Kinetics of protein folding: A lattice model study of the requirements for folding to the native state

Journal of Molecular Biology

Volumn 235, Issue 5, 1994, Pages 1614-1636

  Šali, Andrej ^a   Shakhnovich, Eugene ^a   Karplus, Martin ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Lattice Monte Carlo simulation; Optimization; Protein folding

Indexed keywords

ARTICLE; CHEMICAL REACTION KINETICS; COMPUTER SIMULATION; PRIORITY JOURNAL; PROTEIN FOLDING;

EID: 0028270634     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1994.1110     Document Type: Article

References (54)

1. Anfinsen, C. B. (1973). Principles that govern the folding of protein chains. Science, 181, 223-230.
2. Braun, W. & Go, N. (1985), Calculation of protein conformations by proton-proton distance constraints: a new efficient algorithm. J. Mol. Biol. 186, 611-626.
3. Brooks, C. L., III., Karplus, M. & Pettit, B. M. (1988). Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics. John Wiley & Sons, New York.
4. Brunger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic fi-factor refinement by molecular dynamics. Science, 235, 458-460.
5. Bryngelson, J. D. & Wolynes, P. G. (1987). Spin glasses and the statistical mechanics of protein folding. Proc. Nat. Acad. Sci., U.S.A. 84, 7524-7528.
6. Bryngelson, J. D. & Wolynes, P. G. (1989). Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Pkys. Chem. 93, 6902-6915.
7. Chan, H. S. & Dill, K. A. (1990), The effects of internal constraints on the configurations of chain molecules. J. Chem. Phys. 92, 3118-3135.
8. Chan, H. S. & Dill, K, A. (1991). Polymer principles in protein structure and stability. Anna. Rev. Biophys. Biophys. Chem. 20, 447-490
9. Clore, G. M., Briinger, A. T., Karplus, M. & Gronenborn, A. M. (1986). Application of molecular dynamics with interproton distance restraints to 3D protein structure determination. J. Mol. Biol. 191, 523-551.
10. Derrida, B. (1981). Random-energy model: an exactly solvable model of disordered systems. Phys. Rev. 24, 2613-2624.
11. Elove, G. A., Chaffotte, A. F., Roder, H. & Goldberg, M. E. (1992). Early steps in eytochyme c folding probed by time-resolved circular dichroism and fluorsencce spectroscopy. Biochemistry. 31, 6876-6883.
12. Frauenfelder, H., Sligar, S. G. & Wolynes, P. G. (1991). The energy landscapes and motions of proteins, Science, 254, 1598-1603.
13. Go, N. & Abe, H. (1981). Noninteracting local-structure model of folding and unfolding transition in globular proteins. II. Application to tw'o-dimensional lattice proteins. Biopolymers, 20, 1013-1031.
14. Goldstein, R. A., Luthey-Schulten, Z. A. & Wolynes, P. G. (1992). Optimal protein-folding codes from spin-glass theory. Proc. Nat. Acad. Sci., U.S.A. 89, 4918-4922.
15. Gutin, A. M., Badretdinov, A. Y. & Finkelstein, A. V. (1992). Why are the statistics of globular protein structures Boltzmann-like? Mol. Biol. (USSR), 26, 94-102.
16. Head-Gordon, T. & Stillinger, F. H. (1993). Predicting polypeptide and protein structures from amino acid sequence: anti ion method applied to melittin. Biopolymers, 33, 293- 303.
17. Hilhorst, H. J. & Deutch, J. M. (1975). Analysis of Monte Carlo results on the kinetics of lattice polymer chains w'ith excluded volume. J. Chem. Phys. 63. 5153-5161.
18. Honeycutt, J. D. & Thirumalai, D. (1992). The nature of folded states of globular proteins. Biopolymers, 32. 695-709.
19. Karplus, M. & Shakhnovich, E. (1992). Protein folding: theoretical studies of thermodynamics and dynamics. In Protein Folding (Creighton. T. K., ed.). pp. 127-196, W. H. Freeman and Company, New York.
20. Karplus, M. & Weaver, D. L. (1976). Protein-folding dynamics. Nature (London), 260, 404-406.
21. Karplus, M. & Weaver, D. L. (1979). Diffusion-collision model for protein folding. Biopolymers, 18. 1421-1437.
22. Kim, P. & Baldwin, R. (1982). Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu. Rev. Biockem. 51, 459-489.
23. Kim, P. & Baldwin, R. (1990). Intermediates in the folding reactions of small proteins. Annu. Rev. Biochem. 59, 631-660.
24. Leopold, P. E., Montal, M. & Onuchic, J. N. (1992). Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc. Nat. Acad. Sci., U.S.A. 89, 8721-8725.
25. Levinthal, C. (1968). Are there pathways for protein folding? J. Chim. Phys. 65, 44-45
26. Levinthal, C. (1969). In Mossbauer Spectroscopy in Biological Systems, Proceedings of a Meeting held at Allerton House, Monticello, JL (Debrunner, P., Tsibris, J. C. M. & Miinck, E., eds), pp. 22-24, University of Illinois Press, Urbana, TL.
27. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953). Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087-1092.
28. Miller, R., Danko, C. A., Fasolka, M. J., Balazs, A. C., Chan, H. S. & Dill, K. A. (1992). Folding kinetics of proteins and copolymers. J. Chem. Pkys. 96, 768-780.
29. Miyazawa, S. & Jernigan, R. L. (1985). Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules, 18, 534-552.
30. O’Toole, E. M. & Panagiotopoulos, A. Z. (1992). Monte Carlo simulation of folding transitions of simple model proteins using a chain grow'th algorithm. J. Chem. Phys. 97, 8644-8652.
31. Piela, L., Kostrowicki, J. & Scheraga, H. A. (1989). The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method. J. Phys. Chem. 93, 3339-3346.
32. Ponder, J. W. & Richards, F. M. (1987). Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193, 775-791.
33. Privalov, P. L. (1989). Thermodynamic problems of protein structure. Annu. Rev. Biophys. Biophys. Chem. 18, 47-69.
34. Privalov, P. L. & Khechinashvili, N. N. (1974). A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study. J. Mol. Biol. 86, 665-684.
35. Ptitsyn, O. B. (1987). Protein folding: hypotheses and experiments. J. Protein Chem. 6, 273-293.
36. Ptitsyn, O. B. & Volkenstein, M. V. (1986). Protein structures and neutral theory of evolution., J. Biomol. Struct. Dynam. 4, 137-156.
37. Roder, H, & Elove, G. A. (1993). Early stages of protein folding. In Issues in Protein Folding. Frontiers in Molecular Biology (Pain, R. H., ed.), Academic Press, New' York. In the press.
38. Rooman, M. J. & Wodak, S. J. (1992). Extracting information on folding from the amino acid sequence: consensus regions with preferred conformation in homologous proteins. Biochemistry, 31, 10239-10249.
39. Rooman, M. J., Kocher, J.-P. A. & Wodak, S. J. (1992). Extracting information on folding from the amino acid sequence: accurate predictions for protein regions w'ith preferred conformation in the absence of tertiary interactions. Biochemistry, 31, 10226-10238.
40. Sali, A. & Blundell, T, L. (1993). Comparative protein modelling by satisfaction of spatial restraints.J. Mol. Biol. 234. 779-815.
41. Sali, A. (1991). Modelling three-dimensional structure of proteins from their sequence of amino acid residues. Ph.D. thesis. University of Uondon. London.
42. Seheraga, H. A. (1989). Calculations of stable conformations of polypeptides, proteins, and protein complexes. Chemica Scripta, 29A. 3-Li.
43. Shakhnovich, E. I. & Finkelstein, A. V. (1989). Theory of cooperative transitions in protein molecules. T. Why denaturation of globular protein is a first-order phase transition. Biopolymers, 28, 1667-1680.
44. Shakhnovich, E. I. & Gutin, A. M. (1989). Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach. Biophys. Cham. 34, 187-199.
45. Shakhnovich, E. I. & Gutin, A. M. (1990a). Implications of thermodynamics of protein folding for evolution of primary sequences. Nature (London), 346, 773-775.
46. Shakhnovich, E. I. & Gutin, A. M. (1990ft). Enumeration of all compact conformations of copolymers with random sequence of links. J. Chem. Rhys. 93, 5967-5971.
47. Shakhnovich, E. I. & Gutin, A. M. (1993). A new approach to the design of stable proteins. Protein Eng. In the press.
48. Shakhnovich, E. I. & Gutin, A. M, (1993ft). Engineering of stable and fast-folding sequences of model proteins. Proc. Nat. Acad. Sci., U.S.A. 90, 7195-7199.
49. Shakhnovich, E., Farztdinov, G., Gutin, A. M. & Karplus, M. (1991). Protein folding bottlenecks: a lattice Monte Carlo simulation. Phys. Rev. Letters, 67, 1665-1668.
50. Skolnick, J. & Kolinski, A. (1990). Simulations of the folding of a globular protein. Science, 250. 1121-1125.
51. Skolnick, J. & Kolinski, A. (1991). Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. J. Mol. Biol. 221. 499-531.
52. Wetlaufer, D. B, (1973). Xu cleat ion, rapid folding, and globular intrachain regions in proteins. Proc. Nat. Acad. Sci., U.S.A. 70, 697-701.
53. Wetlaufer, D. B. & Ristow, S. (1973). Acquisition of th ree-dimensional structure of proteins. Anna. Rev. Bloc, hem. 42, 135-158.
54. Zwanzig, R., Szabo, A. & Bagehi, B. (1992). Levinthal’s paradox. Proc. Nat. Acad. Sci., U.S.A. 89, 20-22.