Influence of conservation on calculations of amino acid covariance in multiple sequence alignments

Proteins: Structure, Function and Genetics

Volumn 56, Issue 2, 2004, Pages 211-221

  Fodor, Anthony A ^a   Aldrich, Richard W ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Covariance; Evolution; Genomics; Pfam; Protein Data Bank; Protein engineering; Structure function

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CALCULATION; COVARIANCE; DATA BASE; GENE FREQUENCY; GENE MUTATION; GENETIC CONSERVATION; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; CHEMISTRY, PHYSICAL; DATABASES, PROTEIN; MUTATION; PROBABILITY; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT;

EID: 3042842115     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20098     Document Type: Article

References (24)

1. Olmea O, Valencia A. Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des 1997;2:S25-32.
2. Olmea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 1999;293:1221-1239.
3. Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins 1994;18:309-317.
4. Larson SM, Di Nardo AA, Davidson AR. Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J Mol Biol 2000;303:433-446.
5. Altschuh D, Lesk AM, Bloomer AC, Klug A. Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J Mol Biol 1987;193:693-707.
6. Fariselli P, Olmea O, Valencia A, Casadio R. Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations. Proteins 2001;45(Suppl 5):157-162.
7. Shindyalov IN, Kolchanov NA, Sander C. Can three dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng 1994;7:349-358.
8. Thomas DJ, Casari G, Sander C. The prediction of protein contacts from multiple sequence alignments. Protein Eng 1996;9:941-948.
9. Hatley ME, Lockless SW, Gibson SK, Gilman AG, Ranganathan R. Allosteric determinants in guanine nucleotide-binding proteins. Proc Natl Acad Sci USA 2003;100;14445-14450.
10. Lockless SW, Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999;286:295-299.
11. Suel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 2003;10:59-69.
12. Kass I, Horovitz A. Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 2002;48:611-617.
13. Atchley WR, Wollenberg KR, Fitch WM, Terhalle W, Dress AW. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol Biol Evol 2000;17:164-178.
14. Atchley WR, Terhalle W, Dress A. Positional dependence, cliques, and predictive motifs in the bHLH protein domain. J Mol Evol 1999;48:501-516.
15. McLachlan AD. Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551. J Mol Biol 1971;61: 409-424.
16. Shenkin PS, Erman B, Mastrandrea LD. Information theoretical entropy as a measure of sequence variability. Proteins 1991;11: 297-313.
17. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Res 2002;30:276-280.
18. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
19. Bickel PJ, Kechris KJ, Spector PC, Wedemayer GJ, Glazer AN. Inaugural article: finding important sites in protein sequences. Proc Natl Acad Sci USA 2002;99:14764-14771.
20. Carter PJ, Winter G, Wilkinson AJ, Fersht AR. The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus). Cell 1984; 38:835-840.
21. Jiang Y, Pico A, Cadene M, Chait BT, MacKinnon R. Structure of the RCK domain from the E. coli K+ channel and demonstration of its presence in the human BK channel. Neuron 2001;29:593-601.
22. Dekker J, Fodor A, Aldrich R, Yellen G. A perturbation based method for calculating explicit likelihood of evolutionary covariance in multiple sequence alignments. Bioinformatics, In press.
23. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
24. Aloy P, Stark A, Hadley C, Russell RB. Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins 2003;53(Suppl 6):436-456.