The use of amino acid patterns of classified helices and strands in secondary structure prediction

Journal of Molecular Biology

Volumn 260, Issue 2, 1996, Pages 261-276

  Zhu, Zhan Yang ^a,b   Blundell, Tom L ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Amino acid pattern; Classification; Prediction; Protein secondary structure; Solvent accessibility pattern

Indexed keywords

ADENYLATE KINASE; MYOGLOBIN;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

EID: 0030581145     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0397     Document Type: Article

References (54)

1. Abola, E. E., Bernstein, F. C., Bryant, S. H., Koetzle, T. F. & Weng, J. (1987). Protein Data Bank. In Crystallographic Databases - Information Content, Software Systems, Scientific Applications (Allen, F. H., Bergerhoff, G. & Sievers, R., eds), pp. 107-132, Data Commission of the International Union of Crystallography, Bonn, Cambridge, Chester.
2. Argos, P. & Palau, J. (1982). Amino acid distribution in protein secondary structures. Int. J. Pept. Protein Res. 19, 380-393.
3. Benner, S. A., Cohen, M. A. & Gerloff, D. L. (1993). Predicted secondary structure for the SYC homology-3 domain. J. Mol. Biol. 229, 295-305.
4. Benner, S. A. & Gerloff, D. L. (1991). Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure - a prediction of the structure of the catalytic domain of protein kinases. Advan. Enzyme Regulat. 31, 121-181.
5. 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). Protein data bank: a computer based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
6. Blundell, T. L. & Johnson, M. S. (1993). Catching common folds. Protein Sci. 2, 877-883.
7. Blundell, T. L. & Zhu, Z.-Y. (1995). The α-helix as seen from the protein tertiary structure: a 3D structural classification. Biophys. Chem. 55, 167-184.
8. Bowie, J. U., Lüthy, R. & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 235, 164-170.
9. Chou, P. Y. & Fasman, G. D. (1974a). Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins Biochemistry, 13, 211-222.
10. Chou, P. Y. & Fasman, G. D. (1974b). Prediction of protein conformation Biochem. 13, 222-245.
11. Cohen, F. E., Abarbanel, R. A., Kuntz, I. D. & Fletterick, R. J. (1986). Turn prediction in proteins using a pattern matching approach. Biochemistry, 25, 266-275.
12. Cohen, F. E. & Kuntz, I. D. (1990). Tertiary structure prediction. In Prediction of Protein Structure and the Principles of Protein Conformation (Fasman, G. D., ed.), pp. 647-705, Plenum Press, New York.
13. Dasgupta, S. & Bell, J. A. (1993). Design of helix ends. Int. J. Peptide Protein Res. 41, 499-511.
14. Donnelly, D., Overington, J. P. & Blundell, T. L. (1994). The prediction and orientation of α-helices from sequence alignments - the combined use of environment-dependent substitution tables, fourier-transform methods and helix capping rules. Protein Eng. 7, 645-653.
15. Dunhill, P. (1968). The use of helical net-diagrams to represent protein structures. Biophys. J. 8, 865-875.
16. Gamier, J., Osguthorpe, D. J. & Robson, B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120, 97-120.
17. Gerloff, D. L., Jenny, T. F., Knecht, L. J., Gonnet, G. H. & Benner, S. A. (1993). The nitrogenase mofe protein-a secondary structure prediction. FEBS Letters, 318, 118-124.
18. Gibrat, J.-F., Garnier, J. & Robson, B. (1987). Further developments of protein secondary structure prediction using information theory: new parameters and consideration of residue pairs. J. Mol. Biol., 198, 425-443.
19. Guzzo, A. V. (1965). The influence of amino acid sequence on protein structure. Biophys. J. 5, 809-822.
20. Holley, L. H. & Karplus, M. (1989). Protein secondary structure with a neural network. Proc. Natl Acad. Sci. USA, 86, 152-156.
21. Hubbard, T. J. P. & Blundell, T. L. (1987). Comparison of solvent inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng. 1, 159-171.
22. Johnson, M. S., Overington, J. P. & Blundell, T. L. (1993). Alignment and searching for common protein folds using a data bank of structural templates. J. Mol. Biol. 231, 735-752.
23. Johnson, M. S., Srinivasan, N., Sowdhamini, R. & Blundell, T. L. (1994). Knowledge-based protein modelling. CRC Crit. Rev. Biochem. Mol. Biol. 29, 1-70.
24. Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). A new approach to protein fold recognition. Nature, 358, 86-88.
25. Kabsch, W. & Sander, C. (1983b). Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
26. King, R. D. & Sternberg, J. E. (1990). Machine learning approach for the prediction of protein secondary structure. J. Mol. Biol. 216, 441-457.
27. Levin, J. M., Robson, B. & Gamier, J. (1986). An algorithm for secondary structure determination in proteins based on sequence similarity. FEBS Letters, 205, 303-308.
28. Lewis, P. N., Go, N., Go, M., Kotelchuk, D. & Scheraga, H. A. (1970). Helix propensity profiles of denatured proteins and their correlation with native structures. Proc. Natl Acad. Sci. USA, 65, 810-815.
29. Lewis, P. N., Momany, F. A. & Scheraga, H. A. (1971). Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proc. Natl Acad. Sci. USA, 68, 2293-2297.
30. Lim, V. I. (1974). Algorithms for prediction of α-helical and β-structural regions in globular proteins. J. Mol. Biol. 88, 873-894.
31. Low, B. W., Lovell, F. W. & Rudko, A. D. (1968). Prediction of α-helical regions in proteins of known sequence. Proc. Natl Acad. Sci. USA, 60, 1519-1526.
32. Muggleton, S., King, R. D. & Sternberg, M. J. E. (1992). Protein secondary structure prediction using logic-based machine learning. Protein Eng. 5, 647-657.
33. Overington, J. P., Johnson, M. S., Šali, A. & Blundell, T. L. (1990). Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction, Proc. Roy. Soc. Lond. ser. B, 241, 132-145.
34. Presnell, S. R., Cohen, B. I. & Cohen, F. E. (1992). A segment-based approach to protein secondary structure prediction. Biochemistry, 31, 983-993.
35. Prothero, J. W. (1966). Correlation between the distribution of amino acids and alpha helices. Biophys. J. 6, 367-370.
36. Prothero, J. W. (1968). A model of alpha-helical distribution in proteins. Biophys. J. 8, 1236-1255.
37. Qian, N. & Sejnowski, T. J. (1988). Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol. 202, 865-884.
38. Richardson, J. S. & Richardson, D. C. (1988). Amino acid preferences for specific locations at the ends of a helices. Science, 240, 1648-1652.
39. Richmond, T. J. & Richards, F. M. (1978). Packing of alpha-helices: geometrical constraints and contact areas. J. Mol. Biol. 119, 537-555.
40. Rost, B. & Sander, C. (1993). Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232, 584-599.
41. Rost, B., Sander, C. & Schneider, R. (1994). Redefining the goals of protein secondary structure prediction. J. Mol. Biol. 235, 13-26.
42. Šali, A. (1991). Modelling three-dimensional structure of proteins from their sequence of amino acid residues. PhD thesis, University of London.
43. Šali, A. & Blundell, T. L. (1990). The definition of topological equivalence in homologous and analogous structures: a procedure involving the comparison of local properties and relationships. J. Mol. Biol. 212, 403-428.
44. Schiffer, M. & Edmundson, A. B. (1967). Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys. J. 7, 121-135.
45. Schulz, G. E., Barry, C. D., Friedman, J., Chou, P. Y., Fasman, G. D., Finkelstein, A. V., Lim, V. I., Ptitsyn, O. B., Kabat, E. A., Wu, T. T., Levitt, M., Robson, B. & Nagano, K. (1974). Comparison of predicted and experimentally determined secondary structure of adenylate kinase. Nature, 250, 140-142.
46. Sippl, M. J. (1990). Calculation of conformational ensembles from potentials of mean force. J. Mol. Biol. 213, 859-883.
47. Sternberg, M. J. E. & Thornton, J. M. (1977). On the conformation of proteins: An analysis of β-pleated sheets. J. Mol. Biol. 110, 285-296.
48. Taylor, W. R. & Thornton, J. M. (1983). Prediction of super-secondary structure in proteins. Nature, 301, 540-542.
49. Topham, C. M., McLeod, A., Eisenmenger, F., Overington, J. P., Johnson, M. S. & Blundell, T. L. (1993). Fragment ranking in modelling of protein structures: conformationally-constrained environmental amino acid substitution tables. J. Mol. Biol. 229, 194-220.
50. Wako, H. & Blundell, T. L. (1994). Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structure. J. Mol. Biol. 238, 693-708.
51. Yi, T. M. & Lander, E. S. (1993). Protein secondary structure prediction using nearest-neighbour methods. J. Mol. Biol. 232, 1117-1129.
52. Zhang, X., Mesirov, J. P. & Waltz, D. L. (1992). Hybrid system for protein secondary structure prediction. J. Mol. Biol. 225, 1049-1063.
53. Zhu, Z.-Y. (1995). The assessments of secondary structure prediction at the level of secondary structure elements. Protein Eng. 8, 103-108.
54. Zhu, Z.-Y., Šali, A. & Blundell, T. L. (1992). A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Eng. 5, 43-51.