Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

Proteins: Structure, Function and Genetics

Volumn 38, Issue 2, 2000, Pages 134-148

  Vendruscolo, Michele ^a,b   Najmanovich, Rafael ^a   Domany, Eytan ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Contact maps; Pairwise contact approximation; Protein folding; Protein potential

Indexed keywords

ANALYTIC METHOD; ARTICLE; BASE PAIRING; CRYSTALLOGRAPHY; GENE TARGETING; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; SIMULATION; STRUCTURE ANALYSIS;

ALGORITHMS; DATABASES, FACTUAL; MODELS, CHEMICAL; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 0034141931     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000201)38:2<134::AID-PROT3>3.0.CO;2-A     Document Type: Article

References (68)

1. Anfinsen C. Principles that govern the folding of protein chains. Science 1973;181:223-230.
2. Levitt M. Molecular dynamics of native protein. II. Analysis and nature of motion. J Mol Biol 1983;168:595-620.
3. Lazaridis T, Karplus M. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 1997;278:1928-1931.
4. Brooks CL. Simulations of protein folding and unfolding. Curr Opin Struct Biol 1998;8:222-226.
5. Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 1976;104:59-107.
6. Ueda Y, Taketomi H, Go N. Studies of protein folding, unfolding and fluctuations by computer simulations. II. A three-dimensional lattice model of lysozyme. Biopolymers 1978;17:1531-1548.
7. Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985;18:534-552.
8. Skolnick J, Kolinski A. Simulations of the folding of a globular protein. Science 1990;250:1121-1125.
9. Sali A, Shakhnovich EI, Karplus M. Kinetics of protein folding: a lattice model study of the requirements for folding to the native state. J Mol Biol 1994;235:1614-1636.
10. Dill KA, Bromberg S, Yue K, et al. Principles of protein folding - a perspective from simple exact models. Protein Sci 1995;4:561-602.
11. Guo Z, Thirumalai D. Kinetics and thermodynamics of folding of a do novo designed four-helix bundle protein. J Mol Biol 1996;263: 323-343.
12. Hao MH, Scheraga HA. Molecular mechanisms for cooperative folding of proteins. J Mol Biol 1998;277:973-983.
13. Mirny L, Domany E. Protein fold recognition and dynamics in the space of contact maps. Proteins 1996;26:391-410.
14. Lifson S, Sander C. Antiparallel and parallel beta-strands differ in amino acid residue preferences. Nature 1979;282:109-111.
15. Chan HS, Dill KA. Origins of structure in globular proteins. Proc Natl Acad Sci USA 1990;87:6388-6392.
16. Godzik A, Skolnick J, Kolinski A. Regularities in interaction patterns of globular proteins. Protein Eng 1993;6:801-810.
17. Vendruscolo M, Kussell E, Domany E. Recovery of protein structure from contact maps. Fold Des 1997;2:295-306.
18. Vendruscolo M, Domany E. Efficient dynamics in the space of contact maps. Fold Des 1998;3:329-336.
19. Tanaka S, Scheraga HA. Medium-and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 1976;9:945-950.
20. Wodak S, Rooman M. Generating and testing protein folds. Curr Opin Struct Biol 1993;3:247-259.
21. Sippl M. Knowledge based potentials for proteins. Curr Opin Struct Biol 1995;5:229-235.
22. Jernigan RL, Bahar I. Structure-derived potentials and protein folding. Curr Opin Struct Biol 1996;6:195-209.
23. Kocher JP, Rooman MJ, Wodak SJ. Factors influencing the ability of knowledge-based potentials to identify the native sequence-structure matches. J Mol Biol 1994;235:1598-1623.
24. Thomas PD, Dill KA. Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol 1996;257:457-469.
25. Park B, Levitt M. Energy functions that discriminate x-ray and near-native folds from well-constructed decoys. J Mol Biol 1996; 258:367-392.
26. Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding: when is the quasi-chemical approximation correct? Protein Sci 1997;6:676-688.
27. Rooman M, Gilis D. Different derivations of knowledge based potentials and analysis of their robustness and context-dependent predictive power. Eur J Biochem 1998;254:135-143.
28. Goldstein R, Luthey-Schulten ZA, Wolynes PG. Optimal protein folding codes from spin glass theory. Proc Natl Acad Sci USA 1992;89:4918-4922.
29. Maiorov VN, Grippen GM. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 1992;227:876-888.
30. Vendruscolo M, Domany E. Pairwise contact potentials are unsuitable for protein folding. J Chem Phys 1998;109:11101-11108.
31. Hao MH, Scheraga HA. How optimization of potential function affects protein folding. Proc Natl Acad Sci USA 1996;93:4984-4989.
32. Mirny L, Shakhnovich EI. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 1996;264: 1164-1179.
33. Seno F, Maritan A, Banavar JR. Interaction potentials for protein folding. Proteins 1998;30:244-248.
34. Abkevich VI, Gutin AM, Shakhnovich EI. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J Mol Biol 1995;252:460-471.
35. Bowie D, Luthy JU, Eisenberg D. A method to identify protein sequences that fold into a known 3-dimensional structure. Science 1991;253:164-170.
36. Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
37. Fisher D, Rice D, Bowie JU, Eisenberg D. Assigning amino acid sequences to 3-dimensional protein folds. FASEB J 1996;10:126-136.
38. Hendlich M, Lackner P, Weitckus S, et al. 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 1990;216:167-180.
39. Sippl M, Weitckus S. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a database of known protein conformations. Proteins 1992;13:258-271.
40. Ouzonis C, Sander C, Scharf M, Schneider R. Prediction of protein structure by evaluation of sequence-structure fitness: aligning sequences to contact profiles derived from 3D structures. J Mol Biol 1993;232:805-825.
41. Park B, Huang ES, Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J Mol Biol 1997;266:831-846.
42. Wang Y, Zhang H, Li W, Scott RA. Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci USA 1995;92:709-713.
43. Huang ES, Subbiah S, Tsai J, Levitt M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J Mol Biol 1996;257:716-725.
44. Hinds DA, Levitt M. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 1994;243:668-682.
45. Cohen FE, Richmond TJ, Richards FM. Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example. J Mol Biol 1979;132:275-288.
46. Elofsson A, Le Grand SM, Eisenberg D. Local moves: an efficient algorithm for simulation of protein folding. Proteins 1995;23:73-82.
47. Yue K, Dill KA. Protein folding with a simple energy function and extensive conformational searching. Protein Sci 1996;5:254-261.
48. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-138.
49. Grippen G, Havel TF. "Distance Geometry and Molecular Conformation." New York: John Wiley, 1988.
50. Brünger AT, Adams PD, Rice LM. New applications of simulated annealing in X-rays crystallography and solution NMR. Curr Opin Struct Biol 1997;5:325-336.
51. Bernstein FC, Koetzle TF, Williams GJB, et al. The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542. The PDB database is available on-line at http://www.pdb.bnl.gov
52. Heringa J, Sommerfeldt H, Higgins D, Argos P. OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. CA-BIOS 1992;8:599-600. The on-line material is available at http:// www.embl-heidelberg.de/obstruct.
53. Hobohm U, Sander C. Enlarged representative set of protein structure. Protein Sci 1994;3:522-524.
54. Hooft RW, Vriend G, Sander C, Abola EE. Errors in protein structures. Nature 1996;381:272.
55. Jurs PC. "Computer Software Applications in Chemistry." New York: John Wiley, 1986.
56. Press WH, Teukolsky SA, Wtterling WT, Flannery BP. "Numerical Recipes in Fortran: The Art of Scientific Computing." New York: Cambridge University Press, 1992.
57. Van Mourik J, Clementi C, Maritan A, Seno F, Banavar JR. Determination of interaction potentials of amino acids from native protein structures: tests on simple lattice models. J Chem Phys 1999;110:10123-10133.
58. Fisher D, Elofsson A, Rice D, Eisenberg D. Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Proceedings of the 1st Pacific Symposium on Biocomputing 1996:300-318.
59. Mirny L, Shakhnovich EI. Protein structure prediction by threading: why it works and why it does not. J Mol Biol 1998;283:507-526.
60. Hooft RW, Sander C, Vriend G. Verification of protein structures: side-chain planarity. J App Crystallogr 1996;29:714-716.
61. Orengo CA, Michie AD, Jones S, Swindells MB, Thornton JM. CATH - a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108. The CATH database is available on-line at http://www.biochem.ucl.ac.uk/bsm/cath/
62. Hertz J, Krogh A, Palmer RG. "Introduction to the Theory of Neural Computation. Santa Fe Institute Studies in the Science of Complexity." Lecture Notes v. 1 (Computation and Neural Systems Series). Redwood City, CA: Addison-Wesley Publishing Company, 1991.
63. Watkin TLH, Rau A, Biehl M. The statistical mechanics of learning a rule. Rev Mod Phys 1993;65:499-556.
64. Minsky ML, Papert SA. "Perceptions." Cambridge, MA: MIT Press, 1969.
65. Nabutovsky D, Domany E. Learning the Unlearnable. Neural Comput 1991;3:604-616.
66. Krauth W, Mezard M. Learning algorithms with optimal stability in neural networks. J Phys A 1987;20:L745-L752.
67. Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 1996;256: 623-644.
68. Thomas PD, Dill KA. An iterative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci USA 1996;93:11628-11633.