Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Ackerman, Sharon H ^a   Tillier, Elisabeth R ^b   Gatti, Domenico L ^a  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b PRINCESS MARGARET HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COEVOLUTION; COMPUTER ANALYSIS; COMPUTER PROGRAM; COMPUTER SIMULATION; CRYSTAL STRUCTURE; MOLECULAR SIZE; PROTEIN FAMILY; PROTEIN FUNCTION; SEQUENCE ALIGNMENT; STOCHASTIC MODEL; X RAY ANALYSIS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT;

EID: 84867605737     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047108     Document Type: Article

References (50)

1. Wollenberg KR, Atchley WR, (2000) Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. Proc Natl Acad Sci U S A 97: 3288-3291.
2. Atchley WR, Wollenberg KR, Fitch WM, Terhalle W, Dress AW, (2000) Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol Biol Evol 17: 164-178.
3. Sigala PA, Kraut DA, Caaveiro JM, Pybus B, Ruben EA, et al. (2008) Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. J Am Chem Soc 130: 13696-13708.
4. Fares MA, Travers SA, (2006) A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. Genetics 173: 9-23.
5. Horner DS, Pirovano W, Pesole G, (2008) Correlated substitution analysis and the prediction of amino acid structural contacts. Brief Bioinform 9: 46-56.
6. Caporaso JG, Smit S, Easton B, Hunter L, Huttley G, et al. (2008) Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics. BMC Evolutionary Biology 8: 327.
7. Codoner FM, Fares MA, (2008) Why should we care about molecular coevolution? Evol Bioinform Online 4: 29-38.
8. Kass I, Horovitz A, (2002) Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 48: 611-617.
9. Fodor AA, Aldrich RW, (2004) Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins 56: 211-221.
10. Dekker JP, Fodor A, Aldrich RW, Yellen G, (2004) A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. Bioinformatics 20: 1565-1572.
11. Lockless SW, Ranganathan R, (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286: 295-299.
12. Halabi N, Rivoire O, Leibler S, Ranganathan R, (2009) Protein sectors: evolutionary units of three-dimensional structure. Cell 138: 774-786.
13. Gobel U, Sander C, Schneider R, Valencia A, (1994) Correlated mutations and residue contacts in proteins. Proteins 18: 309-317.
14. Reza FM (1994) An Introduction to Information Theory. New York: Dover Publications, Inc.
15. Tillier ER, Lui TW, (2003) Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. Bioinformatics 19: 750-755.
16. Martin LC, Gloor GB, Dunn SD, Wahl LM, (2005) Using information theory to search for co-evolving residues in proteins. Bioinformatics 21: 4116-4124.
17. Gloor GB, Martin LC, Wahl LM, Dunn SD, (2005) Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. Biochemistry 44: 7156-7165.
18. Dunn SD, Wahl LM, Gloor GB, (2008) Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics 24: 333-340.
19. Brown CA, Brown KS, (2010) Validation of coevolving residue algorithms via pipeline sensitivity analysis: ELSC and OMES and ZNMI, oh my!. PLoS One 5: e10779.
20. Little DY, Chen L, (2009) Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution. PLoS One 4: e4762.
21. Gloor GB, Tyagi G, Abrassart DM, Kingston AJ, Fernandes AD, et al. (2010) Functionally Compensating Coevolving Positions Are Neither Homoplasic Nor Conserved in Clades. Mol Biol Evol 27: 1181-1191.
22. Burger L, van Nimwegen E, (2010) Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comput Biol 6: e1000633.
23. Jones DT, Buchan DW, Cozzetto D, Pontil M, (2012) PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 28: 184-190.
24. Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, et al. (2011) Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A 108: E1293-1301.
25. Codoner FM, O'Dea S, Fares MA, (2008) Reducing the false positive rate in the non-parametric analysis of molecular coevolution. BMC Evol Biol 8: 106.
26. Fernandes AD, Gloor GB, (2010) Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself? Bioinformatics 26: 1135-1139.
27. Suel GM, Lockless SW, Wall MA, Ranganathan R, (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10: 59-69.
28. Weigt M, White RA, Szurmant H, Hoch JA, Hwa T, (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A 106: 67-72.
29. Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, et al. (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS One 6: e28766.
30. Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, et al. (2012) Three-dimensional structures of membrane proteins from genomic sequencing. Cell 149: 1607-1621.
31. Nugent T, Jones DT, (2012) Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc Natl Acad Sci U S A 109: E1540-E1547.
32. Pang A, Smith AD, Nuin PA, Tillier ER, (2005) SIMPROT: using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics 6: 236.
33. Radaev S, Dastidar P, Patel M, Woodard RW, Gatti DL, (2000) Structure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase. J Biol Chem 275: 9476-9484.
34. Ludlam A, Brunzelle J, Pribyl T, Xu X, Gatti DL, et al. (2009) Chaperones of F1-ATPase. J Biol Chem 284: 17138-17146.
35. Zhou T, Radaev S, Rosen BP, Gatti DL, (2000) Structure of the ArsA ATPase: the catalytic subunit of a heavy metal resistance pump. Embo J 19: 4838-4845.
36. Martin P, DeMel S, Shi J, Gladysheva T, Gatti DL, et al. (2001) Insights into the structure, solvation, and mechanism of ArsC arsenate reductase, a novel arsenic detoxification enzyme. Structure 9: 1071-1081.
37. Gatti DL, Palfey BA, Lah MS, Entsch B, Massey V, et al. (1994) The mobile flavin of 4-OH benzoate hydroxylase. Science 266: 110-114.
38. Gassner GT, Ludwig ML, Gatti DL, Correll CC, Ballou DP, (1995) Structure and mechanism of the iron-sulfur flavoprotein phthalate dioxygenase reductase. FASEB J 9: 1411-1418.
39. Sukumar N, Xu Y, Gatti DL, Mitra B, Mathews FS, (2001) Structure of an active soluble mutant of the membrane-associated (S)-mandelate dehydrogenase. Biochemistry 40: 9870-9878.
40. Olmea O, Rost B, Valencia A, (1999) Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 293: 1221-1239.
41. Russ WP, Lowery DM, Mishra P, Yaffe MB, Ranganathan R, (2005) Natural-like function in artificial WW domains. Nature 437: 579-583.
42. Friedman J, Hastie T, Tibshirani R, (2008) Sparse inverse covariance estimation with the graphical lasso. Biostatistics 9: 432-441.
43. Hyvärinen A, Oja E, (2000) Independent Component Analysis: Algorithms and Applications. Neural Networks 13: 411-430.
44. Erdogmus D, Hild KE 2nd, Rao YN, Principe JC, (2004) Minimax mutual information approach for independent component analysis. Neural Comput 16: 1235-1252.
45. Notredame C, Higgins DG, Heringa J, (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302: 205-217.
46. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
47. Katoh K, Misawa K, Kuma K-i, Miyata T, (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl Acids Res 30: 3059-3066.
48. Fritsch FN, Carlson RE, (1980) Monotone Piecewise Cubic Interpolation. SIAM J Numerical Analysis 17: 238-246.
49. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York: Academic Press. pp. 21-123.
50. Felsenstein J (2004) Inferring Phylogenies. Sunderland, MA: Sinauer Associates, Inc.