Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

Protein Science

Volumn 8, Issue 2, 1999, Pages 361-369

  Betancourt, Marcos R ^a   Thirumalai, D ^a,b  

^a UNIVERSITY OF MARYLAND   (United States)

^b University of Maryland   (United States)

Author keywords

Inter residue pair potentials; Native state sensitivity to perturbations; Protein folding; Protein stability; Quasi chemical approximation

Indexed keywords

PROTEIN;

ARTICLE; HYDROPHOBICITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE;

EID: 0033005899     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.2.361     Document Type: Article

References (29)

1. Axilrod RM, Teller E. 1943. Interaction of the van der Waals type between three atoms. J Chem Phys 11:299-300.
2. Bryngelson J. 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. Bussemaker HJ, Thirumalai D, Bhattacharjee JK. 1997. Thermodynamic stability of folded proteins against mutations. Phys Rev Lett 79:3530-3533.
4. Camacho J, Thirumalai D. 1993. Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci USA 90:6369-6372.
5. Chan HS, Dill KA. 1990. On the origins of structure in globular proteins. Proc Natl Acad Sci USA 87:6388-6392.
6. de Gennes PG. 1985. Scaling concepts in polymer physics. Ithaca, NY: Cornell University Press.
7. Du R, Grosberg AY, Tanaka T. 1998. Models of protein interactions: How to choose one. Fold Des 3:203-211.
8. Edwards SF. 1965. Statistical mechanics of polymers with excluded volume. Proc Phys Soc (London) 85:613-624.
9. Fauchere JL, Pliska V. 1983. Hydrophobic parameters π of amino acid side chains from the partitioning of N-acetyl-amino acid amides. Eur J Med Chem 18:639-375.
10. Ferrenberg AM, Swendsen RH. 1989. Optimized Monte Carlo data analysis. Phys Rev Lett 63:1195-1198.
11. Finkelstein AV, Badretdinov AY, Gutin AM. 1995. Why do protein architecture have Boltzmann-like statistics? Proteins Struct Funct Genet 23:142-150.
12. Godzik A, Kolinski A, Skolnick J. 1995. Are proteins ideal mixtures of amino acids? Analysis of energy parameters sets. Protein Sci 4:2107-2117.
13. Godzik A, Kolinski A, Skolnick J. 1996. Knowledge-based potentials for protein folding: What can we learn from protein structures? Structure 4:363-366.
14. Jernigan RL, Bahar J. 1996. Structure-derived potentials and protein simulations. Curr Opin Struct Biol 6:195-209.
15. Levitt M. 1976. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 104:59-107.
16. Li H, Tang C, Wingreen NS. 1997. Nature of driving force for protein folding: A result from analyzing the statistical potential. Phys Rev Lett 79:765-768.
17. Mirny LA, Shakhnovich EI. 1996. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 264:1164-1179.
18. Miyazawa S, Jernigan RL. 1985. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552.
19. Miyazawa S, Jernigan RL. 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256:623-644.
20. Moult J. 1997. Comparison of database potentials and molecular mechanics for fields. Curr Opin Struct Biol 7:194-199.
21. Nozaki Y, Tanford C. 1971. A simplified representation of protein conformations from rapid simulations of protein folding. J Biol Chem 246:2211-2217.
22. Pande VS, Grosberg AY, Tanaka T. 1995. How accurate must potentials be for successful modeling of protein folding. J Chem Phys 103:9482-9491.
23. Roseman MA. 1988. Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds. J Mol Biol 200:513-522.
24. Sippl MJ. 1995. Knowledge-based potentials for proteins. Curr Opin Struct Biol 5:229-235.
25. Skolnick J, Jaroszewski L, Kolinski A, Godzik A. 1997. Derivation and testing of pair potentials for protein folding: When is the quasichemical approximation correct? Protein Sci 6:676-688.
26. Sun S. 1993. Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms. Protein Sci 2:762-785.
27. Tanaka S, Scheraga HA. 1976. Medium and long range interaction parameters between amino acids for predicting three dimensional structures of proteins Macromolecules 9:945-950.
28. Thomas PD, Dill KA. 1996. Statistical potentials extracted from protein structures: How accurate are they? J Mol Biol 257:457-469.
29. Zhang L, Skolnick J. 1998. How do potentials derived from structural databases relate to "true" potentials? Protein Sci 7:112-122.