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

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Title
Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map(PSIMAP)
Author(s)
W K Kim; D M Bolser; Jong Park
Bibliographic Citation
Bioinformatics, vol. 20, no. 7, pp. 1138-1150
Publication Year
2004
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%.
ISSN
1367-4803
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/bioinformatics/bth053
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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