Relative solvent accessible surface area predicts protein conformational changes upon binding

Structure

Volumn 19, Issue 6, 2011, Pages 859-867

  Marsh, Joseph A ^a   Teichmann, Sarah A ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MONOMER; PROTEIN SUBUNIT;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL ANALYSIS; CONFORMATIONAL TRANSITION; MOLECULAR MODEL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SOLVENT ACCESSIBLE SURFACE AREA;

MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEINS; SOLVENTS; SURFACE PROPERTIES; WATER;

EID: 79958093841     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2011.03.010     Document Type: Article

References (44)

1. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402 (Pubitemid 27359211)
2. N. Andrusier, E. Mashiach, R. Nussinov, and H.J. Wolfson Principles of flexible protein-protein docking Proteins 73 2008 271 289
3. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne The Protein Data Bank Nucleic Acids Res. 28 2000 235 242 (Pubitemid 30047768)
4. M.J. Betts, and M.J. Sternberg An analysis of conformational changes on protein-protein association: implications for predictive docking Protein Eng. 12 1999 271 283 (Pubitemid 29209937)
5. D.D. Boehr, R. Nussinov, and P.E. Wright The role of dynamic conformational ensembles in biomolecular recognition Nat. Chem. Biol. 5 2009 789 796
6. A.M.J.J. Bonvin Flexible protein-protein docking Curr. Opin. Struct. Biol. 16 2006 194 200
7. CCP4 (Collaborative Computational Project, Number 4) The CCP4 suite: programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50 1994 760 763
8. J.J. Chou, S. Li, C.B. Klee, and A. Bax Solution structure of Ca(2+)-calmodulin reveals flexible hand-like properties of its domains Nat. Struct. Biol. 8 2001 990 997 (Pubitemid 33032370)
9. S.E. Dobbins, V.I. Lesk, and M.J.E. Sternberg Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking Proc. Natl. Acad. Sci. USA 105 2008 10390 10395
10. J.H. Fong, B.A. Shoemaker, S.O. Garbuzynskiy, M.Y. Lobanov, O.V. Galzitskaya, and A.R. Panchenko Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis PLoS Comput. Biol. 5 2009 e1000316
11. M. Gerstein, A.M. Lesk, and C. Chothia Structural mechanisms for domain movements in proteins Biochemistry 33 1994 6739 6749 (Pubitemid 24190795)
12. J. Gsponer, J. Christodoulou, A. Cavalli, J.M. Bui, B. Richter, C.M. Dobson, and M. Vendruscolo A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction Structure 16 2008 736 746 (Pubitemid 351615020)
13. K. Gunasekaran, and R. Nussinov How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding J. Mol. Biol. 365 2007 257 273 (Pubitemid 44821204)
14. K. Gunasekaran, C. Tsai, S. Kumar, D. Zanuy, and R. Nussinov Extended disordered proteins: targeting function with less scaffold Trends Biochem. Sci. 28 2003 81 85 (Pubitemid 36165136)
15. K. Gunasekaran, C. Tsai, and R. Nussinov Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers J. Mol. Biol. 341 2004 1327 1341 (Pubitemid 39092318)
16. J. Janin Surface area of globular proteins J. Mol. Biol. 105 1976 13 14
17. J. Janin, S. Miller, and C. Chothia Surface, subunit interfaces and interior of oligomeric proteins J. Mol. Biol. 204 1988 155 164 (Pubitemid 19011740)
18. J. Janin, F. Rodier, P. Chakrabarti, and R.P. Bahadur Macromolecular recognition in the Protein Data Bank Acta Crystallogr. D Biol. Crystallogr. 63 2007 1 8
19. M.R. Jensen, P.R.L. Markwick, S. Meier, C. Griesinger, M. Zweckstetter, S. Grzesiek, P. Bernadó, and M. Blackledge Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings Structure 17 2009 1169 1185
20. C.M. Johnson, A. Cooper, and P.G. Stockley Differential scanning calorimetry of thermal unfolding of the methionine repressor protein (MetJ) from Escherichia coli Biochemistry 31 1992 9717 9724
21. E. Krissinel, and K. Henrick Inference of macromolecular assemblies from crystalline state J. Mol. Biol. 372 2007 774 797 (Pubitemid 47321791)
22. O.F. Lange, N. Lakomek, C. Fars, G.F. Schröder, K.F.A. Walter, S. Becker, J. Meiler, H. Grubmüller, C. Griesinger, and B.L. de Groot Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution Science 320 2008 1471 1475 (Pubitemid 351929422)
23. E.D. Levy PiQSi: protein quaternary structure investigation Structure 15 2007 1364 1367 (Pubitemid 350051933)
24. Y. Levy, P.G. Wolynes, and J.N. Onuchic Protein topology determines binding mechanism Proc. Natl. Acad. Sci. USA 101 2004 511 516 (Pubitemid 38084667)
25. Y. Liu, and D. Eisenberg 3D domain swapping: as domains continue to swap Protein Sci. 11 2002 1285 1299 (Pubitemid 34547201)
26. L. Lo Conte, C. Chothia, and J. Janin The atomic structure of protein-protein recognition sites J. Mol. Biol. 285 1999 2177 2198 (Pubitemid 29078179)
27. J.A. Marsh, B. Dancheck, M.J. Ragusa, M. Allaire, J.D. Forman-Kay, and W. Peti Structural diversity in free and bound states of intrinsically disordered protein phosphatase 1 regulators Structure 18 2010 1094 1103
28. B. Mészáros, P. Tompa, I. Simon, and Z. Dosztányi Molecular principles of the interactions of disordered proteins J. Mol. Biol. 372 2007 549 561 (Pubitemid 47267965)
29. S. Miller, J. Janin, A.M. Lesk, and C. Chothia Interior and surface of monomeric proteins J. Mol. Biol. 196 1987 641 656
30. S. Miller, A.M. Lesk, J. Janin, and C. Chothia The accessible surface area and stability of oligomeric proteins Nature 328 1987 834 836 (Pubitemid 17125965)
31. T. Mittag, L.E. Kay, and J.D. Forman-Kay Protein dynamics and conformational disorder in molecular recognition J. Mol. Recognit. 23 2010 105 116
32. T. Mittag, J. Marsh, A. Grishaev, S. Orlicky, H. Lin, F. Sicheri, M. Tyers, and J.D. Forman-Kay Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase Structure 18 2010 494 506
33. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
34. I.M.A. Nooren, and J.M. Thornton Diversity of protein-protein interactions EMBO J. 22 2003 3486 3492 (Pubitemid 36898326)
35. J. Prilusky, C.E. Felder, T. Zeev-Ben-Mordehai, E.H. Rydberg, O. Man, J.S. Beckmann, I. Silman, and J.L. Sussman FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded Bioinformatics 21 2005 3435 3438 (Pubitemid 41222454)
36. M.J. Ragusa, B. Dancheck, D.A. Critton, A.C. Nairn, R. Page, and W. Peti Spinophilin directs protein phosphatase 1 specificity by blocking substrate binding sites Nat. Struct. Mol. Biol. 17 2010 459 464
37. D.C. Teller Accessible area, packing volumes and interaction surfaces of globular proteins Nature 260 1976 729 731
38. D. Tobi, and I. Bahar Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state Proc. Natl. Acad. Sci. USA 102 2005 18908 18913 (Pubitemid 43049540)
39. P. Tompa, and M. Fuxreiter Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions Trends Biochem. Sci. 33 2008 2 8
40. C.J. Tsai, S. Kumar, B. Ma, and R. Nussinov Folding funnels, binding funnels, and protein function Protein Sci. 8 1999 1181 1190 (Pubitemid 29264948)
41. C. Wang, P. Bradley, and D. Baker Protein-protein docking with backbone flexibility J. Mol. Biol. 373 2007 503 519 (Pubitemid 47445567)
42. M. Wells, H. Tidow, T.J. Rutherford, P. Markwick, M.R. Jensen, E. Mylonas, D.I. Svergun, M. Blackledge, and A.R. Fersht Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain Proc. Natl. Acad. Sci. USA 105 2008 5762 5767 (Pubitemid 351758446)
43. P.E. Wright, and H.J. Dyson Linking folding and binding Curr. Opin. Struct. Biol. 19 2009 31 38
44. D. Xu, C.J. Tsai, and R. Nussinov Mechanism and evolution of protein dimerization Protein Sci. 7 1998 533 544 (Pubitemid 28130874)