The dependence of amino acid pair correlations on structural environment

Proteins: Structure, Function and Genetics

Volumn 32, Issue 2, 1998, Pages 175-189

  Cootes, Adrian P ^a   Curmi, Paul M G ^b   Cunningham, Ross ^a   Donnelly, Christine ^a   Torda, Andrew E ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

Nonlocal interactions; Pairwise statistics; Secondary structure

Indexed keywords

AMINO ACID ANALYSIS; ARTICLE; DATA BASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS;

AMINO ACIDS; DATABASES, FACTUAL; HYDROGEN BONDING; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; STATISTICS;

EID: 0032147021     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980801)32:2<175::AID-PROT4>3.0.CO;2-K     Document Type: Article

References (42)

1. Dahiyat, B.I., Mayo, S.L. De novo protein design: Fully automated sequence selection. Science 278:82-87, 1997.
2. Thomas, P.D., Dill, K.A. Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation. Protein Sci. 2:2050-2065, 1993.
3. Abkevich, V.I., Gutin, A.M., Shakhnovich, E.I. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J. Mol. Biol. 252:460-471, 1995.
4. Dill, K.A., Bromberg, S., Yue, K. et al. Principles of protein folding - A perspective from simple exact models. Protein Sci. 4:561-602, 1995.
5. Govindajaran, S., Goldstein, R.A. Optimal local propensities for model proteins. Proteins 22:413-418, 1995.
6. Minor, D.L. Jr., Kim, P.S. Context is a major determinant of β-sheet propensity. Nature 371:264-267, 1994.
7. Smith, C.K., Regan, L. Guidelines for protein design: The energetics of β-sheet sidechain interactions. Science 270: 980-982, 1995.
8. Minor, D.L. Jr., Kim, P.S. Context-dependent secondary structure formation of a designed protein sequence. Nature 380:730-734, 1996.
9. Muñoz, V., Cronet, P., Lopez-Hernandez, E., Serrano, L. Analysis of the effect of local interactions on protein stability. Fold. Des. 1:167-178, 1996.
10. Rooman, M.J., Kocher, J.-P.A., Wodak, S.J. Extracting information on folding from the amino acid sequence: Accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry 31:10226-10238, 1992.
11. Gilis, D., Rooman, M. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J. Mol. Biol. 257:1112-1126, 1996.
12. Gilis, D., Rooman, M. Predicting protein stability changes upon mutation using database-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence. J. Mol. Biol. 272:276-290, 1997.
13. Chou, P.Y., Fasman, G.D. Prediction of protein conformation. Biochemistry 13:222-245, 1974.
14. Gamier, J., Osguthorpe, D.J., Robson, B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120:97-120, 1978.
15. Muñoz, V., Serrano, L. Intrinsic secondary structure propensities of the amino acids, using statistical (-( matrices: Comparison with experimental scales. Proteins 20:301-311, 1994.
16. Overington, J., Johnson, M.S., Šali, A., Blundell, T.L. Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction. Proc. R. Soc. Lond. B 241:132-145, 1990.
17. Overington, J., Donelly, D., Johnson, M.S., Šali, A., Blundell, T.L. Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds. Protein Sci. 1:216-226, 1992.
18. Tomii, K., Kanehisa, M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9:27-36, 1996.
19. von Heijne, G., Blomberg, C. The β structure: Inter-strand correlations. J. Mol. Biol. 117:821-824, 1977.
20. Lifson, S., Sander, C. Specific recognition in the tertiary structure of β-sheets of proteins. J. Mol. Biol. 139:627-639, 1980.
21. Klinger, T.M., Brutlag, D.L. Discovering structural correlations in alpha-helices. Protein Sci. 3:1847-1857, 1994.
22. Wouters, M.A., Curmi, P.M.G. An analysis of side chain interactions and pair correlations within antiparallel β-sheets: The difference between backbone hydrogen-bonded and non-hydrogen bonded residue pairs. Proteins 22:119-131, 1995.
23. Bishop, Y.M.M., Fienberg, S.E., Holland, P.W. "Discrete Multivariate Analysis." Cambridge, MA: The MIT Press, 1975.
24. Everitt, B.S. "The Analysis of Contingency Tables." London: Chapman and Hall, 1977.
25. Fingleton, B. "Models of Category Counts." Cambridge, UK: Cambridge University Press, 1984.
26. Andersen, E.B. "The Statistical Analysis of Categorical Data." Berlin: Springer-Veriag, 1990.
27. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B. et al. The Protein Data Bank: A computer-based archival file for macromolecular structures. Eur. J. Biochem 80:319-324, 1977.
28. Hobohm, U., Scharf, M., Schneider, R., Sander, C. Selection of representative protein data sets. Protein Sci. 1:409-417, 1992.
29. Kabsch, W., Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
30. Hubbard, T.J.P. Use of β-strand interaction pseudopotentials in protein structure prediction and modelling. In: "Proceedings of the Biotechnology Computing Track, Protein Structure Prediction Minitrack of the 27th HICSS." Lathrop, R.H., ed. IEEE Computer Society Press. 1994:336-354.
31. Payne, R.W. "Genstat 5 Reference Manual." New York: Oxford University Press, 1989.
32. Richardson, J.S. β-sheet topology and the relatedness of proteins. Nature 268:495-500, 1977.
33. Presta, L.G., Rose, G.D. Helix signals in proteins. Science 240:1632-1641, 1988.
34. Richardson, J.S., Richardson, D.C. Amino acid preferences for specific locations at the ends of alpha helices. Science 240:1648-1652, 1988.
35. Sippl, M.J. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5:229-235, 1995.
36. Böhm, G. New approaches in molecular structure prediction. Biophys. Chem. 59:1-32, 1996.
37. Jones, D.T., Thornton, J.M. Potential energy functions for threading. Curr. Opin. Struct. Biol. 6:210-216, 1996.
38. Jernigan, R.L., Bahar, I. Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol. 6:195-209, 1996.
39. Torda, A.E. Perspectives in protein fold recognition. Curr. Opin. Struct. Biol. 7:200-205, 1997.
40. Munson, P.J., Singh, R.K. Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Sci. 6:1467-1481, 1997.
41. Sippl, M.J. Calculations 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, 1990.
42. Jones, D.T., Taylor, W.R., Thornton, J.M. A new approach to protein fold recognition. Nature 358:86-89, 1990.