Bioinformatics Advance Access originally published online on February 5, 2004
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Bioinformatics 20(7) © Oxford University Press 2004; all rights reserved.
Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)
1 MRC Rosalind Franklin Centre for Genome Research, Hinxton, Cambridge, CB10 1SB, UK, 2 MRC-DUNN Human Nutrition Unit, Hills Road, Cambridge, CB2 2XY, UK, 3 NGIC, KRIBB, DaeJeon, Korea and 4 Biomatics Lab, BioSystems Dept. KAIST, DaeJeon, Korea
Received on September 2, 2003; revised on November 30, 2003; accepted on December 1, 2003
Advance Access Publication February 5, 2004
Motivation: Interacting pairs of proteins should co-evolve to maintain functional and structural complementarity. Consequently, such a pair of protein families shows similarity between their phylogenetic trees. Although the tendency of co-evolution has been known for various ligand–receptor pairs, it has not been studied systematically in the widest possible scope. We investigated the degree of co-evolution for more than 900 family pairs in a global protein structural interactome map (PSIMAP—a map of all the structural domain–domain interactions in the PDB).
Results: There was significant correlation in 45% of the total SCOPs Family level pairs, rising to 78% in 454 reliable family interactions. Expectedly, the intra-molecular interactions between protein families showed stronger co-evolution than inter-molecular interactions. However, both types of interaction have a fundamentally similar pattern of co-evolution except for cases where different interfaces are involved. These results validate the use of co-evolution analysis with predictive methods such as PSIMAP to improve the accuracy of prediction based on ‘homologous interaction’. The tendency of co-evolution enabled a nearly 5-fold enrichment in the identification of true interactions among the potential interlogues in PSIMAP. The estimated sensitivity was 79.2%, and the specificity was 78.6%.
Availability: The results of co-evolution analysis are available online at http://www.biointeraction.org
Contact: biopark{at}kaist.ac.kr; j{at}bio.cc
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  H. Madaoui and R. Guerois Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking PNAS, June 3, 2008; 105(22): 7708 - 7713. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Dawelbait, C. Winter, Y. Zhang, C. Pilarsky, R. Grutzmann, J.-C. Heinrich, and M. Schroeder Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data Bioinformatics, July 1, 2007; 23(13): i115 - i124. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Hakes, S. C. Lovell, S. G. Oliver, and D. L. Robertson Specificity in protein interactions and its relationship with sequence diversity and coevolution PNAS, May 8, 2007; 104(19): 7999 - 8004. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Sato, Y. Yamanishi, K. Horimoto, M. Kanehisa, and H. Toh Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions Bioinformatics, October 15, 2006; 22(20): 2488 - 2492. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. G. Izarzugaza, D. Juan, C. Pons, J. A. G. Ranea, A. Valencia, and F. Pazos TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W315 - W319. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Henschel, W. K. Kim, and M. Schroeder Equivalent binding sites reveal convergently evolved interaction motifs Bioinformatics, March 1, 2006; 22(5): 550 - 555. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Winter, A. Henschel, W. K. Kim, and M. Schroeder SCOPPI: a structural classification of protein-protein interfaces Nucleic Acids Res., January 1, 2006; 34(suppl_1): D310 - D314. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Mintseris and Z. Weng Structure, function, and evolution of transient and obligate protein-protein interactions PNAS, August 2, 2005; 102(31): 10930 - 10935. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. S. Moon, J. Bhak, K. H. Lee, and D. Lee Architecture of basic building blocks in protein and domain structural interaction networks Bioinformatics, April 15, 2005; 21(8): 1479 - 1486. [Abstract] [Full Text] [PDF]
|
|