Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 9, 2011, Pages 3504-3509

  Li, Wenfei ^a,b,c   Wolynes, Peter G ^d   Takada, Shoji ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c NANJING UNIVERSITY   (China)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Allosteric motions; Energy decomposition; Interaction nonlinearity; Multiscale simulations; Sequence design principle

Indexed keywords

ADENYLATE KINASE;

ALLOSTERISM; ARTICLE; CONFORMATIONAL TRANSITION; ENERGY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION; STATISTICAL MODEL;

ADENYLATE KINASE; ALLOSTERIC REGULATION; AMINO ACID SEQUENCE; AMINO ACIDS; DATABASES, PROTEIN; MOLECULAR DYNAMICS SIMULATION; NONLINEAR DYNAMICS; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 79952774013     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1018983108     Document Type: Article

References (39)

1. Csermely P, Palotai R, Nussinov R (2010) Induced fit, conformational selection and independent dynamic segments: An extended view of binding events. Trends Biochem Sci 35:539-546.
2. Grant BJ, Gorfe AA, McCammon JA (2010) Large conformational changes in proteins: Signaling and other functions. Curr Opin Struct Biol 20:142-147.
3. Onuchic JN, Luthey-Schulten Z, Wolynes PG (1997) Theory of protein folding: The energy landscape perspective. Annu Rev Phys Chem 48:545-600. (Pubitemid 127443918)
4. Tirion MM (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77:1905-1908.
5. Haliloglu T, Bahar I, Erman B (1997) Gaussian dynamics of folded proteins. Phys Rev Lett 79:3090-3093. (Pubitemid 127645089)
6. Atilgan AR, et al. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80:505-515.
7. Ma J (2005) Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13:373-380.
8. Yang L, Song G, Jernigan RL (2009) Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci USA 106:12347-12352.
9. Tzeng SR, Kalodimos CG (2009) Dynamic activation of an allosteric regulatory protein. Nature 462:368-372.
10. Henzler-Wildman KA, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450:913-916. (Pubitemid 350231333)
11. Schrank TP, Bolen DW, Hilser VJ (2009) Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins. Proc Natl Acad Sci USA 106:16984-16989.
12. Bae E, Phillips GJ (2006) Roles of static and dynamic domains in stability and catalysis of adenylate kinase. Proc Natl Acad Sci USA 103:2132-2137. (Pubitemid 43271635)
13. Ferreiro DU, Hegler JA, Komives EA, Wolynes PG (2007) Localizing frustration in native proteins and protein assemblies. Proc Natl Acad Sci USA 104:19819-19824.
14. Ferreiro DU, Hegler JA, Komives EA, Wolynes PG (2011) On the role of frustration in the energy landscapes of allosteric proteins. Proc Natl Acad Sci USA 108:3499-3503.
15. Miyashita O, Onuchic JN, Wolynes PG (2003) Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci USA 100:12570-12575. (Pubitemid 37339939)
16. Clementi C, Nymeyer H, Onuchic JN (2000) Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 298:937-953.
17. Go N (1983) Theoretical studies of protein folding. Annu Rev Biophys Bioeng 12:183-210.
18. Koga N, Takada S (2001) Roles of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model. J Mol Biol 313:171-180. (Pubitemid 33001173)
19. Case D, et al. (2008) AMBER10 (University of California, San Francisco).
20. Pande VS, Grosberg AY, Tanaka T (2000) Heteropolymer freezing and design: Towards physical models of protein folding. Rev Mod Phys 72:259-314.
21. Muller CW, Schulz GE (1992) Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution. A model for a catalytic transition state. J Mol Biol 224:159-177.
22. Beckstein O, Denning EJ, Perilla JR, Woolf TB (2009) Zipping and unzipping of adenylate kinase: Atomistic insights into the ensemble of open ↔ closed transitions. J Mol Biol 394:160-176.
23. Whitford PC, Onuchic JN, Wolynes PG (2008) Energy landscape along an enzymatic reaction trajectory: Hinges or cracks? HFSP J 2:61-64.
24. Arora K, Brooks CR (2007) Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci USA 104:18496-18501. (Pubitemid 350210725)
25. Maragakis P, Karplus M (2005) Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase. J Mol Biol 352:807-822. (Pubitemid 41267070)
26. Daily MD, Phillips GJ, Cui Q (2010) Many local motions cooperate to produce the adenylate kinase conformational transition. J Mol Biol 400:618-631.
27. Lu Q, Wang J (2008) Single molecule conformational dynamics of adenylate kinase: Energy landscape, structural correlations, and transition state ensembles. J Am Chem Soc 130:4772-4783. (Pubitemid 351500112)
28. Lu Q, Wang J (2009) Kinetics and statistical distributions of single-molecule conformational dynamics. J Phys Chem B 113:1517-1521.
29. 1-ATPase from bovine heart mitochondria. Nature 370:621-628.
30. Okazaki K, Koga N, Takada S, Onuchic JN, Wolynes PG (2006) Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. Proc Natl Acad Sci USA 103:11844-11849. (Pubitemid 44215774)
31. Whitford PC, Miyashita O, Levy Y, Onuchic JN (2007) Conformational transitions of adenylate kinase: Switching by cracking. J Mol Biol 366:1661-1671. (Pubitemid 46215597)
32. Zhuravlev PI, Papoian GA (2010) Functional versus folding landscapes: The same yet different. Curr Opin Struct Biol 20:16-22.
33. Chu JW, Ayton GS, Izvekov S, Voth GA (2007) Emerging methods for multiscale simulation of biomolecular systems. Mol Phys 105:167-175. (Pubitemid 46447511)
34. Li W, Yoshii H, Hori N, Kameda T, Takada S (2010) Multiscale methods for protein folding simulations. Methods 52:106-114.
35. Li W, Takada S (2010) Characterizing protein energy landscape by self-learning multiscale simulations: Application to a designed β-hairpin. Biophys J 99:3029-3037.
36. Tama F, Sanejouand YH (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng 14:1-6. (Pubitemid 32318932)
37. Torrie GM, Valleau JP (1974) Monte-Carlo free-energy estimates using non-Boltzmann sampling - application to subcritical Lennard-Jones fluid. Chem Phys Lett 28:578-581.
38. Gohlke H, Kiel C, Case D (2003) Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RaIGDS complexes. J Mol Biol 330:891-913.
39. Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and largescale conformational changes with a modified generalized born model. Proteins 55:383-394. (Pubitemid 38437495)