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Media type:
E-Article
Title:
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein–protein docking
Contributor:
Dobbins, Sara E.;
Lesk, Victor I.;
Sternberg, Michael J. E.
Published:
Proceedings of the National Academy of Sciences, 2008
Published in:
Proceedings of the National Academy of Sciences, 105 (2008) 30, Seite 10390-10395
Language:
English
DOI:
10.1073/pnas.0802496105
ISSN:
0027-8424;
1091-6490
Origination:
Footnote:
Description:
Understanding protein interactions has broad implications for the mechanism of recognition, protein design, and assigning putative functions to uncharacterized proteins. Studying protein flexibility is a key component in the challenge of describing protein interactions. In this work, we characterize the observed conformational change for a set of 20 proteins that undergo large conformational change upon association (>2 Å Cα RMSD) and ask what features of the motion are successfully reproduced by the normal modes of the system. We demonstrate that normal modes can be used to identify mobile regions and, in some proteins, to reproduce the direction of conformational change. In 35% of the proteins studied, a single low-frequency normal mode was found that describes well the direction of the observed conformational change. Finally, we find that for a set of 134 proteins from a docking benchmark that the characteristic frequencies of normal modes can be used to predict reliably the extent of observed conformational change. We discuss the implications of the results for the mechanics of protein recognition.