|Journal of Molecular Biology (2003) 325:377-87|
|Northeast Structural Genomics Consortium|
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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 contradictory answers. Here, we introduced a new data-mining method that yielded the largest high-resolution data set of interactions analysed. We introduced an information theory-based analysis method. On the basis of sequence features, we were able to 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-oligomers and hetero-oligomers. The differences between the six types were so substantial that, using amino acid composition alone, we could predict statistically 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 suggest that the interface type could be predicted from sequence and that interface-type specific mean-field potentials may be adequate for certain applications.
|analysis chemistry metabolism |
|Amino Acids Databases, Protein Protein Conformation Protein Folding Amino Acid Sequence Proteins Mathematics |
|280 (Last update: 03/18/2017 12:14:40pm)|
|J Mol Biol. 2003 Jan 10;325(2):377-87.|