Cyrus Chothia: Classified List Of Publications
PROTEIN STRUCTURE
Overview Papers
The Conformation of Secondary Structures and Loop regions
The Packing of -helices and -sheets
Accessible and Buried Surfaces
Packing Density in Proteins
PROTEIN-PROTEIN AND PROTEIN-SMALL MOLECULE RECOGNITION
PROTEIN DYNAMICS
Overview Paper
Conformational Change And Its Transmission
The Allosteric Mechanism Of Haemoglobulin
IMMUNE SYSTEM: CANONICAL STRUCTURES AND THE REPTOIRES
FOUND IN VARIABLE DOMAINS OF ANTIBODIES AND T-CELL RECPTORS
Canonical Structures
Canonical Structure Repertoires in Humans and Mice
The Packing Of Variable Domains
IMMUNOGLOBULINS INVOLVED IN CELL ADDHESION AND RELATED
PROCESSES
EVOLUTION OF PROTEINS
Divergence Of Sequence And Structure
Divergence of Sequence and the Conservation of Fold
THE DETECTION OF HOMOLOGOUS RELATIONSHIPS
GENOMICS
Overview papers
Protein Domain Families
Whole Proteins
Immunoglobulin and Cadherin Families in Genomes
Small Molecule Metabolic Pathways
SCOP, SUPERFAMLY AND 3D-COMPLEX DATABASES
PROTEIN STRUCTURES DETERMINED BY X-RAY CRYSTALLOGRAPHY
THE STRUCTURE OF SMALL MOLECULES ACTIVE IN THE NERVOUS SYSTEM
OTHER PAPERS
1
PROTEIN STRUCTURE
Overview Papers
24. Chothia, C. Structural invariants in protein folding. Nature 254, 304-308
(1975).
53. Chothia, C.
Principles that determine the structure of proteins.
Ann.
Rev. Biochem. 53, 537-572 (1984); reprinted in
Protein and Nucleic Acid Structure and Dynamics pp. 39-74 ed J. King.
Benjamin/Cummings, Menlo Park (1985).
79. Chothia, C. & Finkelstein, A.V. The classification and origins of protein
folding patterns. Ann. Rev. Biochem. 59, 1007-1039 (1990).
119. Chothia, C., Hubbard, T., Brenner, S., Barns, H. & Murzin A. Protein
folds in the all- and all- classes. Annu. Rev. Biophys. Biomol. Struc.
26 597-627. (1997).
The Conformation of Secondary Structures and Loop regions
20. Chothia, C. Conformation of twisted -sheets in proteins. J. Mol. Biol.
75, 295-302 (1973).
49. Chothia, C.
Coiling of -pleated sheets.
J. Mol. Biol. 163, 107-117
(1983).
78. Tramontano, A., Chothia, C. & Lesk, A.M. Structural determinants of the
conformation of medium-sized loops in proteins. Proteins, 6, 382-394
(1989).
85. Chothia, C., & Lesk, A.M. Conformations for strand entry into parallel sheets.
In Molecular Conformation and Biological Interactions (P.
Balarum & S.
Ramaseshan, eds.) Indian Academy of Sciences,
Bangalore. pp. 49-58 (1991).
The Packings of -helices and -sheets
28. Levitt, M. & Chothia, C. Structural patterns in globular proteins. Nature
261, 552-558 (1976).
31. Chothia, C., Levitt, M. & Richardson, D. Structure of proteins: packing of
-helices and pleated sheets.
Proc. Natl. Acad. Sci. USA 74, 4130-
4134 (1977).
40. Janin, J. & Chothia, C.
Packing of -helices onto -sheets and the
anatomy of proteins. J. Mol. Biol. 143, 95-128 (1980).
41. Chothia, C., Levitt, M. & Richardson, D. Helix to helix packing in proteins.
J. Mol. Biol. 145, 215-250 (1981).
74. Chothia, C. Polyhedra for helical proteins. Nature 337, 204-205 (1989).
2
42. Chothia, C. & Janin, J.
Relative orientation of close-packed -pleated
sheets in proteins. Proc. Natl. Acad. Sci. USA 78, 4146-4150 (1981).
43. Janin, J. & Chothia, C.
The anatomy of  proteins.
in Structural
Aspects of Recognition and Assembly in Biological Macromolecules.
eds. M. Balaban, J.L. Sussman, W. Traul and A. Yonath. Balaban ISS
(1981).
45. Chothia, C. & Janin, J.
Orthogonal packing of -pleated sheets in
proteins. Biochemistry 21, 3955-3965 (1982).
70. Chothia, C.
Protein structure: the fourteenth barrel rolls out.
Nature
333, 598-599 (1988).
75. Lesk, A.M., Branden, C.-I. & Chothia, C. Structural principles of barrel
proteins: the packing at the interior of the sheet. Proteins 5, 139-148
(1989).
97. Murzin, A.G., Lesk, A.M. & Chothia, C.
Principles determining the
structure of -sheet barrels in proteins: I a theoretical analysis. J.
Mol. Biol. 236, 1369-1381 (1994).
98. Murzin, A.G., Lesk, A.M. & Chothia, C.
Principles determining the
structure of -sheet barrels in proteins: II the observed structures. J.
Mol. Biol. 236, 1382-1400 (1994).
88. Murzin, A.G., Lesk, A.M. & Chothia, C. -trefoil fold: patterns of structure
and sequence in the Kunitz inhibitors, interleukins-1 and -1a and the
fibroblast growth factors. J Mol. Biol. 223, 531-543, (1992).
33. Chothia, C. & Janin, J. Geometrical principles that determine the three
dimensional structure of proteins.
in 12th FEBS meeting: Proteins:
structure, function and industrial applications. Vol. 52, pp. 117-126.
Pergamon Press, Oxford (1978).
92. Murzin A. & Chothia, C. Protein architecture: new superfamilies. Curr.
Opin struct. Biol. 2, 895-903 (1992).
95. Chothia, C. & Murzin, A.G.
New folds for all- proteins.
Structure 1,
217-222 (1993).
Accessible and Buried Surfaces
21. Chothia, C. Hydrophobic bonding and accessible surface area in proteins.
Nature 248, 338-339 (1974).
29. Chothia, C. The nature of the accessible and buried surfaces in proteins.
J. Mol. Biol. 105, 1-14 (1976).
39. Lesk, A.M. & Chothia, C.
Solvent accessibility, protein surfaces and
protein folding. Biophys. J. 32, 35-42 (1980).
65. Miller, S., Janin, J. Lesk, A.M. & Chothia, C.
Interior and surface of
monomeric proteins. J. Mol. Biol. 196, 641-656 (1987).
3
67. Miller, S., Lesk, A.M., Janin, J. & Chothia, C. The accessible surface area
and stability of oligomeric proteins. Nature 328, 834-836 (1987).
72. Janin, J., Miller, S. & Chothia, C. Surface, subunit interfaces and interior
of oligomeric proteins. J. Mol. Biol. 204, 155-164 (1988).
69. Miller, S., Janin, J. & Chothia, C. Protein-protein interfaces in oligomeric
proteins.
in Protein Recognition of Immobilised Ligands.
ed. T.
William Hutchens, UCLA symposia on molecular and cellular biology,
new series. Vol. 80, pp. 193-202. Alan R. Liss Inc., New York (1988).
Packing Density in Proteins
63. Chothia, C. & Lesk, A.M. The "crystalline molecule" image of proteins.
Gazz. Chim. Ital. 116, 557-560 (1986).
102. Harpaz, Y., Gerstein, M. & Chothia, C.
Volume changes on protein
folding. Structure 2, 641-649 (1994).
110. Gerstein, M. and Chothia, C. Packing at the Protein-Water Interface.
Proc. Natl. Acad. Sci. 93, 10167-10172 (1996).
134. Tsai, J., Taylor, R., Chothia, C. & Gerstein M. The packing density in
proteins: standard radii and volumes.
J Mol. Biol. 290, 253-266
(1999).
PROTEIN-PROTEIN AND PROTEIN-SMALL MOLECULE RECOGNITION
26. Chothia, C. & Janin, J. Principles of protein-protein recognition. Nature
256, 705-708 (1975).
27. Janin, J. & Chothia, C.
Stability and specificity of protein-protein
interactions: the case of the trypsin-trypsin inhibitor complexes.
J.
Mol. Biol. 100, 197-211 (1976).
34. Janin, J. & Chothia, C.
Structural aspects of protein interactions:
accessible surface area and the role of hydrophobicity. in 12th FEBS
meeting: Proteins: structure, function and industrial applications. Vol.
52, pp. 227-237. Pergamon Press, Oxford (1978).
81. Janin, J. & Chothia, C. The structure of protein-protein recognition sites.
J. Biol. Chem. 265, 16027-16030 (1990).
133. Lo Conte, L., Chothia, C. & Janin, J. The atomic structure of proteinprotein recognition sites. J. Mol. Biol. 285, 2177-2198 (1999).
32. Janin, J. & Chothia, C.
Role of hydrophobicity in the binding of
coenzymes. Biochemistry 17, 2943-2948 (1978).
117. Chothia, C. Protein-Protein and Protein-carbohydrate recognition in
Molecular aspects of host-pathogen interactions (ed. M.A. McCrae,
J.R. Saunders, C.J. Smyth & N.D. Stow) Society for General
4
Microbiology Symposium 55. Cambridge University Press, Cambridge
(1997)
PROTEIN DYNAMICS
Overview Paper
100. Gerstein, M., Lesk, A.M. & Chothia, C.
Structural Mechanisms for
Domain Movements in Proteins. Biochemistry 33 6739-6749 (1994).
Conformational Change And Its Transmission
50. Chothia, C., Lesk, A.M., Dodson, G.G. & Hodgkin, D.M.C. Transmission of
conformational change in insulin. Nature 302, 500-505 (1983).
51. Lesk, A.M. & Chothia, C. Mechanisms of domain closure in proteins. J.
Mol. Biol. 174, 175-191 (1984).
56. Chothia, C. & Lesk, A.M. Helix movements in proteins. Trends Biochem.
Sci. 10, 116-118 (1985).
71. Lesk, A.M. & Chothia, C. Elbow motion in the immunoglobulins involves a
molecular ball-and-socket joint. Nature 335, 188-190 (1988).
86. Gerstein M. & Chothia, C. Analysis of protein loop closure: two types of
hinges produce one motion in lactate dehydrogenase.
J. Mol. Biol.
220, 133-149 (1991).
87. Stein, P. & Chothia, C. Serpin tertiary structure transformation. J. Mol.
Biol. 221, 615-621 (1991).
89. McPhalen, C.A., Vincent, M.G., Picot, D., Jansonius, J.N., Lesk, A.M. &
Chothia,
C.
Domain
closure
in
mitochondrial
aspartate
aminotransferase. J. Mol. Biol. 227, 197-213 (1992).
93. Gerstein, M., Schulz, G. & Chothia, C.
Domain closure in adenylate
kinase: joints on either side of two helices close like neighbouring
fingers. J. Mol. Biol. 229, 494-501 (1993).
94. Gerstein, M., Anderson, B.F., Norris, G.E., Baker, E.N., Lesk, A.M. &
Chothia, C. Domain closure in lactoferrin: two hinges produce a seesaw motion between alternative close-packed interfaces. J. Mol. Biol.
234, 357-372 (1993).
137. Gerstein, M & Chothia, C. Signal Transduction: Proteins in Motion.
Science 285 1682-1683 (1999)
The Allosteric Mechanism Of Haemoglobulin
30. Chothia, C., Wodak, S. & Janin, J.
Role of subunit interfaces in the
allosteric mechanism of haemoglobin. Proc. Natl. Acad. Sci. USA 73,
3793-3797 (1976).
5
35. Baldwin, J. & Chothia, C. Haemoglobin: the structural changes related to
ligand binding and its allosteric mechanism. J. Mol. Biol. 129, 175220 (1979).
48. Baldwin, J. & Chothia, C.
Deoxy and liganded haemoglobin: the
differences in structure and their relation to cooperativity in ligand
binding. in Hemoglobin and oxygen binding. pp. 119-123 ed, Chien
Ho, Elsevier-North Holland, Amsterdam (1982).
55. Lesk, A.M., Janin, J., Wodak, S. & Chothia, C. Haemoglobin: the surface
buried between the 1 1 and 2 2 dimers in the deoxy and oxy
structures. J. Mol. Biol. 183, 267-270 (1985).
IMMUNE SYSTEM: CANONICAL STRUCTURES AND THEIR REPTOIRES IN
THE VARIABLE DOMAINS OF ANTIBODIES AND T-CELL RECPTORS
Canonical Structures
61. Chothia, C., Lesk, A.M., Levitt, M., Amit, A.G., Mariuzza, R.A., Phillips,
S.E.V. and Poljak, R.J.
The predicted structure of immunoglobulin
D1.3 and its comparison with the crystal structure.
Science 233,
755-758 (1986).
66. Chothia, C. & Lesk, A.M.
Canonical structures for the hypervariable
regions of immunoglobulins. J. Mol. Biol. 196, 901-916 (1987).
77. Chothia, C., Lesk, A.M., Tramontano, A., Levitt, M., Smith-Gill, S.J., Air,
G., Sheriff, S., Padlan, E.A., Davies, D., Tulip, W.R., Colman, P.M.
Spinelli,
S.,
Alzari,
P.M.
&
Poljak,
R.J.
Conformations
of
immunoglobulin hypervariable regions. Nature 342, 877-883 (1989).
80. Tramontano. A., Chothia, C. & Lesk, A.M.
Framework residue 71 is a
major determinant of the position and conformation of the second
hypervariable region in the VH domains of immunoglobulins. J. Mol.
Biol. 215, 175-182 (1990).
82. Chothia, C.
Antigen Recognition.
Curr. Opin. Struct .Biol. 1, 53-59
(1991).
104. Barré, S., Greenberg, A.S., Flajnik, M.F. & Chothia, C. Structural
conservation
of
hypervariable
regions
in the
evolution of the
immunoglobulins. Nature structural biology 1, 915-920 (1994).
124. Al-Lazikani, B. Lesk, A. & Chothia, C. Standard conformations for the
canonical structures of immunoglobulins. J. Mol. Biol. 273 927-948
(1997).
6
123. Morea, V. Tramontano, A., Rustici, M., Chothia. C., & Lesk A.M.
Antibody structure, prediction and redesign. Biophys Chem 68 9-16
(1997).
125. Morea, V., Tramontano, A., Rustici, M., Chothia, C. & Lesk, A.
Conformations of the third hypervariable in the VH domain of
immunoglobulins. J. Mol. Biol. 275, 269-294 (1998).
73. Chothia, C., Boswell, D.R. & Lesk, A.M. The outline structure of the T cell
 receptor. EMBO J. 7, 3745-3755 (1988).
140. Al-Lazikani, B. Lesk, A. & Chothia, C. Canonical Structures for the
hypervariable regions of T cell  receptors. J. Mol. Biol. 295, 979994 (2000).
Cannonical Structure Repetoires in Humans and Mice
90. Chothia, C. Lesk, A.M. Gherardi. E., Tomlinson, I.M. Walter, G., Marks,
J.D. Llewelyn, M.B. & Winter, G. Structural repertoire of the human
VH segments. J. Mol. Biol. 227, 799-817 (1992).
106. Tomlinson, I.M., Cox, J.P.L., Gherardi, E., Lesk, A.M. & Chothia, C. The
structural repertoire of the human V domains. EMBO J. 14, 46284638 (1995).
163. de Bono, B. and Chothia, C. VH gene segments in the human and
mouse genomes. J. Mol. Biol. 342, 131-143 (2004).
The Packing Of Variable Domains
57. Chothia, C., Novotny, J., Bruccoleri, R. & Karplus, M.
Domain
associations in immunoglobulin molecules: I. the packing of variable
domains. J. Mol. Biol. 186, 651-663 (1985).
IMMUNOGLOBULINS INVOLVED IN CELL ADDHESION AND RELATED
PROCESSES
99. Harpaz Y. & Chothia, C.
Many of the immunoglobulin superfamily
domains that form cell adhesion molecules and surface receptors have
structures similar to variable domains.
J. Mol. Biol. 238, 528-539
(1994).
107. Bateman, A. & Chothia, C.
Outline structures for the extracellular
domains of the fibroblast growth factor receptors. Nature structural
biology 2, 1068-1074 (1995).
111.
Bateman,
A.,
Eddy,
S.R.
and
Chothia,
C.
Members
Immunoglobulin Superfamily in Bacteria. Protein Sci.
(1996).
7
of
the
5, 1939-1941
112. Fong, S., Hammill, S.J., Proctor, M., Freund, S.M.V., Benian, G.M.,
Chothia, C., Bycroft, M. and Clarke, J. Structure and stability of an
immunoglobulin superfamily domain from twitchin: a muscle protein
of the nematode Carnorhabdites elegans. J. Mol. Biol. 264, 624-639
(1996).
113. Bateman,
A., Jouet, M., MacFarlane, J., Du, J.-S., Kenwrick, S. &
Chothia, C. Outline structure of the human L1 cell adhesion molecule
and the sites where mutations cause neurological disorders. EMBO J.,
15, 6048-6057 (1996).
120. Chothia, C. & Jones, E.Y. Molecular structure of cell Adhesion molecules.
Annu. Rev. Biochem. 66, 823-862 (1997).
EVOLUTION OF PROTEINS
Divergence Of Sequence And Structure
36. Lesk, A.M. & Chothia, C. How different amino acid sequences determine
similar protein structures: the structure and evolutionary dynamics of
the globins. J. Mol. Biol. 136 223-268 (1980).
37. Chothia, C. & Lesk, A.M.
Protein evolution and helix packing in the
globins. in Protein Folding. pp. 63-77. ed. R. Jaenicke, Elsevier-North
Holland, Amsterdam (1979).
46. Chothia. C. & Lesk, A.M. The evolution of proteins formed by -sheets: I.
plastocyanin and azurin. J. Mol. Biol. 160, 309-323 (1982).
47. Lesk, A.M. & Chothia. C. The evolution of proteins formed by -sheets:
II. the core of the immunoglobulin domains. J. Mol. Biol. 160, 325342 (1982).
54. Chothia, C. & Lesk, A.M. Helix movements and the reconstruction of the
haem pocket during the evolution of the cytochrome c family. J. Mol.
Biol. 182, 151-158 (1985).
59. Lesk, A.M. & Chothia, C.
The response of protein structures to amino
acid sequence changes.
Phil. Trans R. Soc. Lond. A 317, 345-356
(1986).
60. Chothia, C. & Lesk, A.M.
The relation between the divergence of
sequence and structure in proteins. EMBO J. 5, 823-826 (1986).
68. Chothia, C. & Lesk, A.M. The evolution of protein structures. Cold Spring
Habor Symp. Quant. Biol. 52, 399-405 (1987).
116. Chothia, C. & Gerstein, M. Protein evolution: how far can sequences
diverge? Nature 385 379-380 (1997).
8
Divergence of sequence and the conservation of fold
96. Gerstein, M., Sonnhammer, E.L.L. & Chothia, C.
Volume changes in
protein evolution. J. Mol. Biol. 236, 1067-1078 (1994).
64. Bashford, D., Chothia, C. & Lesk, A.M. Determinants of a protein fold:
unique features of the globin amino acid sequences. J. Mol. Biol. 196,
199-216 (1987).
83. Van Beeuman, J., Van Bun, S., Canters, G.W., Lommen, A. & Chothia, C.
The Structual Homology of Amicyanin from Thiobacillus versutus to
Plant Plastocyanins. J. Biol. Chem. 266, 4869-4877 (1991).
126. Chothia, C., Gelfand, I. & Kister, A. Structural determinants in the
sequences of immunoglobulin variable domains.
J. Mol. Biol. 278,
457-479 (1998).
139. Hamill, S.J., Cota, E., Chothia, C. & Clarke, J. Conservation of folding
and stability within a protein family: the tyrosine corner as an
evolutionary cul-de-sac. J. Mol. Biol. 295 641-649 (2000)
153. Hill, E.E., Morea V. & Chothia, C. Sequence conservation in families
whose members have little or no sequence similarity. J. Mol. Biol.
322 205-233 2002.
162. Gough J. & Chothia C. The Linked Conservation of Structure and
Fuction in a Family of High Diversity: the Monomeric Cupredoxins.
Structure. 12, 917-925 2004.
165. Han J.H., Kerrison N., Chothia C. & Teichmann S.A. Divergence of
interdomain geometry in two-domain proteins. Structure 14, 935945 2006
136. Chothia, C., Lesk, A.M., Kister, A. & Gelfend, I. Why structure changes
more slowly than sequence in protein evolution. in Simplicity and
Complexity in Proteins and Nucleic Acids (ed. Frauenfelder, H.,
Deisenhofer, J. & Wolynes, P.G.) Dahlem University Press, Berlin
(1999).
169. Sasidharan, R. & Chothia C. The Selection of Acceptable Mutations.
Proc. Natl. Acad. Sci. USA 104, 10080-10085 (2007).
THE DETECTION OF HOMOLOGOUS RELATIONSHIPS
62. Lesk, A.M., Levitt, M. & Chothia, C.
Alignment of the amino acid
sequences of distantly related proteins using variable gap penalties.
Prot. Eng. 1, 77-78 (1986).
122. Park, J., Teichmann, S.A., Hubbard, T. & Chothia, C. Intermediate
sequences increase the detection of distant sequence homologies. J.
Mol. Biol. 273, 349-354 (1997).
9
127. Brenner, S.E., Chothia, C. & Hubbard T. Assessing sequence comparison
methods with reliable structurally identified distant evolutionary
relationships. Proc. Natl. Acad. Sci. USA 95, 6073-6078 (1998).
128. Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T.
& Chothia, C. Sequence comparisons using multiple sequences detect
three times as many remote homologues as pairwise methods.
J.
Mol. Biol. 284, 1201-1210 (1998).
141. Teichmann, S.A., Chothia, C., Church, G.M. & Park, J. Fast assignment
of protein structures to sequences using the intermediate sequence
library PDB-ISL. Bioinformatics 16, 117-124 (2000).
143. Park, J., Holm, L., Heger, A. & Chothia, C.
protein
sequence
databases
have
high
RSDB; representative
information
content.
Bioinformatics 16 458-464 (2000).
156. de Bono B. & Chothia C. EXEGESIS: A Procedure to Improve Gene
Predictions and its use to find Immunoglobulin Superfamily Proteins in
the Human and Mouse Genomes. Nucleic Acids Res. 30 264-267
(2002).
GENOMICS
Overview papers
173 Chothia, C. & Gough J. Genomic and Structural Aspects of Protein
Evolution. Biochem. J. 419, 15-28 (2009).
160. Vogel, C., Bashton, M., Kerrison, N.D., Chothia, C. & Teichmann, S.A.
Structure, Function and Evolution of Multidomain Proteins.. Curr.
Opin. Struc. Biol. 14 208-216. (2004).
145. Teichmann, S.A., Murzin, A.G. and Chothia, C. Determination of protein
function, evolution and interactions by structural genomics.
Curr.
Opin. Struc. Biol. 11 354-363. (2001).
135. Teichmann, S.A., Chothia, C. & Gerstein M. Advances in structural
geomics. Curr. Opin. Struc. Biol. 9, 390-399 (1999).
118. Brenner, S.E., Chothia, C. & Hubbard, T.J.P. Population statistics of
protein structures: lessons from structural classifications. Curr.
Opin. Struct. Biol. 7, 369-376 (1997).
Protein Domain Families
91. Chothia, C. One thousand families for the molecular biologist. Nature
357, 543-544 (1992).
10
103. Chothia, C.
Protein families in the metazoan genome.
Development
supplement: the evolution of development, 27-33 (1994).
114. Bateman, A & Chothia, C. Fibronectin type III domains in yeast detected
by a Hidden Markov model. Curr. Biol. 6, 1544-1547 (1996).
155. Chothia, C., Gough, J., Vogel, C. & Teichmann S.A. Evolution of the
Protein repertoire. Science 300 1701-1703 (2003).
164. Vogel C. & Chothia C. Protein family expansions and biological
complexity. PLOS Computational Biology 2, 370-382 (2006).
58. Janin, J. & Chothia, C.
Domains in proteins: definitions, location and
structural principles. in Meth. Enzym. 115, 420-430 Academic Press,
New York (1985).
Whole Proteins
108. Brenner, S.E., Hubbard, T., Murzin, A. and Chothia, C.
At least one
third of the proteins in Haemophilus influenzae arose from gene
duplications. Nature 378, 140 (1995).
130. Teichmann, S.A., Park, J. & Chothia C. Structural assignments to the
Mycoplasma genitalium proteins show extensive gene duplications
and domain rearrangements. Proc. Natl. Acad. Sci. USA 95, 1465814663 (1998).
151. Bashton M. & Chothia C. The Geometry of Domain Combination in
Proteins. J. Mol. Biol. 315 927-939 (2002).
168. Bashton, M & Chothia C. The Generation of New Protein Functions
by the Combination of Domains. Structure, 15, 85-99 (2007).
154. Okazaki et al. Analysis of the mouse transcriptome based on
functional annotation of 60,770 full-length cDNAs. Nature 420 563573 (2002).
Immuniglobulin and Cadherin Families in Genomes
142. Teichmann, S.A. & Chothia, C. Immunoglobulin Superfamily Proteins in
C. elegans. J. Mol. Biol. 296 1371-1387 (2000).
157. Vogel, C., Teichmann S.A. and Chothia, C. The Immunoglobulin
Superfamily in Drosophila melanogaster and Caenorhabditis elegans
and the Evolution of Complexity. Development 130, 6317-6328
(2003).
161. Vogel C., Teichmann S.A. & Chothia, C. Looking at the bigger picture.
Development 131, 2238-2240 (2004).
144. Hill, E., Broardbent, I.D., Chothia C. & Pettitt, J. Cadherin superfamily
proteins in Caenorhabditis elegans and Drosophila melanogaster.
Mol. Biol. 305 1011-1024 (2001).
11
J.
Small Molecule Metabolic Pathways
146. Teichmann, S.A., Rison, S.C.G., Thornton J.M., Riley, M. Gough, J. &
Chothia, C. The evolution and structural anatomy of the small
molecule metabolic pathways in Escherichia coli. J. Mol. Biol. 311
693-708 (2001).
148. Teichmann, S.A., Rison, S.C.G., Thornton J.M., Riley, M. Gough, J. &
Chothia, C. Small-molecue metabolism: an enzyme mosaic. Trends in
Biotechnology. 19 482-486 (2001).
152. Jardine, O., Gough, J., Chothia, C. & Teichmann, S.A. Comparison of the
Small
Molecule
Metabolic
Enzymes
of
Escherichia
coli
and
Saccharomyces cerevisiae. Genome Res 12 916-929 (2002).
SCOP, SUPERFAMLY AND 3D-COMPLEX DATABASES
SCOP Database
105. Murzin, A.G., Brenner, S., Hubbard, T. & Chothia, C.
SCOP: the
structural classification of proteins database. J. Mol. Biol. 247, 536540 (1995).
109. Brenner, S.E., Chothia, C., Hubbard, T. & Murzin, A.
Understanding
protein structure: using SCOP for fold interpretation. in Meth. Enzym.
266, 635-653 Academic Press, New York (1996).
115. Hubbard, T., Murzin, A.G., Brenner, S. & Chothia, C. SCOP: a structural
classification of proteins database. Nucl.eic Acids Res. 25, 236-239
(1997).
129. Hubbard, T.J.P., Ailey, B., Brenner, S.E., Murzin, A.G. & Chothia, C.
SCOP, Structural Classification of Proteins Database: applications to
evaluation of the effectiveness of sequence alignment methods and
statics of protein structural data. Acta Cryst. D54, 1147-1154 (1998).
131. Hubbard, T.J.P. Ailey, B., Brenner, S.E., Murzin, A.G. & Chothia, C.
SCOP: a structural classification of proteins database. Nucleic Acids
Res. 27, 254-256 (1999).
138. Lo Conte, L., Ailey, B., Hubbard, T.J.P., Brenner, S.E., Murzin, A.G. &
Chotrhia C. SCOP: a Structural Classification of Proteins Database.
Nucleic Acids Res. 28 257-259 (2000).
149. Lo Conte, L., Brenner, S. E., Hubbard, T.J.P., Chothia, C. & Murzin, A.G.
SCOP database in 2002: refinements accomodate structural genomics.
Nucleic Acids Res. 30 264-267 (2002)
12
158. Andreeva, A., Howorth, D., Brenner, S.E., Hubbard, T.J.P. Chothia, C. &
Murzin, A.G. SCOP database in 2004: refinements integrate structure
and sequence family data. Nucleic Acids Res. 30 264-267 (2004).
170.
Andreeva, A., Howorth, D., Chandonia, J.-M., Brenner, E.E.,
Hubbard, T.J.P. Chothia, C. & Murzin, A.G. Data Growth and its
Impact on the SCOP database: New Developments. . Nucl. Acids
Res. 36: D419-D425, (2008).
SUPERFAMILY Database
147. Gough, J., Karplus, K., Hughey, R & Chothia, C. Assignment of
homology to genome sequences using a library of hidden Markov
models that represent all proteins of known structure. J. Mol. Biol.
313 903-919 (2001).
150. Gough, J. & Chothia, C. SUPERFAMILY: HMMs representing all proteins
of known structure: SCOP sequence searches, alignments and
genome assignments. Nucleic Acids Res. 30 264-267 (2002).
159. Madera, M., Vogel, C., Kummerfeld, S.K. Chothia C. & Gough, J. The
SUPERFAMILY database in 2004: additions and improvements. Nucleic
Acids Res. 30 268-272 (2004).
167. Wilson, D., Madera M., Vogel, C., Chothia, C. and Gough J. The
SUPERFAMILY database in 2007: families and function. Nucl. Acids
Res. 35: D308-D313, (2007).
171.
Wilson, D, Pethica, R., Zhou, Y., Talbot, C., Vogel, C., Madera, M.,
Chothia, C. & Gough, J, SUPERFAMILY-sophisticated comparative
genomics, datamining, visualization and phylogeny. Nucl. Acids
Res. 37: D380-D386, (2009).
3D COMPLEX Database
166. Levy ED, Pereira-Leal JB, Chothia C & Teichmann SA. 3D complex: A
structural classification of protein complexes. PLOS Computational
Biology 2, 1395-1406 (2006).
PROTEIN STRUCTURES DETERMINED BY X-RAY CRYSTALLOGRAPHY AND
NMR
23. Sweet, R.M., Wright, H.T., Janin, J., Chothia, C. & Blow, D.M.
Crystal
structure of the complex of porcine trypsin with soybean trypsin
inhibitor (Kunitz) at 2.6 Å resolution.
(1974).
13
Biochemistry 13, 4212-4228
25. Chothia, C. Acetylcholinesterase: the structure of crystals of a globular
form from electric eel. J. Mol. Biol. 97, 55-60 (1975).
44. Mauguen, Y., Hartley, R.W., Dodson, E.J., Dodson, G.G., Bricogne, G.,
Chothia, C. & Jack, A..
Molecular structure of a new family of
ribonucleases. Nature 297, 162-164 (1982).
121. Sandford, R., Sgotto, B., Aparicio, S., Brenner, S., Vaudin, M., Wilson
R.K. Chissoe, S., Pepin, K., Bateman A., Chothia, C., Hughes J. &
Harris P. Comparative analysis of the polycystic kidney disease 1
(PKD1) gene reveals an integral membrane glycoprotein with multiple
evolutionary conserved domains. Hum. Mol. Genet. 6, 1483-1489
(1997).
132. Bycroft, M., Bateman, A., Clarke, J., Hamill. S.J., Sandford, R., Thomas,
R.L. & Chothia, C. The structure of a PKD domain from polycystin-1:
implications for polycystic kidney disease.
EMBO J. 18, 297-305
(1999).
22. Chothia, C. X-ray studies of proteins and amino acids. in Amino-acids,
Peptides and Proteins. vol. 6, pp163-205. Chemical Society. London
(1974).
THE STRUCTURE OF SMALL MOLECULES ACTIVE IN THE NERVOUS SYSTEM
1. Chothia, C. & Pauling, P. Conformations of acetylcholine. Nature 219,
1156-1157 (1968).
2. Chothia, C. & Pauling, P. The structure of the potent muscarinic agonist
L-(+)-acetyl-b-methylcholine iodide. J. Chem. Soc. Chem. Commun.
626-627 (1969).
3. Chothia, C. & Pauling, P.
Two conformations of the cholinergic agonist
acetyl-a-methylcholine: a new conformation for cholinergic molecules.
J. Chem. Soc. Chem. Commun. 746-747 (1969).
4. Chothia, C. & Pauling, P. Conformation of cholinergic molecules relevant
to acetylcholinesterase. Nature 223, 919-921 (1969).
5. Chothia, C. & Pauling, P. On the conformation of hallucinogenic molecules
and their correlations.
Proc. Natl. Acad. Sci. USA 63, 1063-1070
(1969).
6. Chothia, C. & Pauling, P.
The conformation of cholinergic molecules at
nicotinic nerve receptors.
Proc. Natl. Acad. Sci. USA 65, 477-482
(1970).
7. Chothia, C.
Interaction of acetylcholine with different cholinergic nerve
receptors. Nature 225, 36-41 (1970).
14
8. Chothia, C., Pauling, P. & Petcher, T.J. The conformation of cholinergic
agonists. Brit. J. Pharmacol. 39, 219P (1970).
9. Chothia, C. & Pauling, P. Absolute configurations of cholinergic molecules:
the
crystal
structure
of
(+)-trans-2-acetoxy
cyclopropyl
trimethylammonium iodide. Nature 226, 541-542 (1970).
10. Chothia, C. Structure activity relationships of some muscarinic agonists.
Nature 227, 1355-1356 (1970).
11. Chothia C. & Pauling P. Molecular Models. Nature 229, 281 1971
12. Baker, R.W., Chothia, C., Pauling, P. & Petcher, T.J.
Structure and
activity of muscarinic stimulants. Nature 230, 439-445 (1972).
13. Baker, R.W., Chothia, C., Pauling, P. & Weber, H.P. Molecular structure
of LSD. Science 178, 614-615 (1972).
14. Baker, R.W., Chothia, C., Pauling, P. & Weber, H.P. Molecular structures
of hallucinogenic substances: lysergic acid diethylamide, psilocybin
and 2,4,5-trimethoxyamphetamine. Mol. Pharm.. 9, 23-32 (1973).
15. Baker, R.W., Chothia, C. & Pauling, P. Conformation of acetylcholine at
muscarinic nerve receptors: crystal and molecular structure of 2trimethylammonium-methyl-5-methyl furan iodide.
J. Mol. Biol. 105,
517-526 (1976).
16. Chothia, C. & Pauling, P.
The crystal and molecular structure of DL-
lactoylcholine iodide. Acta Cryst. B33, 1851-1854 (1977).
17. Chothia, C. & Pauling, P.
The crystal and molecular structure and
absolute configuration of L-(+)-S-acetyl-b-methylcholine iodide. Acta
Cryst. B34, 152-155 (1978).
18. Chothia, C. & Pauling, P.
The crystal and molecular structure and
absolute configuration of (+)-(1S, 2S)-trans-acetoxy-cyclopropyltrimethyl-ammonium. Acta Cryst. B34, 156-160 (1977).
19. Chothia, C. & Pauling, P.
The crystal and molecular structure of 1,1-
dimethyl-4-phenylpiperazinium iodide.
Acta Cryst. B34, 2986-2989
(1978).
OTHER PAPERS
38. Chothia, C. Concluding remarks. in Protein Folding. pp. 583-585 ed. R.
Jaenicke, Elsevier-North Holland, Amsterdam (1979).
52. Dodson, G., & Chothia C, Protein Crystallography: 50 Years of Pepsin
Crystals. Nature 309 309-309 1984
76. Creighton, T.E. & Chothia, C. Selecting buried residues. Nature 339, 1415 (1989).
15
84. Chothia, C. Asymmetry in protein structures. in Ciba Found. Symp. 162:
Biological Asymmetry and Handedness. pp. 36-57 eds. G.R. Bock & J.
Marsh. John Wiley. Chichester (1991).
101. Chothia, C. & Taylor, W.R. Sequences and topology: Editorial overview.
Curr. Opin struct. Biol. 4, 381-382 (1994).
16