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Protein-Peptide Interactions Adopt the Same Structural Motifs as Monomeric Protein Folds

par Vanhee, Peter;Stricher, Francois F.;Baeten, Lies L.;Verschueren, Erik;Lenaerts, Tom ;Serrano, Luis;Rousseau, Frédéric;Schymkowitz, Joost J.
Référence Structure, 17, 8, page (1128-1136)
Publication Publié, 2009-08

Article révisé par les pairs

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Résumé :

We compared the modes of interaction between protein-peptide interfaces and those observed within monomeric proteins and found surprisingly few differences. Over 65% of 731 protein-peptide interfaces could be reconstructed within 1 Å RMSD using solely fragment interactions occurring in monomeric proteins. Interestingly, more than 80% of interacting fragments used in reconstructing a protein-peptide binding site were obtained from monomeric proteins of an entirely different structural classification, with an average sequence identity below 15%. Nevertheless, geometric properties perfectly match the interaction patterns observed within monomeric proteins. We show the usefulness of our approach by redesigning the interaction scaffold of nine protein-peptide complexes, for which five of the peptides can be modeled within 1 Å RMSD of the original peptide position. These data suggest that the wealth of structural data on monomeric proteins could be harvested to model protein-peptide interactions and, more importantly, that sequence homology is no prerequisite. © 2009 Elsevier Ltd. All rights reserved.