Classification of proteins: Available structural space for molecular modeling

Methods in Molecular Biology

Volumn 857, Issue , 2012, Pages 1-31

  Andreeva, Antonina ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

Chameleon sequences; Circular permutation; Conformational changes; Fold decay; Fold transitions; Oligomeric complex; Protein classification; Protein domain; Protein motif; Protein repeat

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN MULTIMERIZATION; PROTEIN TERTIARY STRUCTURE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 84858129259     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-588-6_1     Document Type: Article

References (152)

1. Kendrew, J. C., Bodo, G., Dintzis, H. M., Parrish, R. G., Wyckoff, H., and Phillips, D. C. (1958) A three-dimensional model of the myoglobin molecule obtained by x-ray analysis, Nature 181, 662-666.
2. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank, Nucleic Acids Res 28, 235-242. (Pubitemid 30047768)
3. Chothia, C. (1984) Principles that determine the structure of proteins, Annu. Rev. Biochem. 53, 537-572.
4. Chothia, C., Levitt, M., and Richardson, D. (1977) Structure of proteins: packing of alpha-helices and pleated sheets, Proc. Natl. Acad. Sci. USA 74, 4130-4134. (Pubitemid 8228367)
5. Levitt, M., and Chothia, C. (1976) Structural patterns in globular proteins, Nature 261, 552-558.
6. Richardson, J. S. (1977) beta-Sheet topology and the relatedness of proteins, Nature 268, 495-500.
7. Richardson, J. S. (1981) The anatomy and taxonomy of protein structure, Adv. Protein Chem. 34, 167-339.
8. Holm, L., and Sander, C. (1994) The FSSP database of structurally aligned protein fold families, Nucleic Acids Res 22, 3600-3609. (Pubitemid 24299833)
9. Ohkawa, H., Ostell, J., and Bryant, S. (1995) MMDB: an ASN.1 specifi cation for macromolecular structure, Proc Int Conf Intell Syst Mol Biol 3, 259-267.
10. Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) SCOP: a structural classifi cation of proteins database for the investigation of sequences and structures, J Mol Biol 247, 536-540.
11. Orengo, C. A., Pearl, F. M., Bray, J. E., Todd, A. E., Martin, A. C., Lo Conte, L., and Thornton, J. M. (1999) The CATH Database provides insights into protein structure/function relationships, Nucleic Acids Res 27, 275-279. (Pubitemid 29211857)
12. Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B., and Thornton, J. M. (1997) CATH-a hierarchic classifi cation of protein domain structures, Structure 5, 1093-1108. (Pubitemid 27393093)
13. Wetlaufer, D. B. (1973) Nucleation, rapid folding, and globular intrachain regions in proteins, Proc Natl Acad Sci USA 70, 697-701.
14. Rossmann, M. G., Moras, D., and Olsen, K. W. (1974) Chemical and biological evolution of nucleotide-binding protein, Nature 250, 194-199.
15. Remaut, H., Bompard-Gilles, C., Goffi n, C., Frere, J. M., and Van Beeumen, J. (2001) Structure of the Bacillus subtilis D-aminopeptidase DppA reveals a novel selfcompartmentalizing protease, Nat Struct Biol 8, 674-678. (Pubitemid 32757925)
16. Alden, K., Veretnik, S., and Bourne, P. E. (2010) dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment, BMC Bioinformatics 11, 310.
17. Alexandrov, N., and Shindyalov, I. (2003) PDP: protein domain parser, Bioinformatics 19, 429-430. (Pubitemid 36284946)
18. Holm, L., and Sander, C. (1994) Parser for protein folding units, Proteins 19, 256-268. (Pubitemid 24215052)
19. Redfern, O. C., Harrison, A., Dallman, T., Pearl, F. M., and Orengo, C. A. (2007) CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures, PLoS Comput Biol 3, e232.
20. Siddiqui, A. S., and Barton, G. J. (1995) Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain defi nitions, Protein Sci 4, 872-884.
21. Sowdhamini, R., and Blundell, T. L. (1995) An automatic method involving cluster analysis of secondary structures for the identifi cation of domains in proteins, Protein Sci 4, 506-520.
22. Swindells, M. B. (1995) A procedure for detecting structural domains in proteins, Protein Sci 4, 103-112.
23. Taylor, W. R. (1999) Protein structural domain identifi cation, Protein Eng 12, 203-216. (Pubitemid 29158755)
24. Veretnik, S., Bourne, P. E., Alexandrov, N. N., and Shindyalov, I. N. (2004) Toward consistent assignment of structural domains in proteins, J Mol Biol 339, 647-678. (Pubitemid 38625911)
25. Zhou, H., Xue, B., and Zhou, Y. (2007) DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profi le, Protein Sci 16, 947-955. (Pubitemid 46683199)
26. Sigrist, C. J., Cerutti, L., de Castro, E., Langendijk-Genevaux, P. S., Bulliard, V., Bairoch, A., and Hulo, N. (2010) PROSITE, a protein domain database for functional characterization and annotation, Nucleic Acids Res 38, D161-166.
27. Levy, E. D., Pereira-Leal, J. B., Chothia, C., and Teichmann, S. A. (2006) 3D complex: a structural classifi cation of protein complexes, PLoS Comput Biol 2, e155.
28. Andreeva, A., Prlic, A., Hubbard, T. J., and Murzin, A. G. (2007) SISYPHUS-structural alignments for proteins with non-trivial relationships, Nucleic Acids Res 35, D253-259. (Pubitemid 46056209)
29. Hemmingsen, J. M., Gernert, K. M., Richardson, J. S., and Richardson, D. C. (1994) The tyrosine corner: a feature of most Greek key beta-barrel proteins, Protein Sci 3, 1927-1937.
30. Brennan, R. G., and Matthews, B. W. (1989) The helix-turn-helix DNA binding motif, J Biol Chem 264, 1903-1906. (Pubitemid 19057656)
31. Doherty, A. J., Serpell, L. C., and Ponting, C. P. (1996) The helix-hairpin-helix DNAbinding motif: a structural basis for nonsequence-specifi c recognition of DNA, Nucleic Acids Res 24, 2488-2497. (Pubitemid 26237145)
32. Religa, T. L., Johnson, C. M., Vu, D. M., Brewer, S. H., Dyer, R. B., and Fersht, A. R. (2007) The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain, Proc Natl Acad Sci USA 104, 9272-9277. (Pubitemid 47185769)
33. Andreeva, A., and Murzin, A. G. (2006) Evolution of protein fold in the presence of functional constraints, Current Opinion in Structural Biology 16, 399-408. (Pubitemid 43831641)
34. Grishin, N. V. (2001) KH domain: one motif, two folds, Nucleic Acids Res 29, 638-643.
35. Bellamacina, C. R. (1996) The nicotinamide dinucleotide binding motif: a comparison of nucleotide binding proteins, FASEB J 10, 1257-1269. (Pubitemid 26307511)
36. Rigden, D. J., and Galperin, M. Y. (2004) The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution, J Mol Biol 343, 971-984. (Pubitemid 39345957)
37. Saraste, M., Sibbald, P. R., and Wittinghofer, A. (1990) The P-loop-a common motif in ATP-and GTP-binding proteins, Trends Biochem Sci 15, 430-434. (Pubitemid 20376582)
38. Jonassen, I. (1997) Effi cient discovery of conserved patterns using a pattern graph, Comput Appl Biosci 13, 509-522. (Pubitemid 27480211)
39. Jonassen, I., Collins, J. F., and Higgins, D. G. (1995) Finding fl exible patterns in unaligned protein sequences, Protein Sci 4, 1587-1595.
40. Rigoutsos, I., and Floratos, A. (1998) Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm, Bioinformatics 14, 55-67. (Pubitemid 28397726)
41. Ye, K., Kosters, W. A., and Ijzerman, A. P. (2007) An effi cient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences, Bioinformatics 23, 687-693. (Pubitemid 46554719)
42. Kleywegt, G. J. (1999) Recognition of spatial motifs in protein structures, J Mol Biol 285, 1887-1897. (Pubitemid 29060478)
43. Lee, M. C., Scanlon, M. J., Craik, D. J., and Anderson, M. A. (1999) A novel two-chain proteinase inhibitor generated by circularization of a multidomain precursor protein, Nat Struct Biol 6, 526-530. (Pubitemid 29252829)
44. Neer, E. J., Schmidt, C. J., Nambudripad, R., and Smith, T. F. (1994) The ancient regulatory-protein family of WD-repeat proteins, Nature 371, 297-300. (Pubitemid 24300613)
45. Murray, K. B., Gorse, D., and Thornton, J. M. (2002) Wavelet transforms for the characterization and detection of repeating motifs, J Mol Biol 316, 341-363. (Pubitemid 34722149)
46. Heger, A., and Holm, L. (2000) Rapid automatic detection and alignment of repeats in protein sequences, Proteins 41, 224-237.
47. Andrade, M. A., Ponting, C. P., Gibson, T. J., and Bork, P. (2000) Homology-based method for identifi cation of protein repeats using statistical signifi cance estimates, J Mol Biol 298, 521-537.
48. Murray, K. B., Taylor, W. R., and Thornton, J. M. (2004) Toward the detection and validation of repeats in protein structure, Proteins 57, 365-380. (Pubitemid 39223742)
49. Levy, E. D., Boeri Erba, E., Robinson, C. V., and Teichmann, S. A. (2008) Assembly refl ects evolution of protein complexes, Nature 453, 1262-1265. (Pubitemid 351913589)
50. Chothia, C., and Janin, J. (1975) Principles of protein-protein recognition, Nature 256, 705-708.
51. Jones, S., and Thornton, J. M. (1997) Analysis of protein-protein interaction sites using surface patches, J Mol Biol 272, 121-132. (Pubitemid 27395542)
52. Levy, E. D. (2007) PiQSi: protein quaternary structure investigation, Structure 15, 1364-1367. (Pubitemid 350051933)
53. Janin, J., Bahadur, R. P., and Chakrabarti, P. (2008) Protein-protein interaction and quaternary structure, Q Rev Biophys 41, 133-180.
54. Stetefeld, J., Jenny, M., Schulthess, T., Landwehr, R., Engel, J., and Kammerer, R. A. (2000) Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer, Nat Struct Biol 7, 772-776.
55. Kuhnel, K., Jarchau, T., Wolf, E., Schlichting, I., Walter, U., Wittinghofer, A., and Strelkov, S. V. (2004) The VASP tetramerization domain is a right-handed coiled coil based on a 15-residue repeat, Proc Natl Acad Sci USA 101, 17027-17032. (Pubitemid 39627768)
56. Cabezon, E., Runswick, M. J., Leslie, A. G., and Walker, J. E. (2001) The structure of bovine IF(1), the regulatory subunit of mitochondrial F-ATPase, EMBO J 20, 6990-6996. (Pubitemid 34062291)
57. Nooren, I. M., Kaptein, R., Sauer, R. T., and Boelens, R. (1999) The tetramerization domain of the Mnt repressor consists of two right-handed coiled coils, Nat Struct Biol 6, 755-759. (Pubitemid 29360237)
58. Walshaw, J., and Woolfson, D. N. (2001) Socket: a program for identifying and analysing coiled-coil motifs within protein structures, J Mol Biol 307, 1427-1450. (Pubitemid 33027651)
59. Strelkov, S. V., and Burkhard, P. (2002) Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation, J Struct Biol 137, 54-64. (Pubitemid 35430421)
60. Orgel, J. P., Irving, T. C., Miller, A., and Wess, T. J. (2006) Microfi brillar structure of type I collagen in situ, Proc Natl Acad Sci USA 103, 9001-9005. (Pubitemid 43902523)
61. Henderson, R., and Unwin, P. N. (1975) Three-dimensional model of purple membrane obtained by electron microscopy, Nature 257, 28-32.
62. Walters, R. F., and DeGrado, W. F. (2006) Helix-packing motifs in membrane proteins, Proc Natl Acad Sci USA 103, 13658-13663. (Pubitemid 44413963)
63. Guan, L., Mirza, O., Verner, G., Iwata, S., and Kaback, H. R. (2007) Structural determination of wild-type lactose permease, Proc Natl Acad Sci USA 104, 15294-15298. (Pubitemid 47502911)
64. Abramson, J., Smirnova, I., Kasho, V., Verner, G., Kaback, H. R., and Iwata, S. (2003) Structure and mechanism of the lactose permease of Escherichia coli, Science 301, 610-615. (Pubitemid 36927939)
65. Gupta, S., Bavro, V. N., D'Mello, R., Tucker, S. J., Venien-Bryan, C., and Chance, M. R. (2010) Conformational changes during the gating of a potassium channel revealed by structural mass spectrometry, Structure 18, 839-846.
66. Toyoshima, C., and Nomura, H. (2002) Structural changes in the calcium pump accompanying the dissociation of calcium, Nature 418, 605-611.
67. Olesen, C., Sorensen, T. L., Nielsen, R. C., Moller, J. V., and Nissen, P. (2004) Dephosphorylation of the calcium pump coupled to counterion occlusion, Science 306, 2251-2255. (Pubitemid 40024461)
68. Huang, Y., Lemieux, M. J., Song, J., Auer, M., and Wang, D. N. (2003) Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli, Science 301, 616-620. (Pubitemid 36927940)
69. Oomen, C. J., van Ulsen, P., van Gelder, P., Feijen, M., Tommassen, J., and Gros, P. (2004) Structure of the translocator domain of a bacterial autotransporter, EMBO J 23, 1257-1266. (Pubitemid 38524998)
70. Locher, K. P., Rees, B., Koebnik, R., Mitschler, A., Moulinier, L., Rosenbusch, J. P., and Moras, D. (1998) Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes, Cell 95, 771-778. (Pubitemid 29014457)
71. Dyson, H. J., and Wright, P. E. (2005) Intrinsically unstructured proteins and their functions, Nat Rev Mol Cell Biol 6, 197-208. (Pubitemid 40314921)
72. Dunker, A. K., Silman, I., Uversky, V. N., and Sussman, J. L. (2008) Function and structure of inherently disordered proteins, Curr Opin Struct Biol 18, 756-764.
73. Uversky, V. N., and Dunker, A. K. (2010) Understanding protein non-folding, Biochim Biophys Acta 1804, 1231-1264.
74. Uversky, V. N. (2002) Natively unfolded proteins: a point where biology waits for physics, Protein Sci 11, 739-756. (Pubitemid 34241284)
75. Tompa, P. (2002) Intrinsically unstructured proteins, Trends Biochem Sci 27, 527-533. (Pubitemid 35279598)
76. Joerger, A. C., and Fersht, A. R. (2010) The tumor suppressor p53: from structures to drug discovery, Cold Spring Harb Perspect Biol 2, a000919.
77. Rajagopalan, S., Andreeva, A., Rutherford, T. J., and Fersht, A. R. (2010) Mapping the physical and functional interactions between the tumor suppressors p53 and BRCA2, Proc Natl Acad Sci USA 107, 8587-8592.
78. Rajagopalan, S., Andreeva, A., Teufel, D. P., Freund, S. M., and Fersht, A. R. (2009) Interaction between the transactivation domain of p53 and PC4 exemplifi es acidic activation domains as single-stranded DNA mimics, J Biol Chem 284, 21728-21737.
79. Jonker, H. R., Wechselberger, R. W., Boelens, R., Folkers, G. E., and Kaptein, R. (2005) Structural properties of the promiscuous VP16 activation domain, Biochemistry 44, 827-839. (Pubitemid 40129643)
80. Uversky, V. N. (2003) A protein-chameleon: conformational plasticity of alpha-synuclein, a disordered protein involved in neurodegenerative disorders, J Biomol Struct Dyn 21, 211-234. (Pubitemid 37204199)
81. Linding, R., Jensen, L. J., Diella, F., Bork, P., Gibson, T. J., and Russell, R. B. (2003) Protein disorder prediction: implications for structural proteomics, Structure 11, 1453-1459. (Pubitemid 37412427)
82. Romero, P., Obradovic, Z., Li, X., Garner, E. C., Brown, C. J., and Dunker, A. K. (2001) Sequence complexity of disordered protein, Proteins 42, 38-48.
83. Ward, J. J., Sodhi, J. S., McGuffi n, L. J., Buxton, B. F., and Jones, D. T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life, J Mol Biol 337, 635-645. (Pubitemid 38326883)
84. Sickmeier, M., Hamilton, J. A., LeGall, T., Vacic, V., Cortese, M. S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V. N., Obradovic, Z., and Dunker, A. K. (2007) DisProt: the Database of Disordered Proteins, Nucleic Acids Res 35, D786-793. (Pubitemid 46056310)
85. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res 25, 3389-3402. (Pubitemid 27359211)
86. Johnson, L. S., Eddy, S. R., and Portugaly, E. (2010) Hidden Markov model speed heuristic and iterative HMM search procedure, BMC Bioinformatics 11, 431.
87. Madera, M. (2008) Profile Comparer: a program for scoring and aligning profi le hidden Markov models, Bioinformatics 24, 2630-2631.
88. Sadreyev, R. I., Tang, M., Kim, B. H., and Grishin, N. V. (2009) COMPASS server for homology detection: improved statistical accuracy, speed and functionality, Nucleic Acids Res 37, W90-94.
89. Andreeva, A., Prlic, A., Hubbard, T. J., and Murzin, A. G. (2007) SISYPHUS-structural alignments for proteins with non-trivial relationships, Nucleic Acids Res. 35, D253-259. (Pubitemid 46056209)
90. Grishin, N. V. (2001) Fold change in evolution of protein structures, J Struct Biol 134, 167-185.
91. Kinch, L. N., and Grishin, N. V. (2002) Evolution of protein structures and functions, Curr Opin Struct Biol 12, 400-408. (Pubitemid 34804624)
92. Alva, V., Koretke, K. K., Coles, M., and Lupas, A. N. (2008) Cradle-loop barrels and the concept of metafolds in protein classifi cation by natural descent, Curr Opin Struct Biol 18, 358-365.
93. Anfi nsen, C. B. (1973) Principles that govern the folding of protein chains, Science 181, 223-230.
94. Anfi nsen, C. B., Haber, E., Sela, M., and White, F. H., Jr. (1961) The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain, Proc Natl Acad Sci USA 47, 1309-1314.
95. Luo, X., Tang, Z., Xia, G., Wassmann, K., Matsumoto, T., Rizo, J., and Yu, H. (2004) The Mad2 spindle checkpoint protein has two distinct natively folded states, Nat Struct Mol Biol 11, 338-345. (Pubitemid 38436798)
96. Tuinstra, R. L., Peterson, F. C., Kutlesa, S., Elgin, E. S., Kron, M. A., and Volkman, B. F. (2008) Interconversion between two unrelated protein folds in the lymphotactin native state, Proc Natl Acad Sci USA 105, 5057-5062. (Pubitemid 351738509)
97. Cabrita, L. D., and Bottomley, S. P. (2004) How do proteins avoid becoming too stable? Biophysical studies into metastable proteins, Eur Biophys J 33, 83-88. (Pubitemid 38987094)
98. Bullough, P. A., Hughson, F. M., Skehel, J. J., and Wiley, D. C. (1994) Structure of infl uenza haemagglutinin at the pH of membrane fusion, Nature 371, 37-43. (Pubitemid 24277462)
99. Chan, D. C., Fass, D., Berger, J. M., and Kim, P. S. (1997) Core structure of gp41 from the HIV envelope glycoprotein, Cell 89, 263-273. (Pubitemid 27199898)
100. Stiasny, K., Allison, S. L., Mandl, C. W., and Heinz, F. X. (2001) Role of metastability and acidic pH in membrane fusion by tick-borne encephalitis virus, J Virol 75, 7392-7398. (Pubitemid 32737997)
101. Orosz, A., Wisniewski, J., and Wu, C. (1996) Regulation of Drosophila heat shock factor trimerization: global sequence requirements and independence of nuclear localization, Mol Cell Biol 16, 7018-7030. (Pubitemid 26389761)
102. Xiao, T., Gardner, K. H., and Sprang, S. R. (2002) Cosolvent-induced transformation of a death domain tertiary structure, Proc Natl Acad Sci USA 99, 11151-11156. (Pubitemid 34920894)
103. Kuloglu, E. S., McCaslin, D. R., Markley, J. L., and Volkman, B. F. (2002) Structural rearrangement of human lymphotactin, a C chemokine, under physiological solution conditions, J Biol Chem 277, 17863-17870. (Pubitemid 34967595)
104. Zubkov, S., Gronenborn, A. M., Byeon, I. J., and Mohanty, S. (2005) Structural consequences of the pH-induced conformational switch in A. polyphemus pheromone-binding protein: mechanisms of ligand release, J Mol Biol 354, 1081-1090. (Pubitemid 41698917)
105. Joerger, A. C., Rajagopalan, S., Natan, E., Veprintsev, D. B., Robinson, C. V., and Fersht, A. R. (2009) Structural evolution of p53, p63, and p73: implication for heterotetramer formation, Proc Natl Acad Sci USA 106, 17705-17710.
106. Cordell, S. C., Anderson, R. E., and Lowe, J. (2001) Crystal structure of the bacterial cell division inhibitor MinC, EMBO J 20, 2454-2461. (Pubitemid 32452863)
107. Xu, Q., and Minor, D. L., Jr. (2009) Crystal structure of a trimeric form of the K(V)7.1 (KCNQ1) A-domain tail coiled-coil reveals structural plasticity and context dependent changes in a putative coiled-coil trimerization motif, Protein Sci 18, 2100-2114.
108. Schellenberg, M. J., Ritchie, D. B., Wu, T., Markin, C. J., Spyracopoulos, L., and Macmillan, A. M. (2010) Context-Dependent Remodeling of Structure in Two Large Protein Fragments, J Mol Biol 402, 720-730.
109. Guo, J. T., Jaromczyk, J. W., and Xu, Y. (2007) Analysis of chameleon sequences and their implications in biological processes, Proteins 67, 548-558. (Pubitemid 46625572)
110. Mezei, M. (1998) Chameleon sequences in the PDB, Protein Eng 11, 411-414. (Pubitemid 28347248)
111. Tan, S., and Richmond, T. J. (1998) Crystal structure of the yeast MATalpha2/MCM1/ DNA ternary complex, Nature 391, 660-666. (Pubitemid 28113205)
112. Abel, K., Yoder, M. D., Hilgenfeld, R., and Jurnak, F. (1996) An alpha to beta conformational switch in EF-Tu, Structure 4, 1153-1159. (Pubitemid 27005383)
113. Polekhina, G., Thirup, S., Kjeldgaard, M., Nissen, P., Lippmann, C., and Nyborg, J. (1996) Helix unwinding in the effector region of elongation factor EF-Tu-GDP, Structure 4, 1141-1151. (Pubitemid 27005382)
114. Chen, Y. W., Allen, M. D., Veprintsev, D. B., Lowe, J., and Bycroft, M. (2004) The structure of the AXH domain of spinocerebellar ataxin-1, J Biol Chem 279, 3758-3765. (Pubitemid 38140620)
115. de Chiara, C., Menon, R. P., Adinolfi, S., de Boer, J., Ktistaki, E., Kelly, G., Calder, L., Kioussis, D., and Pastore, A. (2005) The AXH domain adopts alternative folds the solution structure of HBP1 AXH, Structure 13, 743-753. (Pubitemid 40704663)
116. Hamada, K., Shimizu, T., Yonemura, S., Tsukita, S., and Hakoshima, T. (2003) Structural basis of adhesion-molecule recognition by ERM proteins revealed by the crystal structure of the radixin-ICAM-2 complex, EMBO J 22, 502-514. (Pubitemid 36193595)
117. Kitano, K., Yusa, F., and Hakoshima, T. (2006) Structure of dimerized radixin FERM domain suggests a novel masking motif in C-terminal residues 295-304, Acta Crystallogr Sect F Struct Biol Cryst Commun 62, 340-345.
118. Zimmer, J., Li, W., and Rapoport, T. A. (2006) A novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA, J Mol Biol 364, 259-265. (Pubitemid 44715923)
119. Tidow, H., Lauber, T., Vitzithum, K., Sommerhoff, C. P., Rosch, P., and Marx, U. C. (2004) The solution structure of a chimeric LEKTI domain reveals a chameleon sequence, Biochemistry 43, 11238-11247. (Pubitemid 39180367)
120. Ditzel, L., Lowe, J., Stock, D., Stetter, K. O., Huber, H., Huber, R., and Steinbacher, S. (1998) Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT, Cell 93, 125-138. (Pubitemid 28173558)
121. Klumpp, M., Baumeister, W., and Essen, L. O. (1997) Structure of the substrate binding domain of the thermosome, an archaeal group II chaperonin, Cell 91, 263-270. (Pubitemid 27456393)
122. Chothia, C. (1984) Principles that determine the structure of proteins, Annu Rev Biochem 53, 537-572.
123. Chothia, C., and Finkelstein, A. V. (1990) The classifi cation and origins of protein folding patterns, Annu Rev Biochem 59, 1007-1039.
124. Sternberg, M. J., and Thornton, J. M. (1976) On the conformation of proteins: the handedness of the beta-strand-alpha-helix-betastrand unit, J Mol Biol 105, 367-382.
125. Sternberg, M. J., and Thornton, J. M. (1977) On the conformation of proteins: the handedness of the connection between parallel beta-strands, J Mol Biol 110, 269-283. (Pubitemid 8045659)
126. Belogurov, G. A., Vassylyeva, M. N., Svetlov, V., Klyuyev, S., Grishin, N. V., Vassylyev, D. G., and Artsimovitch, I. (2007) Structural basis for converting a general transcription factor into an operon-specifi c virulence regulator, Mol Cell 26, 117-129. (Pubitemid 46553793)
127. Guzzo, C. R., Nagem, R. A., Barbosa, J. A., and Farah, C. S. (2007) Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif, Proteins 69, 644-651. (Pubitemid 47623878)
128. Essen, L. O., Perisic, O., Cheung, R., Katan, M., and Williams, R. L. (1996) Crystal structure of a mammalian phosphoinositide-specifi c phospholipase C delta, Nature 380, 595-602. (Pubitemid 26119011)
129. Sutton, R. B., Davletov, B. A., Berghuis, A. M., Sudhof, T. C., and Sprang, S. R. (1995) Structure of the fi rst C2 domain of synaptotagmin I: a novel Ca2+/phospholipidbinding fold, Cell 80, 929-938.
130. Andreeva, A., Howorth, D., Brenner, S. E., Hubbard, T. J., Chothia, C., and Murzin, A. G. (2004) SCOP database in 2004: refi nements integrate structure and sequence family data, Nucleic Acids Res 32, D226-229. (Pubitemid 38081644)
131. Andreeva, A., Howorth, D., Chandonia, J. M., Brenner, S. E., Hubbard, T. J., Chothia, C., and Murzin, A. G. (2008) Data growth and its impact on the SCOP database: new developments, Nucleic Acids Res 36, D419-425. (Pubitemid 351149760)
132. Cuff, A., Redfern, O. C., Greene, L., Sillitoe, I., Lewis, T., Dibley, M., Reid, A., Pearl, F., Dallman, T., Todd, A., Garratt, R., Thornton, J., and Orengo, C. (2009) The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space, Structure 17, 1051-1062.
133. Hadley, C., and Jones, D. T. (1999) A systematic comparison of protein structure classifi cations: SCOP, CATH and FSSP, Structure 7, 1099-1112. (Pubitemid 29436507)
134. Day, R., Beck, D. A., Armen, R. S., and Daggett, V. (2003) A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary, Protein Sci 12, 2150-2160. (Pubitemid 37163350)
135. Holm, L., and Park, J. (2000) DaliLite workbench for protein structure comparison, Bioinformatics 16, 566-567.
136. Suhrer, S. J., Wiederstein, M., Gruber, M., and Sippl, M. J. (2009) COPS-a novel workbench for explorations in fold space, Nucleic Acids Res 37, W539-544.
137. Li, Z., Ye, Y., and Godzik, A. (2006) Flexible Structural Neighborhood-a database of protein structural similarities and alignments, Nucleic Acids Res 34, D277-280.
138. Bray, J. E., Todd, A. E., Pearl, F. M., Thornton, J. M., and Orengo, C. A. (2000) The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues, Protein Eng 13, 153-165. (Pubitemid 30237590)
139. Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M., and Barton, G. J. (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench, Bioinformatics 25, 1189-1191.
140. Ashkenazy, H., Erez, E., Martz, E., Pupko, T., and Ben-Tal, N. (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids, Nucleic Acids Res 38 Suppl, W529-533.
141. -(2010) The Universal Protein Resource (UniProt) in 2010, Nucleic Acids Res 38, D142-148.
142. Sayers, E. W., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., Feolo, M., Geer, L. Y., Helmberg, W., Kapustin, Y., Landsman, D., Lipman, D. J., Madden, T. L., Maglott, D. R., Miller, V., Mizrachi, I., Ostell, J., Pruitt, K. D., Schuler, G. D., Sequeira, E., Sherry, S. T., Shumway, M., Sirotkin, K., Souvorov, A., Starchenko, G., Tatusova, T. A., Wagner, L., Yaschenko, E., and Ye, J. (2009) Database resources of the National Center for Biotechnology Information, Nucleic Acids Res 37, D5-15.
143. Holm, L., and Rosenstrom, P. (2010) Dali server: conservation mapping in 3D, Nucleic Acids Res 38 Suppl, W545-549.
144. Pearson, W. R., and Lipman, D. J. (1988) Improved tools for biological sequence comparison, Proc Natl Acad Sci USA 85, 2444-2448.
145. Gibrat, J. F., Madej, T., and Bryant, S. H. (1996) Surprising similarities in structure comparison, Curr Opin Struct Biol 6, 377-385. (Pubitemid 26197439)
146. Orengo, C. A., and Taylor, W. R. (1996) SSAP: sequential structure alignment program for protein structure comparison, Methods Enzymol 266, 617-635.
147. Ye, Y., and Godzik, A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists, Bioinformatics 19 Suppl 2, ii246-255. (Pubitemid 41296662)
148. Shindyalov, I. N., and Bourne, P. E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Eng 11, 739-747. (Pubitemid 28434482)
149. Ortiz, A. R., Strauss, C. E., and Olmea, O. (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison, Protein Sci 11, 2606-2621. (Pubitemid 35191136)
150. Sippl, M. J., and Wiederstein, M. (2008) A note on diffi cult structure alignment problems, Bioinformatics 24, 426-427. (Pubitemid 351189021)
151. Zhang, Y., and Skolnick, J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score, Nucleic Acids Res 33, 2302-2309. (Pubitemid 41439897)
152. Jayasinghe, S., Hristova, K., and White, S. H. (2001) MPtopo: A database of membrane protein topology, Protein Sci 10, 455-458. (Pubitemid 32225666)