzhak Tor, Susan Del Valle, David Jaramillo, Seergazhi
G. Srivatsan, Andro Rios and Haim Weizman, Designing
new isomorphic fluorescent nucleobase analogues: the thieno
[3,2-d]pyrimidine core, Tetrahedron, 63, 3608-3614 (2007).
Seergazhi Srivatsan, Nicholas J. Greco and Yitzhak Tor, A
highly emissive fluorescent nucleoside that signals the activity of toxic ribosome-inactivation proteins, Angew. Chem.,
Int. Ed, 47, 6661-6665 (2008).
Renatus W. Sinkeldam, Nicholas J. Greco and Yitzhak
Tor, Polarity of major grooves explored by using isosteric
emissive nucleoside, ChemBioChem, 9, 706-709 (2008).
Seergazhi G. Srivatsan, Haim Weizman and Yitzhak Tor,
A highly fluorescent nucleoside analog based on thieno[3,4d]pyrimidine senses mismatched pairing, Org. Biomol.
Chem, 6, 1334-1338 (2008).
Manuela Schuksz, Mark M. Fuster, Jillian R. Brown, Brett
E. Crawford, David P. Ditto, Roger Lawrence, Charles A.
Glass, Lianxhun Wang, Yitzhak Tor and Jeffrey D. Esko,
Surfen, a small molecule antagonist of heparan sulfate, Proc.
Natl. Acad. Sci. U. S. A, 105, 13075-13080 (2008).
Nicholas J. Greco, Design, synthesis and application of
novel fluorescent nucleosides. (D)
Victor K. Tam, Targeting unique nucleic acid structures
with small molecules. (D)
TROGLER, WILLIAM C. Professor. B.A, 1974,
Johns Hopkins; M.A, 1974, Johns Hopkins; Ph.D, 1977,
California Institute of Technology. Materials Chemistry;
Nanochemistry. Inorganic polymers and nanoparticles as
luminescent and electronic sensors for explosives. Characterization of the chemoselectivity of field effect tran-
16
CALIFORNIA, SAN DIEGO
sistor and interdigitated electrode chemical sensors based
on metallophthalocyanines. Use of hollow porous silica
and titania nanoparticles in drug and gene delivery. TEL:
(858) 534-6175 FAX: (858) 534-5383
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C02165
Email: wtrogler@ucsd.edu
Richard D. Yang, T. Gredig, Corneliu N. Colesniuc, Jeongwon Park, Ivan K. Schuller, William C. Trogler and Andrew C. Kummel, Ultrathin organic transistors for chemical
sensing, Appl. Phys. Lett, 90, 263506/1-263506/3 (2007).
Jason C. Sanchez, Antonio G. DiPasquale, Arnold L.
Rheingold and William C. Trogler, Synthesis, Luminescence
Properties, and Explosives Sensing with 1,1-Tetraphenylsilole- and 1,1-Silafluorene-vinylene Polymers, Chem. Mater, 19, 6459-6470 (2007).
Forest I. Bohrer, Amos Sharoni, Corneliu Colesniuc, Jeongwon Park, Ivan K. Schuller, Andrew C. Kummel and
William C. Trogler, Gas Sensing Mechanism in Chemiresistive Cobalt and Metal-Free Phthalocyanine Thin Films, J.
Am. Chem. Soc, 129, 5640-5646 (2007).
Richard D. Yang, Jeongwon Park, Corneliu N. Colesniuc,
Ivan K. Schuller, William C. Trogler and Andrew C. Kummel, Ultralow drift in organic thin-film transistor chemical
sensors by pulsed gating, J. Appl. Phys, 102, 034515/1034515/7 (2007).
Sarah J. Toal, Jason C. Sanchez, Regina E. Dugan and
William C. Trogler, Visual detection of trace nitroaromatic
explosive residue using photoluminescent metallole-containing polymers, J. Forensic Sci, 52, 79-83 (2007).
Sarah L. Blair, Jessica Wang-Rodriguez, Maria J. Cortes,
Davorka Messmer, Andrew C. Kummel and William C. Trogler, Enhanced touch preps to improve the ease of interpretation of intra-operative breast cancer margins, The American
Surgeon, 73, 973-976 (2007).
Jeongwon Park, Richard D. Yang, Corneliu N. Colesniuc,
Amos Sharoni, Sungho Jin, Ivan K. Schuller, William C.
Trogler and Andrew C. Kummel, Bilayer processing for an
enhanced organic-electrode contact in ultrathin bottom contact organic transistors, Appl. Phys. Lett, 92, 193311/1193311/3 (2008).
Jian Yang, Johan U. Lind and William C. Trogler, Synthesis of Hollow Silica and Titania Nanospheres, Chem. Mater,
20, 2875-2877 (2008).
Forest I. Bohrer, Corneliu N. Colesniuc, Jeongwon Park,
Ivan K. Schuller, Andrew C. Kummel and William C. Trogler, Selective Detection of Vapor Phase Hydrogen Peroxide
with Phthalocyanine Chemiresistors, J. Am. Chem. Soc, 130,
3712-3713 (2008).
Jason C. Sanchez and William C. Trogler, Efficient blueemitting silafluorene-fluorene-conjugated copolymers: selective turn-off/turn-on detection of explosives, J. Mater. Chem,
18, 3143-3156 (2008).
Jason C. Sanchez and William C. Trogler, Hydrosilylation
of diynes as a route to functional polymers delocalized
through silicon, Macromol. Chem. Phys, 209, 1527-1540
(2008).
Jason C. Sanchez, Sara A. Urbas, Sarah J. Toal, Antonio
G. DiPasquale, Arnold L. Rheingold and William C. Trogler,
Catalytic Hydrosilylation Routes to Divinylbenzene Bridged
Silole and Silafluorene Polymers. Applications to Surface
Imaging of Explosive Particulates, Macromolecules (Washington, DC, U. S.), 41, 1237-1245 (2008).
Forest I. Bohrer, Gas sensing mechanisms in chemiresistive metal phthalocyanine nanofilms. (D)
Jason C. Sanchez, Design and optimization of polymeric
silole and boronate photoluminescent probes for improved
explosives detection applications. (D)
TSIEN, ROGER Y. (b.1952) Professor. A.B, 1972,
Harvard; Ph.D, 1977, University of Cambridge, Cambridge, UK. Comyns Berkeley Research Fellowship,
1977-1981, Gonville & Caius College, Cambridge, U.K.
Design, synth. and use of fluorescent indicators and photoreleasable messengers to probe intracellular signs such
as Ca, inositol phosphates, cyclic nucleotides and nitric
oxide; eng. of Green Fluorescent Protein; pharma’l ultrahigh-throughput screening. TEL: (858) 534-4891 FAX:
(858) 534-5270
Web: www.tsienlab.ucsd.edu
Email: rtsien@ucsd.edu
Hui-Wang Ai, Nathan C. Shaner, Zihao Cheng, Roger Y.
Tsien and Robert E. Campbell, Exploration of New Chromophore Structures Leads to the Identification of Improved
Blue Fluorescent Proteins, Biochemistry, 46, 5904-5910
(2007).
Brent R. Martin, Thomas J. Deerinck, Mark H. Ellisman,
Susan S. Taylor and Roger Y. Tsien, Isoform-Specific PKA
Dynamics Revealed by Dye-Triggered Aggregation and DAKAP1␣-Mediated Localization in Living Cells, Chem. Biol.
(Cambridge, MA, U. S.), 14, 1031-1042 (2007).
Stephen R. Adams and Roger Y. Tsien, Imaging the influx
of cell-penetrating peptides into the cytosol of individual live
cells, Handb. Cell-Penetrating Pept. (2nd Ed.), 505-513
(2007).
Maya T. Kunkel, Alex Toker, Roger Y. Tsien and Alexandra C. Newton, Calcium-dependent Regulation of Protein Ki-
nase D Revealed by a Genetically Encoded Kinase Activity
Reporter, J. Biol. Chem, 282, 6733-6742 (2007).
Oded Tour, Stephen R. Adams, Rex A. Kerr, Rene M. Meijer, Terrence J. Sejnowski, Richard W. Tsien and Roger Y.
Tsien, Calcium Green FlAsH as a genetically targeted smallmolecule calcium indicator, Nat. Chem. Biol, 3, 423-431
(2007).
Christina T. Hauser and Roger Y. Tsien, A hexahistidineZn2+-dye label reveals STIM1 surface exposure, Proc. Natl.
Acad. Sci. U. S. A, 104, 3693-3697 (2007).
Nathan C. Shaner, Michael Z. Lin, Michael R. McKeown,
Paul A. Steinbach, Kristin L. Hazelwood, Michael W. Davidson and Roger Y. Tsien, Improving the photostability of
bright monomeric orange and red fluorescent proteins, Nat.
Methods, 5, 545-551 (2008).
Damian J. Wallace, Stephan Meyer zum Alten Borgloh, Simone Astori, Ying Yang, Melanie Bausen, Sebastian Kuegler, Amy E. Palmer, Roger Y. Tsien, Rolf Sprengel, Jason
N. D. Kerr, Winfried Denk and Mazahir T. Hasan, Singlespike detection in vitro and in vivo with a genetic Ca2+ sensor, Nat. Methods, 5, 797-804 (2008).
Stephen R. Adams and Roger Y. Tsien, Preparation of the
membrane-permeant biarsenicals FlAsH-EDT2 and ReAsHEDT2 for fluorescent labeling of tetracysteine-tagged proteins, Nat. Protoc, 3, 1527-1534 (2008).
Samuel Andrew Hires, Yongling Zhu and Roger Y. Tsien,
Optical measurement of synaptic glutamate spillover and reuptake by linker optimized glutamate-sensitive fluorescent
reporters, Proc. Natl. Acad. Sci. U. S. A, 105, 4411-4416
(2008).
Michael Z. Lin, Jeffrey S. Glenn and Roger Y. Tsien, A
drug-controllable tag for visualizing newly synthesized proteins in cells and whole animals, Proc. Natl. Acad. Sci. U. S.
A, 105, 7744-7749 (2008).
Emilia Olson, Detecting pathological protease activity with
activatable cell penetrating peptides (ACPP’s). (D)
TUKEY, ROBERT H. (b.1949) Professor. B.Sc,
1973, University of Minnesota; Ph.D, 1980, University
of Iowa. Pharmacology. Environmental toxicology: The
role of environmental and chemical toxicants on gene expression. TEL: (858) 822-0288 FAX: (858) 822-0363
Web: superfund.ucsd.edu/
Email: rtukey@ucsd.edu
Kathy Senekeo-Effenberger, Shujuan Chen, Erin BraceSinnokrak, Jessica A. Bonzo, Mei-Fei Yueh, Upendra Argikar, Jenny Kaeding, Jocelyn Trottier, Rory P. Remmel, Joseph K. Ritter, Olivier Barbier and Robert H. Tukey, Expression of the human UGT1 locus in transgenic mice by 4-chloro-6-(2,3-xylidino)-2-pyrimidinylthioacetic acid (WY-14643)
and implications on drug metabolism through peroxisome
proliferator-activated receptor ␣ activation, Drug Metab.
Dispos, 35, 419-427 (2007).
Jessica A. Bonzo, Alain Belanger and Robert H. Tukey,
The role of chrysin and the Ah receptor in induction of the
human UGT1A1 gene in vitro and in transgenic UGT1 mice,
Hepatology (Hoboken, NJ, U. S.), 45, 349-360 (2007).
Theresa N. Operana and Robert H. Tukey, Oligomerization
of the UDP-glucuronosyltransferase 1A Proteins: Homo- and
heterodimerization analysis by fluorescence resonance energy transfer and co-immunoprecipitation, J. Biol. Chem, 282,
4821-4829 (2007).
Mei-Fei Yueh and Robert H. Tukey, Nrf2-Keap1 Signaling
Pathway Regulates Human UGT1A1 Expression in Vitro and
in Transgenic UGT1 Mice, J. Biol. Chem, 282, 8749-8758
(2007).
Theresa N. Operana, Nghia Nguyen, Shujuan Chen, Deirdre Beaton and Robert H. Tukey, Human CYP1A1GFP Expression in Transgenic Mice Serves as a Biomarker for Environmental Toxicant Exposure, Toxicol. Sci, 95, 98-107
(2007).
Nghia Nguyen, Jessica A. Bonzo, Shujuan Chen, Sarah
Chouinard, Michael J. Kelner, Gary Hardiman, Alain Belanger and Robert H. Tukey, Disruption of the Ugt1 Locus in
Mice Resembles Human Crigler-Najjar Type I Disease, J.
Biol. Chem, 283, 7901-7911 (2008).
Sarah Chouinard, Mei-Fei Yueh, Robert H. Tukey, Frank
Giton, Jean Fiet, Georges Pelletier, Olivier Barbier and Alain
Belanger, Inactivation by UDP-glucuronosyltransferase enzymes: The end of androgen signaling, J. Steroid Biochem.
Mol. Biol, 109, 247-253 (2008).
VIADIU, HECTOR Assistant Professor. TEL: (858)
822-4486 FAX: (858) 822-4499
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C20803
Email: viadiu@ucsd.edu
Publication list has not been verified by the department.
Hector Viadiu, Tamir Gonen and Thomas Walz, Projection
Map of Aquaporin-9 at 7 Å Resolution, J. Mol. Biol, 367, 8088 (2007).
WANG, LEI (b.1972) Assistant Professor. B.S, 1994,
Peking University; Ph.D, 2002, University of California
at Berkeley. Merck Fellow of the Damon Runyon Cancer
Research Foundation, 2002-2005, University of California, San Diego. Chemical Biology. Genetically encoding
novel amino acids to investigate biological processes in
live cells and in vivo. Study the origin and evolution of
the genetic code using genetic engineering and synthetic
biology methods. TEL: (858) 453-4100 FAX: (858) 5970855
Web: wang.salk.edu
Email: lwang@salk.edu
L. Wang and P. G. Schultz, Expanding the genetic code,
Angewandte Chemie International Edition, 44, 34-66 (2005).
Y. Zhang, L. Wang, P. G. Schultz and I. A. Wilson, Crystal structures of apo Wild-Type M. jannaschii TyrRS and a
mutant synthetase specific for O-Methyl-L-Tyrosine, Protein
Science, 14, 1340-1349 (2005).
L. Wang, J. Xie and P. G. Schultz, Exanding the genetic
code, Annual Review of Biophysics and Biomolecular Structure, 35, 225-249 (2006).
A. R. Parrish, W. Wang and L. Wang, Manipulating proteins for neuroscience, Current Opinion in Neurobiology, 16,
585-592 (2006).
L. Wang and R. Y. Tsien, Evolving proteins in mammalian
cells using somatic hypermutation, Nature Protocols, 1,
1346-1350 (2006).
W. Wang, J. K. Takimoto, G. V. Louie, T. J. Baiga, J. P.
Noel, K.-F. Lee, P. A. Slesinger and L. Wang, Genetically
encoding unnatural amino acids for cellular and neuronal
studies, Nature Neuroscience, 10, 1063-1072 (2007).
D. B. F. Johnson, J. K. Takimoto, J. Xu and L. Wang, Unnatural amino acids to investigate biological processes, Wiley
Encyclopedia
of
Chemical
Biology,
doi:10.1002/
9780470048672 (2007).
Q. Wang and L. Wang, New methods enabling efficient incorporation of unnatural amino acids in yeast, Journal of the
American Chemical Society, 130, 6066-6067 (2008).
M. Z. Lin and L. Wang, Selective labeling of proteins with
chemical probes in living cells, Physiology, 23, 131-141
(2008).
WANG, WEI Associate Professor. Postdoctoral Fellow, 2001-2003, Stanoford University. Bioinformatics;
Computational Chemistry. TEL: (858) 822-4240 FAX:
(858) 822-4236
Web: wanglab.ucsd.edu
Email: wei-wang@ucsd.edu
No publication information submitted for this edition.
WATSON, JOSEPH W.
No publication information submitted for this edition.
WEARE, JOHN H. (b.1940) Professor. B.S, 1962,
Harvey Mudd College; Ph.D, 1968, The Johns Hopkins
University. AFOSR Fellowship, 1968-1969, M.I.T; Guggenheim Fellowship, 1976-1977, Harvard University.
Theoretical chemistry; ab initio molecular dynamics;
theory of clusters, surfaces, and condensed matter; theory of geochemical processes. TEL: (858) 534-3286 FAX:
(858) 534-7244
Web: www.chem.ucsd.edu/Faculty/Research_text/
weare.html
Email: jweare@ucsd
Publication list has not been verified by the department.
Eric J. Bylaska, Marat Valiev, James R. Rustad and John
H. Weare, Structure and dynamics of the hydration shells of
the Al3+ ion, J. Chem. Phys, 126, 104505/1-104505/8 (2007).
Marat Valiev, Jie Yang, Joseph A. Adams, Susan S. Taylor
and John H. Weare, Phosphorylation Reaction in cAPK Protein Kinase-Free Energy Quantum Mechanical/Molecular
Mechanics Simulations, J. Phys. Chem. B, 111, 13455-13464
(2007).
WEINBERGER, LEOR S. Assistant Professor. Ph.D,
2004, UC Berkeley. Lewis Thomas Fellow, 2005-2007,
Princeton University. Biochemistry. TEL: (858) 5348671 FAX: (858) 246-0864
Web: weinbergerlab.ucsd.edu
Email: lsw@ucsd.edu
Leor S. Weinberger and Thomas Shenk, An HIV feedback
resistor: Auto-regulatory circuit deactivator and noise buffer,
Los Alamos Natl. Lab., Prepr. Arch., Quant. Biol, 1-15
(2007).
Leor S. Weinberger and Thomas Shenk, An HIV feedback
resistor: Auto-regulatory circuit deactivator and noise buffer,
PLoS Biol, 5, 67-81 (2007).
Leor S. Weinberger, Roy D. Dar and Michael L. Simpson,
Transient-mediated fate determination in a transcriptional
circuit of HIV, Nat. Genet, 40, 466-470 (2008).
WEIZMAN, HAIM (b.1965) LPSOE. B.Sc, 1992, The
Hebrew University of Jerusalem; M.S, 1994, The Weizmann Institute of Science; Ph.D, 1999, The Weizmann
Institute of Science. Postdoctoral research fellow, 19992003, University of California, San Diego; Project Scientist, 2003-2005, University of California, San Diego;
Lecturer, 2003-2005, University of California, San Diego. Organic Chemistry. Chemical education: representations, development of curriculum for organic and bioorganic chemistry, and cognitive process related to teaching of chemistry. TEL: (858) 534-2963 FAX: (858) 5340202
CALIFORNIA, SAN DIEGO
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C03537
Email: hweizman@ucsd.edu
K. C. Nguyen and H. Weizman, Greening Wittig reactions:
Solvent –free synthesis of Ethyl trans-Cinnamate and E-3-(9Anthryl)-2-Propenoic Acid Ethyl Ester, J. Chem. Ed, 84,
119-121 (2007).
R. Hwa and H. Weizman, Revisiting the separation of Ferrocene and Acetylferrocene by adsorption chromatography:
Adding a third component, J. Chem. Ed, 84, 1497-1498
(2007).
Y. Tor, S. Del Valle, D. Jaramillo, S. G. Srivatsan and H.
Weizman, Designing new isomorphic fluorescent nucleobase
analogues: The thieno[3,2-d]pyrimidine core, Tetrahedron,
63, 3608-3614 (2007).
H. Weizman, Why are 1H NMR integrations not perfect?
An inquiry based exercise for exploring the relationship between spin-dynamics and NMR integration in the organic
laboratory, J. Chem. Ed, 85, 294-296 (2008).
S. G. Srivatsan, H. W. Weizman and H. Y. Tor, A highly
fluorescent nucleoside analog based on thieno[3,4-d]pyrimidine senses mismatched pairing, Org. Biomol. Chem, 6,
1334—1338 (2008).
WENKERT, ERNEST (b.1925) Professor Emeritus.
B.S, 1945, University of Washington; M.S, 1947, University of Washington; Ph.D, 1951, Harvard University.
Synthesis and structure analysis of organic natural products; development of new methods of organochemical
synthesis; synthesis based on transition metal-mediated
reactions. TEL: (619) 534-4942 FAX: (858) 534-4864
Email: ewenkert@ucsd.edu
No publication information submitted for this edition.
WHEELER, JOHN C. (b.1941) Professor. B.A, 1963,
Oberlin College; Ph.D, 1968, Cornell University. NSF
Fellowship, 1967-1969, Harvard University; Alfred P.
Sloan Foundation Fellowship, 1972-1976, University of
California, San Diego; Guggenheim Foundation Fellowship, 1983-1984, Université de Paris-Sud Centre
d’Orsay. Theoretical chemistry: statistical mechanics,
thermodynamics; phase transitions, critical phenomena
in mixtures; moment analysis of spectral densities. Polymers and polymerization. Vibrational motion at solid
surfaces. Phase equilibria in micellar solutions. TEL:
(858) 534-3287 FAX: (858) 534-7244
Web: www.chem.ucsd.edu/Faculty/Research_text/
wheeler.html
Email: jwheeler@ucsd.edu
No publication information submitted for this edition.
WHITESELL, JAMES K. (b.1944) Professor. B.S,
1966, Pennsylvania State University; Ph.D, 1971, Harvard University. Postdoctoral, 1971-1973, Woodward
Research Institute. Organic Chemistry. Stereochemistry,
both in a molecular and a supramolecular sense. Solar
energy harvesting. Materials for photonic applications.
TEL: (858) 534-5870 FAX: (858) 534-5383
Email: jkw@ucsd.edu
No publication information submitted for this edition.
WOLYNES, PETER GUY (b.1953) Francis H. C.
Crick Professor. A.B, 1971, Indiana University; A.M,
1972, Harvard University; Ph.D, 1976, Harvard University; D.Sc, 1988, Indiana University. Research Associate,
1975-1976, M. I. T. Biophysics/Biophysical Chemistry;
Physical Chemistry. Protein folding and function;
glasses; dynamics of biomolecules; stochastic cell biology; theoretical chemical physics. TEL: (858) 822-4825
FAX: (858) 822-4560
Web: www.chem.ucsd.edu/Faculty/bios/wolynes.html
Email: pwolynes@ucsd.edu
V. Lubchenko, R. J. Silbey and P. G. Wolynes, The microscopic quantum theory of low temperature amorphous solids,
Adv. Chem. Phys, 136, 95-206 (2007).
V. Lubchenko and P. G. Wolynes, Theory of structural
glasses and supercooled liquids, Ann. Rev. Phys. Chem, 58,
235-266 (2007).
D. U. Ferreiro, C. F. Cervantes, M. E. Truhlar, S. S. Cho,
P. G. Wolynes and E. A. Komives, Stabilizing IkBk by “consensus” design, J. Mol. Bio, 365, 1201-1216 (2007).
J. Latzer, G. Papoian, M. Prentiss, E. Komives and P. G.
Wolynes, Induced fit, folding, and recognition of the NF-kBnuclear localization signals by IkBa and IdBb, J. Mol. Bio,
376, 262-274 (2007).
D. Schultz, J. N. Onuchic and P. G. Wolynes, Understanding stochastic simulations of the smallest genetic networks, J.
Phys. Chem, 126, 245102-1-11 (2007).
Y. Levy, J. N. Onuchic and P. G. Wolynes, Fly-casting in
Protein-DNA binding: Frustration between protein folding
and electrostatics facilitates target recognition, JACS, 3, 738739 (2007).
M. Gruebele and P. G. Wolynes, Quantizing ULam’s control conjecture, Phys. Rev. Lett, 99, 060201-1-4 (2007).
S. S. Cho, P. Weinkam and P. G. Wolynes, Origins of barriers and barrierless folding in BBL, PNAS, 104, 112-123
(2007).
D. Schultz, E. Ben Jacob, J. N. Onuchic and P. G. Wolynes, Molecular level stochastic model for competence cycles in Bacillus subtilis, PNAS, 104, 17582-17587 (2007).
T. Lu, T. Shen, M. Bennett, P. G. Wolynes and J. Hasty,
Phenotypic variability of growing cellular populations,
PNAS, 104, 18982-18987 (2007).
D. Ferreiro, J. Hegler, E. Komives and P. G. Wolynes, Localizing frustration in native proteins and protein assemblies,
PNAS, 104, 19819-19824 (2007).
L. Sutto, J. Latzer, J. Hegler, D. Ferreiro and P. G. Wolynes, Consequences of localized frustration for the folding
mechanism of the IM7 protein, PNAS, 104, 19825-19830
(2007).
C. Zong, C. J. Wilson, T. Shen, P. Wittung-Staffshede, S.
Mayo and P. Wolynes, Establishing the entatic state in folding metallated pseudomonas aeruginosa azurin, PNAS, 104,
3159-3164 (2007).
P. G. Wolynes, Lectures on biomolecular energy landscapes, Proceedings of the International School of Physics
“Enrico Fermi” Course CLXV, 27-46 (2007).
J. Latzer, T. Shen and P. Wolynes, Conformational switching upon phosphorylation: A predictive framework based on
energy landscape principles, Biochem, 47, 2110-2122 (2008).
L. S. Itzhaki and P. G. Wolynes, The quest to understand
protein folding, Curr. Op. Struct. Bio, 18, 1-3 (2008).
J. A. Hegler, P. Weinkam and P. G. Wolynes, The spectrum of biomolecular states and motions, HFSP Journal, 2,
307-313 (2008).
P. G. Whitford, J. N. Onuchic and P. G. Wolynes, The energy landscape along an enzymatic reaction trajectory:
Hinges or cracks?, HFSP Journal, 2, 61-64 (2008).
J. D. Stevenson, A. M. Walczak, R. W. Hall and P. G.
Wolynes, Constructing explicit magnetic analogies for the
dynamics of glass forming liquids, J. Chem. Phys, 129,
194505-1-6 (2008).
M. C. Prentiss, D. J. Wales and P. G. Wolynes, Protein
structure prediction using basin hopping, J. Chem. Phys, 128,
225106-1-9 (2008).
J. D. Stevenson and P. G. Wolynes, On the surface of
glasses, J. Chem. Phys, 129, 234514-1-4 (2008).
T. Shen, C. Zong, J. Portman and P. G. Wolynes, Variationally determined free energy profiles for structural models
of proteins: Characteristic temperatures for folding and trapping, J. Phys. Chem .B, 112, 6074-6082 (2008).
R. W. Hall and P. G. Wolynes, Intermolecular forces and
the glass transition, J. Phys. Chem. B, 112, 301-312 (2008).
P. G. Wolynes, Protein folding and beyond: Energy landscapes and the organization of living matter in space and
time, Physical Biology from Atoms to Medicine, 267-288
(2008).
D. U. Ferreiro, A. M. Walczak, E. A. Komives and P. G.
Wolynes, The energy landscapes of repeat-containing proteins: Topology, cooperativity and the folding funnels of onedimensional architectures, PLOS Computational Biology, 4,
1-12 (2008).
S. Bhattacharyya, B. Bagchi and P. G. Wolynes, Facilitation, complexity growth, mode coupling and activated dynamics in supercooled liquids, PNAS, 105, 16067-16082
(2008).
D. Schultz, A. M. Walczak, J. N. Onuchic and P. G. Wolynes, Extinction and resurrection in gene networks, PNAS,
105, 19165-19170 (2008).
D. U. Ferreiro and P. G. Wolynes, The capillarity picture
and the kinetics of one-dimensional protein folding, PNAS,
105, 9853-9854 (2008).
P. G. Wolynes, The protein folding energy landscape: A
primer, Protein Folding, Misfolding and Aggregation, 49-69
(2008).
Aleksandra Walczak, Many body theory of stochastic gene
networks. (D)
Chenghang Zong, Theoretical studies of biomolecular selfassembly near equilibrium and far from equilibrium. (D)
Joachim Laetzer, Computational tools based on energy
landscape theory to predict structurally diverse ensembles of
transcription factors. (D)
Samuel S. Cho, Energy landscapes for protein folding,
binding, and aggregation: Simple funnels and beyond. (D)
Ting Lu, Stochasticity in biological networks: Two sides of
a golden coin. (D)
WOOLEY, JOHN (b.1945) Professor. B.S, 1967,
Michigan State University; Ph.D, 1975, The University
of Chicago. Research Fellow/ Postdoc, 1975, G. D.
Searle Pharmaceuticals, Ltd; research associate/Postdoc,
1976-1977, Harvard University Dept of Biochemical
Sciences; Physiology Course Instructor, 1978, Marine
Biological Labs; Assistant Professor, 1978-1983, Princeton University/ Dept of Biology and Dept of Biochemical Sciences; Program Director, 1984-1988, NSF Biological Instrumentation Program; Division Director, 19881992, NSF Instrumentaion and Resources Division; Deputy Associate Director, 1992-1999, DOE Biological and
Environmental Research; Associate VC of Research,
1999-2008, UC San Diego. Bioinformatics; Structural
Biology. In structural genomics, the research focuses on
obtaining insight, by way of experimental and computational studies on protein structures, into the protein universe. In metagenomics, the research focuses on characterizing, by way of coupled analysis of sequence data
17
and contextual or ecology data, the role of microbes in
the environment and the impact of environments on microbial communities. TEL: (858) 534-2494 FAX: (858)
822-1452
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C03721
Email: jwooley@ucsd.edu
Y. Ye and J. Wooley, A historical perspective and overview of protein structure prediction, Computational Methods
for Protein Structure Prediction and Modeling, (2007).
Chloe Zubieta, S. Sri Krishna, Mili Kapoor, Piotr Kozbial,
Daniel McMullan, Herbert L. Axelrod, Mitchell D. Miller,
Polat Abdubek, Eileen Ambing, Tamara Astakhova, Dennis
Carlton, Hsiu-Ju Chiu, Thomas Clayton, Marc C. Deller,
Lian Duan, Marc-Andre Elsliger, Julie Feuerhelm, Slawomir
K. Grzechnik, Joanna Hale, Eric Hampton, Gye Won Han,
Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W.
Knuth, Abhinav Kumar, David Marciano, Andrew T. Morse,
Edward Nigoghossian, Linda Okach, Silvya Oommachen,
Ron Reyes, Christopher L. Rife, Paul Schimmel, Henry van
den Bedem, Dana Weekes, Aprilfawn White, Qingping Xu,
Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam
Godzik, Scott A. Lesley and Ian A. Wilson, Crystal structures of two novel dye-decolorizing peroxidases reveal a ␤barrel fold with a conserved heme-binding motif, Proteins:
Struct., Funct., Bioinf, 69, 223-233 (2007).
Chloe Zubieta, Rosanne Joseph, S. Sri Krishna, Daniel
McMullan, Mili Kapoor, Herbert L. Axelrod, Mitchell D.
Miller, Polat Abdubek, Claire Acosta, Tamara Astakhova,
Dennis Carlton, Hsiu-Ju Chiu, Thomas Clayton, Marc C.
Deller, Lian Duan, Ylva Elias, Marc-Andre Elsliger, Julie
Feuerhelm, Slawomir K. Grzechnik, Joanna Hale, Gye Won
Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock,
Mark W. Knuth, Piotr Kozbial, Abhinav Kumar, David Marciano, Andrew T. Morse, Kevin D. Murphy, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Ron Reyes,
Christopher L. Rife, Paul Schimmel, Christina V. Trout,
Henry van den Bedem, Dana Weekes, Aprilfawn White,
Qingping Xu, Keith O. Hodgson, John Wooley, Ashley M.
Deacon, Adam Godzik, Scott A. Lesley and Ian A. Wilson,
Identification and structural characterization of heme binding
in a novel dye-decolorizing peroxidase, TyrA, Proteins:
Struct., Funct., Bioinf, 69, 234-243 (2007).
Dana Weekes, Mitchell D. Miller, S. Sri Krishna, Daniel
McMullan, Timothy M. McPhillips, Claire Acosta, Jaume M.
Canaves, Marc-Andre Elsliger, Ross Floyd, Slawomir K.
Grzechnik, Lukasz Jaroszewski, Heath E. Klock, Eric Koesema, John S. Kovarik, Andreas Kreusch, Andrew T. Morse,
Kevin Quijano, Glen Spraggon, Henry van den Bedem,
Guenter Wolf, Keith O. Hodgson, John Wooley, Ashley M.
Deacon, Adam Godzik, Scott A. Lesley and Ian A. Wilson,
Crystal structure of a transcription regulator (TM1602) from
Thermotoga maritima at 2.3 Å resolution, Proteins: Struct.,
Funct., Bioinf, 67, 247-252 (2007).
S. Sri Krishna, Lutz Tautz, Qingping Xu, Daniel McMullan, Mitchell D. Miller, Polat Abdubek, Eileen Ambing, Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton, HsiuJu Chiu, Thomas Clayton, Michael DiDonato, Lian Duan,
Marc-Andre Elsliger, Slawomir K. Grzechnik, Joanna Hale,
Eric Hampton, Gye Won Han, Justin Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Eric
Koesema, Andrew T. Morse, Tomas Mustelin, Edward Nigoghossian, Silvya Oommachen, Ron Reyes, Christopher L.
Rife, Henry van den Bedem, Dana Weekes, Aprilfawn
White, Keith O. Hodgson, John Wooley, Ashley M. Deacon,
Adam Godzik, Scott A. Lesley and Ian A. Wilson, Crystal
structure of NMA 1982 from Neisseria meningitidis at 1.5 Å
resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases, Proteins: Struct., Funct., Bioinf,
69, 415-421 (2007).
Qingping Xu, Kumar Singh Saikatendu, S. Sri Krishna,
Daniel McMullan, Polat Abdubek, Sanjay Agarwalla, Eileen
Ambing, Tamara Astakhova, Herbert L. Axelrod, Dennis
Carlton, Hsiu-Ju Chiu, Thomas Clayton, Michael DiDonato,
Lian Duan, Marc-Andre Elsliger, Julie Feuerhelm, Slawomir
K. Grzechnik, Joanna Hale, Eric Hampton, Gye Won Han,
Justin Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E.
Klock, Mark W. Knuth, Eric Koesema, Mitchell D. Miller,
Andrew T. Morse, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Jessica Paulsen, Ron Reyes, Christopher L.
Rife, Robert Schwarzenbacher, Henry van den Bedem, Aprilfawn White, Guenter Wolf, Keith O. Hodgson, John Wooley,
Ashley M. Deacon, Adam Godzik, Scott A. Lesley and Ian
A. Wilson, Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 Å resolution provides a structural basis
for bipartite phosphomonoester hydrolysis of 2-hydroxy-3keto-5-methylthiopentenyl-1-phosphate, Proteins: Struct.,
Funct., Bioinf, 69, 433-439 (2007).
Irimpan I. Mathews, Daniel McMullan, Mitchell D. Miller,
Jaume M. Canaves, Marc-Andre Elsliger, Ross Floyd, Slawomir K. Grzechnik, Lukasz Jaroszewski, Heath E. Klock,
Eric Koesema, John S. Kovarik, Andreas Kreusch, Peter
Kuhn, Timothy M. McPhillips, Andrew T. Morse, Kevin
Quijano, Christopher L. Rife, Robert Schwarzenbacher, Glen
Spraggon, Raymond C. Stevens, Henry van den Bedem,
Dana Weekes, Guenter Wolf, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley and
Ian A. Wilson, Crystal structure of 2-keto-3-deoxygluconate
kinase (TM0067) from Thermotoga maritima at 2.05 Å resolution, Proteins: Struct., Funct., Bioinf, 70, 603-608 (2007).
18
CALIFORNIA, SAN DIEGO
Chloe Zubieta, S. Sri Krishna, Daniel McMullan, Mitchell
D. Miller, Polat Abdubek, Sanjay Agarwalla, Eileen Ambing,
Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton,
Hsiu-Ju Chiu, Thomas Clayton, Marc Deller, Michael DiDonato, Lian Duan, Marc-Andre Elsliger, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Gye Won Han, Justin Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock,
Mark W. Knuth, Eric Koesema, Abhinav Kumar, David Marciano, Andrew T. Morse, Edward Nigoghossian, Silvya
Oommachen, Ron Reyes, Christopher L. Rife, Henry van den
Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, Keith
O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley and Ian A. Wilson, Crystal structure of
homoserine O-succinyltransferase from Bacillus cereus at 2.4
Å resolution, Proteins: Struct., Funct., Bioinf, 68, 999-1005
(2007).
K. Arima and J. Wooley, Metagenomics, Computational
Methods for Understanding Bacterial and Archaeal Genomes, 7, 345-396 (2008).
L. Weizhong, J. C. Wooley and A. Godzik, Probing metagenomics by rapid cluster analysis of very large datasets,
PLoS one, 3, e3375 (2008).
Herbert L. Axelrod, Daniel McMullan, S. Sri Krishna,
Mitchell D. Miller, Marc-Andre Elsliger, Polat Abdubek, Eileen Ambing, Tamara Astakhova, Dennis Carlton, Hsiu-Ju
Chiu, Thomas Clayton, Lian Duan, Julie Feuerhelm, Slawomir K. Grzechnik, Joanna Hale, Gye Won Han, Justin
Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock,
Mark W. Knuth, Eric Koesema, Andrew T. Morse, Edward
Nigoghossian, Linda Okach, Silvya Oommachen, Jessica
Paulsen, Kevin Quijano, Ron Reyes, Christopher L. Rife,
Henry van den Bedem, Dana Weekes, Aprilfawn White,
Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley and
Ian A. Wilson, Crystal structure of AICAR transformylase
IMP cyclohydrolase (TM1249) from Thermotoga maritima at
1.88 Å resolution, Proteins: Struct., Funct., Bioinf, 71, 10421049 (2008).
Qingping Xu, Piotr Kozbial, Daniel McMullan, S. Sri
Krishna, Scott M. Brittain, Scott B. Ficarro, Michael DiDonato, Mitchell D. Miller, Polat Abdubek, Herbert L. Axelrod,
Hsiu-Ju Chiu, Thomas Clayton, Lian Duan, Marc-Andre Elsliger, Julie Feuerhelm, Slawomir K. Grzechnik, Joanna
Hale, Gye Won Han, Lukasz Jaroszewski, Heath E. Klock,
Andrew T. Morse, Edward Nigoghossian, Jessica Paulsen,
Ron Reyes, Christopher L. Rife, Henry van den Bedem,
Aprilfawn White, Keith O. Hodgson, John Wooley, Ashley
M. Deacon, Adam Godzik, Scott A. Lesley and Ian A. Wilson, Crystal structure of an ADP-ribosylated protein with a
cytidine deaminase-like fold, but unknown function
(TM1506), from Thermotoga maritima at 2.70 Å resolution,
Proteins: Struct., Funct., Bioinf, 71, 1546-1552 (2008).
Piotr Kozbial, Qingping Xu, Hsiu-Ju Chiu, Daniel McMullan, S. Sri Krishna, Mitchell D. Miller, Polat Abdubek, Claire
Acosta, Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton, Thomas Clayton, Marc Deller, Lian Duan, Ylva Elias,
Marc-Andre Elsliger, Julie Feuerhelm, Slawomir K. Grzechnik, Joanna Hale, Gye Won Han, Lukasz Jaroszewski, Kevin
K. Jin, Heath E. Klock, Mark W. Knuth, Eric Koesema,
Abhinav Kumar, David Marciano, Andrew T. Morse, Kevin
D. Murphy, Edward Nigoghossian, Linda Okach, Silvya
Oommachen, Ron Reyes, Christopher L. Rife, Glen Spraggon, Christina V. Trout, Henry van den Bedem, Dana
Weekes, Aprilfawn White, Guenter Wolf, Chloe Zubieta,
Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam
Godzik, Scott A. Lesley and Ian A. Wilson, Crystal structures of MW1337R and lin2004: representatives of a novel
protein family that adopt a four-helical bundle fold, Proteins:
Struct., Funct., Bioinf, 71, 1589-1596 (2008).
L. Jaroszewski, L. Slabinski, J. Wooley, A. M. Deacon, S.
A. Lesley, I. A. Wilson and A. Godzik, Genome pool strategy for structural coverage of protein families, Structure, 16,
1659-1667 (2008).
Lukasz Jaroszewski, Lukasz Slabinski, John Wooley, Ashley M. Deacon, Scott A. Lesley, Ian A. Wilson and Adam
Godzik, Genome Pool Strategy for Structural Coverage of
Protein Families, Structure (Cambridge, MA, U. S.), 16,
1659-1667 (2008).
YANG, JERRY (b.1972) Assistant Professor. B.S,
1995, University of California, Berkeley; M.A, 1998,
Columbia University; M.Ph, 2000, Columbia University;
Ph.D, 2001, Columbia University. Postdoctoral Fellow,
2001-2003, Harvard University. Bioorganic Chemistry;
Biotechnology. Development of new therapeutics for Alzheimer’s disease; construction of functional nanosensors using artificial ion channels for use in medical and
environmental diagnostics; design and synthesis of cancer drug delivery systems. TEL: (858) 534-6006 FAX:
(858) 534-4554
Web: www-chem.ucsd.edu/research/profile.cfm?cid=
C04652
Email: jerryyang@ucsd.edu
Seong Deok Kong, Alice Luong, Gerald Manorek, Stephen
B. Howell and Jerry Yang, Acidic Hydrolysis of NEthoxybenzylimidazoles (NEBIs): Potential Applications as
pH-Sensitive Linkers for Drug Delivery, Bioconjugate Chem,
18, 293-296 (2007).
Ricardo Capone, Steven Blake, Marcela Rincon Restrepo,
Jerry Yang and Michael Mayer, Designing Nanosensors
Based on Charged Derivatives of Gramicidin A, J. Am.
Chem. Soc, 129, 9737-9745 (2007).
Petra Inbar, Mahealani R. Bautista, Stacy A. Takayama
and Jerry Yang, Assay To Screen for Molecules That Associate with Alzheimer’s Related ␤-Amyloid Fibrils, Anal.
Chem. (Washington, DC, U. S.), 80, 3502-3506 (2008).
Steven Blake, Ricardo Capone, Michael Mayer and Jerry
Yang, Chemically Reactive Derivatives of Gramicidin A for
Developing Ion Channel-Based Nanoprobes, Bioconjugate
Chem, 19, 1614-1624 (2008).
Michael Mayer, Vincent Semetey, Irina Gitlin, Jerry Yang
and George M. Whitesides, Using Ion Channel-Forming Peptides to Quantify Protein-Ligand Interactions, J. Am. Chem.
Soc, 130, 1453-1465 (2008).
Steven Blake, Designing nanosensors based on ion channel-forming peptides of gramicidin A. (D)