title: Methylation-targeted specificity of the DNA binding proteins R.DpnI and MeCP2 studied by molecular dynamics simulations.
abstract: DNA methylation plays a major role in organismal development and the regulation of gene expression. Methylation of cytosine bases and the cellular roles of methylated cytosine in eukaryotes are well established, as well as methylation of adenine bases in bacterial genomes. Still lacking, however, is a general mechanistic understanding, in structural and thermodynamic terms, of how proteins recognize methylated DNA. Toward this aim, we present the results of molecular dynamics simulations, alchemical free energy perturbation, and MM-PBSA calculations to explain the specificity of the R.DpnI enzyme from Streptococcus pneumonia in binding to adenine-methylated DNA with both its catalytic and winged-helix domains. We found that adenine-methylated DNA binds more favorably to the catalytic subunit of R.DpnI (-4 kcal mol-1) and to the winged-helix domain (-1.6 kcal mol-1) than non-methylated DNA. In particular, N6-adenine methylation is found to enthalpically stabilize binding to R.DpnI. In contrast, C5-cytosine methylation entropically favors complexation by the MBD domain of the human MeCP2 protein with almost no contribution of the binding enthalpy.
authors.affiliation: Center for Bioinformatics, Saarland University, PO Box/15 11 50, 66041, Saarbrücken, Germany.|Department of Biology and Biotechnology, Faculty of Science, Arab American University, PO Box 240, Jenin, Palestinian Territories, Israel.
authors.forename: Siba
authors.initials: S
authors.lastname: Shanak
authors.affiliation: Center for Bioinformatics, Saarland University, PO Box/15 11 50, 66041, Saarbrücken, Germany.
authors.forename: Ozlem
authors.initials: O
authors.lastname: Ulucan
authors.affiliation: Center for Bioinformatics, Saarland University, PO Box/15 11 50, 66041, Saarbrücken, Germany. volkhard.helms@bioinformatik.uni-saarland.de.
authors.forename: Volkhard
authors.identifier: http://orcid.org/0000-0002-2180-9154
authors.initials: V
authors.lastname: Helms
mesh_terms: D000225:Adenine / Q000737:chemistry; D020134:Catalytic Domain / Q000235:genetics; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D004262:DNA Restriction Enzymes / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D006801:Humans; D051783:Methyl-CpG-Binding Protein 2 / Q000737:chemistry / Q000235:genetics*; D056004:Molecular Dynamics Simulation; D013296:Streptococcus pneumoniae / Q000201:enzymology; D013816:Thermodynamics
chemical_list: D004268:DNA-Binding Proteins; C497392:MECP2 protein, human; D051783:Methyl-CpG-Binding Protein 2; D003596:Cytosine; D004247:DNA; D004262:DNA Restriction Enzymes; D000225:Adenine
keywords: Binding free energy; Conformational entropy; DNA methylation; Free energy perturbation; MM-PBSA; Restriction endonuclease; Sequence specificity; m5C; m6A