期刊
JOURNAL OF MOLECULAR BIOLOGY
卷 365, 期 5, 页码 1596-1606出版社
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2006.11.020
关键词
protein-protein interactions; principles of biomolecular recognition; positive and negative design; protein networks; homodimers and heterodimers
资金
- NIGMS NIH HHS [R01 GM052126-08, R56 GM052126, R01 GM052126-09A2, R01 GM052126-11, GM 52126, R01 GM052126-10, R01 GM052126] Funding Source: Medline
We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar structures. The effects originate in the fact that the probability to find a pattern self-match between two identical, even randomly organized interacting protein surfaces is always higher compared with the probability for a pattern match between two different, promiscuous protein surfaces. This theoretical finding explains statistical prevalence of homodimers in protein-protein interaction networks reported earlier. Further, our findings are confirmed by the analysis of curated database of protein complexes that showed highly statistically significant overrepresentation. of dimers formed by structurally similar proteins with highly divergent sequences (superfamily heterodimers). We suggest that promiscuous homodimeric interactions pose strong competitive interactions for heterodimers evolved from homodimers. Such evolutionary bottleneck is overcome using the negative design evolutionary pressure applied against promiscuous homodimer formation. This is achieved through the formation of highly specific contacts formed by charged residues as demonstrated both in model and real superfamily heterodimers. (c) 2006 Elsevier Ltd. All rights reserved.
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