title: Accurate prediction of the dynamical changes within the second PDZ domain of PTP1e.
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 thses kinds of methods.
authors.affiliation: MLG, Département d'Informatique, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Elisa
authors.initials: E
authors.lastname: Cilia
authors.forename: Geerten W
authors.initials: GW
authors.lastname: Vuister
authors.forename: Tom
authors.initials: T
authors.lastname: Lenaerts
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D054731:PDZ Domains; D011487:Protein Conformation; D060066:Protein Interaction Maps; D054595:Protein Tyrosine Phosphatase, Non-Receptor Type 13 / Q000737:chemistry* / Q000378:metabolism*; D016415:Sequence Alignment
chemical_list: C516742:PTPN13 protein, human; D054595:Protein Tyrosine Phosphatase, Non-Receptor Type 13