On the origin of the cooperativity of protein folding: Implications from model simulations

Proteins: Structure, Function and Genetics

Volumn 26, Issue 3, 1996, Pages 271-287

  Kolinski, Andrzej ^a,b   Galazka, Wojciech ^b   Skolnick, Jeffrey ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONFORMATIONAL TRANSITION; MODEL; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

AMINO ACIDS; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; THERMODYNAMICS;

EID: 0029809182     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199611)26:3<271::AID-PROT4>3.0.CO;2-H     Document Type: Article

References (39)

1. Anfinsen, C.B., Scheraga, H.A. Experimental and theoretical aspects of protein folding. Adv. Protein Chem. 29:205-300, 1975.
2. Ptitsyn, O.B. Protein folding: Hypotheses and experiments. J. Protein Chem. 6:273-293, 1987.
3. Grosberg, A.Y., Khokhlov, A.R. Physics of phase transition in solutions of macro molecules. Sov. Sci. Rev. A 8:147-252, 1987.
4. Shakhnovich, E.I., Finkelstein, A.V. Theory of cooperative transitions in protein molecules. I. Why denaturation of a globular protein is a first-order phase transition. Biopolymers 28:1667-1680, 1989.
5. Karplus, M., Sali, A. Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5:58-73, 1995.
6. 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. Protein Sci. 4:561-602, 1995.
7. Frauenfelder, H., Wolynes, P.G. Biomolecules: Where the physics of complexity and simplicity meet. Phys. Today 47:58-64, 1994.
8. 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.
9. Shakhnovich, E.I., Gutin, A.M. Engineering of stable and fast-folding sequences of model proteins. Proc. Natl. Acad. Sci. USA 90:7195-7199, 1993.
10. Sali, A., Shakhnovich, E.I., Karplus, M. Kinetics of protein folding. A lattice model study of requirements for folding of the native state. J. Mol. Biol. 235:1614-1636, 1994.
11. Kolinski, A., Godrik, 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. 98:7420-7433, 1993.
12. Kolinski, A., Skolnick, J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18:338-352, 1994.
13. Kolinski, A., Skolnick, J. Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin. Proteins 18:353-366, 1994.
14. Vieth, M., Kolinski, A., Brooks III, C., Skolnick, J. Prediction of the folding pathways and structure of the GCN4 leucine zipper. J. Mol. Biol. 237:361-367, 1994.
15. Kuwajima, K. The molten globule state as a clue for understanding the folding and cooperativity of globular protein structure. Proteins 6:87-103, 1989.
16. Ptitsyn, O.B., Pain, R.H., Semisotnov, G.V., Zerovnik, E., Razgulyaev, O.I. Evidence for a molten globule state as a general intermediate in protein folding. FEBS Lett. 262: 20-24, 1990.
17. Godzik, A., Kolinski, A., Skolnick, J. Lattice representation of globular proteins: How good are they? J. Comp. Chem. 14:1194-1202, 1993.
18. Skolnick, J., Kolinski, A., Ortiz, A.R. MONSSTER: A method for folding globular proteins with a small number of distance restraints. J. Mol. Biol., in press.
19. Hao, M.-H., Scheraga, H.A. Monte Carlo simulations of a first-order transition for protein folding. J. Phys. Chem. 98:4940-4948, 1994.
20. Hao, M.-H., Scheraga, H.A. Statistical thermodynamics of protein folding: Sequence dependence. J. Phys. Chem. 98: 9882-9893, 1994.
21. Berg, B. A., Neuhaus, T. Multicanonical ensemble: A new approach to simulate first-order phase transitions. Phys. Rev. Lett. 68:9-12, 1991.
22. Hansmann, U.H.E., Okamoto, Y. Prediction of peptide conformation by a multicanonical algorithm: New approach to the multiple minima problem. J. Comput. Chem. 14:1333-1338, 1993.
23. Kolinski, A., Galazka, W., Skolnick, J. Computer design of idealized β-motifs. J. Chem. Phys. 103: 10286-10296, 1995.
24. Kolinski, A., Milik, M., Rycombel, J., Skolnick, J. A reduced model of short-range interactions in polypeptide chains. J. Chem. Phys. 103:4312-4323, 1995.
25. Milik, M., Kolinski, A., Skolnick, J. An algorithm for rapid reconstruction of a protein backbone from alpha carbon coordinates. J. Comput. Chem. In press, 1996.
26. Kolinski, A., Skolnick, J. Parameters of statistical potentials. Available by ftp from public directory, scripps.edu (pub/andr/MCSP)
27. Kabseh, W., Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
28. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer Jr., E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Simanouchi, T., Tasumi, M. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
29. PDB, Quarterly Newsletter, No. 71, January 1995.
30. Handel, T., DeGrado, W.F. A designed 4-helical bundle shows characteristics of both molten globule and native state. Biophys. J. 61:A265, 1992.
31. Raleigh, D.P., DeGrado, W.F. A de novo designed protein shows a thermally induced transition from a native to a molten globule like state. J. Am. Chem. Soc. 114:10079-10081, 1992.
32. Betz, S.F., Bryson, J.W., DeGrado, W.F. Nativelike and structurally characterized designed α-helical bundles. Curr. Biol. 5:457-463, 1995.
33. Lee, J. New Monte Carlo algorithm: Entropic sampling. Phys. Rev. Lett. 71:211-214, 1993.
34. Elofsson, A., Nilsson, L. How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin, J. Mol. Biol. 223:766-780, 1993.
35. DeBolt, S., Skolnick, J. Protein Eng. 9:637-655, 1996.
36. Zimm, B.H., Bragg, J.K. Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 31:526-535, 1959.
37. Mattice, W.L. Annu. Rev. Biophys. Biophys. Chem. 18:93, 1989.
38. Milik, M., Kolinski, A., Skolnick, J. Neural network system for the evaluation of side chain packing in protein structures. Protein Eng. 8:225-236, 1995.
39. Ponder, J.W., Richards, F.M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193:775-791, 1987.