Context dependence and coevolution among amino acid residues in proteins

Methods in Enzymology

Volumn 395, Issue , 2005, Pages 779-790

  Wang, Zhengyuan O ^a   Pollock, David D ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CYTOCHROME C OXIDASE; PROTEIN DERIVATIVE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; HUMAN; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; STATISTICAL ANALYSIS; VERTEBRATE;

ANIMALS; CATTLE; DATABASES, PROTEIN; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; MOLECULAR STRUCTURE; PROTEINS;

VERTEBRATA;

EID: 19944406094     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)95040-4     Document Type: Article

References (36)

1. Atchley W.R., Wollenberg K.R., Fitch W.M., Terhalle W., Dress A.W. Correlation among amino acid sites in bHLH protein domains: An information theoretic analysis. Mol. Biol. Evol. 17:2000;164-178
2. Brasseura G., Ragob J.-P. D., Slonimskic P.P., Lemesle-Meuniera D. Analysis of suppressor mutation reveals long distance interactions in the bc1 complex of Saccharomyces cerevisiae. Biochim. Biophys. Acta Bioenergetics. 1506:2001;89-102
3. Chelvanayagam G., Eggenschwiler A., Knecht L., Connet G.H., Benner S.A. An analysis of simultaneous variation in protein structures. Protein Eng. 10:1997;307-316
4. Dean A.M., Golding G.B. Enzyme evolution explained (sort of). Pac. Symp. Biocomput. 2000;6-17
5. Felsenstein J. Phylogeny inference package. Cladistics. 5:1989;164-166
6. Fukami-Kobayashi K., Schreiber D.R., Benner S.A. Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J. Mol. Biol. 319:2002;729-743
7. Gobel U., Sander C., Schneider R., Valencia A. Correlated mutations and residue contacts in proteins. Proteins. 18:1994;309-317
8. Goldberg A., Wildman D.E., Schmidt T.R., Huttemann M., Goodman M., Weiss M.L., Grossman L.I. Adaptive evolution of cytochrome c oxidase subunit VIII in anthropoid primates. PNAS. 100:2003;5873-5878
9. Govindarajan S., Ness J.E., Kim S., Mundorff E.C., Minshull J., Gustafsson C. Systematic variation of amino acid substitutions for stringent assessment of pairwise covariation. J. Mol. Biol. 328:2003
10. Gribaldo S., Casane D., Lopez P., Philippe H. Functional divergence prediction from evolutionary analysis: A case study of vertebrate hemoglobin. Mol. Biol. Evol. 20:2003;1754-1759
11. Korber B.T., Farber R.M., Wolpert D.H., Lapedes A.S. Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis. Proc. Natl. Acad. Sci. USA. 90:1993;7176-7180
12. Krishnan N.M., Seligmann H., Stewart C.-B., de Koning A.P.J., Pollock D.D. Ancestral sequence reconstruction in primate mitochondrial DNA: Compositional bias and effect on functional inference. Mol. Biol. Evol. 21:(10):2004;1871-1883
13. Lapedes A.S., Giraud B.G., Liu L.C., Stormo G.D. Correlated Mutations In Protein Sequences: Phylogenetic and Structural Effects. Correlated Mutations in Protein. Proceedings of the AMS/SIAM Conference: Statistics in Molecular Biology:1997;. Seattle, WA.
14. Lopez P., Casane D., Philippe H. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19:2002;1-7
15. Neher E. How frequent are correlated changes in families of protein sequences? Proc. Natl. Acad. Sci. USA. 91:1994;98-102
16. Pazos F., Helmer-Citterich M., Ausiello G., Valencia A. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271:1997;511-523
17. Pazos F., Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14:2001;609-614
18. Philippe H., Casane D., Gribaldo S., Lopez P., Meunier J. Heterotachy and functional shift in protein evolution. IUBMB Life. 55:2003;257-265
19. Pollock D.D. Genomic diversity, phylogenetics and coevolution in proteins. Applied Bioinformatics. 1:2002;25-36
20. Pollock D.D., Taylor W.R. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10:1997;647-657
21. Pollock D.D., Taylor W.R., Goldman N. Coevolving protein residues: Maximum likelihood identification and relationship to structure. J. Mol. Biol. 287:1999;187-198
22. Pritchard L., Bladon P., Mitchell J.M.O., Dufton M.J. Evaluation of a novel method for the identification of coevolving protein residues. Protein Eng. 14:(8):2001;549-555
23. Saitou N., Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425
24. Shindyalov I., Kolchanov N., Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng. 7:1994;349-358
25. Taylor W., Hatrick K. Compensating changes in protein multiple sequence alignments. Protein Eng. 7:1994;341-348
26. Thompson J., Higgins D., Gibson T. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680
27. Tsukihara T., Aoyama H., Yamashita E., Tomizaki T., Yamaguchi H., Shinzawa-Itoh K., Nakashima R., Yaono R., Yoshikawa S. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Science. 272:1996;1136-1144
28. Tsukihara T., Shimokata K., Katayama Y., Shimada H., Muramoto K., Aoyama H., Mochizuki M., Shinzawa-Itoh K., Yamashita E., Yao M., Ishimura Y., Yoshikawa S. The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process. Proc. Natl. Acad. Sci. USA. 100:2003;15304-15309
29. Tuff P., Darlu P. Exploring a phylogenetic approach for the detection of correlated substitutions in proteins. Mol. Biol. Evol. 17:2000;1753-1759
30. Valencia A., Pazos F. Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol. 12:2002;368-373
31. Wikström M. Cytochrome c oxidase: 25 years of the elusive proton pump. Biochim. Biophys. Acta Bioenergetics. 1655:2004;241
32. Williams P.D., Pollock D.D., Goldstein R.A. Evolution of functionality in lattice proteins. J. Mol. Graph Model. 19:2001;150-156
33. Williams, P. D., Pollock, D. D., and Goldstein, R. A. (in revision). Why are proteins marginally stable? II: Functionality strikes back. Proteins: Structure, function, and genetics.
34. Wollenberg K.R., Atchley W.R. Separation of phylogenetic and functional association in biological sequences by using the parametric bootstrap. Proc. Natl. Acad. Sci. USA. 97:2000;3288-3291
35. Wu W., Schmidt T.R., Goodman M., Grossman L.I. Molecular evolution of cytochrome c oxidase subunit I in primates: Is there coevolution between mitochondrial and nuclear genomes? Mol. Phylogenet. Evol. 17:2000;294-304
36. Xu, Y. O. Hall, R. W., Goldstein, R. A., and Pollock, D. D. (in review). Divergence, recombination, and retention of functionality during protein evolution. Human Genomics.