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Title: Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e
Authors: Cilia, Elisa
Vuister, Geerten W.
Lenaerts, Tom
First Published: 29-Nov-2012
Publisher: Public Library of Science on behalf of the International Society for Computational Biology (ISCB)
Citation: PLoS Computational Biology, 2012, 8 (11), e1002794
Abstract: Experimental NMR relaxation studies have shown that peptide binding induces dynamical changes at the side-chain level throughout the second PDZ domain of PTP1e, identifying as such the collection of residues involved in long-range communication. Even though different computational approaches have identified subsets of residues that were qualitatively comparable, no quantitative analysis of the accuracy of these predictions was thus far determined. Here, we show that our information theoretical method produces quantitatively better results with respect to the experimental data than some of these earlier methods. Moreover, it provides a global network perspective on the effect experienced by the different residues involved in the process. We also show that these predictions are consistent within both the human and mouse variants of this domain. Together, these results improve the understanding of intra-protein communication and allostery in PDZ domains, underlining at the same time the necessity of producing similar data sets for further validation of these kinds of methods.
DOI Link: 10.1371/journal.pcbi.1002794
ISSN: 1553-734X
eISSN: 1553-7358
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright: © 2012 Cilia et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Appears in Collections:Published Articles, Dept. of Biochemistry

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