How MeCP2 and R.DpnI Proteins Recognize Methylated DNA

Abstract

DNA methylation plays a major role in organismal development and the regulation of gene expression. Methylation of cytosine bases and its cellular roles in eukaryotes are well established, as well as methylation of adenine bases in bacterial genomes. Here, we present results from molecular dynamics simulations, alchemical free energy perturbation, and MM-PBSA calculations to explain the specificity of the R.DpnI enzyme for binding to adenine-methylated DNA in both its catalytic and winged-helix domains. We find that adenine-methylated DNA binds more favorably to the catalytic subunit of R.DpnI (−4 kcal/mol) and to the winged-helix domain (−1.6 kcal/mol) than unmethylated DNA.In particular, N6-adenine methylation is found to enthalpically stabilize binding to R.DpnI. In contrast, C5-cytosine methylation stabilizes binding to the MBD domain of the MeCP2 entropically with almost no difference in binding enthalpy.