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


BACKGROUND
The results of co-evolution analysis are available online at http://www.biointeraction.org
Kim
Wan K
WK
MRC Rosalind Franklin Centre for Genome Research, Hinxton, Cambridge CB10 1SB, UK.
Bolser
Dan M
DM
Park
Jong H
JH
D000595:Amino Acid Sequence; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D008969:Molecular Sequence Data; D010802:Phylogeny; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*
D011506:Proteins; D020543:Proteome