The emergence of protein complexes: Quaternary structure, dynamics and allostery

Biochemical Society Transactions

Volumn 40, Issue 3, 2012, Pages 475-491

  Perica, Tina ^a   Marsh, Joseph A ^a   Sousa, Filipa L ^a   Natan, Eviatar ^a   Colwell, Lucy J ^a   Ahnert, Sebastian E ^b   Teichmann, Sarah A ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Allostery; Dynamics; Oligomerization; p53; Protein complex; Quaternary structure

Indexed keywords

CASPASE 9; G PROTEIN COUPLED RECEPTOR; PROTEIN P53; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; TRANSCRIPTION FACTOR;

ALLOSTERISM; AUTOREGULATION; CONFERENCE PAPER; DIMERIZATION; DNA BINDING; ENZYME ACTIVE SITE; HETEROZYGOSITY LOSS; MOLECULAR RECOGNITION; OLIGOMERIZATION; OXIDATION; PHENOTYPE; POINT MUTATION; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DNA INTERACTION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STABILITY; THERMOSTABILITY; WILD TYPE;

ALLOSTERIC REGULATION; ANIMALS; AWARDS AND PRIZES; EVOLUTION, MOLECULAR; HUMANS; MULTIPROTEIN COMPLEXES; NUMISMATICS; PROTEIN STRUCTURE, QUATERNARY; PROTEINS;

EID: 84861511557     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20120056     Document Type: Conference Paper

References (161)

1. Monod, J., Wyman, J. and Changeux, J.P. (1965) On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88-118
2. Kühner, S., van Noort, V., Betts, M.J., Leo-Macias, A., Batisse, C., Rode, M., Yamada, T., Maier, T., Bader, S., Beltran-Alvarez, P. et al. (2009) Proteome organization in a genome-reduced bacterium. Science 326, 1235-1240
3. Levy, E.D., Erba, E.B., Robinson, C.V. and Teichmann, S.A. (2008) Assembly reflects evolution of protein complexes. Nature 453, 1262-1265 (Pubitemid 351913589)
4. Levy, E.D., Pereira-Leal, J.B., Chothia, C. and Teichmann, S.A. (2006) 3D complex: a structural classification of protein complexes. PLoS Comput. Biol. 2, e155
5. Jacob, F. (1977) Evolution and tinkering. Science 196, 1161-1166
6. Alon, U. (2003) Biological networks: the tinkerer as an engineer. Science 301, 1866-1867
7. Pereira-Leal, J.B., Levy, E.D. and Teichmann, S.A. (2006) The origins and evolution of functional modules: lessons from protein complexes. Philos. Trans. R. Soc. London Ser. B 361, 507-517 (Pubitemid 44870107)
8. Nooren, I.M.A. and Thornton, J.M. (2003) Diversity of protein-protein interactions. EMBO J. 22, 3486-3492 (Pubitemid 36898326)
9. Hartwell, L.H., Hopfield, J.J., Leibler, S. and Murray, A.W. (1999) From molecular to modular cell biology. Nature 402, C47-C52
10. Hodgkin, J. (1998) Seven types of pleiotropy. Int. J. Dev. Biol. 42, 501-505
11. Yu, H., Braun, P., Yildirim, M.A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N. et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322, 104-110
12. Krogan, N.J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A.P. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643
13. Soundararajan, V., Raman, R., Raguram, S., Sasisekharan, V. and Sasisekharan, R. (2010) Atomic interaction networks in the core of protein domains and their native folds. PLoS ONE 5, e9391
14. Amitai, G., Shemesh, A., Sitbon, E., Shklar, M., Netanely, D., Venger, I. and Pietrokovski, S. (2004) Network analysis of protein structures identifies functional residues. J. Mol. Biol. 344, 1135-1146 (Pubitemid 39491254)
15. Böde, C., Kovács, I.A., Szalay, M.S., Palotai, R., Korcsmáros, T. and Csermely, P. (2007) Network analysis of protein dynamics. FEBS Lett. 581, 2776-2782 (Pubitemid 46874391)
16. Ahnert, S.E., Johnston, I.G., Fink, T.M.A., Doye, J.P.K. and Louis, A.A. (2010) Self-assembly, modularity, and physical complexity. Phys. Rev. E Stat. Nonlinear Soft Matter Phys. 82, 026117
17. Kolmogorov, A.N. (1965) Three approaches to the definition of the concept "quantity of information". Probl. Inf. Transm. (Engl. Trans.) 1, 3-11
18. Chaitin, G. (1966) On the length of programs for computing finite binary sequences. J. Assoc. Comput. Mach. 13, 547-569
19. Soloveichik, D. and Winfree, E. (2007) Complexity of self-assembled shapes. SIAM J. Comput. 36, 1544-1569
20. Tarassov, K., Messier, V., Landry, C.R., Radinovic, S., Serna Molina, M.M., Shames, I., Malitskaya, Y., Vogel, J., Bussey, H. and Michnick, S.W. (2008) An in vivo map of the yeast protein interactome. Science 320, 1465-1470 (Pubitemid 351929421)
21. Dobson, R.C.J., Valegård, K. and Gerrard, J.A. (2004) The crystal structure of three site-directed mutants of Escherichia coli dihydrodipicolinate synthase: further evidence for a catalytic triad. J. Mol. Biol. 338, 329-339 (Pubitemid 38447089)
22. Navia, M.A., Fitzgerald, P.M., McKeever, B.M., Leu, C.T., Heimbach, J.C., Herber, W.K., Sigal, I.S., Darke, P.L. and Springer, J.P. (1989) Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1. Nature 337, 615-620 (Pubitemid 19054290)
23. Devenish, S.R.A. and Gerrard, J.A. (2009) The role of quaternary structure in (β/α;)γ-barrel proteins: evolutionary happenstance or a higher level of structure-function relationships? Org. Biomol. Chem. 7, 833-839
24. Cansu, S. and Doruker, P. (2008) Dimerization affects collective dynamics of triosephosphate isomerase. Biochemistry 47, 1358-1368 (Pubitemid 351198712)
25. Wait, A.F., Parkin, A., Morley, G.M., dos Santos, L. and Armstrong, F.A. (2010) Characteristics of enzyme-based hydrogen fuel cells using an oxygen-tolerant hydrogenase as the anodic catalyst. J. Phys. Chem. C. 114, 12003-12009
26. Volbeda, A., Amara, P., Darnault, C., Mouesca, J.M., Parkin, A., Roessler, M.M., Armstrong, F.A. and Fontecilla-Camps, J.C. (2012) X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli. Proc. Natl. Acad., Sci. U.S.A. 109, 5305-5310
27. Marianayagam, N.J., Sunde, M. and Matthews, J.M. (2004) The power of two: protein dimerization in biology. Trends Biochem. Sci. 29, 618-625 (Pubitemid 39389082)
28. Goodsell, D.S. and Olson, A.J. (2000) Structural symmetry and protein function. Annu. Rev. Biophys. Biomol. Struct. 29, 105-153 (Pubitemid 30599590)
29. Janin, J., Bahadur, R.P. and Chakrabarti, P. (2008) Protein-protein interaction and quaternary structure. Q. Rev. Biophys. 41, 133-180
30. Chothia, C. and Janin, J. (1975) Principles of protein-protein recognition. Nature 256, 705-708
31. Robinson-Rechavi, M., Alibés, A. and Godzik, A. (2006) Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. J. Mol. Biol. 356, 547-557
32. Malay, A.D., Allen, K.N. and Tolan, D.R. (2005) Structure of the thermolabile mutant aldolase B, A149P: molecular basis of hereditary fructose intolerance. J. Mol. Biol. 347, 135-144 (Pubitemid 40283634)
33. Bennett, M.J., Schlunegger, M.P. and Eisenberg, D. (1995) 3D domain swapping: a mechanism for oligomer assembly. Protein Sci. 4, 2455-2468
34. Rousseau, F., Wilkinson, H., Villanueva, J., Serrano, L., Schymkowitz, J.W.H. and Itzhaki, L.S. (2006) Domain swapping in p13suc1 results in formation of native-like, cytotoxic aggregates. J. Mol. Biol. 363, 496-505 (Pubitemid 44436250)
35. Ding, F., Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E. and Shakhnovich, E.I. (2002) Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J. Mol. Biol. 324, 851-857 (Pubitemid 36044117)
36. Liu, Y. and Eisenberg, D. (2002) 3D domain swapping: as domains continue to swap. Protein Sci. 11, 1285-1299 (Pubitemid 34547201)
37. Messina, D.N., Glasscock, J., Gish, W. and Lovett, M. (2004) An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression. Genome Res. 14, 2041-2047 (Pubitemid 39440184)
38. Klemm, J.D., Schreiber, S.L. and Crabtree, G.R. (1998) Dimerization as a regulatory mechanism in signal transduction. Annu. Rev. Immunol. 16, 569-592 (Pubitemid 28183377)
39. Bundschuh, R., Hayot, F. and Jayaprakash, C. (2003) The role of dimerization in noise reduction of simple genetic networks. J. Theor. Biol. 220, 261-269 (Pubitemid 36027130)
40. Morimoto, R.I. (1993) Cells in stress: transcriptional activation of heat shock genes. Science 259, 1409-1410
41. Ou, H.D., Lohr, F., Vogel, V., Mantele, W. and Dotsch, V. (2007) Structural evolution of C-terminal domains in the p53 family. EMBO J. 26, 3463-3473 (Pubitemid 47123529)
42. McLure, K.G. and Lee, P.W. (1998) How p53 binds DNA as a tetramer. EMBO J. 17, 3342-3350 (Pubitemid 28279508)
43. Rajagopalan, S., Huang, F. and Fersht, A.R. Single-molecule characterization of oligomerization kinetics and equilibria of the tumor suppressor p53. Nucleic Acids Res. 39, 2294-2303
44. Kitayner, M., Rozenberg, H., Rohs, R., Suad, O., Rabinovich, D., Honig, B. and Shakked, Z. (2010) Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat. Struct. Mol. Biol. 17, 423-429
45. Weinberg, R.L., Veprintsev, D.B. and Fersht, A.R. (2004) Cooperative binding of tetrameric p53 to DNA. J. Mol. Biol. 341, 1145-1159 (Pubitemid 39092307)
46. Menendez, D., Inga, A. and Resnick, M.A. (2009) The expanding universe of p53 targets. Nat. Rev. Cancer 9, 724-737
47. de Vienne, D. and Rodolphe, F. (1985) Biochemical and genetic properties of oligomeric structures: a general approach. J. Theor. Biol. 116, 527-568
48. Natan, E., Baloglu, C., Pagel, K., Freund, S.M., Morgner, N., Robinson, C.V., Fersht, A.R. and Joerger, A.C. (2011) Interaction of the p53 DNA-binding domain with its N-terminal extension modulates the stability of the p53 tetramer. J. Mol. Biol. 409, 358-368
49. Mateu, M.G., Sanchez Del Pino, M.M. and Fersht, A.R. (1999) Mechanism of folding and assembly of a small tetrameric protein domain from tumor suppressor p53. Nat. Struct. Biol. 6, 191-198 (Pubitemid 29069783)
50. Nicholls, C.D., McLure, K.G., Shields, M.A. and Lee, P.W. (2002) Biogenesis of p53 involves cotranslational dimerization of monomers and posttranslational dimerization of dimers: implications on the dominant negative effect. J. Biol. Chem. 277, 12937-12945 (Pubitemid 34952661)
51. Brachmann, R.K., Vidal, M. and Boeke, J.D. (1996) Dominant-negative p53 mutations selected in yeast hit cancer hot spots. Proc. Natl. Acad. Sci. U.S.A. 93, 4091-4095 (Pubitemid 26144248)
52. Blagosklonny, M.V. (2000) p53 from complexity to simplicity: mutant p53 stabilization, gain-of-function, and dominant-negative effect. FASEB J. 14, 1901-1907
53. Dearth, L.R., Qian, H., Wang, T., Baroni, T.E., Zeng, J., Chen, S.W., Yi, S.Y. and Brachmann, R.K. (2007) Inactive full-length p53 mutants lacking dominant wild-type p53 inhibition highlight loss of heterozygosity as an important aspect of p53 status in human cancers. Carcinogenesis 28, 289-298 (Pubitemid 46321844)
54. Frebourg, T., Sadelain, M., Ng, Y.S., Kassel, J. and Friend, S.H. (1994) Equal transcription of wild-type and mutant p53 using bicistronic vectors results in the wild-type phenotype. Cancer Res. 54, 878-881 (Pubitemid 24085432)
55. Natan, E., Hirschberg, D., Morgner, N., Robinson, C.V. and Fersht, A.R. (2009) Ultraslow oligomerization equilibria of p53 and its implications. Proc. Natl. Acad. Sci. U.S.A. 106, 14327-14332
56. Demidenko, Z.N., Fojo, T. and Blagosklonny, M.V. (2005) Complementation of two mutant p53: implications for loss of heterozygosity in cancer. FEBS Lett. 579, 2231-2235 (Pubitemid 40469698)
57. Bhatia, K., Goldschmidts, W., Gutierrez, M., Gaidano, G., Dalla-Favera, R. and Magrath, I. (1993) Hemi- or homozygosity: a requirement for some but not other p53 mutant proteins to accumulate and exert a pathogenetic effect. FASEB J. 7, 951-956 (Pubitemid 23225554)
58. Gannon, J.V., Greaves, R., Iggo, R. and Lane, D.P. (1990) Activating mutations in p53 produce a common conformational effect: a monoclonal antibody specific for the mutant form. EMBO J. 9, 1595-1602
59. Garcia-Alai, M.M., Tidow, H., Natan, E., Townsley, F.M., Veprintsev, D.B. and Fersht, A.R. (2008) The novel p53 isoform "delta p53" is a misfolded protein and does not bind the p21 promoter site. Protein Sci. 17, 1671-1678
60. Milner, J. and Medcalf, E.A. (1991) Cotranslation of activated mutant p53 with wild type drives the wild-type p53 protein into the mutant conformation. Cell 65, 765-774 (Pubitemid 121001308)
61. Xu, J., Reumers, J., Couceiro, J.R., De Smet, F., Gallardo, R., Rudyak, S., Cornelis, A., Rozenski, J., Zwolinska, A., Marine, J.C. et al. (2011) Gain of function of mutant p53 by coaggregation with multiple tumor suppressors. Nat. Chem. Biol. 7, 285-295
62. Draghi, J.A., Parsons, T.L., Wagner, G.P. and Plotkin, J.B. (2010) Mutational robustness can facilitate adaptation. Nature 463, 353-355
63. Vousden, K.H. and Ryan, K.M. (2009) p53 and metabolism. Nat. Rev. Cancer 9, 691-700
64. Kawamura, T., Suzuki, J., Wang, Y.V., Menendez, S., Morera, L.B., Raya, A., Wahl, G.M. and Belmonte, J.C. (2009) Linking the p53 tumour suppressor pathway to somatic cell reprogramming. Nature 460, 1140-1144
65. Marion, R.M., Strati, K., Li, H., Murga, M., Blanco, R., Ortega, S., Fernandez-Capetillo, O., Serrano, M. and Blasco, M.A. (2009) A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity. Nature 460, 1149-1153
66. Lynch, C.J. and Milner, J. (2006) Loss of one p53 allele results in four-fold reduction of p53 mRNA and protein: a basis for p53 haplo-insufficiency. Oncogene 25, 3463-3470 (Pubitemid 43877049)
67. Harrison, R.S., Sharpe, P.C., Singh, Y. and Fairlie, D.P. (2007) Amyloid peptides and proteins in review. Rev. Physiol. Biochem. Pharmacol. 159, 1-77
68. Wright, C.F., Teichmann, S.A., Clarke, J. and Dobson, C.M. (2005) The importance of sequence diversity in the aggregation and evolution of proteins. Nature 438, 878-881 (Pubitemid 41753072)
69. André, I., Strauss, C.E.M., Kaplan, D.B., Bradley, P. and Baker, D. (2008) Emergence of symmetry in homooligomeric biological assemblies. Proc. Natl. Acad. Sci. U.S.A. 105, 16148-16152
70. Todd, A.E., Orengo, C.A. and Thornton, J.M. (2001) Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307, 1113-1143 (Pubitemid 33029957)
71. Beltrao, P. and Serrano, L. (2007) Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput. Biol. 3, e25
72. Levy, E.D. (2010) A simple definition of structural regions in proteins and its use in analyzing interface evolution. J. Mol. Biol. 403, 660-670
73. Lukatsky, D.B., Shakhnovich, B.E., Mintseris, J. and Shakhnovich, E.I. (2007) Structural similarity enhances interaction propensity of proteins. J. Mol. Biol. 365, 1596-1606 (Pubitemid 46048849)
74. Lukatsky, D.B., Zeldovich, K.B. and Shakhnovich, E.I. (2006) Statistically enhanced self-attraction of random patterns. Phys. Rev. Lett. 97, 178101
75. Fleishman, S.J., Whitehead, T.A., Ekiert, D.C., Dreyfus, C., Corn, J.E., Strauch, E.-M., Wilson, I.A. and Baker, D. (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332, 816-821
76. Grueninger, D., Treiber, N., Ziegler, M.O.P., Koetter, J.W.A., Schulze, M.-S. and Schulz, G.E. (2008) Designed protein-protein association. Science 319, 206-209
77. Karanicolas, J., Corn, J.E., Chen, I., Joachimiak, L.A., Dym, O., Peck, S.H., Albeck, S., Unger, T., Hu, W., Liu, G. et al. (2011) A de novo protein binding pair by computational design and directed evolution. Mol. Cell 42, 250-260
78. Altschuh, D., Lesk, A.M., Bloomer, A.C. and Klug, A. (1987) Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J. Mol. Biol. 193, 693-707
79. Neher, E. (1994) How frequent are correlated changes in families of protein sequences? Proc. Natl. Acad. Sci. U.S.A. 91, 98-102
80. Shindyalov, I.N., Kolchanov, N.A. and Sander, C. (1994) Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng. 7, 349-358 (Pubitemid 24063134)
81. Lockless, S.W. and Ranganathan, R. (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286, 295-299 (Pubitemid 29484693)
82. Pollock, D.D. and Taylor, W.R. (1997) Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10, 647-657 (Pubitemid 27332071)
83. Yeang, C.H. and Haussler, D. (2007) Detecting coevolution in and among protein domains. PLoS Comput. Biol. 3, e211
84. Skerker, J.M., Perchuk, B.S., Siryaporn, A., Lubin, E.A., Ashenberg, O., Goulian, M. and Laub, M.T. (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133, 1043-1054 (Pubitemid 351787742)
85. Dunn, S.D., Wahl, L.M. and Gloor, G.B. (2008) Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics 24, 333-340 (Pubitemid 351189008)
86. Callahan, B., Neher, R.A., Bachtrog, D., Andolfatto, P. and Shraiman, B.I. (2011) Correlated evolution of nearby residues in Drosophilid proteins. PLoS Genet. 7, e1001315
87. Choi, S.S., Li, W. and Lahn, B.T. (2005) Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis. Nat. Genet. 37, 1367-1371 (Pubitemid 41722194)
88. Pazos, F., Helmer-Citterich, M., Ausiello, G. and Valencia, A. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271, 511-523 (Pubitemid 27373087)
89. Halperin, I., Wolfson, H. and Nussinov, R. (2006) Correlated mutations: advances and limitations: a study on fusion proteins and on the Cohesin-Dockerin families. Proteins 63, 832-845 (Pubitemid 43765137)
90. Kass, I. and Horovitz, A. (2002) Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 48, 611-617 (Pubitemid 34925449)
91. Halabi, N., Rivoire, O., Leibler, S. and Ranganathan, R. (2009) Protein sectors: evolutionary units of three-dimensional structure. Cell 138, 774-786
92. Lapedes, A.S., Giraud, B.G., Liu, L.C. and Stormo, G.D. (1999) Correlated mutations in models of protein sequences: phylogenetic and structural effects. Stat. Mol. Biol. 33, 236-256
93. Burger, L. and van Nimwegen, E. (2008) Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Mol. Syst. Biol. 4, 165
94. Burger, L. and van Nimwegen, E. (2010) Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comput. Biol. 6, e1000633
95. Weigt, M., White, R.A., Szurmant, H., Hoch, J.A. and Hwa, T. (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc. Natl. Acad. Sci. U.S.A. 106, 67-72
96. Marks, D.S., Colwell, L.J., Sheridan, R., Hopf, T.A., Pagnani, A., Zecchina, R. and Sander, C. (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS ONE 6, e28766
97. Davis, F.P. and Sali, A. (2005) PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21, 1901-1907 (Pubitemid 40668025)
98. Dahirel, V., Shekhar, K., Pereyra, F., Miura, T., Artyomov, M., Talsania, S., Allen, T.M., Altfeld, M., Carrington, M., Irvine, D.J. et al. (2011) Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proc. Natl. Acad. Sci. U.S.A. 108, 11530-11535
99. Suel, G.M., Lockless, S.W., Wall, M.A. and Ranganathan, R. (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10, 59-69 (Pubitemid 36034178)
100. Kuriyan, J. and Eisenberg, D. (2007) The origin of protein interactions and allostery in colocalization. Nature 450, 983-990 (Pubitemid 350273628)
101. Huang, Z., Zhu, L., Cao, Y., Wu, G., Liu, X., Chen, Y., Wang, Q., Shi, T., Zhao, Y., Wang, Y. et al. (2011) ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Res. 39, D663-D669
102. Marcos, E., Crehuet, R. and Bahar, I. (2011) Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members. PLoS Comput. Biol. 7, e1002201
103. Koshland, Jr, D.E., Nemethy, G. and Filmer, D. (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5, 365-385
104. Hilser, V.J., Dowdy, D., Oas, T.G. and Freire, E. (1998) The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble. Proc. Natl. Acad. Sci. U.S.A. 95, 9903-9908 (Pubitemid 28415267)
105. Hammes, G.G., Chang, Y.C. and Oas, T.G. (2009) Conformational selection or induced fit: a flux description of reaction mechanism. Proc. Natl. Acad. Sci. U.S.A. 106, 13737-13741
106. Okazaki, K. and Takada, S. (2008) Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms. Proc. Natl. Acad. Sci. U.S.A. 105, 11182-11187
107. Dodla, R. and Wilson, C.J. (2010) A phase function to quantify serial dependence between discrete samples. Biophys. J. 98, L5-L7
108. Horovitz, A. and Fersht, A.R. (1990) Strategy for analysing the co-operativity of intramolecular interactions in peptides and proteins. J. Mol. Biol. 214, 613-617
109. Elber, R. (2011) Simulations of allosteric transitions. Curr. Opin. Struct. Biol. 21, 167-172
110. del Sol, A., Fujihashi, H., Amoros, D. and Nussinov, R. (2006) Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol. Syst. Biol. 2, 2006.0019
111. Daily, M.D. and Gray, J.J. (2009) Allosteric communication occurs via networks of tertiary and quaternary motions in proteins. PLoS Comput. Biol. 5, e1000293
112. Greene, L.H. and Higman, V.A. (2003) Uncovering network systems within protein structures. J. Mol. Biol. 334, 781-791 (Pubitemid 37433891)
113. Atilgan, A.R., Akan, P. and Baysal, C. (2004) Small-world communication of residues and significance for protein dynamics. Biophys. J. 86, 85-91 (Pubitemid 38067438)
114. Daily, M.D. and Gray, J.J. (2007) Local motions in a benchmark of allosteric proteins. Proteins 67, 385-399 (Pubitemid 46449415)
115. Yang, L.W., Rader, A.J., Liu, X., Jursa, C.J., Chen, S.C., Karimi, H.A. and Bahar, I. (2006) oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res. 34, W24-W31 (Pubitemid 44529729)
116. Cooper, A. and Dryden, D.T. (1984) Allostery without conformational change: a plausible model. Eur. Biophys. J. 11, 103-109
117. Rafferty, J.B., Somers, W.S., Saint-Girons, I. and Phillips, S.E. (1989) Three-dimensional crystal structures of Escherichia coli met repressor with and without corepressor. Nature 341, 705-710 (Pubitemid 19260883)
118. Stacklies, W., Xia, F. and Grater, F. (2009) Dynamic allostery in the methionine repressor revealed by force distribution analysis. PLoS Comput. Biol. 5, e1000574
119. Swint-Kruse, L. and Matthews, K.S. (2009) Allostery in the LacI/GalR family: variations on a theme. Curr. Opin. Microbiol. 12, 129-137
120. Lewis, M., Chang, G., Horton, N.C., Kercher, M.A., Pace, H.C., Schumacher, M.A., Brennan, R.G. and Lu, P. (1996) Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science 271, 1247-1254
121. Bell, C.E. and Lewis, M. (2000) A closer view of the conformation of the Lac repressor bound to operator. Nat. Struct. Biol. 7, 209-214 (Pubitemid 30140766)
122. Markiewicz, P., Kleina, L.G., Cruz, C., Ehret, S. and Miller, J.H. (1994) Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence. J. Mol. Biol. 240, 421-433 (Pubitemid 24249917)
123. Kalodimos, C.G., Boelens, R. and Kaptein, R. (2002) A residue-specific view of the association and dissociation pathway in protein-DNA recognition. Nat. Struct. Biol. 9, 193-197 (Pubitemid 34171311)
124. Tungtur, S., Meinhardt, S. and Swint-Kruse, L. (2010) Comparing the functional roles of nonconserved sequence positions in homologous transcription repressors: implications for sequence/function analyses. J. Mol. Biol. 395, 785-802
125. Ma, B., Tsai, C.J., Haliloglu, T. and Nussinov, R. (2011) Dynamic allostery: linkers are not merely flexible. Structure 19, 907-917
126. Swint-Kruse, L. (2004) Using networks to identify fine structural differences between functionally distinct protein states. Biochemistry 43, 10886-10895
127. Demerdash, O.N., Daily, M.D. and Mitchell, J.C. (2009) Structure-based predictive models for allosteric hot spots. PLoS Comput. Biol. 5, e1000531
128. Zhan, H., Camargo, M. and Matthews, K.S. (2010) Positions 94-98 of the lactose repressor N-subdomain monomer-monomer interface are critical for allosteric communication. Biochemistry 49, 8636-8645
129. Flynn, T.C., Swint-Kruse, L., Kong, Y., Booth, C., Matthews, K.S. and Ma, J. (2003) Allosteric transition pathways in the lactose repressor protein core domains: asymmetric motions in a homodimer. Protein Sci. 12, 2523-2541 (Pubitemid 37310792)
130. Su, J.G., Jin Xu, X., Hua Li, C., Chen, W.Z. and Wang, C.X. (2011) Identification of key residues for protein conformational transition using elastic network model. J. Chem. Phys. 135, 174101
131. Mukherjee, S. and Zhang, Y. (2011) Protein-protein complex structure predictions by multimeric threading and template recombination. Structure 19, 955-966
132. Stein, A., Mosca, R. and Aloy, P. (2011) Three-dimensional modeling of protein interactions and complexes is going 'omics. Curr. Opin. Struct. Biol. 21, 200-208
133. Fermi, G., Perutz, M.F., Shaanan, B. and Fourme, R. (1984) The crystal structure of human deoxyhaemoglobin at 1.74 Å resolution. J. Mol. Biol. 175, 159-174 (Pubitemid 15243353)
134. Arakawa, T., Kawano, Y., Kataoka, S., Katayama, Y., Kamiya, N., Yohda, M. and Odaka, M. (2007) Structure of thiocyanate hydrolase: a new nitrile hydratase family protein with a novel five-coordinate cobalt(III) center. J. Mol. Biol. 366, 1497-1509 (Pubitemid 46215603)
135. Cramer, P., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863-1876 (Pubitemid 32538356)
136. Stock, D., Leslie, A.G. and Walker, J.E. (1999) Molecular architecture of the rotary motor in ATP synthase. Science 286, 1700-1705 (Pubitemid 129515869)
137. Marsh, J.A. and Teichmann, S.A. (2011) Relative solvent accessible surface area predicts protein conformational changes upon binding. Structure 19, 859-867
138. Dobbins, S.E., Lesk, V.I. and Sternberg, M.J.E. (2008) Insights into protein flexibility: the relationship between normal modes and conformational change upon protein-protein docking. Proc. Natl. Acad. Sci. U.S.A. 105, 10390-10395
139. Babu, M.M., van der Lee, R., de Groot, N.S. and Gsponer, J. (2011) Intrinsically disordered proteins: regulation and disease. Curr. Opin. Struct. Biol. 21, 432-440
140. Wright, P.E. and Dyson, H.J. (2009) Linking folding and binding. Curr. Opin. Struct. Biol. 19, 31-38
141. Hegyi, H., Schad, E. and Tompa, P. (2007) Structural disorder promotes assembly of protein complexes. BMC Struct. Biol. 7, 65
142. Tompa, P. and Fuxreiter, M. (2008) Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends Biochem. Sci. 33, 2-8
143. Marsh, J.A., Dancheck, B., Ragusa, M.J., Allaire, M., Forman-Kay, J.D. and Peti, W. (2010) Structural diversity in free and bound states of intrinsically disordered protein phosphatase 1 regulators. Structure 18, 1094-1103
144. Mittag, T., Marsh, J., Grishaev, A., Orlicky, S., Lin, H., Sicheri, F., Tyers, M. and Forman-Kay, J.D. (2010) Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure 18, 494-506
145. Wells, M., Tidow, H., Rutherford, T.J., Markwick, P., Jensen, M.R., Mylonas, E., Svergun, D.I., Blackledge, M. and Fersht, A.R. (2008) Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. Proc. Natl. Acad. Sci. U.S.A. 105, 5762-5767 (Pubitemid 351758446)
146. Pereira-Leal, J.B., Levy, E.D., Kamp, C. and Teichmann, S.A. (2007) Evolution of protein complexes by duplication of homomeric interactions. Genome Biol. 8, R51-R51
147. Enright, A.J., Iliopoulos, I., Kyrpides, N.C. and Ouzounis, C.A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 86-90
148. Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O. and Eisenberg, D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753
149. Jabri, E. and Karplus, P.A. (1996) Structures of the Klebsiella aerogenes urease apoenzyme and two active-site mutants. Biochemistry 35, 10616-10626 (Pubitemid 26279640)
150. Ha, N.C., Oh, S.T., Sung, J.Y., Cha, K.A., Lee, M.H. and Oh, B.H. (2001) Supramolecular assembly and acid resistance of Helicobacter pylori urease. Nat. Struct. Biol. 8, 505-509 (Pubitemid 32525008)
151. Balasubramanian, A. and Ponnuraj, K. (2010) Crystal structure of the first plant urease from jack bean: 83 years of journey from its first crystal to molecular structure. J. Mol. Biol. 400, 274-283
152. Kummerfeld, S.K. and Teichmann, S.A. (2005) Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet. 21, 25-30 (Pubitemid 40178845)
153. Meenan, N.A., Sharma, A., Fleishman, S.J., Macdonald, C.J., Morel, B., Boetzel, R., Moore, G.R., Baker, D. and Kleanthous, C. (2010) The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction. Proc. Natl. Acad. Sci. U.S.A. 107, 10080-10085
154. Hurley, J.H., Lee, S. and Prag, G. (2006) Ubiquitin-binding domains. Biochem. J. 399, 361-372 (Pubitemid 44672627)
155. Lo Conte, L., Chothia, C. and Janin, J. (1999) The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285, 2177-2198 (Pubitemid 29078179)
156. Ozbabacan, S.E., Engin, H.B., Gursoy, A. and Keskin, O. (2011) Transient protein-protein interactions. Protein Eng. Des. Sel. 24, 635-648
157. Cox, J. and Mann, M. (2011) Quantitative, high-resolution proteomics for data-driven systems biology. Annu. Rev. Biochem. 80, 273-299
158. Kodandapani, R., Pio, F., Ni, C.Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R.A. and Ely, K.R. (1996) A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex. Nature 380, 456-460
159. Venkatachalam, S., Shi, Y.P., Jones, S.N., Vogel, H., Bradley, A., Pinkel, D. and Donehower, L.A. (1998) Retention of wild-type p53 in tumors from p53 heterozygous mice: reduction of p53 dosage can promote cancer formation. EMBO J. 17, 4657-4667 (Pubitemid 28377166)
160. Martin, A.J., Vidotto, M., Boscariol, F., Di Domenico, T., Walsh, I. and Tosatto, S.C. (2011) RING: networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics 27, 2003-2005
161. Vehlow, C., Stehr, H., Winkelmann, M., Duarte, J.M., Petzold, L., Dinse, J. and Lappe, M. (2011) CMView: interactive contact map visualization and analysis. Bioinformatics 27, 1573-1574