title: Structural Effects of Some Relevant Missense Mutations on the MECP2-DNA Binding: A MD Study Analyzed by Rescore+, a Versatile Rescoring Tool of the VEGA ZZ Program.
abstract: DNA methylation plays key roles in mammalian cells and is modulated by a set of proteins which recognize symmetrically methylated nucleotides. Among them, the protein MECP2 shows multifunctional roles repressing and/or activating genes by binding to both methylated and unmethylated regions of the genome. The interest for this protein markedly increased from the observation that its mutations are the primary cause of Rett syndrome, a neurodevelopmental disorder which causes mental retardation in young females. Thus, the present study is aimed to investigate the effects of some of these known pathogenic missense mutations (i.e. R106Q, R106W, R111G, R133C and R133H) on the MECP2 folding and DNA binding by molecular dynamics simulations. The effects of the simulated mutations are also parameterized by using a here proposed new tool, named Rescore+, implemented in the VEGA ZZ suite of programs, which calculates a set of scoring functions on all frames of a trajectory or on all complexes contained in a database thus allowing an easy rescoring of results coming from MD or docking simulations. The obtained results revealed that the reported loss of the MECP2 function induced by the simulated mutations can be ascribed to both stabilizing and destabilizing effect on DNA binding. The study confirms that MD simulations are particularly useful to rationalize and predict the mutation effects offering insightful information for diagnostics and drug design.
authors.affiliation: Dipartimento di Scienze Farmaceutiche "Pietro Pratesi", Facoltà di Farmacia, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133, Milano, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Pedretti
authors.affiliation: Dipartimento di Scienze Farmaceutiche "Pietro Pratesi", Facoltà di Farmacia, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133, Milano, Italy.
authors.forename: Cinzia
authors.initials: C
authors.lastname: Granito
authors.affiliation: Dipartimento di Scienze Farmaceutiche "Pietro Pratesi", Facoltà di Farmacia, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133, Milano, Italy.
authors.forename: Angelica
authors.initials: A
authors.lastname: Mazzolari
authors.affiliation: Dipartimento di Scienze Farmaceutiche "Pietro Pratesi", Facoltà di Farmacia, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133, Milano, Italy. Giulio.Vistoli@unimi.it.
authors.forename: Giulio
authors.initials: G
authors.lastname: Vistoli
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D051783:Methyl-CpG-Binding Protein 2 / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D020125:Mutation, Missense / Q000235:genetics*; D011485:Protein Binding / Q000235:genetics; D015518:Rett Syndrome / Q000235:genetics
chemical_list: D004268:DNA-Binding Proteins; C497392:MECP2 protein, human; D051783:Methyl-CpG-Binding Protein 2; D004247:DNA
keywords: DNA binding; MECP2; missense mutations; molecular dynamics; rescoring tool