CURRICULUM VITAE
Steven C. Almo, Ph.D.
Department of Biochemistry
Department of Physiology & Biophysics
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
phone: (718) 430-2746
fax:
(718) 430-8565
e-mail: almo@aecom.yu.edu
EDUCATION
B.S. Biology, 1982
Massachusetts Institute of Technology
Cambridge, MA
Ph.D. Biophysics, 1990
Harvard University
Cambridge, MA
Post Doctoral,1992
Johns Hopkins School of Medicine
Cell Biology and Biophysics
Baltimore, MD
POSITIONS/AWARDS
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Teaching Assistant, Stanford University Medical School, Dept. of Biochemistry, September 1982.
Teaching Assistant, Harvard University, Dept. of Biochemistry and Molecular Biology, Sept. 1983-85.
Recipient, Institute for Biological Recognition and Catalysis, Inc., Travel Grant, March 1988
Recipient, Institute for Biological Recognition and Catalysis, Inc., Travel Grant, November 1988
Instructor in Molecular Graphics Course, MIT, Department of Chemistry, 1988-1989.
Instructor, Woods Hole Marine Biology Laboratories, Physiology Summer Course, Summer 1990.
Assistant Professor of Biochemistry, Albert Einstein College of Medicine, Dept. of Biochemistry, March
1992-June 1997.
Member, Albert Einstein Comprehensive Cancer Research Center, 1996-present
Associate Professor of Biochemistry, Albert Einstein College of Medicine, Dept. of Biochemistry, July
1997-May 2001.
Professor of Biochemistry, Albert Einstein College of Medicine, Dept. of Biochemistry, June 2001present.
Associate Director for Crystallography, Center for Synchrotron Biosciences, 1997-2006.
Irma T. Hirschl/Monique Weill-Caulier Career Development Award, 2000-2004
Professor of Physiology & Biophysics, Albert Einstein College of Medicine, Department of Physiology
& Biophysics, June 2003-Present
AMGEN AWARD, American Society for Biochemistry and Molecular Biology, 2004
The LaDonne Schulman Faculty Recognition Award for Graduate Teaching at the Albert Einstein
College of Medicine, 2005
Director of Structural Proteomics, New York Structural Biology Center, November 2006-present
Director, Albert Einstein Macromolecular Therapeutic Development Facility 2007-present
AECOM SERVICE
 Faculty Senate, 1993-1995, 1998-2007
 Sue Golding Graduate Admissions Committee, 1993-1996
 MSTP Steering Committee, 1996-present
 Molecular Biophysics Training Grant Steering Committee, 1997-2010
 Associate Professor Promotion Committee, 1997-2000
 Advisory Committee, Analytical Imaging Facility, 2000-present
 Professor Promotion Committee, 2002-2004
 Tenure Committee, 2005-present
 Chair, Strategic Planning Committee on Structural Biology and Proteomics, 2007
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NATIONAL SERVICE
Special NCI Study Section for Program Project Review, 4/97
American Cancer Society, Peer Review Committee on Cancer Drug Development, 1/98-12/01
National Center for Research Resources Special Emphasis Panel ZRR1 BRT-1, April 1, 1998
Special NCI Study Section for Program Project Review, 5/98
NIH BBCB Study Section, Ad hoc, 7/98
NIH Physical Biochemistry Study Section, Ad hoc, 6/00
Editorial Board, International Archives of Allergy and Immunology, 1/98-12/00
Proposal Study Panel, Brookhaven National Laboratory, 1999-present
User Executive Committee, National Synchrotron Light Source, Brookhaven National
Laboratory, 2001-2003, 2005-2007
National Center for Research Resources Review Panel ZRG1 BBCA, October, 2001
Reviewer for J. Biol. Chem., Biochemistry, Science, Nat. Struct. Biol., Biophys. J., Structure,
Acta. Cryst, Chemistry & Biology, Nature, Proc. Natl. Acad. Sci., J. Cell Biol., Protein
Science, Proteins
Faculty of 1000, Electronic Reviews, Biology Reports Ltd.
NIH CDF-4 Study Section, Ad hoc, 2/02
NIH CSF (formerly CDF-4) Study Section, 10/02-10/06
NIH Scientific Advisory Board, Epitope Discovery Working Group, NIAID, 9/04-12/05
NIH Administrative Chairman of Division of Molecular and Cellular Mechanisms Special
Emphasis Panel, 7/04-6/06
NIH ZRG1-SBMI Review Panel, Ad hoc, 03/05
Chairman, NIH ZRG1 CB-B 02 S, Review Panel (Bioengineering Research Partnership), 6/05
NIH IDM-G (2) Review Panel, Ad hoc, 03/05
NIH ZRG1 IDM-G (02) Drug Development 08/06
NIH ZRG1 BST-D (50) Technology Centers for Networks and Pathways 3/09/09 – 3/10/09
NIH CSF Study Section, Ad hoc, 6/09
ZRG1 BCMB-B (99) R Review Panel 7/30/09
Member, Beamline Advisory Team, National Synchrotron Light Source, 2009-present
Scientific Advisory Committee, HIVRAD (Michael Cho, PI; Iowa State) 2009-present
Scientific Advisory Committee, Center for Synchrotron Biosciences (Mark Chance, PI; Case
Western Reserve) 2009-present
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Scientific Advisory Committee, PXRR (Robert Sweet, PI; Brookhaven National Laboratory)
2009-present; Chair 2011
College of CSR Reviewers, 2010-present
Organizer, 2012 Keystone Meeting “Structural Biology of Cellular Processes: From Atoms to
Cells”
PROFESSIONAL SOCIETIES
 American Society for Cell Biology
 American Crystallographic Association
PUBLICATIONS:
1. Farber GK, Machin P, Almo SC, Petsko GA, Hajdu J. X-ray Laue diffraction from crystals of xylose
isomerase. Proc Natl Acad Sci U S A. 1988;85(1):112-5. PMCID: 279493.
2. Mondragon A, Subbiah S, Almo SC, Drottar M, Harrison SC. Structure of the amino-terminal domain
of phage 434 repressor at 2.0 A resolution. J Mol Biol. 1989;205(1):189-200.
3. Smith DL, Almo SC, Toney MD, Ringe D. 2.8-A-resolution crystal structure of an active-site mutant of
aspartate aminotransferase from Escherichia coli. Biochemistry. 1989;28(20):8161-7.
4. Schlichting I, Almo SC, Rapp G, Wilson K, Petratos K, Lentfer A, Wittinghofer A, Kabsch W, Pai EF,
Petsko GA, et al. Time-resolved X-ray crystallographic study of the conformational change in Ha-Ras p21
protein on GTP hydrolysis. Nature. 1990;345(6273):309-15.
5. Howell PL, Almo SC, Parsons MR, Hajdu J, Petsko GA. Structure determination of turkey egg-white
lysozyme using Laue diffraction data. Acta Crystallogr B. 1992;48 ( Pt 2):200-7.
6. Almo SC, Pollard TD, Way M, Lattman EE. Purification, characterization and crystallization of
Acanthamoeba profilin expressed in Escherichia coli. J Mol Biol. 1994;236(3):950-2.
7. Almo SC, Smith DL, Danishefsky AT, Ringe D. The structural basis for the altered substrate
specificity of the R292D active site mutant of aspartate aminotransferase from E. coli. Protein Eng.
1994;7(3):405-12.
8. Fedorov AA, Magnus KA, Graupe MH, Lattman EE, Pollard TD, Almo SC. X-ray structures of
isoforms of the actin-binding protein profilin that differ in their affinity for phosphatidylinositol phosphates.
Proc Natl Acad Sci U S A. 1994;91(18):8636-40. PMCID: 44661.
9. Fedorov AA, Pollard TD, Almo SC. Purification, characterization and crystallization of human platelet
profilin expressed in Escherichia coli. J Mol Biol. 1994;241(3):480-2.
10. Pollard TD, Almo S, Quirk S, Vinson V, Lattman EE. Structure of actin binding proteins: insights about
function at atomic resolution. Annu Rev Cell Biol. 1994;10:207-49.
11. Fedorov AA, Joseph-McCarthy D, Fedorov E, Sirakova D, Graf I, Almo SC. Ionic interactions in
crystalline bovine pancreatic ribonuclease A. Biochemistry. 1996;35(50):15962-79.
12. Joseph-McCarthy D, Fedorov AA, Almo SC. Comparison of experimental and computational
functional group mapping of an RNase A structure: implications for computer-aided drug design. Protein
Eng. 1996;9(9):773-80.
13. Wiedemann P, Giehl K, Almo SC, Fedorov AA, Girvin M, Steinberger P, Rudiger M, Ortner M, Sippl
M, Dolecek C, Kraft D, Jockusch B, Valenta R. Molecular and structural analysis of a continuous birch
profilin epitope defined by a monoclonal antibody. J Biol Chem. 1996;271(47):29915-21.
14. Fedorov AA, Ball T, Mahoney NM, Valenta R, Almo SC. The molecular basis for allergen crossreactivity: crystal structure and IgE-epitope mapping of birch pollen profilin. Structure. 1997;5(1):33-45.
15. Fedorov AA, Ball T, Valenta R, Almo SC. X-ray crystal structures of birch pollen profilin and Phl p 2.
Int Arch Allergy Immunol. 1997;113(1-3):109-13.
16. Fedorov AA, Lappalainen P, Fedorov EV, Drubin DG, Almo SC. Structure determination of yeast
cofilin. Nat Struct Biol. 1997;4(5):366-9.
17. Goldsmith SC, Pokala N, Matsudaira P, Almo SC. Crystallization and preliminary crystallographic
analysis of the N-terminal actin binding domain of human fimbrin. Proteins. 1997;28(3):452-3.
18. Goldsmith SC, Pokala N, Shen W, Fedorov AA, Matsudaira P, Almo SC. The structure of an actincrosslinking domain from human fimbrin. Nat Struct Biol. 1997;4(9):708-12.
19. Lappalainen P, Fedorov EV, Fedorov AA, Almo SC, Drubin DG. Essential functions and actin-binding
surfaces of yeast cofilin revealed by systematic mutagenesis. Embo J. 1997;16(18):5520-30. PMCID:
1170184.
20. Mahoney NM, Janmey PA, Almo SC. Structure of the profilin-poly-L-proline complex involved in
morphogenesis and cytoskeletal regulation. Nat Struct Biol. 1997;4(11):953-60.
21. Puius YA, Zhao Y, Sullivan M, Lawrence DS, Almo SC, Zhang ZY. Identification of a second aryl
phosphate-binding site in protein-tyrosine phosphatase 1B: a paradigm for inhibitor design. Proc Natl
Acad Sci U S A. 1997;94(25):13420-5. PMCID: 28320.
22. Degano M, Almo SC, Sacchettini JC, Schramm VL. Trypanosomal nucleoside hydrolase. A novel
mechanism from the structure with a transition-state inhibitor. Biochemistry. 1998;37(18):6277-85.
23. Eads JC, Mahoney NM, Vorobiev S, Bresnick AR, Wen KK, Rubenstein PA, Haarer BK, Almo SC.
Structure determination and characterization of Saccharomyces cerevisiae profilin. Biochemistry.
1998;37(32):11171-81.
24. Hanein D, Volkmann N, Goldsmith S, Michon AM, Lehman W, Craig R, DeRosier D, Almo S,
Matsudaira P. An atomic model of fimbrin binding to F-actin and its implications for filament crosslinking
and regulation. Nat Struct Biol. 1998;5(9):787-92.
25. Liu S, Fedorov AA, Pollard TD, Lattman EE, Almo SC, Magnus KA. Crystal packing induces a
conformational change in profilin-I from Acanthamoeba castellanii. J Struct Biol. 1998;123(1):22-9.
26. Mahoney NM, Almo SC. Crystallization and preliminary X-ray analysis of human platelet profilin
complexed with an oligo proline peptide. Acta Crystallogr D Biol Crystallogr. 1998;54(Pt 1):108-10.
27. Mao C, Cook WJ, Zhou M, Federov AA, Almo SC, Ealick SE. Calf spleen purine nucleoside
phosphorylase complexed with substrates and substrate analogues. Biochemistry. 1998;37(20):7135-46.
28. Mitra J, Tang X, Almo SC, Shields D. Temperature-induced conformational changes in
prosomatostatin-II: implications for processing. Biochem J. 1998;334 ( Pt 1):275-82. PMCID: 1219689.
29. Patskovska LN, Fedorov AA, Patskovsky YV, Almo SC, Listowsky I. Expression, crystallization and
preliminary X-ray analysis of ligand-free human glutathione S-transferase M2-2. Acta Crystallogr D Biol
Crystallogr. 1998;54(Pt 3):458-60.
30. Puius YA, Mahoney NM, Almo SC. The modular structure of actin-regulatory proteins. Curr Opin Cell
Biol. 1998;10(1):23-34.
31. Puius YA, Zou M, Ho NT, Ho C, Almo SC. Novel water-mediated hydrogen bonds as the structural
basis for the low oxygen affinity of the blood substitute candidate rHb(alpha 96Val-->Trp). Biochemistry.
1998;37(26):9258-65.
32. Valenta R, Almo S, Ball T, Dolecek C, Steinberger P, Laffer S, Eibensteiner P, Flicker S, Vrtala S,
Spitzauer S, Valent P, Denepoux S, Kraft D, Banchereau J, Lebecque S. The immunoglobulin E-allergen
interaction: a target for therapy of type I allergic diseases. Int Arch Allergy Immunol. 1998;116(3):167-76.
33. Burley SK, Almo SC, Bonanno JB, Capel M, Chance MR, Gaasterland T, Lin D, Sali A, Studier FW,
Swaminathan S. Structural genomics: beyond the human genome project. Nat Genet. 1999;23(2):151-7.
34. Fedorov AA, Fedorov E, Gertler F, Almo SC. Structure of EVH1, a novel proline-rich ligand-binding
module involved in cytoskeletal dynamics and neural function. Nat Struct Biol. 1999;6(7):661-5.
35. Levin S, Almo SC, Satir BH. Functional diversity of the phosphoglucomutase superfamily: structural
implications. Protein Eng. 1999;12(9):737-46.
36. Mahoney NM, Rozwarski DA, Fedorov E, Fedorov AA, Almo SC. Profilin binds proline-rich ligands in
two distinct amide backbone orientations. Nat Struct Biol. 1999;6(7):666-71.
37. Shi W, Li CM, Tyler PC, Furneaux RH, Cahill SM, Girvin ME, Grubmeyer C, Schramm VL, Almo SC.
The 2.0 A structure of malarial purine phosphoribosyltransferase in complex with a transition-state
analogue inhibitor. Biochemistry. 1999;38(31):9872-80.
38. Shi W, Li CM, Tyler PC, Furneaux RH, Grubmeyer C, Schramm VL, Almo SC. The 2.0 A structure of
human hypoxanthine-guanine phosphoribosyltransferase in complex with a transition-state analog
inhibitor. Nat Struct Biol. 1999;6(6):588-93.
39. Shi W, Schramm VL, Almo SC. Nucleoside hydrolase from Leishmania major. Cloning, expression,
catalytic properties, transition state inhibitors, and the 2.5-a crystal structure. J Biol Chem.
1999;274(30):21114-20.
40. Apgar J, Tseng Y, Fedorov E, Herwig MB, Almo SC, Wirtz D. Multiple-particle tracking measurements
of heterogeneities in solutions of actin filaments and actin bundles. Biophys J. 2000;79(2):1095-106.
PMCID: 1301005.
41. Burke E, Mahoney NM, Almo SC, Barik S. Profilin is required for optimal actin-dependent
transcription of respiratory syncytial virus genome RNA. J Virol. 2000;74(2):669-75. PMCID: 111586.
42. Melian A, Watts GF, Shamshiev A, De Libero G, Clatworthy A, Vincent M, Brenner MB, Behar S,
Niazi K, Modlin RL, Almo S, Ostrov D, Nathenson SG, Porcelli SA. Molecular recognition of human CD1b
antigen complexes: evidence for a common pattern of interaction with alpha beta TCRs. J Immunol.
2000;165(8):4494-504.
43. Ostrov DA, Shi W, Schwartz JC, Almo SC, Nathenson SG. Structure of murine CTLA-4 and its role in
modulating T cell responsiveness. Science. 2000;290(5492):816-9.
44. Puius YA, Fedorov EV, Eichinger L, Schleicher M, Almo SC. Mapping the functional surface of
domain 2 in the gelsolin superfamily. Biochemistry. 2000;39(18):5322-31.
45. Sarmiento M, Puius YA, Vetter SW, Keng YF, Wu L, Zhao Y, Lawrence DS, Almo SC, Zhang ZY.
Structural basis of plasticity in protein tyrosine phosphatase 1B substrate recognition. Biochemistry.
2000;39(28):8171-9.
46. Shi W, Munagala NR, Wang CC, Li CM, Tyler PC, Furneaux RH, Grubmeyer C, Schramm VL, Almo
SC. Crystal structures of Giardia lamblia guanine phosphoribosyltransferase at 1.75 A(,). Biochemistry.
2000;39(23):6781-90.
47. Wolven AK, Belmont LD, Mahoney NM, Almo SC, Drubin DG. In vivo importance of actin nucleotide
exchange catalyzed by profilin. J Cell Biol. 2000;150(4):895-904. PMCID: 2175289.
48. Fedorov A, Shi W, Kicska G, Fedorov E, Tyler PC, Furneaux RH, Hanson JC, Gainsford GJ, Larese
JZ, Schramm VL, Almo SC. Transition state structure of purine nucleoside phosphorylase and principles
of atomic motion in enzymatic catalysis. Biochemistry. 2001;40(4):853-60.
49. Goldsmith SC, Guan JQ, Almo S, Chance M. Synchrotron protein footprinting: a technique to
investigate protein-protein interactions. J Biomol Struct Dyn. 2001;19(3):405-18.
50. Rustandi R, Vallely KM, Varlamova O, Klein MG, Almo SC, Bresnick AR, Weber DJ. 1H, 13C, 15N
NMR sequence-specific resonance assignments for human apo-Mts1 (S100A4). J Biomol NMR.
2001;19(4):381-2.
51. Schwartz JC, Zhang X, Fedorov AA, Nathenson SG, Almo SC. Structural basis for co-stimulation by
the human CTLA-4/B7-2 complex. Nature. 2001;410(6828):604-8.
52. Shi W, Basso LA, Santos DS, Tyler PC, Furneaux RH, Blanchard JS, Almo SC, Schramm VL.
Structures of purine nucleoside phosphorylase from Mycobacterium tuberculosis in complexes with
immucillin-H and its pieces. Biochemistry. 2001;40(28):8204-15.
53. Shi W, Tanaka KS, Crother TR, Taylor MW, Almo SC, Schramm VL. Structural analysis of adenine
phosphoribosyltransferase from Saccharomyces cerevisiae. Biochemistry. 2001;40(36):10800-9.
54. Tseng Y, Fedorov E, McCaffery JM, Almo SC, Wirtz D. Micromechanics and ultrastructure of actin
filament networks crosslinked by human fascin: a comparison with alpha-actinin. J Mol Biol.
2001;310(2):351-66.
55. Zhang X, Schwartz JC, Nathenson SG, Almo SC. Crystallization and preliminary X-ray analysis of the
complex between human CTLA-4 and B7-2. Acta Crystallogr D Biol Crystallogr. 2001;57(Pt 6):898-9.
56. Bobkov AA, Muhlrad A, Kokabi K, Vorobiev S, Almo SC, Reisler E. Structural effects of cofilin on
longitudinal contacts in F-actin. J Mol Biol. 2002;323(4):739-50.
57. Bubb MR, Govindasamy L, Yarmola EG, Vorobiev SM, Almo SC, Somasundaram T, Chapman MS,
Agbandje-McKenna M, McKenna R. Polylysine induces an antiparallel actin dimer that nucleates filament
assembly: crystal structure at 3.5-A resolution. J Biol Chem. 2002;277(23):20999-1006.
58. Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA,
Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK.
Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 2002;11(4):723-38.
PMCID: 2373525.
59. Dewan JC, Feeling-Taylor A, Puius YA, Patskovska L, Patskovsky Y, Nagel RL, Almo SC, Hirsch RE.
Structure of mutant human carbonmonoxyhemoglobin C (betaE6K) at 2.0 A resolution. Acta Crystallogr D
Biol Crystallogr. 2002;58(Pt 12):2038-42.
60. Guan JQ, Vorobiev S, Almo SC, Chance MR. Mapping the G-actin binding surface of cofilin using
synchrotron protein footprinting. Biochemistry. 2002;41(18):5765-75.
61. Kicska GA, Tyler PC, Evans GB, Furneaux RH, Shi W, Fedorov A, Lewandowicz A, Cahill SM, Almo
SC, Schramm VL. Atomic dissection of the hydrogen bond network for transition-state analogue binding to
purine nucleoside phosphorylase. Biochemistry. 2002;41(49):14489-98.
62. Ostrov DA, Roden MM, Shi W, Palmieri E, Christianson GJ, Mendoza L, Villaflor G, Tilley D, Shastri
N, Grey H, Almo SC, Roopenian D, Nathenson SG. How H13 histocompatibility peptides differing by a
single methyl group and lacking conventional MHC binding anchor motifs determine self-nonself
discrimination. J Immunol. 2002;168(1):283-9.
63. Schwartz JC, Zhang X, Nathenson SG, Almo SC. Structural mechanisms of costimulation. Nat
Immunol. 2002;3(5):427-34.
64. Shi W, Sarver AE, Wang CC, Tanaka KS, Almo SC, Schramm VL. Closed site complexes of adenine
phosphoribosyltransferase from Giardia lamblia reveal a mechanism of ribosyl migration. J Biol Chem.
2002;277(42):39981-8.
65. Tseng Y, Schafer BW, Almo SC, Wirtz D. Functional synergy of actin filament cross-linking proteins.
J Biol Chem. 2002;277(28):25609-16.
66. Zhang X, Schwartz JC, Almo SC, Nathenson SG. Expression, refolding, purification, molecular
characterization, crystallization, and preliminary X-ray analysis of the receptor binding domain of human
B7-2. Protein Expr Purif. 2002;25(1):105-13.
67. Guan JQ, Almo SC, Reisler E, Chance MR. Structural reorganization of proteins revealed by
radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependent. Biochemistry.
2003;42(41):11992-2000.
68. Huang RY, Boulton SJ, Vidal M, Almo SC, Bresnick AR, Chance MR. High-throughput expression,
purification, and characterization of recombinant Caenorhabditis elegans proteins. Biochem Biophys Res
Commun. 2003;307(4):928-34.
69. Kiselar JG, Janmey PA, Almo SC, Chance MR. Structural analysis of gelsolin using synchrotron
protein footprinting. Mol Cell Proteomics. 2003;2(10):1120-32.
70. Kiselar JG, Janmey PA, Almo SC, Chance MR. Visualizing the Ca2+-dependent activation of gelsolin
by using synchrotron footprinting. Proc Natl Acad Sci U S A. 2003;100(7):3942-7. PMCID: 153027.
71. Lewandowicz A, Shi W, Evans GB, Tyler PC, Furneaux RH, Basso LA, Santos DS, Almo SC,
Schramm VL. Over-the-barrier transition state analogues and crystal structure with Mycobacterium
tuberculosis purine nucleoside phosphorylase. Biochemistry. 2003;42(20):6057-66.
72. Sun JP, Fedorov AA, Lee SY, Guo XL, Shen K, Lawrence DS, Almo SC, Zhang ZY. Crystal structure
of PTP1B complexed with a potent and selective bidentate inhibitor. J Biol Chem. 2003;278(14):12406-14.
73. Sun JP, Wu L, Fedorov AA, Almo SC, Zhang ZY. Crystal structure of the Yersinia protein-tyrosine
phosphatase YopH complexed with a specific small molecule inhibitor. J Biol Chem. 2003;278(35):333929.
74. Vorobiev S, Strokopytov B, Drubin DG, Frieden C, Ono S, Condeelis J, Rubenstein PA, Almo SC.
The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism. Proc Natl Acad Sci U
S A. 2003;100(10):5760-5. PMCID: 156274.
75. Zhang X, Schwartz JC, Almo SC, Nathenson SG. Crystal structure of the receptor-binding domain of
human B7-2: insights into organization and signaling. Proc Natl Acad Sci U S A. 2003;100(5):2586-91.
PMCID: 151384.
76. Bobkov AA, Muhlrad A, Shvetsov A, Benchaar S, Scoville D, Almo SC, Reisler E. Cofilin (ADF)
affects lateral contacts in F-actin. J Mol Biol. 2004;337(1):93-104.
77. Dodatko T, Fedorov AA, Grynberg M, Patskovsky Y, Rozwarski DA, Jaroszewski L, Aronoff-Spencer
E, Kondraskina E, Irving T, Godzik A, Almo SC. Crystal structure of the actin binding domain of the
cyclase-associated protein. Biochemistry. 2004;43(33):10628-41.
78. Guan JQ, Almo SC, Chance MR. Synchrotron radiolysis and mass spectrometry: a new approach to
research on the actin cytoskeleton. Acc Chem Res. 2004;37(4):221-9.
79. Klein MG, Shi W, Ramagopal U, Tseng Y, Wirtz D, Kovar DR, Staiger CJ, Almo SC. Structure of the
actin crosslinking core of fimbrin. Structure. 2004;12(6):999-1013.
80. Mattila PK, Quintero-Monzon O, Kugler J, Moseley JB, Almo SC, Lappalainen P, Goode BL. A highaffinity interaction with ADP-actin monomers underlies the mechanism and in vivo function of
Srv2/cyclase-associated protein. Mol Biol Cell. 2004;15(11):5158-71. PMCID: 524793.
81. Mohri K, Vorobiev S, Fedorov AA, Almo SC, Ono S. Identification of functional residues on
Caenorhabditis elegans actin-interacting protein 1 (UNC-78) for disassembly of actin depolymerizing
factor/cofilin-bound actin filaments. J Biol Chem. 2004;279(30):31697-707.
82. Muhlrad A, Kudryashov D, Michael Peyser Y, Bobkov AA, Almo SC, Reisler E. Cofilin induced
conformational changes in F-actin expose subdomain 2 to proteolysis. J Mol Biol. 2004;342(5):1559-67.
83. Shi W, Ting LM, Kicska GA, Lewandowicz A, Tyler PC, Evans GB, Furneaux RH, Kim K, Almo SC,
Schramm VL. Plasmodium falciparum purine nucleoside phosphorylase: crystal structures, immucillin
inhibitors, and dual catalytic function. J Biol Chem. 2004;279(18):18103-6.
84. Singh V, Shi W, Evans GB, Tyler PC, Furneaux RH, Almo SC, Schramm VL. Picomolar transition
state analogue inhibitors of human 5'-methylthioadenosine phosphorylase and X-ray structure with MTimmucillin-A. Biochemistry. 2004;43(1):9-18.
85. Sukumvanich P, DesMarais V, Sarmiento CV, Wang Y, Ichetovkin I, Mouneimne G, Almo S,
Condeelis J. Cellular localization of activated N-WASP using a conformation-sensitive antibody. Cell Motil
Cytoskeleton. 2004;59(2):141-52.
86. Zhang X, Schwartz JC, Guo X, Bhatia S, Cao E, Lorenz M, Cammer M, Chen L, Zhang ZY, Edidin
MA, Nathenson SG, Almo SC. Structural and functional analysis of the costimulatory receptor
programmed death-1. Immunity. 2004;20(3):337-47.
87. Ball T, Edstrom W, Mauch L, Schmitt J, Leistler B, Fiebig H, Sperr WR, Hauswirth AW, Valent P,
Kraft D, Almo SC, Valenta R. Gain of structure and IgE epitopes by eukaryotic expression of the major
Timothy grass pollen allergen, Phl p 1. Febs J. 2005;272(1):217-27.
88. Bhatia S, Edidin M, Almo SC, Nathenson SG. Different cell surface oligomeric states of B7-1 and B72: implications for signaling. Proc Natl Acad Sci U S A. 2005;102(43):15569-74. PMCID: 1266120.
89. Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW,
Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM,
Wasserman SR, Emtage S, D'Amico KL, Burley SK. New York-Structural GenomiX Research Consortium
(NYSGXRC): a large scale center for the protein structure initiative. J Struct Funct Genomics. 2005;6(23):225-32.
90. Dulyaninova NG, Malashkevich VN, Almo SC, Bresnick AR. Regulation of myosin-IIA assembly and
Mts1 binding by heavy chain phosphorylation. Biochemistry. 2005;44(18):6867-76.
91. Guan JQ, Takamoto K, Almo SC, Reisler E, Chance MR. Structure and dynamics of the actin
filament. Biochemistry. 2005;44(9):3166-75.
92. Parsa T, Cunningham SJ, Wall SP, Almo SC, Crain EF. The usefulness of urine fluorescence for
suspected antifreeze ingestion in children. Am J Emerg Med. 2005;23(6):787-92.
93. Patskovska LN, Patskovsky YV, Almo SC, Hirsch RE. COHbC and COHbS crystallize in the R2
quaternary state at neutral pH in the presence of PEG 4000. Acta Crystallogr D Biol Crystallogr.
2005;61(Pt 5):566-73.
94. Quintero-Monzon O, Rodal AA, Strokopytov B, Almo SC, Goode BL. Structural and functional
dissection of the Abp1 ADFH actin-binding domain reveals versatile in vivo adapter functions. Mol Biol
Cell. 2005;16(7):3128-39. PMCID: 1165398.
95. Ramagopal UA, Dauter Z, Thirumuruhan R, Fedorov E, Almo SC. Radiation-induced site-specific
damage of mercury derivatives: phasing and implications. Acta Crystallogr D Biol Crystallogr. 2005;61(Pt
9):1289-98.
96. Strokopytov BV, Fedorov A, Mahoney NM, Kessels M, Drubin DG, Almo SC. Phased translation
function revisited: structure solution of the cofilin-homology domain from yeast actin-binding protein 1
using six-dimensional searches. Acta Crystallogr D Biol Crystallogr. 2005;61(Pt 3):285-93.
97. Sun JP, Wang WQ, Yang H, Liu S, Liang F, Fedorov AA, Almo SC, Zhang ZY. Structure and
biochemical properties of PRL-1, a phosphatase implicated in cell growth, differentiation, and tumor
invasion. Biochemistry. 2005;44(36):12009-21.
98. Tseng Y, Kole TP, Lee JS, Fedorov E, Almo SC, Schafer BW, Wirtz D. How actin crosslinking and
bundling proteins cooperate to generate an enhanced cell mechanical response. Biochem Biophys Res
Commun. 2005;334(1):183-92.
99. Zhan C, Fedorov EV, Shi W, Ramagopal UA, Thirumuruhan R, Manjasetty BA, Almo SC, Fiser A,
Chance MR, Fedorov AA. The ybeY protein from Escherichia coli is a metalloprotein. Acta Crystallogr
Sect F Struct Biol Cryst Commun. 2005;61(Pt 11):959-63. PMCID: 1978141.
100.
Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA. D-Ribulose 5phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate
binding (beta/alpha)8-barrel superfamily. Biochemistry. 2006;45(8):2493-503.
101.
Bhatia S, Edidin M, Almo SC, Nathenson SG. B7-1 and B7-2: similar costimulatory ligands with
different biochemical, oligomeric and signaling properties. Immunol Lett. 2006;104(1-2):70-5.
102.
Cao E, Ramagopal UA, Fedorov A, Fedorov E, Yan Q, Lary JW, Cole JL, Nathenson SG, Almo
SC. NTB-A receptor crystal structure: insights into homophilic interactions in the signaling lymphocytic
activation molecule receptor family. Immunity. 2006;25(4):559-70.
103.
Chattopadhyay K, Bhatia S, Fiser A, Almo SC, Nathenson SG. Structural basis of inducible
costimulator ligand costimulatory function: determination of the cell surface oligomeric state and functional
mapping of the receptor binding site of the protein. J Immunol. 2006;177(6):3920-9.
104.
Chiu W, Baker ML, Almo SC. Structural biology of cellular machines. Trends Cell Biol.
2006;16(3):144-50.
105.
Flicker S, Steinberger P, Ball T, Krauth MT, Verdino P, Valent P, Almo S, Valenta R. Spatial
clustering of the IgE epitopes on the major timothy grass pollen allergen Phl p 1: importance for allergenic
activity. J Allergy Clin Immunol. 2006;117(6):1336-43.
106.
Kim J, Malashkevich V, Roday S, Lisbin M, Schramm VL, Almo SC. Structural and kinetic
characterization of Escherichia coli TadA, the wobble-specific tRNA deaminase. Biochemistry.
2006;45(20):6407-16.
107.
Lazar-Molnar E, Almo SC, Nathenson SG. The interchain disulfide linkage is not a prerequisite
but enhances CD28 costimulatory function. Cell Immunol. 2006;244(2):125-9. PMCID: 1976262.
108.
Patskovsky Y, Patskovska L, Almo SC, Listowsky I. Transition state model and mechanism of
nucleophilic aromatic substitution reactions catalyzed by human glutathione S-transferase M1a-1a.
Biochemistry. 2006;45(12):3852-62.
109.
Roden MM, Brims DR, Fedorov AA, DiLorenzo TP, Almo SC, Nathenson SG. Structural analysis
of H2-Db class I molecules containing two different allelic forms of the type 1 diabetes susceptibility factor
beta-2 microglobulin: implications for the mechanism underlying variations in antigen presentation. Mol
Immunol. 2006;43(9):1370-8.
110.
Singh V, Shi W, Almo SC, Evans GB, Furneaux RH, Tyler PC, Painter GF, Lenz DH, Mee S,
Zheng R, Schramm VL. Structure and inhibition of a quorum sensing target from Streptococcus
pneumoniae. Biochemistry. 2006;45(43):12929-41. PMCID: 2517848.
111.
Yew WS, Fedorov AA, Fedorov EV, Rakus JF, Pierce RW, Almo SC, Gerlt JA. Evolution of
enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris.
Biochemistry. 2006;45(49):14582-97.
112.
Yew WS, Fedorov AA, Fedorov EV, Wood BM, Almo SC, Gerlt JA. Evolution of enzymatic
activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum.
Biochemistry. 2006;45(49):14598-608.
113.
Zhang Y, Vorobiev SM, Gibson BG, Hao B, Sidhu GS, Mishra VS, Yarmola EG, Bubb MR, Almo
SC, Southwick FS. A CapG gain-of-function mutant reveals critical structural and functional determinants
for actin filament severing. Embo J. 2006;25(19):4458-67. PMCID: 1589989.
114.
Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR,
Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y,
Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang ZY, Lawrence DS, Burley
SK. Structural genomics of protein phosphatases. J Struct Funct Genomics. 2007;8(2-3):121-40.
115.
Benchaar SA, Xie Y, Phillips M, Loo RR, Galkin VE, Orlova A, Thevis M, Muhlrad A, Almo SC,
Loo JA, Egelman EH, Reisler E. Mapping the interaction of cofilin with subdomain 2 on actin.
Biochemistry. 2007;46(1):225-33.
116.
Cao E, Zang X, Ramagopal UA, Mukhopadhaya A, Fedorov A, Fedorov E, Zencheck WD, Lary
JW, Cole JL, Deng H, Xiao H, Dilorenzo TP, Allison JP, Nathenson SG, Almo SC. T cell immunoglobulin
mucin-3 crystal structure reveals a galectin-9-independent ligand-binding surface. Immunity.
2007;26(3):311-21.
117.
Chattopadhyay K, Ramagopal UA, Mukhopadhaya A, Malashkevich VN, Dilorenzo TP, Brenowitz
M, Nathenson SG, Almo SC. Assembly and structural properties of glucocorticoid-induced TNF receptor
ligand: Implications for function. Proc Natl Acad Sci U S A. 2007;104(49):19452-7. PMCID: 2148310.
118.
Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, Raushel FM. Structural
diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate
deacetylase. Biochemistry. 2007;46(27):7953-62.
119.
Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM.
Structure-based activity prediction for an enzyme of unknown function. Nature. 2007;448(7155):775-9.
PMCID: 2254328.
120.
Imker HJ, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA. Mechanistic diversity in the RuBisCO
superfamily: the "enolase" in the methionine salvage pathway in Geobacillus kaustophilus. Biochemistry.
2007;46(13):4077-89.
121.
Kiselar JG, Mahaffy R, Pollard TD, Almo SC, Chance MR. Visualizing Arp2/3 complex activation
mediated by binding of ATP and WASp using structural mass spectrometry. Proc Natl Acad Sci U S A.
2007;104(5):1552-7. PMCID: 1785275.
122.
McLachlan GD, Cahill SM, Girvin ME, Almo SC. Acid-induced equilibrium folding intermediate of
human platelet profilin. Biochemistry. 2007;46(23):6931-43.
123.
Murkin AS, Birck MR, Rinaldo-Matthis A, Shi W, Taylor EA, Almo SC, Schramm VL. Neighboring
group participation in the transition state of human purine nucleoside phosphorylase. Biochemistry.
2007;46(17):5038-49. PMCID: 2526054.
124.
Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA.
Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from
Novosphingobium aromaticivorans. Biochemistry. 2007;46(45):12896-908.
125.
Rinaldo-Matthis A, Wing C, Ghanem M, Deng H, Wu P, Gupta A, Tyler PC, Evans GB, Furneaux
RH, Almo SC, Wang CC, Schramm VL. Inhibition and structure of Trichomonas vaginalis purine
nucleoside phosphorylase with picomolar transition state analogues. Biochemistry. 2007;46(3):659-68.
PMCID: 2517847.
126.
Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt
PC, Almo SC, Jacobson MP, Gerlt JA. Prediction and assignment of function for a divergent N-succinyl
amino acid racemase. Nat Chem Biol. 2007;3(8):486-91.
127.
Taylor EA, Rinaldo-Matthis A, Li L, Ghanem M, Hazleton KZ, Cassera MB, Almo SC, Schramm
VL. Anopheles gambiae purine nucleoside phosphorylase: catalysis, structure, and inhibition.
Biochemistry. 2007;46(43):12405-15.
128.
Velge P, Herler M, Johansson J, Roche SM, Temoin S, Fedorov AA, Gracieux P, Almo SC,
Goebel W, Cossart P. A naturally occurring mutation K220T in the pleiotropic activator PrfA of Listeria
monocytogenes results in a loss of virulence due to decreasing DNA-binding affinity. Microbiology.
2007;153(Pt 4):995-1005.
129.
Vrtala S, Focke M, Kopec J, Verdino P, Hartl A, Sperr WR, Fedorov AA, Ball T, Almo S, Valent P,
Thalhamer J, Keller W, Valenta R. Genetic engineering of the major timothy grass pollen allergen, Phl p
6, to reduce allergenic activity and preserve immunogenicity. J Immunol. 2007;179(3):1730-9.
130.
Yan Q, Malashkevich VN, Fedorov A, Fedorov E, Cao E, Lary JW, Cole JL, Nathenson SG, Almo
SC. Structure of CD84 provides insight into SLAM family function. Proc Natl Acad Sci U S A.
2007;104(25):10583-8. PMCID: 1965556.
131.
Yew WS, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA. Evolution of enzymatic activities in the
enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2. Biochemistry.
2007;46(33):9564-77.
132.
Chan KK, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA. Structural basis for substrate specificity
in phosphate binding (beta/alpha)8-barrels: D-allulose 6-phosphate 3-epimerase from Escherichia coli K12. Biochemistry. 2008;47(36):9608-17. PMCID: 2597415.
133.
Chao JA, Patskovsky Y, Almo SC, Singer RH. Structural basis for the coevolution of a viral RNAprotein complex. Nat Struct Mol Biol. 2008;15(1):103-5.
134.
Chattopadhyay K, Ramagopal UA, Brenowitz M, Nathenson SG, Almo SC. Evolution of GITRL
immune function: murine GITRL exhibits unique structural and biochemical properties within the TNF
superfamily. Proc Natl Acad Sci U S A. 2008;105(2):635-40. PMCID: 2206588.
135.
Graslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U,
Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R,
Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y,
Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A,
Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage
JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A,
Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L,
Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M,
Montelione GT, Stuart DI, Owens RJ, Daenke S, Schutz A, Heinemann U, Yokoyama S, Bussow K,
Gunsalus KC. Protein production and purification. Nat Methods. 2008;5(2):135-46.
136.
Hudkins RL, Diebold JL, Tao M, Josef KA, Park CH, Angeles TS, Aimone LD, Husten J, Ator MA,
Meyer SL, Holskin BP, Durkin JT, Fedorov AA, Fedorov EV, Almo SC, Mathiasen JR, Bozyczko-Coyne D,
Saporito MS, Scott RW, Mallamo JP. Mixed-lineage kinase 1 and mixed-lineage kinase 3 subtypeselective dihydronaphthyl[3,4-a]pyrrolo[3,4-c]carbazole-5-ones: optimization, mixed-lineage kinase 1
crystallography, and oral in vivo activity in 1-methyl-4-phenyltetrahydropyridine models. J Med Chem.
2008;51(18):5680-9.
137.
Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt
JA, Jacobson MP. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling
and virtual screening. Structure. 2008;16(11):1668-77. PMCID: 2714228.
138.
Kim J, Tsai PC, Chen SL, Himo F, Almo SC, Raushel FM. Structure of diethyl phosphate bound
to the binuclear metal center of phosphotriesterase. Biochemistry. 2008;47(36):9497-504. PMCID:
2725523.
139.
Lazar-Molnar E, Gacser A, Freeman GJ, Almo SC, Nathenson SG, Nosanchuk JD. The PD1/PD-L costimulatory pathway critically affects host resistance to the pathogenic fungus Histoplasma
capsulatum. Proc Natl Acad Sci U S A. 2008;105(7):2658-63. PMCID: 2268192.
140.
Lazar-Molnar E, Yan Q, Cao E, Ramagopal U, Nathenson SG, Almo SC. Crystal structure of the
complex between programmed death-1 (PD-1) and its ligand PD-L2. Proc Natl Acad Sci U S A.
2008;105(30):10483-8. PMCID: 2492495.
141.
Malashkevich VN, Varney KM, Garrett SC, Wilder PT, Knight D, Charpentier TH, Ramagopal UA,
Almo SC, Weber DJ, Bresnick AR. Structure of Ca2+-bound S100A4 and its interaction with peptides
derived from nonmuscle myosin-IIA. Biochemistry. 2008;47(18):5111-26. PMCID: 2633413.
142.
Nguyen TT, Brown S, Fedorov AA, Fedorov EV, Babbitt PC, Almo SC, Raushel FM. At the
periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the
isomerization of D-galacturonate to D-tagaturonate. Biochemistry. 2008;47(4):1194-206.
143.
Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC,
Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.
Biochemistry. 2008;47(38):9944-54. PMCID: 2562705.
144.
Rinaldo-Matthis A, Murkin AS, Ramagopal UA, Clinch K, Mee SP, Evans GB, Tyler PC, Furneaux
RH, Almo SC, Schramm VL. L-Enantiomers of transition state analogue inhibitors bound to human purine
nucleoside phosphorylase. J Am Chem Soc. 2008;130(3):842-4. PMCID: 2531256.
145.
Alvarado JJ, Nemkal A, Sauder JM, Russell M, Akiyoshi DE, Shi W, Almo SC, Weiss LM.
Structure of a microsporidian methionine aminopeptidase type 2 complexed with fumagillin and TNP-470.
Mol Biochem Parasitol. 2009;168(2):158-67. PMCID: 2759695.
146.
Ball T, Linhart B, Sonneck K, Blatt K, Herrmann H, Valent P, Stoecklinger A, Lupinek C,
Thalhamer J, Fedorov AA, Almo SC, Valenta R. Reducing allergenicity by altering allergen fold: a mosaic
protein of Phl p 1 for allergy vaccination. Allergy. 2009;64(4):569-80.
147.
Burgos ES, Ho MC, Almo SC, Schramm VL. A phosphoenzyme mimic, overlapping catalytic sites
and reaction coordinate motion for human NAMPT. Proc Natl Acad Sci U S A. 2009;106(33):13748-53.
PMCID: 2728965.
148.
Chan KK, Wood BM, Fedorov AA, Fedorov EV, Imker HJ, Amyes TL, Richard JP, Almo SC, Gerlt
JA. Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for
substrate destabilization. Biochemistry. 2009;48(24):5518-31. PMCID: 2697262.
149.
Chattopadhyay K, Lazar-Molnar E, Yan Q, Rubinstein R, Zhan C, Vigdorovich V, Ramagopal UA,
Bonanno J, Nathenson SG, Almo SC. Sequence, structure, function, immunity: structural genomics of
costimulation. Immunol Rev. 2009;229(1):356-86. PMCID: 3001128.
150.
Chattopadhyay K, Ramagopal UA, Nathenson SG, Almo SC. 1.8 A structure of murine GITR
ligand dimer expressed in Drosophila melanogaster S2 cells. Acta Crystallogr D Biol Crystallogr.
2009;65(Pt 5):434-9. PMCID: 2672815.
151.
Cummings JA, Fedorov AA, Xu C, Brown S, Fedorov E, Babbitt PC, Almo SC, Raushel FM.
Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the
amidohydrolase superfamily. Biochemistry. 2009;48(27):6469-81. PMCID: 2748305.
152.
Drumm JE, Mi K, Bilder P, Sun M, Lim J, Bielefeldt-Ohmann H, Basaraba R, So M, Zhu G,
Tufariello JM, Izzo AA, Orme IM, Almo SC, Leyh TS, Chan J. Mycobacterium tuberculosis universal stress
protein Rv2623 regulates bacillary growth by ATP-Binding: requirement for establishing chronic persistent
infection. PLoS Pathog. 2009;5(5):e1000460. PMCID: 2682197.
153.
Gutierrez JA, Crowder T, Rinaldo-Matthis A, Ho MC, Almo SC, Schramm VL. Transition state
analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing. Nat Chem Biol. 2009;5(4):251-7.
PMCID: 2743263.
154.
Ho MC, Cassera MB, Madrid DC, Ting LM, Tyler PC, Kim K, Almo SC, Schramm VL. Structural
and metabolic specificity of methylthiocoformycin for malarial adenosine deaminases. Biochemistry.
2009;48(40):9618-26. PMCID: 2771402.
155.
Ho MC, Sturm MB, Almo SC, Schramm VL. Transition state analogues in structures of ricin and
saporin ribosome-inactivating proteins. Proc Natl Acad Sci U S A. 2009;106(48):20276-81. PMCID:
2787146.
156.
Leiman PG, Basler M, Ramagopal UA, Bonanno JB, Sauder JM, Pukatzki S, Burley SK, Almo
SC, Mekalanos JJ. Type VI secretion apparatus and phage tail-associated protein complexes share a
common evolutionary origin. Proc Natl Acad Sci U S A. 2009;106(11):4154-9. PMCID: 2657435.
157.
Nguyen TT, Fedorov AA, Williams L, Fedorov EV, Li Y, Xu C, Almo SC, Raushel FM. The
mechanism of the reaction catalyzed by uronate isomerase illustrates how an isomerase may have
evolved from a hydrolase within the amidohydrolase superfamily. Biochemistry. 2009;48(37):8879-90.
PMCID: 2773443.
158.
Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM,
Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM,
Jacobson MP, Babbitt PC, Sali A. Target selection and annotation for the structural genomics of the
amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009;10(2):107-25. PMCID:
2693957.
159.
Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J,
Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA. Computation-facilitated assignment of
the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from
Oceanobacillus iheyensis. Biochemistry. 2009;48(48):11546-58. PMCID: 2787699.
160.
Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, Rutter ME, Bain K,
Chang S, Gheyi T, Sauder JM, Burley SK, Babbitt PC, Almo SC, Gerlt JA. Evolution of enzymatic
activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cismuconate lactonizing enzymes. Biochemistry. 2009;48(7):1445-53. PMCID: 2746992.
161.
Sampaleanu LM, Bonanno JB, Ayers M, Koo J, Tammam S, Burley SK, Almo SC, Burrows LL,
Howell PL. Periplasmic domains of Pseudomonas aeruginosa PilN and PilO form a stable heterodimeric
complex. J Mol Biol. 2009;394(1):143-59.
162.
Subach FV, Malashkevich VN, Zencheck WD, Xiao H, Filonov GS, Almo SC, Verkhusha VV.
Photoactivation mechanism of PAmCherry based on crystal structures of the protein in the dark and
fluorescent states. Proc Natl Acad Sci U S A. 2009;106(50):21097-102. PMCID: 2795494.
163.
Xiang DF, Kolb P, Fedorov AA, Meier MM, Fedorov LV, Nguyen TT, Sterner R, Almo SC,
Shoichet BK, Raushel FM. Functional annotation and three-dimensional structure of Dr0930 from
Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily.
Biochemistry. 2009;48(10):2237-47.
164.
Xiang DF, Patskovsky Y, Xu C, Meyer AJ, Sauder JM, Burley SK, Almo SC, Raushel FM.
Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of
enzymes. Biochemistry. 2009;48(17):3730-42. PMCID: 2683473.
165.
Zencheck WD, Xiao H, Nolen BJ, Angeletti RH, Pollard TD, Almo SC. Nucleotide- and activatordependent structural and dynamic changes of arp2/3 complex monitored by hydrogen/deuterium
exchange and mass spectrometry. J Mol Biol. 2009;390(3):414-27. PMCID: 2983480.
166.
Zhan C, Yan Q, Patskovsky Y, Li Z, Toro R, Meyer A, Cheng H, Brenowitz M, Nathenson SG,
Almo SC. Biochemical and structural characterization of the human TL1A ectodomain. Biochemistry.
2009;48(32):7636-45. PMCID: 2790920.
167.
Achkar JM, Jenny-Avital E, Yu X, Burger S, Leibert E, Bilder PW, Almo SC, Casadevall A, Laal
S. Antibodies against immunodominant antigens of Mycobacterium tuberculosis in subjects with
suspected tuberculosis in the United States compared by HIV status. Clin Vaccine Immunol.
2010;17(3):384-92. PMCID: 2837951.
168.
Bhatia S, Sun K, Almo SC, Nathenson SG, Hodes RJ. Dynamic equilibrium of B7-1 dimers and
monomers differentially affects immunological synapse formation and T cell activation in response to
TCR/CD28 stimulation. J Immunol. 2010;184(4):1821-8.
169.
Brims DR, Qian J, Jarchum I, Mikesh L, Palmieri E, Ramagopal UA, Malashkevich VN, Chaparro
RJ, Lund T, Hattori M, Shabanowitz J, Hunt DF, Nathenson SG, Almo SC, Dilorenzo TP. Predominant
occupation of the class I MHC molecule H-2Kwm7 with a single self-peptide suggests a mechanism for its
diabetes-protective effect. Int Immunol. 2010;22(3):191-203. PMCID: 2829095.
170.
Chao JA, Patskovsky Y, Patel V, Levy M, Almo SC, Singer RH. ZBP1 recognition of beta-actin
zipcode induces RNA looping. Genes Dev. 2010;24(2):148-58. PMCID: 2807350.
171.
Cummings JA, Nguyen TT, Fedorov AA, Kolb P, Xu C, Fedorov EV, Shoichet BK, Barondeau
DP, Almo SC, Raushel FM. Structure, mechanism, and substrate profile for Sco3058: the closest bacterial
homologue to human renal dipeptidase. Biochemistry. 2010;49(3):611-22. PMCID: 2808448.
172.
Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK,
Almo SC, Raushel FM. The hunt for 8-oxoguanine deaminase. J Am Chem Soc. 2010;132(6):1762-3.
PMCID: 2820149.
173.
Ho MC, Shi W, Rinaldo-Matthis A, Tyler PC, Evans GB, Clinch K, Almo SC, Schramm VL. Four
generations of transition-state analogues for human purine nucleoside phosphorylase. Proc Natl Acad Sci
U S A. 2010;107(11):4805-12. PMCID: 2841916.
174.
Hudkins RL, Zulli AL, Underiner TL, Angeles TS, Aimone LD, Meyer SL, Pauletti D, Chang H,
Fedorov EV, Almo SC, Fedorov AA, Ruggeri BA. 8-THP-DHI analogs as potent Type I dual TIE-2/VEGFR2 receptor tyrosine kinase inhibitors. Bioorg Med Chem Lett. 2010;20(11):3356-60.
175.
Lazar-Molnar E, Chen B, Sweeney KA, Wang EJ, Liu W, Lin J, Porcelli SA, Almo SC, Nathenson
SG, Jacobs WR, Jr. Programmed death-1 (PD-1)-deficient mice are extraordinarily sensitive to
tuberculosis. Proc Natl Acad Sci U S A. 2010;107(30):13402-7. PMCID: 2922129.
176.
Li ZH, Dulyaninova NG, House RP, Almo SC, Bresnick AR. S100A4 regulates macrophage
chemotaxis. Mol Biol Cell. 2010;21(15):2598-610. PMCID: 2912347.
177.
Malashkevich VN, Dulyaninova NG, Ramagopal UA, Liriano MA, Varney KM, Knight D, Brenowitz
M, Weber DJ, Almo SC, Bresnick AR. Phenothiazines inhibit S100A4 function by inducing protein
oligomerization. Proc Natl Acad Sci U S A. 2010;107(19):8605-10. PMCID: 2889333.
178.
Piatkevich KD, Malashkevich VN, Almo SC, Verkhusha VV. Engineering ESPT pathways based
on structural analysis of LSSmKate red fluorescent proteins with large Stokes shift. J Am Chem Soc.
2010;132(31):10762-70. PMCID: 2919691.
179.
Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD,
Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S,
Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, Burley SK. Structure of a putative BenFlike porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution. Proteins. 2010;78(14):3056-62.
PMCID: 2989796.
180.
Sedeh RS, Fedorov AA, Fedorov EV, Ono S, Matsumura F, Almo SC, Bathe M. Structure,
evolutionary conservation, and conformational dynamics of Homo sapiens fascin-1, an F-actin
crosslinking protein. J Mol Biol. 2010;400(3):589-604.
181.
Seffernick JL, Reynolds E, Fedorov AA, Fedorov E, Almo SC, Sadowsky MJ, Wackett LP. X-ray
structure and mutational analysis of the atrazine Chlorohydrolase TrzN. J Biol Chem.
2010;285(40):30606-14. PMCID: 2945555.
182.
Subach OM, Malashkevich VN, Zencheck WD, Morozova KS, Piatkevich KD, Almo SC,
Verkhusha VV. Structural characterization of acylimine-containing blue and red chromophores in
mTagBFP and TagRFP fluorescent proteins. Chem Biol. 2010;17(4):333-41. PMCID: 2862997.
183.
Tsai PC, Fan Y, Kim J, Yang L, Almo SC, Gao YQ, Raushel FM. Structural determinants for the
stereoselective hydrolysis of chiral substrates by phosphotriesterase. Biochemistry. 2010;49(37):7988-97.
PMCID: 2945819.
184.
Wisedchaisri G, Dranow DM, Lie TJ, Bonanno JB, Patskovsky Y, Ozyurt SA, Sauder JM, Almo
SC, Wasserman SR, Burley SK, Leigh JA, Gonen T. Structural underpinnings of nitrogen regulation by
the prototypical nitrogen-responsive transcriptional factor NrpR. Structure. 2010;18(11):1512-21. PMCID:
2996049.
185.
Wood BM, Amyes TL, Fedorov AA, Fedorov EV, Shabila A, Almo SC, Richard JP, Gerlt JA.
Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize
the active conformation. Biochemistry. 2010;49(17):3514-6.
186.
Xiang DF, Patskovsky Y, Xu C, Fedorov AA, Fedorov EV, Sisco AA, Sauder JM, Burley SK, Almo
SC, Raushel FM. Functional identification and structure determination of two novel prolidases from
cog1228 in the amidohydrolase superfamily. Biochemistry. 2010;49(31):6791-803. PMCID: 2914802.
187.
Cassera MB, Ho MC, Merino EF, Burgos ES, Rinaldo-Matthis A, Almo SC, Schramm VL. A HighAffinity Adenosine Kinase from Anopheles gambiae. Biochemistry. 2011;50(11):1885-93. PMCID:
3059358.
188.
Guan R, Ho MC, Almo SC, Schramm VL. Methylthioinosine phosphorylase from Pseudomonas
aeruginosa. Structure and annotation of a novel enzyme in quorum sensing. Biochemistry.
2011;50(7):1247-54. PMCID: 3040260.
189.
Wang L, Rubinstein R, Lines JL, Wasiuk A, Ahonen C, Guo Y, Lu LF, Gondek D, Wang Y, Fava
RA, Fiser A, Almo S, Noelle RJ. VISTA, a novel mouse Ig superfamily ligand that negatively regulates T
cell responses. J Exp Med. 2011;208(3):577-92. PMCID: 3058578.
190.
Zhan C, Patskovsky Y, Yan Q, Li Z, Ramagopal U, Cheng H, Brenowitz M, Hui X, Nathenson
SG, Almo SC. Decoy strategies: the structure of TL1A:DcR3 complex. Structure. 2011;19(2):162-71.
PMCID: 3065972.
191.
Magalhães ML, Czekster CM, Guan R, Malashkevich VN, Almo SC, Levy M. Evolved streptavidin
mutants reveal key role of loop residue in high-affinity binding. Protein Sci. 2011 Jul;20(7):1145-54. PMID:
21520321.
192.
Roche CJ, Malashkevich V, Balazs TC, Dantsker D, Chen Q, Moreira J, Almo SC, Friedman JM,
Hirsch RE. Structural and functional studies indicating altered redox properties of hemoglobin E:
implications for production of bioactive nitric oxide. J Biol Chem. 2011 Jul 1;286(26):23452-66. PMID:
21531715.
193.
Hall RS, Fedorov AA, Xu C, Fedorov EV, Almo SC, Raushel FM. Three-dimensional structure
and catalytic mechanism of cytosine deaminase. Biochemistry. 2011 Jun 7;50(22):5077-85. PMID:
21545144.
194.
Hitchcock DS, Fedorov AA, Fedorov EV, Dangott LJ, Almo SC, Raushel FM. Rescue of the
orphan enzyme isoguanine deaminase. Biochemistry. 2011 Jun 28;50(25):5555-7. PMID: 21604715.
195.
Dulyaninova NG, Hite KM, Zencheck WD, Scudiero DA, Almo SC, Shoemaker RH, Bresnick AR.
Cysteine 81 Is Critical for the Interaction of S100A4 and Myosin-IIA. Biochemistry. 2011 Aug
23;50(33):7218-27.PMID: 21749055.
196.
Samanta D, Mukherjee G, Ramagopal UA, Chaparro RJ, Nathenson SG, Dilorenzo TP, Almo
SC. Structural and functional characterization of a single-chain peptide-MHC molecule that modulates
both naive and activated CD8+ T cells. Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13682-7. PMID:
21825122.
197.
Iiams V, Desai B, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA. Mechanism of the Orotidine 5'
Monophosphate Decarboxylase Catalyzed Reaction: Importance of Residues in the Orotate Binding Site.
Biochemistry. 2011 Aug 26. [Epub ahead of print]PMID: 21870810.
Research Support
U54 GM094662
Almo, Steven (PI)
9/1/10-6/30/15
NIH/NIGMS
The NYSGRC: A Large Scale Center for PSI:Biology
The New York Structural Genomic Research Consortium (NYSGRC) is one of the four NIGMSsupported Protein Structure Initiative (PSI) high-throughput production centers. The goals of this center
are the development and establishment of platforms and technologies that support high-throughput
structure, with a particular focus on eukaryotic protein secreted proteins and multi-protein assemblies.
U01 GM94665
Nathenson, Stan (PI)
9/1/10-6/30/15
NIH/NIGMS
Atoms-to-Animals: Structural Genomics of Immunity
This is a PSI Partnership Center focusing on the secreted and cell surface molecules that control
innate and adaptive immunity. This Center will direct the efforts of the NYSGRC to target immune
regulatory proteins for high-throughput expression, purification and structure determination. Based on
these structures, this grant will support the generation of proteins and mouse models for mechanistic
dissection and therapeutic development. A major aspect of this work is the establishment of the Immune
Function Network (IFN), a national consortium on immunologists that will exploit the protein reagents
and mouse model systems.
P01 GM071790
Gerlt, John (PI)
9/15/09-4/30/14
NIH/NIGMS
Structural Bases for Catalytic Efficiency and Substrate Specificity
This initiative focuses on the functional annotation of enzymes within the enolase and amidohydrolase
superfamilies. Sali is a Co-PI on the grant.
U54 GM093342
Gerlt, John (PI)
5/20/10-4/30/15
NIH/NIGMS
This multi-institutional U54 Center is focused on the development of new approaches and the
establishment of the infrastructure for the large-scale annotation of function. These efforts include
high-throughput protein production, structure determination, computational docking, experimental library
screening and in vivo validation of in vitro functions using microbiology and metabolomics. Sali is a CoPI on the grant.
U54-AI057158-06S1; Lipkin
Almo, Steve (PI)
9/17/09–8/31/11
NIH/NIAID
Northeast Biodefense Center
Genes-to-vaccines: a novel platform for genome-wide T cell epitope discovery
The overall goal of this ARRA-supported project is to develop a new experimental platform for the rapid
and systematic identification of all relevant T cell epitopes from NIAID Category A, B, and C pathogens
as well as emerging/re-emerging infectious diseases.
RO1 AI07289
Nathenson, PI; Almo, Co-PI
6/01/02-5/31/12
NIH/NIAID
NIH
Molecular and Structural Basis for Costimulation
This grant supports detailed structural and biochemical studies on the CD28 family, the TIM family and
PD-1.
Northeast Biodefense Center (NBC)
Lipkin, Ian (PI)
3/01/08-2/28/14
NIH/NIAID
Protein Reagent Core
The overall goal this work is to establish high-throughput eukaryotic protein expression capabilities to
support the investigators of the NBC.
R01 GM41916
Schramm, Vern (PI)
8/01/98-7/31/12
NIH/NIGMS
"Transition State Analysis of Enzymatic Reactions"
X-ray crystallography on nucleoside hydrolase from Crithidia fasciculata.
P30 CA013330
NIH/NCI
Structural Biology Facility
Goldman, David, (PI)
7/01/07-6/30/11