ArticleComputational and structural biotechnology journal2020
Both intra and inter-domain interactions define the intrinsic dynamics and allosteric mechanism in DNMT1s.
Article in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 23 citations in OpenAlex.
- Disease-Associated Mutations Impact DNA Methyltransferase 1 Function through Dynamic Allosteric Effects and Solvent Exposure.Journal of chemical theory and computation · 2026Article
- Decoding Mechanisms of PTEN Missense Mutations in Cancer and Autism Spectrum Disorder using Interpretable Machine Learning Approaches.bioRxiv : the preprint server for biology · 2025Article
- Prediction of the binding mechanism of a selective DNA methyltransferase 3A inhibitor by molecular simulation.Scientific reports · 2024Article
- Mechanism studies of the activation of DNA methyltransferase DNMT1 triggered by histone H3 ubiquitination, revealed by multi-scale molecular dynamics simulations.Science China. Life sciences · 2023Article
- Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect.Frontiers in molecular biosciences · 2022Article
- DNMT3A and DNMT3B in Breast Tumorigenesis and Potential Therapy.Frontiers in cell and developmental biology · 2022Review
- Deciphering the active constituents of Dabushen decoction of ameliorating osteoarthritisFrontiers in pharmacology · 2022Article
- How does nintedanib overcome cancer drug-resistant mutation of RET protein-tyrosine kinase: insights from molecular dynamics simulations.Journal of molecular modeling · 2021Article
- Markov State Models and Molecular Dynamics Simulations Provide Understanding of the Nucleotide-Dependent Dimerization-Based Activation of LRRK2 ROC Domain.Molecules (Basel, Switzerland) · 2021Article
- Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions.Molecules (Basel, Switzerland) · 2021Article
- Untangling Dual-Targeting Therapeutic Mechanism of Epidermal Growth Factor Receptor (EGFR) Based on Reversed Allosteric Communication.Pharmaceutics · 2021Article
- Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism ofComputational and structural biotechnology journal · 2021Article
- Deciphering the Mechanism of Gilteritinib Overcoming Lorlatinib Resistance to the Double Mutant I1171N/F1174I in Anaplastic Lymphoma Kinase.Frontiers in cell and developmental biology · 2021Article
- Is Crocin a Potential Anti-tumor Candidate Targeting Microtubules? Computational Insights From Molecular Docking and Dynamics Simulations.Frontiers in molecular biosciences · 2020Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methyltransferase 1 (DNMT1), a large multidomain enzyme, is believed to be involved in the passive transmission of genomic methylation patterns via methylation maintenance. Yet, the molecular mechanism of interaction networks underlying DNMT1 structures, dynamics, and its biological significance has yet to be fully characterized. In this work, we used an integrated computational strategy that combined coarse-grained and atomistic simulations with coevolution information and network modeling of the residue interactions for the systematic investigation of allosteric dynamics in DNMT1. The elastic network modeling has proposed that the high plasticity of RFTS has strengthened the correlated behaviors of DNMT1 structures through the hinge sites located at the RFTS-CD interface, which mediate the collective motions between domains. The perturbation response scanning (PRS) analysis combined with the enrichment analysis of disease mutations have further highlighted the allosteric potential of the RFTS domain. Furthermore, the long-range paths connect the intra-domain interactions through the TRD interface and catalytic interface, emphasizing some key inter-domain interactions as the bridges in the global allosteric regulation of DNMT1. The observed interplay between conserved intra-domain networks and dynamical plasticity encoded by inter-domain interactions provides insights into the intrinsic dynamics and functional evolution, as well as the design of allosteric modulators of DNMT1 based on the TRD interface.
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