Correlated Evolution of Interacting Proteins: Looking Behind the Mirrortree

Journal of Molecular Biology

Volumn 385, Issue 1, 2009, Pages 91-98

  Kann, Maricel G ^a   Shoemaker, Benjamin A ^b   Panchenko, Anna R ^b   Przytycka, Teresa M ^b  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

domain domain interactions; mirrortree; phylogenetic tree; protein coevolution; protein protein interactions

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CORRELATION ANALYSIS; EVOLUTION; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION;

EID: 57849099132     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.09.078     Document Type: Article

References (31)

1. Goh C.S., Bogan A.A., Joachimiak M., Walther D., and Cohen F.E. Co-evolution of proteins with their interaction partners. J. Mol. Biol. 299 (2000) 283-293
2. Pazos F., Helmer-Citterich M., Ausiello G., and Valencia A. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271 (1997) 511-523
3. Pazos F., and Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14 (2001) 609-614
4. Goh C.S., and Cohen F.E. Co-evolutionary analysis reveals insights into protein-protein interactions. J. Mol. Biol. 324 (2002) 177-192
5. Jothi R., Kann M.G., and Przytycka T.M. Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics 21 (2005) i241-i250
6. Kann M.G., Jothi R., Cherukuri P.F., and Przytycka T.M. Predicting protein domain interactions from coevolution of conserved regions. Proteins 67 (2007) 811-820
7. Jothi R., Cherukuri P.F., Tasneem A., and Przytycka T.M. Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J. Mol. Biol. 362 (2006) 861-875
8. Ramani A.K., and Marcotte E.M. Exploiting the co-evolution of interacting proteins to discover interaction specificity. J. Mol. Biol. 327 (2003) 273-284
9. Gertz J., Elfond G., Shustrova A., Weisinger M., Pellegrini M., Cokus S., and Rothschild B. Inferring protein interactions from phylogenetic distance matrices. Bioinformatics 19 (2003) 2039-2045
10. Pazos F., and Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47 (2002) 219-227
11. Sato T., Yamanishi Y., Kanehisa M., and Toh H. The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 21 (2005) 3482-3489
12. Tan S.H., Zhang Z., and Ng S.K. ADVICE: Automated Detection and Validation of Interaction by Co-Evolution. Nucleic Acids Res. 32 (2004) W69-W72
13. Craig R.A., and Liao L. Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices. BMC Bioinformatics 8 (2007) 6
14. Pazos F., Ranea J.A., Juan D., and Sternberg M.J. Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J. Mol. Biol. 352 (2005) 1002-1015
15. Juan D., Pazos F., and Valencia A. Co-evolution and co-adaptation in protein networks. FEBS Lett. 582 (2008) 1225-1230
16. Fraser H.B., Hirsh A.E., Steinmetz L.M., Scharfe C., and Feldman M.W. Evolutionary rate in the protein interaction network. Science 296 (2002) 750-752
17. Kim W.K., Bolser D.M., and Park J.H. Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinformatics 20 (2004) 1138-1150
18. Mintseris J., and Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc. Natl Acad. Sci. USA 102 (2005) 10930-10935
19. Chakrabarti S., and Panchenko A. Coevolution in defining the functional specificity. Proteins (2008) [Epub ahead of print]
20. Fraser H.B., Hirsh A.E., Wall D.P., and Eisen M.B. Coevolution of gene expression among interacting proteins. Proc. Natl Acad. Sci. USA 101 (2004) 9033-9038
21. Drummond D.A., Bloom J.D., Adami C., Wilke C.O., and Arnold F.H. Why highly expressed proteins evolve slowly. Proc. Natl Acad. Sci. USA 102 (2005) 14338-14343
22. Rocha E.P., and Danchin A. An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol. Biol. Evol. 21 (2004) 108-116
23. Hakes L., Lovell S.C., Oliver S.G., and Robertson D.L. Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proc. Natl Acad. Sci. USA 104 (2007) 7999-8004
24. Juan D., Pazos F., and Valencia A. High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc. Natl Acad. Sci. USA 105 (2008) 934-939
25. Yeang C.H., and Haussler D. Detecting coevolution in and among protein domains. PLoS Comput. Biol. 3 (2007) e211
26. Shoemaker B.A., Panchenko A.R., and Bryant S.H. Finding biologically relevant protein domain interactions: conserved binding mode analysis. Protein Sci. 15 (2006) 352-361
27. Swets J.A. Measuring the accuracy of diagnostic systems. Science 240 (1988) 1285-1293
28. McClish D.K. Analyzing a portion of the ROC curve. Med. Decis. Mak. 9 (1989) 190-195
29. Gribskov M., and Robinson N.L. Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem. 20 (1996) 25-33
30. Marchler-Bauer A., Anderson J.B., Cherukuri P.F., DeWeese-Scott C., Geer L.Y., Gwadz M., et al. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 33 (2005) D192-D196
31. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637