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

TitleLarge-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP).
Publication TypeJournal Article
Year of Publication2004
AuthorsKim, WK, Bolser, DM, Park, JH
Date Published2004 May 01
KeywordsAmino Acid Sequence, Binding Sites, Chromosome Mapping, Evolution, Molecular, Gene Expression Profiling, Molecular Sequence Data, Phylogeny, Protein Binding, Protein Conformation, Protein Interaction Mapping, Protein Structure, Tertiary, Proteins, Proteome, Reproducibility of Results, Sensitivity and Specificity, Sequence Alignment, Sequence Analysis, Protein

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

Alternate JournalBioinformatics
Citation Key10.1093/bioinformatics/bth053
PubMed ID14764552