Statistical mechanics of simple models of protein folding and design

Biophysical Journal

Volumn 73, Issue 6, 1997, Pages 3192-3210

  Pande, Vijay S ^a   Grosberg, Alexander Yu ^b,c   Tanaka, Toyoichi ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ENTROPY; MATHEMATICAL MODEL; PROTEIN CONFORMATION; PROTEIN FOLDING; STATISTICAL ANALYSIS; THERMODYNAMICS;

EID: 0030735693     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78345-0     Document Type: Article

References (47)

1. Abkevich, V. I., A. M. Gutin, and E. I. Shakhnovich. 1994. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry. 33:10026-10036.
2. Bryngelson, J. D. 1994. When is a potential accurate enough for structure prediction? Theory and application to a random heteropolymer model of protein folding. J. Chem. Phys. 100:6038-6045.
3. Bryngelson, J. D., and P. G. Wolynes. 1987. Spin glasses and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. USA. 84: 7524-7528.
4. Chan, H. S., and K. A. Dill. 1993. The protein folding problem. Phys. Today. 46:24-31.
5. Derrida, B. 1980. Random-energy model: limit of a family of disordered models. Phys. Rev. Lett. 45:79-82.
6. Derrida, B. 1985. A generalization of the random energy model which includes correlations between energies. J. Phys. Lett. 46:L401-L407.
7. Dinner, A., A. Sali, M. Karplus, and E. Shakhnovich. 1994. Phase diagram of a model protein derived by exhaustive enumeration of the conformations. J. Chem. Phys. 101:1444-1451.
8. Franz, S., M. Mezard, and G. Parisi. 1994. On the mean field theory of random heteropolymers. Int. J. Neural Syst. 3:195-199.
9. Frauenfelder, H., and P. G. Wolynes. 1994. Biomolecules: where the physics of complexity and simplicity meet. Phys. Today, 47:58-64.
10. Garel, T., L. Leibler, and H. Orland. 1994. Random hydrophilic-hydrophobic copolymers. J. Phys. II (France). 4:2139-2148.
11. Garel, T., and H. Orland. 1988a. Chemical sequence and spatial structure in simple models of biopolymers. Europhys. Lett. 6:597-601.
12. Garel, T., and H. Orland. 1988b. Mean-field model for protein folding. Europhys. Lett. 6:307-310.
13. Godzik, A., A. Kolinski, and J. Skolnick. 1995. Lattice representations of globular proteins: how good are they? J. Comput. Chem. 14:1194-1202.
14. Goldenfeld, N. 1992. Lectures on Phase Transitions and the Renormalization group. Addison-Wesley, Reading, MA.
15. Grosberg, A. Yu., and A. R. Khokhlov. 1994. Statistical Physics of Macromolecules. American Institute of Physics, New York.
16. Gutin, A. M., and E. I. Shakhnovich. 1994. Statistical mechanics of polymers with distance constraints. J. Chem. Phys. 100:5290-5293.
17. Hecht, M. H., J. S. Richardson, and D. C. Richardson. 1990. De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science. 249:884-888.
18. Holden, C., editor. 1995. Random samples. Science. 269:1821-1822.
19. Klimov, D. K., and D. Thirumalai. 1996. A criterion that determines the foldability of proteins. Phys. Rev. Lett. 76:4070-4073.
20. Koukiou, F. 1993. Analyticity of the partition function of the random energy model. J. Phys. A. 26:L1207-1210.
21. Li, H., R. Helling, C. Tang, and N. Wingreen. 1996. Why do proteins look like proteins? Emergence of preferred structures in a simple model of protein folding. Science. 273:666-669.
22. Mezard, M., G. Parisi, and M. Virasoro. 1987. Spin Glass Theory and Beyond. World Scientific, Singapore.
23. Miyazawa, S., and R. Jernigan. 1985. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:534-552.
24. Monod, J. 1971. Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology. Knopf, New York.
25. Onuchic, J. N., P. G. Wolynes, Z. Luthey-Schulten, and N. D. Socci. 1995. Toward an outline of the topography of a realistic protein-folding funnel. Proc. Natl. Acad. Sci. USA. 92:3626-3630.
26. Panchenko, A., Z. Luthey-Schulten, and P. G. Wolynes. 1995. Foldons, protein structural modules, and exons. Proc. Natl. Acad. Sci. USA. 93:2008-2013.
27. Pande, V. S., A. Yu. Grosberg, C. Joerg, and T. Tanaka. 1996a. Is heteropolymer freezing well described by a random energy model? Phys. Rev. Lett. 76:3987-3990.
28. Pande, V. S., A. Yu. Grosberg, M. Kardar, C. Joerg, and T. Tanaka. 1996b. Freezing transition of compact polyampholytes. Phys. Rev. Lett. 77: 3565-3568.
29. Pande, V. S., A. Yu. Grosberg, and T. Tanaka. 1994a. Nonrandomness in protein sequences: evidence for a physically driven stage of evolution? Proc. Natl. Acad. Sci. USA. 91:12972-12975.
30. Pande, V. S., A. Yu. Grosberg, and T. Tanaka. 1994b. Thermodynamic procedure to synthesize heteropolymers that can renature to recognize a given target molecule. Proc. Natl. Acad. Sci. USA. 91:12976-12979
31. Pande, V. S., A. Yu. Grosberg, and T. Tanaka. 1995a. Freezing transition of random heteropolymers consisting of an arbitrary set of monomers. Phys. Rev. E. 51:3381-3392.
32. Pande, V. S., A. Yu. Grosberg, and T. Tanaka. 1995b. Phase diagram of heteropolymers with an imprinted conformation. Macromolecules. 28: 2218-2227.
33. Pande, V. S., A. Yu. Grosberg, and T. Tanaka. 1995c. How accurate must potentials be for successful modeling of protein folding? J. Chem. Phys. 103:9482-9491.
34. Pande, V. S., A. Yu. Grosberg, and T. Tanaka. 1997a. On the theory of folding kinetics for short proteins. Folding Design. 2:109-114.
35. Pande, V. S., A. Yu. Grosberg, and T. Tanaka. 1997b. Thermodynamics of the coil to frozen globule transition in heteropolymers. J. Chem. Phys. 107: 5118-5124.
36. Pande, V. S., C. Joerg, A. Yu. Grosberg, and T. Tanaka. 1994c. Enumerations of the Hamiltonian walks on a cubic sublattice. J. Phys. A. 27:6231-6236.
37. Plotkin, S. S., J. Wang, and P. G. Wolynes. 1996. Correlated energy landscape model for finite, random heteropolymers. Phys. Rev. E. 53: 6271-6296.
38. Plotkin, S. S., J. Wang, and P. G. Wolynes. 1997. Statistical mechanics of a correlated energy landscape model for protein folding funnels. J. Chem. Phys. 106:2932-2948.
39. Ptitsyn, O. B., and M. V. Volkenstein. 1986. Protein structures and neutral theory of evolution. J. Biomol. Struct. Dyn. 4:137-156.
40. Ramanathan, S., and E. I. Shakhnovich. 1994. Statistical mechanics of proteins with "evolutionary selected" sequences. Phys. Rev. E. 50: 1303-1312.
41. Sfatos, C., A. Gutin, and E. Shakhnovich. 1993. Phase diagram of random copolymers. Phys. Rev. E. 48:465-475.
42. Shakhnovich, E., and A. Gutin. 1989. Formation of unique structure in polypeptide chains: theoretical investigation with the aid of a replica approach. Biophys. Chem. 34:187-199.
43. Shakhnovich, E., and A. Gutin. 1990. Enumeration of all compact conformations of copolymers with random sequence of links. J. Chem. Phys. 93:5967-5971.
44. Shakhnovich, E. I., and A. M. Gutin. 1993. Engineering of stable and fast-folding sequences of model proteins. Proc. Natl. Acad. Sci. USA. 90:7195-7199.
45. Socci, N. D., and J. N. Onuchic. 1995. Kinetic and thermodynamic analysis of protein-like heteropolymers: Monte Carlo histogram technique. J. Chem. Phys. 103:4732-4741.
46. Volkenstein, M. V. 1994. Physical Approaches to Biological Evolution. Springer Verlag, Berlin and New York.
47. Yue, K., K. M. Fiebig, P. D. Thomas, H. S. Chan, E. I. Shakhnovich, and K. A. Dill. 1995. A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci. USA. 92:325-329.