ScriptBiochemistry. Author manuscript; available in PMC 2014 April 23.Published in final edited type as: Biochemistry. 2013 April 23; 52(16): 2828?838. doi:10.1021/bi400163k.NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptDNA cytosine methylation: Structural and thermodynamic characterization in the epigenetic marking mechanismJin Yang? Lee Lior-Hoffmann?, Shenglong Wang? Yingkai Zhang?*, and Suse Broyde,* �Department of Chemistry, New York University, New York, New York 10003, United StatesDepartmentof Biology, New York University, New York, New York 10003, United StatesAbstractDNA cytosine methyltransferases regulate the expression on the genome through the precise epigenetic marking of particular cytosines using a methyl group, and aberrant methylation is actually a hallmark of human diseases which includes cancer. Targeting these enzymes for drug design and style is currently a high priority. We have utilized ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations to extensively investigate the reaction mechanism with the representative DNA methyltransferase HhaI (M.HhaI) from prokaryotes, whose overall mechanism is shared together with the mammalian enzymes. We receive for the initial time complete no cost power profiles for the full reaction, together with reaction dynamics in atomistic detail. Our final results show an energetically preferred mechanism in which nucleophilic attack of cytosine C5 around the S-adenosyl-L-methionine (AdoMet) methyl group is concerted with formation in the Michael adduct among a conserved Cys inside the active site with cytosine C6.Perfluoroundecanoic acid Chemscene Spontaneous and reversible proton transfer among a conserved Glu in the active site and cytosine N3 in the transition state was observed in our simulations, revealing the chemical participation of this Glu residue inside the catalytic mechanism. Subsequently, the ?elimination on the C5 proton utilizes as base an OH- derived from a conserved crystal water that’s aspect of a proton wire water channel, and this syn limination reaction is the rate-limiting step. Design and style of novel cytosine methylation inhibitors could be sophisticated by our structural and thermodynamic characterization on the reaction mechanism.Search phrases DNA cytosine methylation mechanism; QM/MM-MD simulation; Epigenetics The DNA methyl transferases play crucial roles in lots of biological functions. They are important players in regulating gene expression1: in embryonic development2, three, in X-chromosome inactivation4, in genomic imprinting5 and, all round, in epigenetic mechanisms that transmit genetic data devoid of altering the actual base sequence of the DNA through regulation of your methylation status6-8. Aberrant methylation is usually a feature of cancers and also other diseases9-11.Formula of 1885090-83-4 Methyl transferase activity is impaired by DNA harm resulting from environmental carcinogens, notably benzo[a]pyrene12, 13 and methylation status has an important effect around the reactivity of DNA with benzo[a]pyrene metabolites14.PMID:23357584 The design*Corresponding authors: (212) 998-7882, Fax (212) 995-4475, [email protected] (212) 998-8231, Fax (212) 995-4015, [email protected]. Conflict of interest statement. None declared. Supporting Information Extra facts regarding MD simulation protocol and other tested mechanisms. Protonation state of charged residue assignments (Table S1), and force field parameters (Table S2). Figures S1 – S14 and Movies S1 – S2 as described inside the text. This material is readily available no cost of charge via the online world at htt.