Coordinated Residue Motions at the Enzyme-Substrate Interface Promote DNA Translocation in Polymerases

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• DNA polymerase (Pol) enzymes are crucial for nucleic acid polymerization, enabling genetic information storage and transmission.
• DNA translocation is a fundamental step in the Pol catalytic cycle, allowing enzymes to reposition after nucleotide addition.
• The precise atomic-level mechanism of DNA translocation by Pol enzymes remains incompletely understood.

Purpose of the Study:

• To elucidate the dynamic translocation mechanism of DNA polymerase η (Polη) at the atomistic level.
• To investigate the role of specific enzyme residues in facilitating DNA translocation.
• To provide new insights into the fundamental process of DNA polymerization.

Main Methods:

• Utilized recent structural data of DNA polymerase η (Polη).
• Employed equilibrium molecular dynamics simulations.
• Incorporated deep-learning-guided enhanced sampling simulations.

Main Results:

• Elucidated Polη translocation mechanism involving asynchronous shifting along DNA strands.
• Identified a coordinated action of positively charged residues at the Polη·DNA interface.
• Described residue movement akin to 'screen wipers' that promotes DNA translocation.

Conclusions:

• The translocation mechanism of Polη relies on a coordinated dynamic motion of specific charged residues.
• This mechanism allows for efficient repositioning of the enzyme on DNA without dissociation.
• Findings offer new perspectives on the fundamental process of DNA polymerization.