Statistical potentials extracted from protein structures: How accurate are they?

Journal of Molecular Biology

Volumn 257, Issue 2, 1996, Pages 457-469

  Thomas, Paul D ^a   Dill, Ken A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Boltzmann ensemble; Knowledge based potential; Protein folding; Protein structure recognition; Residue partitioning

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; DATA BASE; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; STATISTICS;

EID: 0029976427     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0175     Document Type: Article

References (52)

1. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
2. Bowie, J. U., Lüthy R. & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
3. Bryant, S. H. & Amzel, L. M. (1987). Correctly folded proteins make twice as many hydrophobic contacts. Int. J. Peptide Protein Res. 29, 46-52.
4. Bryant, S. H. & Lawrence, C. E. (1991). The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions. Proteins: Struct. Funct. Genet. 9, 108-119.
5. Bryant, S. H. & Lawrence, C. E. (1993). An empirical energy function for threading protein sequence through the folding motif. Proteins: Struct. Funct. Genet. 16, 92-112.
6. Camacho, C. J. & Thirumalai, D. (1993a). Kinetics and thermodynamics of folding in model proteins. Proc. Natl Acad. Sci. USA, 90, 6369-6372.
7. Camacho, C. J. & Thirumalai, D. (1993b). Minimum energy compact structures of random sequences of heteropolymers. Phys. Rev. Letters, 71, 2505-2508.
8. Casari, G. & Sippl, M. J. (1992). Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. J. Mol. Biol. 224, 725-732.
9. Chan, H. S. & Dill, K. A. (1991a). Sequence-space soup of proteins and copolymers. J. Chem. Phys. 95, 3775-3787.
10. Chan, H. S. & Dill, K. A. (1991b). Polymer principles in protein structure and stability Annu. Rev. Biophys. Biophys. Chem. 20, 447-449.
11. Chan, H. S. & Dill, K. A. (1994). Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100, 9238-9257.
12. Chan, H. S., Bromberg, S. & Dill, K. A. (1995). Models of cooperativity in protein folding. Phil. Trans. Roy. Soc. Lond. ser. B, 348, 61-70.
13. Dill, K. A., Bromberg, S., Yue, K., Fiebig, K. M., Yee, D. P., Thomas, P. D. & Chan, H. S. (1995). Principles of protein folding - a perspective from simple exact models. Protein Sci. 4, 561-602.
14. Fauchère, J.-L. & Pliska, V. (1983). Hydrophobic parameters II of amino-acid side-chains from the partitioning of N-acetyl-amino acid amides. Eur. J. Med. Chem. Chim. Ther. 18, 369-375.
15. Finkelstein, A. V., Gutun, A. M. & Badretdinov, A. Ya. (1993). Why are the same protein folds used to perform different functions? FEBS Letters, 325, 23-28.
16. Finkelstein, A. V., Gutin, A. M. & Badretdinov, A. Ya. (1995). Boltzmann-like statistics of protein architectures. Origins and consequences. Sub-Cell. Biochem. 24, 1-26.
17. Godzik, A. & Skolnick, J. (1992). Sequence-structure matching in globular proteins: application to super-secondary and tertiary structure determination. Proc. Natl Acad. Sci. USA, 89, 12098-12102.
18. Hendlich, M., Lackner, P., Weitckus, S., Floeckner, H., Froschauer, R., Gottsbacher, K., Casari, G. & Sippl, M. J. (1990). Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 216, 167-180.
19. Hobohm, U. & Sander, C. (1994). Enlarged representative set of protein structures. Protein Sci. 3, 522-524.
20. Janin, J. (1979). Surface and inside volumes in globular proteins. Nature, 277, 491-492.
21. Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). A new approach to protein fold recognition. Nature, 358, 86-89.
22. Kocher, J. P., Rooman, M. J. & Wodak, S. J. (1994). Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235, 1598-1613.
23. Kolaskar, A. S. & Prashanth, D. (1979). Empirical torsional potential functions from protein structure data. Int. J. Peptide Protein Res. 14, 88-98.
24. Kolinski, A. & Skolnick, J. (1994). Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins: Struct. Funct. Genet. 18, 338-352.
25. Lau, K. F. & Dill, K. A. (1989). A lattice statistical mechanics model of the onformational and sequence spaces of proteins. Macromolecules, 22, 3986-3997.
26. Lau, K. F. & Dill, K. A. (1990). Theory for protein mutability and biogenesis. Proc. Natl Acad. Sci. USA, 87, 638-642.
27. Lawrence, C., Auger, I. & Mannella, C. (1987). Distribution of accessible surfaces of amino acids in globular proteins. Proteins: Struct. Funct. Genet. 2, 153-161.
28. Lee, B. K. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility J. Mol. Biol. 55, 379-400.
29. Lipman, D. J. & Wilbur, W. J. (1991). Modelling neutral and selective evolution of potein folding. Proc. Roy. Soc. London, ser. B, 245, 7-11.
30. Lüthy R., Bowie, J. U. & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
31. MacArthur, M. W. & Thornton, J. M. (1991). Influence of proline residues on protein formation. J. Mol. Biol. 218, 397-412.
32. 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. Phys. 96, 768-790.
33. Miller, S., Janin, J., Lesk, A. M. & Chothia, C. (1987). Interior and surface of monomeric proteins. J. Mol. Biol. 196, 641-656.
34. Miyazawa, S. & Jernigan, R. L. (1985). Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules, 18, 534-552.
35. Nishikawa, K. & Matsuo, Y. (1993). Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. Protein Eng. 6, 811-820.
36. Nozaki, Y. & Tanford, C. (1971). The solubility of amino acids and two glycine polypeptides in aqueous ethanol and dioxane solutions. J. Biol. Chem. 246, 2211-2217.
37. O'Toole, E. M. & Panagiotopoulos, A. Z. (1993). Effect of sequence and intermolecular interactions on the number and nature of low-energy states for simple model proteins. J. Chem. Phys. 90, 3185-3190.
38. Pellegrini, M., & Doniach, S. (1993). Computer simulation of antibody binding specificity Proteins: Struct. Funct. Genet. 15, 436-444.
39. Pohl, F. M. (1971). Empirical protein energy maps. Nature New Biol. 234, 277-279.
40. Rashin, A. A., Ionif, M. & Honig, B. (1986). Internal cavities and buried waters in globular proteins. Biochemistry, 25, 3619-3625.
41. Richards, F. M. (1977). Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng. 6, 151-176.
42. Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H. & Zehfus, M. H. (1985). Hydrophobicity of amino acid residues in globular proteins. Science, 229, 834-838.
43. Serrano, L., Sancho, J., Hirshberg, M. & Fersht, A. R. (1992). Alpha-helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N-and C-caps and the replacement of alanine by glycine or serine at solvent-exposed interfaces. J. Mol. Biol. 227, 544-559.
44. Shortle, D., Chan, H. S. & Dill, K. A. (1992). Modeling the effects of mutations on the denatured states of proteins. Protein Sci. 1, 201-215.
45. Sippl, M. J. (1990). Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213, 859-883.
46. Sippl M. J. & Weitckus, S. (1992). Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins: Struct. Funct. Genet. 13, 258-271.
47. Skolnick, J. & Kolinski, A. (1990). Simulations of the folding of a globular protein. Science, 250, 1121-1125.
48. Sun, S. (1993). Reduced representation model of protein structure prediction: statistical potential and genetic algorithms. Protein Sci. 2, 762-785.
49. Tanaka, S. & Scheraga, H. A. (1976). Medium-and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules, 9, 945-950.
50. Unger, R. & Moult, J. (1993). Genetic algorithms for protein folding simulations. J. Mol. Biol. 231, 75-81.
51. Wilmanns, M. & Eisenberg, D. (1993). Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold. Proc. Natl Acad. Sci. USA, 90, 1379-1383.
52. Wilson, C. & Doniach, S. (1989). A computer model to dynamically simulate protein folding: studies with crambin. Proteins: Struct. Funct. Genet. 6, 193-209.