Substrate-dependent millisecond domain motions in DNA polymerase β

Area of Science:

• Biochemistry and Molecular Biology
• Enzymology
• Structural Biology

Background:

• DNA polymerase β (Pol β) is essential for DNA repair, and its mutations are linked to cancer.
• Pol β's fidelity in nucleotide incorporation is critical for repair, potentially influenced by conformational changes.
• Understanding Pol β dynamics is key to elucidating its role in DNA repair and disease.

Purpose of the Study:

• To determine the rate constants for domain motions in apo and substrate-bound DNA polymerase β (Pol β).
• To investigate how substrate binding affects the dynamic landscape and conformational flexibility of Pol β.
• To correlate identified flexible residues with known cancer-associated mutations.

Main Methods:

• Solution NMR relaxation dispersion was employed to measure domain motion rate constants.
• Studies were conducted on both the apo (unbound) and substrate-bound (binary) forms of Pol β.
• Analysis focused on identifying flexible regions and their dynamics in different Pol β states.

Main Results:

• Apo Pol β exhibits molecular motions in the DNA lyase domain at 1400 s(-1), sampling a conformation similar to the substrate-bound state.
• DNA binding significantly quenches lyase domain motions and reveals conformational motions in the polymerase domain.
• Flexible residues identified in this study overlap with mutation sites linked to cancer phenotypes.

Conclusions:

• Substrate binding alters the dynamic landscape of DNA polymerase β (Pol β).
• Protein dynamics play an intimate role in Pol β's DNA repair fidelity.
• The identified flexible regions and their link to cancer mutations highlight the importance of protein dynamics in disease.