Abstract
Divergent evolution has led to families of proteins with similar three-dimensional structures (Bajaj and Blundell, 1984). The identification of sequences that can produce a given fold is one approach that is likely to yield solutions to the protein folding problem, since the three-dimensional structures of proteins place severe constraints on the sequences that can adopt a particular fold. For example, within a family, equivalent amino acids of the solvent inaccessible core are more conserved in identity and position than those on the protein surface (Chothia and Lesk, 1982a, b; Lesk and Chothia, 1986; Hubbard and Blundell, 1987), except where functional restraints such as catalytic activity or ligand binding require the presence of a particular amino acid.
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References
Bajaj, M. and Blundell T. L., 1984 Evolution and tertiary structure of proteins, Ann. Rev. Biophys. Bioeng. 13:453.
Bernstein, F. et al., 1977 The Protein Data Bank: a computer based archival file for macromolecular structures, J. Mol. Biol. 112:535.
Bowie, J. U., Lüthy, R. and Eisenberg, D., A method to identify protein sequences that fold into known three-dimensional structure, 1991 Science 253:164.
Chothia, C. and Lesk A. M., 1982a Evolution of proteins formed by β-sheets: I. plastocyanin and azurin, J. Mol. Biol. 160:309.
Chothia, C. and Lesk A. M., 1982b Evolution of proteins formed by β-sheets: II. the core of the immunoglobulins, J. Mol. Biol. 160:325.
Dayhoff, M. O., Schwartz, R. M. and Orcutt, B. C., 1978 A model for evolutionary change, in: Atlas of Protein Sequence and Structure, Dayhoff, M.O., ed., Vol. 5, Suppl. 3, National Biomedical Research Foundation, Washington, D.C., 345.
Hubbard, T. J. P. and Blundell, T. L., 1987 Compariosn of solvent-inaccessible core of homologous proteins: definitions useful for protein modelling, Prot. Engin. 1:159.
Johnson, M. S., Overington, J. P and Blundell, T. L., Alignment and searching for common protein folds using a data bank of structural templates, submitted.
Johnson, M. S. and Overington, J. P., A structural basis for sequence comparisons: a critical evaluation of scoring methodologies, submitted.
Jones, D. T., Taylor, W. R. and Thornton, J. M., 1992 A new approach to protein fold recognition, Nature 358:86.
Lesk A. M. and Chothia, C., 1986 The response of protein structure to amino acid changes, Phil. Trans. Roy. Soc. Lond. A317:345.
Lüthy, R., McLachlan, A. D. and Eisenberg, D. Secondary structure-based profiles, Proteins 10:229.
Overington, J. P., Johnson, M. S., Sali, A. and Blundell, T. L., 1990a Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediciton, Proc. Roy. Soc. B241:132.
Overington, J. P., Johnson, M. S., Topham, C., McLeod, A., Sali, A., Zhu, Z.-Y., Sibanda, L. and Blundell, T. L., 1990b Applications of environment specific amino acid substitution tables to identify key residues in protein tertiary structure, Current Science (India) 59:867.
Overington, J. P., Donnelly, D., Johnson, M. S., Sali, A. and Blundell, T. L., 1992 Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds, Prot. Sci. 1:216.
Sali, A. and Blundell, T. L. J., 1990 Definition of general topological equivalence in protein structures, Mol. Biol. 212:403.
Sali, A., Overington, J. P., Johnson, M. S. and Blundell, T. L., 1990 From comparisons of protein sequences and structures to protein modelling and design, Trends in Biol. Sci. 15:235.
Topham, C. M., McLeod, A., Eisenmenger, F., Overington, J. P., Johnson, M. S. and Blundell, T. L. J., Fragment ranking in modelling of protein structure: conformationally-constrained environmental amino acid substitution tables, Mol. Biol., in press.
Zhu, Z.-Y., Sali, A. and Blundell, T. L., 1992 A variable gap penalty function and feature weights for protein 3-D structure comparisons, Prot. Engin. 5:43.
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© 1993 Springer Science+Business Media New York
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Johnson, M.S., Blundell, T.L. (1993). Sequence Patterns that Characterize Protein Families with a Common Fold. In: Imahori, K., Sakiyama, F. (eds) Methods in Protein Sequence Analysis. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-1603-7_28
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DOI: https://doi.org/10.1007/978-1-4899-1603-7_28
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