Coevolving protein residues: Maximum likelihood identification and relationship to structure

Journal of Molecular Biology

Volumn 287, Issue 1, 1999, Pages 187-198

  Pollock, David D ^a   Taylor, William R ^a   Goldman, Nick ^b  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Coevolution; Maximum likelihood; Molecular evolution; Protein residues; Protein structure

Indexed keywords

AMINO ACID; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; EVOLUTION; MAXIMUM LIKELIHOOD METHOD; PHYLOGENY; PRIORITY JOURNAL;

EID: 0033582946     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2601     Document Type: Article

References (27)

1. Altschuh D., Lesk A., Bloomer A. C., Klug A. Correlation of coordinated amino-acid substitutions with function in viruses related to tobacco mosaic virus. J. Mol. Biol. 193:1987;643-707.
2. Aszodi A., Munro R. E., Taylor W. R. Distance geometry based comparative modelling. Fold. Design. 2:1997;S3-S6.
3. Bairoch A., Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucl. Acids Res. 26:1998;38-42.
4. Benner S. A. Predicting the conformation of proteins from sequence data. Cleland J. L., Craik C. S. Protein Engineering: Principles and Practice. 1996;71-100 Wiley-Liss.
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. The Protein Databank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
6. Chelvanayagam G., Eggenschwiler A., Kneckt L., Gonnet G. H., Benner S. A. An analysis of simultaneous variation in protein structures. Protein Eng. 10:1997;307-316.
7. Cox D. R. Further results on tests of separate families of hypotheses. J. Roy. Stat. Soc. ser. B. 24:1962;406-424.
8. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:1981;368-376.
9. Felsenstein J. PHYLIP (phylogeny inference package) version 3.5. 1993;University of Washington, Seattle.
10. Gobel U., Sander C., Schneider R., Valencia A. Correlated mutations and residue contacts in proteins. Proteins: Struct. Funct. Genet. 18:1994;309-317.
11. Goldman N. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:1993;182-198.
12. Goldman N., Thorne J. L., Jones D. T. Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J. Mol. Biol. 263:1996;196-208.
13. Jones D. T., Taylor W. R., Thornton J. M. A new approach to protein fold recognition. Nature. 358:1992;86-89.
14. Muse S. V. Evolutionary analyses of DNA sequences subject to constraints on secondary structure. Genetics. 139:1995;1429-1439.
15. Neher E. How frequent are correlated changes in families of protein sequences? Proc. Natl Acad. Sci. USA. 91:1994;98-102.
16. Pagel M. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. Roy. Soc. London ser. B. 255:1994;37-45.
17. Pazos F., Helmer-Citterich M., Ausiello G., Valencia A. Correlated mutations contain information about protein-protein interactions. J. Mol. Biol. 271:1997;511-523.
18. Pollock D. D., Taylor W. R. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10:1997;647-657.
19. Rice J. A. Mathematical Statistics and Data Analysis. 1995;Duxbury Press, Belmont.
20. Rzhetsky A. Estimating substitution rates in ribosomal RNA genes. Mol. Biol. Evol. 141:1995;771-783.
21. Schoniger M., von Haeseler A. A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phylogenet. Evol. 3:1994;240-247.
22. Shindyalov I. N., Kolchanov N. A., Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng. 7:1994;349-358.
23. Taylor W. R. Multiple sequence threading: an analysis of alignment quality and stability. J. Mol. Biol. 269:1997;902-943.
24. Taylor W. R. Dynamic sequence databank searching with templates and multiple alignment. J. Mol. Biol. 280:1998;375-406.
25. Taylor W. R., Hatrick K. Compensating changes in protein multiple sequence alignments. Protein Eng. 7:1994;341-348.
26. Yang Z., Goldman N., Friday A. Maximum likelihood trees from DNA sequences - a peculiar statistical estimation problem. Syst. Biol. 44:1995a;384-399.
27. Yang Z., Kumar S., Nei M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics. 141:1995b;1641-1650.