Factors governing the foldability of proteins

Proteins: Structure, Function and Genetics

Volumn 26, Issue 4, 1996, Pages 411-441

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

^a University of Maryland   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

Author keywords

kinetic accessibility and stability; kinetic partitioning mechanism; lattice Monte Carlo simulations; native conformation nucleation collapse; protein folding

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; SEQUENCE HOMOLOGY; SIMULATION; SYSTEM ANALYSIS; THERMODYNAMICS;

KINETICS; MODELS, CHEMICAL; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEIN FOLDING; THERMODYNAMICS;

EID: 0030443105     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199612)26:4<411::AID-PROT4>3.0.CO;2-E     Document Type: Article

References (56)

1. Bryngelson, J.D., Onuchic, J.N., Socci, N.D., Wolynes,P.G. Funnels, pathways and the energy landscape of protein folding: A synthesis. Proteins 21:167-195, 1995.
2. Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., Yee, D.P., Thomas, P.D., Chan, H.S. Principles of protein folding: A perspective from simple exact models. Prot. Sci. 4:561-602, 1995.
3. Hinds, D.A., Levitt, M.A. Exploring conformational space with a simple lattice model for protein structure. J. Mol. Biol. 243:668-682, 1994.
4. Karplus, M., Shakhnovich, E. Protein folding: Theoretical studies of thermodynamics and dynamics. In: "Protein Folding." Creighton, T.E. (ed.). New York: W.H. Freeman, 1992:127-196.
5. Thirumalai, D. Theoretical perspectives on in vitro and in vivo protein folding. In: "Statistical Mechanics, Protein Structure, and Protein Substrate Interactions." Doniach, S. (ed.), New York: Plenum Press, 1994:115-133.
6. Wolynes, P.G., Onuchic, J.N., Thirumalai, D. Navigating the folding routes. Science 267:1619-1620, 1995.
7. Baldwin, R.L. The nature of protein folding pathways: The classical versus the new view. J. Biomol. NMR 5:103-109, 1995.
8. Radford, S.E., Dobson, C.M. Insights into protein folding using physical techniques: Studies of lysozyme and alpha-lactalbumin. Phil. Trans. R. Soc. Lond. B 348:17-25, 1995.
9. Levinthal, C. In: "Mossbauer Spectroscopy in Biological Systems." Debrunner, P., Tsibris, J.C.M., Münck, E. (eds.). Urbana: University of Illinois Press, 1969:22-24.
10. Amara, P., Straub, J.E. Folding model proteins using kinetic and thermodynamic annealing of the classical density distribution. J. Phys. Chem. 99:14840-14853, 1995.
11. Bryngelson, J.D., Wolynes, P.G. Intermediates and barrier crossing in a random energy model (with application to protein folding). J. Phys. Chem. 93:6902-6915, 1989.
12. Chan, H.S., Dill, K.A. Energy landscapes and the collapse dynamics of homopolymers. J. Chem. Phys. 99:2116-2127, 1993.
13. Chan, H.S., Dill, K.A. Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100:9238-9257, 1994.
14. Covell, D.G., Jernigan, R.L. Conformations of folded proteins in restricted spans. Biochemistry 29:3287-3294, 1990.
15. Hinds, D.A., Levitt, M.A. A lattice model for protein structure prediction at low resolution. Proc. Natl. Acad. Sci. USA 89:2536-2540, 1992.
16. Honeycutt, J.D., Thirumalai, D. Metastability of the folded states of globular proteins. Proc. Natl. Acad. Sci. USA 87:3526-3529, 1990.
17. Guo, Z., Thirumalai, D., Honeycutt, J.D. Folding kinetics of proteins: A model study. J. Chem. Phys. 97:525-535, 1992.
18. Garel, T.R., Orland, H. Mean field model for protein folding. Europhys. Lett. 6:307-310, 1988.
19. Leopold, P.E., Montai, M., Onuchic, J.N. Protein folding funnels: A kinetic approach to the sequence-structure relationship. Proc. Natl. Acad. Sci. USA 89:8721-8725, 1992.
20. Sali, A., Shakhnovich, E., Karplus, M. How does a protein fold. Nature 369:248-251, 1994.
21. Sali, A., Shakhnovich, E., Karplus, M. Kinetics of protein folding: A lattice model study of the requirements for folding to the native state. J. Mol. Biol. 235:1614-1636, 1994.
22. Shakhnovich, E., Gutin, A.M. Formation of unique structure in polypeptide chains: Theoretical investigation with the aid of a replica approach. Biophys. Chem. 34:187-199, 1989.
23. Shakhnovich, E., Farztdinov, G., Gutin, A.M., Karplus, M. Protein folding bottlenecks: A lattice Monte Carlo simulation. Phys. Rev. Lett. 67:1665-1668, 1991.
24. Skolnick, J., Kolinski, A. Simulation of the folding of a globular protein. Science 250:1121-1125, 1990.
25. Skolnick, J., Kolinski, A. Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure, and dynamics. J. Mol. Biol. 221:499-531, 1991.
26. Zwanzig, R. Simple model of protein folding kinetics. Proc. Natl. Acad. Sci. 92:9801-9804, 1995.
27. Zwanzig, R., Szabo, A., Bagchi, B. Levinthal's paradox. Proc. Natl. Acad. Sci. USA 89:20-22, 1992.
28. Camacho, C.J., Thirumalai, D. Modeling the role of disulfide bonds in protein folding: Entropic barriers and pathways. Proteins 22:27-40, 1995.
29. Chan, H.S. Kinetics of protein folding. Nature 373:664-665, 1995.
30. Derrida, B. Random-energy model: Limit of a family of disordered models. Phys. Rev. Lett. 45:79-82, 1980.
31. Goldstein, R.A., Luthey-Schulten, Z.A., Wolynes, P.G. Optimal protein-folding codes from spin-glass theory. Proc. Natl. Acad. Sci. USA 89:4918-4922, 1992.
32. Socci, N.D., Onuchic, J.N. Folding kinetics of protein-like heteropolymers. J. Chem. Phys. 101:1519-1528, 1994.
33. Camacho, C.J., Thirumalai, D. Kinetics and thermodynamics of folding in model proteins. Proc. Natl. Acad. Sci. USA 90:6369-6372, 1993.
34. Thirumalai, D. From minimal models to real proteins: Time scales for protein folding kinetics. J. Phys. (Paris) I 5:1457-1467, 1995.
35. Shakhnovich, E. Gutin, A.M. Enumeration of all compact conformations of copolymers with random sequence of links. J. Chem. Phys. 93:5967-5971, 1990.
36. White, S.H., Jacobs, R.E. The evolution of proteins from random amino acid sequences. I. Evidence from the length-wise distribution of amino acids in modern protein sequences. J. Mol. Evol. 36:79-95, 1993.
37. Garel, T.R., Leibler, L., Orland, H. Random hydrophilic-hydrophobic copolymers. J. Physique (Paris) II 4:2139-2148, 1994.
38. Miller, R., Danko, C.A., Fasolka, M.J., Balazs, A.C., Chan, H.S., Dill, K.A. Folding kinetics of proteins and copolymers. J. Chem. Phys. 96:768-780, 1992.
39. Binder, K.A. Theory and technical aspects of Monte Carlo simulations. In: "Monte Carlo Methods in Statistical Physics." Binder, K.A. (ed.). Berlin: Springer-Verlag, 1986:26-30.
40. Chan, H.S., Dill, K.A. The effects of internal constraints on the configurations of chain molecules. J. Chem. Phys. 92:3118-3135, 1990.
41. Karplus, M., Sali, A. Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5:58-73, 1995.
42. Honeycutt, J.D., Thirumalai, D. The nature of folded states of globular proteins. Biopolymers 32:695-709, 1992.
43. Guo, Z., Thirumalai, D. Kinetics of protein folding: Nucleation mechanism, time scales, and pathways. Biopolymers 36:83-103, 1995.
44. Martin, J.L. Computer enumerations. In: "Phase Transitions and Critical Phenomena." Domb, C., Green, M.S. (eds.). New York: Academic Press, 1974:102.
45. Shakhnovich, E., Gutin, A.M. A new approach to the design of stable proteins. Protein Eng. 6:793-800, 1993.
46. Shakhnovich, E. Proteins with selected sequences fold into unique native conformation. Phys. Rev. Lett. 72:3907-3910, 1994.
47. Mountain, R.D., Thirumalai, D. Quantitative measure of efficiency of Monte Carlo simulations. Physica A 210:453-460, 1994.
48. Karplus, M., Sali, A., Shakhnovich, E. Kinetics of protein folding. Nature 373:665, 1995.
49. Thirumalai, D., Guo, Z. Nucleation mechanism for protein folding and theoretical predictions for hydrogen-exchange labeling experiments. Biopolymers 35:137-140, 1995.
50. Abkevich, V.I., Gutin, A.M., Shakhnovich, E. Specific nucleus as the transition state for protein folding: Evidence from the lattice model. Biochemistry 33:10026-10036, 1994.
51. Abkevich, V.I., Gutin, A.M., Shakhnovich, E. Free energy landscape of protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101:6052-6062, 1994.
52. Otzen, D.E., Itzhaki, L.S., Fersht, A.R. Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. Proc. Natl. Acad. Sci. 91:10422-10425, 1994.
53. Betancourt, M.R., Onuchic, J.N. Kinetics of protein-like models: The energy landscape factors that determine folding. J. Chem. Phys. 103:773-787, 1995.
54. Socci, N.D., Onuchic, J.N. Kinetic and thermodynamic analysis of protein-like heteropolymers: Monte Carlo histogram technique. J. Chem. Phys. 103:4732-4744, 1995.
55. Bai, Y., Sosnick, T.R., Mayne, L., Englander, S.W. Protein folding intermediates: Native-state hydrogen exchange. Science 269:192-197, 1995.
56. Fersht, A.R. Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications. Proc. Natl. Acad. Sci. USA 92:10869-10873, 1995.