Modeling DNA polymerase μ motions: subtle transitions before chemistry

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• DNA polymerases are crucial for DNA replication and repair.
• Understanding the dynamic mechanisms of DNA polymerases, like DNA polymerase mu (pol μ), is key to elucidating their function.
• The existence of an open-to-closed transition and induced-fit mechanism in pol μ remains unclear.

Purpose of the Study:

• To investigate the dynamic mechanisms of DNA polymerase mu (pol μ) during nucleotide incorporation.
• To determine if pol μ undergoes an open-to-closed transition and exhibits an induced-fit mechanism.
• To identify key residues involved in pol μ's function and fidelity.

Main Methods:

• Molecular-dynamics simulations of pol μ were performed.
• Simulations included varying nucleotide forms and mutant systems.
• Analysis focused on protein and DNA domain motions and residue interactions.

Main Results:

• No significant large-scale motions were observed in pol μ's protein or DNA domains.
• Subtle residue motions were identified, particularly His(329), Asp(330), Gln(440), and Glu(443).
• Mutant simulations revealed the roles of Arg(444), Arg(447), Arg(448), and Gln(440) in DNA template and nucleotide stabilization, and identified a DNA frameshift pairing.

Conclusions:

• The study suggests an absence of large-scale motion in pol μ, questioning a classical induced-fit mechanism.
• A distinct open form of pol μ may not exist, consistent with crystallization challenges.
• Residues Arg(448) and Gln(440) are proposed to be critical for preventing insertion frameshift errors in pol μ.