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Bioinformatics Advance Access published online on February 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth053
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received September 2, 2003
Revised November 30, 2003
Accepted December 1, 2003

Article

Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)

Wan K. Kim 1, Dan M. Bolser 2, Jong H. Park 3*

1 MRC Rosalind Franklin Centre for Genome Research, Hinxton, Cambridge, CB10 1SB, UK
2 2MRC-DUNN Human Nutrition Unit, Hills Road, Cambridge, CB2 2XY, UK
3 NGIC, KRIBB, DaeJeon, Korea; Biomatics Lab, BioSystems Dept. KAIST, DaeJeon, Korea

* To whom correspondence should be addressed. E-mail: biopark{at}kaist.ac.kr.


  Abstract

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


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