Fig. 1: Molecular dynamic simulations of DNMT1 binding to unmethylated DNA (UMDNA). | Nature Communications

Fig. 1: Molecular dynamic simulations of DNMT1 binding to unmethylated DNA (UMDNA).

From: DNMT1-mediated regulation of somatostatin-positive interneuron migration impacts cortical architecture and function

Fig. 1: Molecular dynamic simulations of DNMT1 binding to unmethylated DNA (UMDNA).The alternative text for this image may have been generated using AI.

a DNMT1/UMDNA/SAH complex unit in the X-ray structure (PDB ID: 3PTA). Inter-unit DNMT1 protein regions (rose-pink) are mostly positively charged and interact with the UMDNA (blue). Intra-unit DNMT1 regions include the autoinhibitory linker BAH1/BAH2 (white surface), catalytic domain (orange), SAH (red spheres), and CXXC domain (yellow). More information is presented in Supplementary Fig. S1b. b–g Simulations of DNMT1/UMDNA interactions in aqueous solution. b Illustration of the DNMT1/UMDNA complex in solution. c Structure of the complex at the endpoint of one of three MD simulations (same coloring scheme as in (a)), with residues at the CpG site interacting with the catalytic domain highlighted by sticks. Only hydrogen atoms bound to polar groups are shown (as black dashed lines). d–g Number of contacts between DNMT1 and UMDNA (d), the 5’ (e), and 3’ regions (f), as well as between the catalytic domain of DNMT1 and the 5’ region (g) during the last-100-ns simulation (being consistent across replicas (Supplementary Fig. S1g, h). Raw data are available via the hyperlinks listed in the Data Availability Statement.

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