Side-chain rotamer transitions at protein-protein interfaces.

TitleSide-chain rotamer transitions at protein-protein interfaces.
Publication TypeJournal Article
Year of Publication2010
AuthorsGuharoy, M., J. Janin, and C. H. Robert
JournalProteins
Volume78
Issue15
Pagination3219-25
Date Published2010 Nov 15
ISSN1097-0134
KeywordsAlgorithms, Computational Biology, Models, Molecular, Monte Carlo Method, Protein Conformation, Protein Interaction Domains and Motifs, Proteins, Thermodynamics
Abstract

We compare the changes in side chain conformations that accompany the formation of protein-protein complexes, in residues forming either the interface or the remainder of the solvent-accessible surface of the proteins in the Docking Benchmark 3.0. We find that the interface residues undergo significantly more changes than other surface residues, and these changes are more likely to convert them from a high-energy torsion angle state to a lower-energy one than the reverse. Moreover, in both the unbound proteins and the complexes, the interface residues are more frequently found to be in a high-energy torsion angle state than the noninterface residues. As these differences exist before the binding step, they may be relevant to specificity and help in identifying binding sites for docking predictions.

DOI10.1002/prot.22821
Alternate JournalProteins
PubMed ID20737439
Research group: