Side-chain dynamics and protein folding

Proteins: Structure, Function and Genetics

Volumn 52, Issue 2, 2003, Pages 303-321

  Kussell, Edo ^a   Shimada, Jun ^a   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Glass transition; Nucleation mechanism; Protein folding; Side chain dynamics; Side chain packing

Indexed keywords

ARTICLE; EQUILIBRIUM CONSTANT; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SIMULATION;

AMINO ACIDS; BACTERIAL PROTEINS; COMPUTER SIMULATION; KINETICS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 0037999104     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10426     Document Type: Article

References (43)

1. Shimada J, Kussell E, Shakhnovich EI. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J Mol Biol 2001;308:79-95.
2. Richards FM, Lim WA. An analysis of packing in the protein folding problem. Quat Rev Biophys 1994;26:423-498.
3. Heringa J, Argos P. Strain in protein structures as viewed through nonrotameric side chains. I. Their position and interaction. Proteins 1999;37:30-43.
4. Levitt M, Gerstein M, Huang E, Subbiah S, Tsai J. Protein folding: the endgame. Annu Rev Biochem 1997;66:549-579.
5. Dunbrack RL, Karplus M. Conformational-analysis of the backbone-dependent rotamer preferences of protein side-chains. Nat Struct Biol 1994;1:334-340.
6. Fersht A. Structure and Mechanism in Protein Science. New York: WH Freeman and Company; 1999.
7. Shakhnovich EI, Finkelstein AV. Theory of cooperative transitions in protein molecules. I. Why denaturation of globular proteins is a first-order phase transition. Biopolymers 1989;28:1667-1680.
8. Sali A, Shakhnovich EI, Karplus M. How does a protein fold? Nature 1994;369:248-251.
9. Brooks CL, Karplus M, Pettitt BM. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. New York: John Wiley & Sons; 1998.
10. Kussell E, Shimada J, Shakhnovich EI. Excluded volume in protein side-chain packing. J Mol Biol 2001;311:183-193.
11. Bromberg S, Dill KA. Side-chain entropy and packing in proteins. Protein Sci 1994;3:997-1009.
12. Klimov DK, Thirumalai D. Cooperativity in protein folding, from lattice models with sidechains to real proteins. Fold Design 1998;3:127-139.
13. Li L, Mirny LA, Shakhnovich EI. Kinetics, thermodynamics, and evolution of non-native interactions in protein folding nucleus. Nat Struct Biol 2000;7:336-342.
14. Garel T, Orland H, Orlandini E. Phase diagram of magnetic polymers. Eur Phys J B 1999;12:261-268.
15. Muñoz V, Eaton WA. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc Natl Acad Sci USA 1999;96:11311-11316.
16. Morrissey M, Shakhnovich EI. Design of proteins with selected thermal properties. Fold Design 1996;1:391-406.
17. Mirny LA, Abkevich V, Shakhnovich EI. How evolution makes proteins fold quickly. Proc Natl Acad Sci USA 1998;95:4976-4981.
18. Miyazawa S, Jernigan R. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985;18:534-552.
19. Sali A, Shakhnovich EI, Karplus M. Kinetics of protein folding. A lattice model study for the requirements for folding to the native state. J Mol Biol 1994;235:1614-1636.
20. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of state calculations by fast computing machines. J Chem Phys 1953;21:1087-1092.
21. Press WH, Teukolsky SA, Vetterling WT, Flannery BP. Numerical Recipes in C. New York: Cambridge University Press; 1996.
22. Ptitsyn O. Molten globule and protein folding. Adv Protein Chem 1995;47:83-229.
23. Abkevich VI, Gutin AM, Shakhnovich EI. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 1994;33:10026-10036.
24. Shakhnovich E, Abkevich V, Ptitsyn O. Conserved residues and the mechanism of protein folding. Nature 1996;379:96-98.
25. Jackson SE. How do small single-domain proteins fold? Fold Design 1998;3:R81-R91.
26. McCallister EL, Alm E, Baker D. Critical role of beta-hairpin formation in Protein G folding. Nat Struct Biol 2000;7:669-673.
27. Nauli S, Kuhlman B, Baker D. Computer-based redesign of a protein folding pathway. Nat Struct Biol 2001;8:602-605.
28. Park S, Shastry MCR, Roder H. Folding dynamics of the B1 domain of Protein G explored by ultrarapid mixing. Nat Struct Biol 1999;6:943-947.
29. Shimada J, Shakhnovich EI. The ensemble folding kinetics of protein G from an all-atom monte carlo simulation. Proc Natl Acad Sci USA 2002;99:1175-1180.
30. Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich EI. On the transition coordinate for protein folding. J Chem Phys 1998;108:334-350.
31. Fersht AR. Optimization of rates of protein-folding - the nucleation-condensation mechanism and its implications. Proc Natl Acad Sci USA 1995;92:10869-10873.
32. Englander SW. Protein folding intermediates and pathways studied by the hydrogen exchange. Annu Rev Biophys Biomol Struct 2000;29:213-238.
33. Staniforth RA, Dean JLE, Zhong Q, Zerovnik E, Clarke AR, Waltho JP. The major transition state in folding need not involve the immobilization of side chains. Proc Natl Acad Sci USA 2000;97:5790-5795.
34. Ha J, Loh SN. Changes in side chain packing during apomyoglobin folding characterized by pulsed thiol-disulfide exchange. Nat Struct Biol 1998;5:730-737.
35. Northey JGB, Di Nardo AA, Davidson AR. Hydrophobic core packing in the SH3 domain folding transition state, Nat Struct Biol 2002;9:126-130.
36. Sridevi K, Juneja J, Bhuyan AK, Krishnamoorthy G, Udgaonkar JB. The slow folding reaction of barstar: the core tryptophan region attains tight packing before substantial secondary and tertiary structure formation and final compaction of the polypeptide chain. J Mol Biol 2000;302:479-495.
37. Kob W, Andersen HC. Kinetic lattice-gas model of cage effects in high-density liquids and a test of mode-coupling theory of the ideal-glass transition. Phys Rev E 1993;48:4364-4377.
38. Kurchan J, Peliti L, Sellitto M. Aging in lattice-gas models with constrained dynamics. Europhys Lett 1997;39:365-370.
39. Barrat A, Kurchan J, Loreto V, Sellitto M. Edwards' measures: a thermodynamic construction for dense granular media and glasses. Phys Rev E 2001;63:051301.
40. Biroli G, Mezard M. Lattice glass models. Phys Rev Lett 2002;88:025501.
41. De Dominicis C, Orland H, Lainee F. Stretched exponential relaxation in systems with random free energies. J Physique Lett 1985;46:463-466.
42. Koper GJ, Hilhorst HJ. Power law relaxation in the random energy model. Europhys Lett 1987;3:1213-1217.
43. Shakhnovich EI, Gutin AM. Relaxation to equilibrium in the random energy model. Europhys Lett 1989;9:569-574.