Recognizing native folds by the arrangement of hydrophobic and polar residues

Journal of Molecular Biology

Volumn 252, Issue 5, 1995, Pages 709-720

  Huang, Enoch S ^a   Subbiah, S ^a   Levitt, Michael ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Contact potential; Fold recognition; Hydrophobic interaction; Protein folding; Threading

Indexed keywords

EID: 0029101826     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1995.0529     Document Type: Article

References (64)

1. Argos, P. (1987). Analysis of sequence-similar pentapep-tides in unrelated protein tertiary structures. Strategies for protein folding and a guide for site-directed mutagenesis. J. Mol. Biol. 197, 331-348.
2. Bashford, D., Chothia, C. & Lesk, A. M. (1987). Determinants of a protein fold. Unique features of the globin amino acid sequences. J. Mol. Biol. 196, 199-216.
3. Bauer, A. & Beyer, A. (1994). An improved pair potential to recognize native protein folds. Proteins: Struct. Funct. Genet. 18, 254-261.
4. Baumann, G., Frommel, C. & Sander, C. (1989). Polarity as a criterion in protein design. Protein Eng. 2, 329-334.
5. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Jr, Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). Protein Data Bank: a computer-based archival file for macromol-ecular structures. J. Mol. Biol. 112, 535-542.
6. Betz, S. F. (1993). Disulfide bonds and the stability of globular proteins. Protein Sci. 2, 1551-1558.
7. Bowie, J. U., Clarke, N. D., Pabo, C. O. & Sauer, R. T. (1990a). Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins: Struct. Funct. Genet. 7, 257-264.
8. Bowie, J. U., Reidhaar-Olson, J. F., Lim, W. A. & Sauer, R. T. (1990b). Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science, 247, 1306-1310.
9. Bryant, S. H. & Amzel, L. M. (1987). Correctly folded proteins make twice as many hydrophobic contacts. Int. J. Pept. Protein Res. 29, 46-52.
10. Bryant, S. H. & Lawrence, C. E. (1993). An empirical energy function for threading protein sequence through folding motif. Proteins: Struct. Funct. Genet. 16, 92-112.
11. 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.
12. Chiche, L., Gregoret, L. M., Cohen, F. E. & Kollman, P. A. (1990). Protein model structure evaluation using the solvation free energy of folding. Proc. Natl Acad. Sci. USA, 87, 3240-3243.
13. Cohen, B. I., Presnell, S. R. & Cohen, F. E. (1993). Origins of structural diversity within sequentially identical hexapeptides. Protein Sci. 2, 2134-2145.
14. Covell, D. G. & Jernigan, R. L. (1990). Conformations of folded proteins in restricted spaces. Biochemistry, 29, 3287-3294.
15. Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133-7155.
16. Dill, K. A., Fiebig, K. M. & Chan, H.S. (1993). Cooperativity in protein-folding kinetics. Proc. Natl Acad. Sci. USA, 90, 1942-1946.
17. Eisenberg, D. & McLachlan, A. D. (1986). Solvation energy in protein folding and binding. Nature, 319, 199-203.
18. Eriksson, A. E., Basse, W. A., Zhang, X.-J., Heinz, D. W., Blaber, M., Baldwin, E. P. & Matthews, B. W. (1992). Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science, 255, 178-183.
19. Feng, Y, Sligar, S. G. & Wand, A. J. (1994). Solution structure of apocytochrome b562. Nature Struct. Biol. 1, 30-34.
20. 2-terminal domain of phage X repressor. Proc. Natl Acad. Sci. USA, 81, 5685-5689.
21. 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.
22. Hinds, D. A. & Levitt, M. (1992). A lattice model for protein structure prediction at low resolution. Proc. Natl Acad. Sci. USA, 89, 2536-2540.
23. Hinds, D. A. & Levitt, M. (1994). Exploring conformational space with a simple lattice model for protein structure. J. Mol. Biol. 243, 668-682.
24. Janin, J. & Chothia, C. (1990). The structure of protein-protein recognition sites. J. Biol. Chem. 265, 16027-16030.
25. Kabsch, W. & Sander, C. (1984). On the use of sequence homologies to predict protein structure: identical pen-tapeptides can have completely different conformations. Proc. Natl Acad. Sci. USA, 81, 1075-1078.
26. Kamtekar, S., Schiffer, J. M., Xiong, H., Babik, J. M. & Hecht, M. H. (1993). Protein design by binary patterning of polar and nonpolar amino acids. Science, 262, 1680-1685.
27. Kauzmann, W. (1959). Some factors in the interpretation of protein denaturation. Advan. Protein Chem. 14, 1-63.
28. Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
29. Lau, K. F. & Dill, K. A. (1989). A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules, 22, 3986-3997.
30. Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379-400.
31. Lee, C. & Levitt, M. (1991). Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core. Nature, 352, 448-451.
32. Lee, C. & Subbiah, S. (1991). Prediction of protein side-chain conformation by packing optimization. J. Mol. Biol. 217, 373-388.
33. Lesk, A. M. & Chothia, C. (1980). How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J. Mol. Biol. 136, 225-270.
34. Levitt, M. (1976). A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104, 59-107.
35. Lim, W. A. & Sauer, R. T. (1989). Alternative packing arrangements in the hydrophobic core of X repressor. Nature, 339, 31-36.
36. Luthy R., Bowie, J. U. & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
37. Maiorov, V. N. & Crippen, G. M. (1992). Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol. 227, 876-888.
38. Miller, S. (1989). The structures of interfaces between subunits of dimeric and tetrameric proteins. Protein Eng. 3, 77-83.
39. Miyazawa, S. & Jernigan, R. L. (1985). Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules, 18, 534-552.
40. Novotny J., Bruccoleri, R. & Karplus, M. (1984). An analysis of incorrectly folded protein models. Implications for structure predictions. J. Mol. Biol. 177, 787-818.
41. Novotny J., Rashin, A. A. & Bruccoleri, R. E. (1988). Criteria that discriminate between native proteins and incorrectly folded models. Proteins: Struct. Funct. Genet. 4, 19-30.
42. Orengo, C. A., Flores, T. P., Taylor, W. R. & Thornton, J. M. (1993). Identification and classification of protein fold families. Protein Eng. 6, 485-500.
43. Ouzounis, C., Sander, C., Scharf, M. & Schneider, R. (1993). Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. J. Mol. Biol. 232, 805-825.
44. Park, B. & Levitt, M. (1995) The complexity and accuracy of discrete state models of protein structure. J. Mol. Biol. 249, 493-507.
45. Perutz, M. F., Kendrew, J. C. & Watson, H. C. (1965). Structure and function of haemoglobin. II. Some relations between polypeptide chain configuration and amino acid sequence. J. Mol. Biol. 13, 669-678.
46. Ponder, J. W. & Richards, F. M. (1987). Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193, 775-791.
47. Reidhaar-Olson, J. F. & Sauer, R. T. (1988). Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. Science, 241, 53-57.
48. 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.
49. Sali, D., Bycroft, M. & Fersht, A. R. (1991). Surface electrostatic interactions contribute little to stability of barnase. J. Mol. Biol. 220, 779-788.
50. Serrano, L., Kellis, J. T., Jr, Cann, P., Matouschek, A. & Fersht, A. R. (1992). The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol. 224, 783-804.
51. Shortle, D. & Meeker, A. K. (1986). Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation. Proteins: Struct. Funct. Genet. 1, 81-89.
52. Shortle, D., Stites, W. E. & Meeker, A. K. (1990). Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry, 29, 8033-8041.
53. 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.
54. Sippl, M. J. (1993). Recognition of errors in three-dimensional structures of proteins. Proteins: Struct. Funct. Genet. 17, 355-362.
55. Sippl, M. J. (1995). Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5, 229-235.
56. Sun, S. (1993). Reduced representation model of protein structure prediction: statistical potential and genetic algorithms. Protein Sci. 2, 762-785.
57. Sweet, R. M. & Eisenberg, D. (1983). Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J. Mol. Biol. 171, 479-488.
58. 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.
59. Tanford, C. (1980). The Hydrophobic Effect: Formation of Micelles and Biological Membranes, 2nd edit. Wiley, New York.
60. Viswanadhan, V. N. (1987). Hydrophobicity and residue-residue contacts in globular proteins. Int. J. Biol. Macromol. 9, 39-48.
61. Wertz, D. H. & Scheraga, H. A. (1978). Influence of water on protein structure. An analysis of the preferences of amino acid residues for the inside or outside and for specific conformations in a protein molecule. Macromolecules, 11, 9-15.
62. Wodak, S. J. & Rooman, M.J. (1993). Generating and testing protein folds. Curr. Opin. Struct. Biol. 3, 247-259.
63. Yue, K. & Dill, K. A. (1992). Inverse protein folding problem: designing polymer sequences. Proc. Natl Acad. Sci. USA, 89, 4163-4167.
64. Young, L., Jernigan, R. L. & Covell, D. G. (1994). A role for surface hydrophobicity in protein-protein recognition. Protein Sci. 3, 717-729.