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| Title: | Analysing six types of protein-protein interfaces |
| Author: | Yanay Ofran & Burkhard Rost |
| Quote: | J Mol Biol, 325, 377-387 |
Non-covalent residue side-chain interactions occur in many different types of proteins and facilitate many biological functions. Are these differences manifested in the sequence compositions and/or the residue-residue contact preferences of the interfaces? Previous studies analysed small data sets and gave contradicting answers. Here, we introduced a new data-mining method that yielded the largest high-resolution data set of interactions analysed. We also introduced an information theory-based analysis method. Based on sequence features we were able to clearly differentiate six types of protein interfaces, each corresponding to a different functional or structural association between residues. Particularly, we found significant differences in amino acid composition and residue-residue preferences between interactions of residues within the same structural domain and between different domains, between permanent and transient interfaces, and between interactions associating homo- and hetero-oligomers. The differences between the six types were so substantial that using amino acid composition alone, we could statistically predict to which of the six types of interfaces a pool of 1000 residues belongs at 63-100% accuracy. All interfaces differed significantly from the background of all residues in SWISS-PROT, from the group of surface residues, and from internal residues that were not involved in non-trivial interactions. Overall, our results may suggest that the interface type could be predicted from sequence and that interface-type specific mean-field potentials may be adequate for certain applications.