Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches

Proteins: Structure, Function and Genetics

Volumn 29, Issue 3, 1997, Pages 292-308

  Bahar, I ^a,b   Kaplan, M ^b   Jernigan, R L ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b BOGAZICI UNIVERSITY   (Turkey)

Author keywords

Coupling between bond torsions and bond angles; Inverse folding experiments; Knowledge based potentials; Secondary structure propensities; Virtual bonds

Indexed keywords

ARTICLE; MATHEMATICAL ANALYSIS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; SEQUENCE ANALYSIS;

AMINO ACIDS; ENERGY TRANSFER; MATHEMATICAL COMPUTING; PROBABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0030832809     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199711)29:3<292::AID-PROT4>3.0.CO;2-D     Document Type: Article

References (46)

1. Flory, P.J. "Statistical Mechanics of Chain Molecules." New York: Interscience, 1969. (also reprinted by Hanser Publishers, Oxford University, Oxford, 1988.)
2. Bahar, I., Jernigan, R.L. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266:195-214, 1997.
3. Bahar, I., Jernigan, R.L. Coordination geometry of non-bonded residues in globular proteins. Folding Design 1:357-370, 1996.
4. Miyazawa, S., Jernigan, R.L. 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, 1996.
5. Honig, B., Cohen, F.E. Adding backbone to protein folding: Why proteins are polypeptides. Folding Design 1:R17-R20, 1996.
6. Kocher, J.-P.A., Rooman, M.J., Wodak, S. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235:1598-1613, 1994.
7. Park, B.H., Levitt, M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J. Mol. Biol. 258:367-392, 1996.
8. Niefind, K., Schomburg, D. Amino acid similarity coefficients for protein modeling and sequence alignment derived from main-chain folding angles. J. Mol. Biol. 219:481-497, 1991.
9. Sun, S. Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms. Protein Sci. 2:762-785, 1993.
10. Nishikawa, K., Matsuo, Y. Development of pseudoenergy potentials for assessing protein 3d-1d compatibility and detecting weak homologies. Protein Eng. 6:811-820, 1993.
11. Levitt, M. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104:59-107, 1976.
12. Gregoret, L.M., Cohen, F.E. Protein folding: Effect of packing density on chain conformation. J. Mol. Biol. 219: 109-122, 1991.
13. DeWitte, R.S., Shakhnovich, E.I. Pseudodihedrals: Simplified protein backbone representation with knowledge-based energy. Protein Sci. 3:1570-1581, 1994.
14. Park, B.H., Levitt, M. The complexity and accuracy of discrete state models of protein structure. J. Mol. Biol. 249:493-507, 1995.
15. Brant, D.A., Flory, P.J. The configuration of random polypeptide II theory. J. Am. Chem. Soc. 87:2791-2800, 1965.
16. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F.J., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. Tasumi, M. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
17. Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., Weng, J. Protein Data Bank. In: "Crystallographic Databases-Information Content Software Systems, Scientific Applications." Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., Weng, J. (eds.). Bonn, Cambridge, and Chester: Data Commission of the International Union of Crystallography, 1987:107.
18. Chou, P.Y., Fasman, G.D. Prediction of the secondary structure of protein from amino acid sequence. Adv. Enzymol. 47:45-148, 1978.
19. Garnier, J., Osguthorpe, D., Robson, B. An analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120:97-120, 1978.
20. Levitt, M. Conformational preferences of amino acids in globular proteins. Biochemistry 17:4277-4285, 1978.
21. Blundell, T.L., Sibanba, B.L., Sternberg, M.J.E., Thornton, J.M. Knowledge-based prediction of protein structures and design of novel molecules. Nature 326:347-352, 1987.
22. Serrano, L., Sancho, J., Hirshberg, M., Fersht, A.R. α-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 surfaces. J. Mol. Biol. 227:544-559, 1992.
23. Richardson, J., Richardson, D. Amino acid preferences for specific locations at the end of α-helices. Science 240:1648-1652, 1988.
24. Muñoz, V., Serrano, L. Elucidating the folding problem of helical peptides using empirical parameters. Struct. Biol. 1:399-409, 1994.
25. Aurora, R., Srinivasan, R., Rose, G.D. Rules for α-helix termination by glycine. Science 264:1126-1129, 1994.
26. Lyu, C.P., Liff, M.I., Marky, L.A., Kallenbach, N.R. Side chain contributions to the stability of alpha-helical structure in peptides. Science 250:669-673, 1990.
27. Chou P.Y., Fasman, G.D. In: "Peptides." Chou, P.Y., Fasman, G.D. (eds.). New York: Halsted Press, 1977:284-287.
28. Chou, P.Y. Prediction of protein structural classes from amino acid compositions. In: "Prediction of Protein Structures and the Principles of Protein Conformation." Chou, P.Y. (eds.). Plenum Press, New York: 1989:549-586.
29. O'Neil, T.K., DeGrado, W. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250:646-651, 1990.
30. Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T.M., Baldwin, R.L. Relative helix-forming tendencies of nonpolar amino acids. Nature 344:268-270, 1990.
31. Horovitz, A., Matthews, J.M., Fersht, A.R. α-Helix stability in Proteins II. Factors that influence stability at an internal position. J. Mol. Biol. 227:560-568, 1992.
32. Blaber, M., Zhang, X.-J., Matthews, B.W. Structural basis of amino acid α helix propensity. Science 260:1637-1640, 1993.
33. Luque, I., Mayorga, O.L., Freire, E. Structure-based thermodynamic scale of α-helix propensities in amino acids. Biochemistry 35:13681-13688, 1996.
34. Creamer, T.P., Rose, G.D. Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix-forming propensities. Proc. Natl. Acad. Sci. USA 89:5937-5941, 1992.
35. Merutka, G., Stellwagen, E. Positional independence and additivity of amino acid replacements on helix stability in monomeric peptides. Biochemistry 29:894-898, 1990.
36. Hecht, M.H., Sturtevant, J.M., Sauer, R.T. Stabilization of λ repressor against thermal denaturation by site directed Gly → Ala changes in α-helix 3. Proteins 1:43-46, 1986.
37. Dao-Pin, S.T., Baase, B.W., Matthews, B.W. A mutant T4 Lysozyme (Val131Ala) designed to increase thermostability by reduction of strain within an α-helix. Proteins 7:198-204, 1990.
38. Kim, C.A., Berg, J.M. Thermodynamic β-sheet propensities measured using a zinc-finger host peptide. Nature 362:267-270, 1993.
39. Bai, Y., Englander, S.W. Hydrogen bond strength and β-sheet propensities: The role of a side chain blocking effect. Proteins 18:262-266, 1994.
40. Minor, D.L., Kim, P.S. Measurement of the β-sheet propensities of amino acids. Nature 367:660-663, 1994.
41. Minor, D.L., Kim, P.S. Context is a major determinant of β-sheet propensity. Nature 371:264-267, 1994.
42. Minor, D.L., Kim, P.S. Context-dependent secondary structure formation of a designed protein sequence. Nature 380:730-734, 1996.
43. Waterhous, D.V., Johnson, W.C. Importance of environment in determining secondary structure in proteins. Biochemistry 33:2121-2128, 1994.
44. Smith, C.K., Withka, J.M., Regan, L. A thermodynamic scale for the β-sheet forming tendencies of the amino acids. Biochemistry 33:5510-5517, 1994.
45. Hendlich, M., Lackner, P., Weitckus, S., Floeckner, H., Froschauer, R., Gottsbacher, K., Casari, G., Sippl, M.J. 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, 1990.
46. Otzen, D.E., Fersht, A.R. Side chain determinants of β-sheet stability. Biochemistry 17:5718-5724, 1995.