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Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e

TitleAccurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e
Publication TypeJournal Article
Year of Publication2012
AuthorsCilia, E, Vuister, GW, Lenaerts, T
JournalPLoS Comput Biol
Volume8
Issue11
Paginatione1002794 -
Date Published2012/11/29
Abstract

<title>Author Summary</title><p>Intra-protein communication has recently attracted an increasing interest from the scientific community, because of its important functional consequences: allostery and signalling. Unravelling how information is processed and transferred within a protein structure requires the study of the dynamical effects of, for instance, binding events, which may be captured experimentally by NMR relaxation experiments. Given the complexity of this experimental analysis, computational approaches, often based on molecular dynamics simulations, have been proposed for predicting these dynamical effects, using protein structural information as input. We examine here the accuracy of these predictors in the context of a well-studied domain, i.e. the second PSD95/Disc-large/ZO-1 domain (or PDZ domain) of PTP1e, and compare it to our approach that combines Monte-Carlo sampling of the conformational space of the side-chains and an information theoretical analysis. The results we discuss in this manuscript show clearly that the latter method provides very accurate predictions when compared to the experimental results, and has a better predictive quality compared to other computational approaches. The predictions, which are consistent between closely related structures, and the global network perspective provided by this approach, improve our understanding of intra-protein communication and allostery in these domains.</p>

URLhttp://dx.doi.org/10.1371%2Fjournal.pcbi.1002794

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