Phosphorylation Induced Conformational Transitions in DNA Polymerase β

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• DNA polymerase beta (pol β) is crucial for base excision DNA repair.
• Previous in vitro studies showed PKC phosphorylation of pol β at S44 and S55 reduces polymerase activity but not DNA binding.

Purpose of the Study:

• To investigate phosphorylation-induced conformational changes in DNA polymerase beta (pol β) with a focus on S44 phosphorylation.
• To elucidate the role of magnesium ions in these conformational transitions.

Main Methods:

• Comprehensive atomic resolution molecular dynamics (MD) simulations of wild-type and phosphorylated DNA polymerase beta.
• Analysis of internal dynamics, energetics, dynamic cross-correlation, and centrality network analysis.
• Examination of hydrogen bond disruption and salt bridge formation.

Main Results:

• S44 phosphorylation induces drastic conformational changes, shifting pol β from a closed to an open structure.
• Phosphorylation enhances correlated motions between enzyme domains and modulates information flow between the Lyase and base pair binding domains.
• Disruption of a key hydrogen bond (S44-E335) and formation of new salt bridges, particularly in the presence of Mg ions, drive these changes.

Conclusions:

• S44 phosphorylation significantly alters pol β structure and dynamics, impacting its function in DNA repair.
• Magnesium ions play a critical role in mediating the conformational transitions and enrich the structural phase space.
• These findings provide mechanistic insights into pol β regulation and its role in DNA repair pathways.