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Updated: May 22, 2025

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Deciphering the structural consequences of R83 and R152 methylation on DNA polymerase β using molecular modeling.

Amit Srivastava1, Haitham Idriss2,3,4, Gobind Das1

  • 1Department of Physics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.

Plos One
|March 12, 2025
PubMed
Summary
This summary is machine-generated.

Methylation of DNA polymerase β at R83 and R152 by PRMT6 enhances its activity. This study reveals how methylation alters enzyme structure and dynamics, improving DNA binding and processivity at an atomic level.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • DNA polymerase β (Pol β) is crucial for DNA repair and replication.
  • Posttranslational modifications, like methylation, regulate Pol β activity.
  • PRMT6 methylates Pol β at R83 and R152, enhancing its function.

Purpose of the Study:

  • To elucidate the structural and dynamic mechanisms underlying methylation-induced enhancement of Pol β activity.
  • To understand how PRMT6-mediated methylation at R83 and R152 impacts Pol β-DNA interactions.

Main Methods:

  • Molecular modeling of the methylated Pol β/DNA complex.
  • Microsecond-long molecular dynamics simulations with Mg ions.
  • Analysis of structural changes, hydrogen bonding, cross-correlation maps, and graph connectivity networks.

Main Results:

  • Methylation at R83 and R152 induced significant structural changes in Pol β.
  • The DNA fragment moved closer to enzyme subdomains, forming new hydrogen bonds.
  • Methylation enhanced long-range correlations and modulated information pathways within the enzyme-DNA complex.

Conclusions:

  • Methylation at R83 and R152 by PRMT6 enhances Pol β activity through specific structural and dynamic alterations.
  • This study provides atomic-level insights into the mechanism of methylation-driven Pol β functional enhancement.
  • Findings clarify how posttranslational modifications impact DNA polymerase function and regulation.