Multiple protein folding nuclei and the transition state ensemble in two-state proteins

Proteins: Structure, Function and Genetics

Volumn 43, Issue 4, 2001, Pages 465-475

  Klimov, D K ^a,b   Thirumalai, D ^a,b  

^a Bldg 142   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

Author keywords

Cooperativity; Lattice protein models; Non native interactions; Nucleation collapse mechanism; Protein folding kinetics and thermodynamics

Indexed keywords

PROTEIN;

ARTICLE; MOLECULAR INTERACTION; MOLECULAR MODEL; PHASE TRANSITION; PHYSICAL PHASE; PRIORITY JOURNAL; PROBABILITY; PROTEIN DOMAIN; PROTEIN FOLDING; REACTION ANALYSIS; SIMULATION; STRUCTURE ACTIVITY RELATION; SURFACE CHARGE;

ALGORITHMS; AMINO ACID SEQUENCE; CLUSTER ANALYSIS; COMPUTER SIMULATION; KINETICS; MODELS, MOLECULAR; MONTE CARLO METHOD; PEPTIDES; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 0035370662     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.1058     Document Type: Article

References (33)

1. Dill KA, Chan HS. From Levinthal to pathways to funnels. Nature Struct Biol 1997;4:10-19.
2. Onuchic JN, Luthey-Schulten ZA, Wolynes PG. Theory of protein folding: an energy landscape perspective. Annu Rev Phys Chem 1997;48:545-600.
3. Thirumalai D, Klimov DK. Deciphering the time scales and mechanisms of protein folding using minimal off-lattice models. Curr Opin Struct Biol 1999;9:197-207.
4. Fersht A. Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding. New York: WH Freeman; 1999.
5. Wolynes PG. Folding funnels and energy landscapes of larger proteins within the capillarity approximation. Proc Natl Acad Sci USA 1997;94:6170-6175.
6. Guo Z, Thirumalai D. Kinetics of protein folding: nucleation mechanism, time scales, and pathways. Biopolymers 1995;36:83-103.
7. Guo Z, Thirumalai D. The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus. Folding Design 1997;2:377-391.
8. Bryngelson JD, Wolynes PG. A simple statistical field theory of heteropolymer collapse with application to protein folding. Biopolymers 1990;30:177-188.
9. Fersht AR. Nucleation mechanism of protein folding. Curr Opin Struct Biol 1997;7:10-14.
10. Shakhnovich E, Abkevich VI, Ptitsyn O. Conserved residues and the mechanisms of protein folding. Nature 1996;379:96-98.
11. Klimov DK, Thirumalai D. Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J Mol Biol 1998;282:471-492.
12. Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG. Protein folding funnels: the nature of the transition state ensemble. Folding Design 1996;1:441-450.
13. Li L, Mirny LA, Shakhnovich EI. Kinetics, thermodynamics and evolution of non-native interactions in protein folding nucleus. Nature Struct Biol 2000;7:336-342.
14. Go N. Theoretical studies of protein folding. Annu Rev Biophys Bioeng 1983;12:183-210.
15. Clementi C, Jennings PA, Onuchic JN. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1. Proc Natl Acad Sci USA 2000;97:5871-5876.
16. Klimov DK, Thirumalai D. Cooperativity in protein folding: from lattice models with side chains to real proteins. Folding Design 1998;3:127-139.
17. Kolinski A, Godzik A, Skolnick J. A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: application to designed helical proteins. J Chem Phys 1993;98:7420-7433.
18. Ferrenberg AM, Swendsen RH. Optimized Monte Carlo data analysis. Phys Rev Lett 1989;63:1195-1198.
19. Shea JE, Nochomovitz YD, Guo ZY, Brooks CL III. Exploring the space of protein folding hamiltonians: the balance of forces in a minimalist β-barrel model. J Chem Phys 1998;96:12512-12517.
20. Sayle R, Milner-White EJ. RasMol: biomolecular graphics for all. Trends Biochem Sci 1995;20:374.
21. Klimov DK, Thirumalai D. Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics. J Chem Phys 1998;109:4119-4125.
22. Thirumalai D, Klimov DK, Betancourt MR. Exploring the folding mechanisms of proteins using lattice models. In: Grassberger P, Barkema GT, Nadler W, editors. Monte Carlo approach to biopolymers and protein folding. Singapore: World Scientific; 1998. p 19-28.
23. Camacho CJ, Thirumalai D. Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci USA 1993;90:6369-6372.
24. Klimov DK, Thirumalai D. A criterion that determines the foldability of proteins. Phys Rev Lett 1996;76:4070-4073.
25. Bussemaker HJ, Thirumalai D, Bhattacharjee JK. Thermodynamic stability of folded proteins against mutations. Phys Rev Lett 1997;79:3530-3533.
26. Thirumalai D, Klimov DK. Fishing for folding nuclei in lattice models and proteins. Folding Design 1998;3:R112-R118.
27. Grancharova VP, Riddle DS, Santiago JV, Baker D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nature Struct Biol 1998;5:714-720.
28. Socci ND, Onuchic JN, Wolynes PG. Diffusive dynamics of the reaction coordinate for protein folding funnels. J Chem Phys 1996;104:5860-5868.
29. Zwanzig R. Two-state models of protein folding kinetics. Proc Natl Acad Sci USA 1997;94:148-150.
30. Klosek MM, Matkowsky BJ, Schuss Z. The Kramers problem in the turnover regime: the role of the stochastic separatrix. Ber Bunsenges Phys Chem 1991;95:331-337.
31. Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich EI. On the transition coordinate for protein folding. J Chem Phys 1998;108: 334-350.
32. Huo S, Straub JE. The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature. J Chem Phys 1997;107: 5000-5006.
33. Pande VS, Grosberg AY, Tanaka T, Rokhsar DS. Pathways for protein folding: is a new view needed? Curr Opin Struct Biol 1998;8:68-79.