Modeling DNA polymerase m motions: Subtle transitions before chemistry

Yunlang Li, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

To investigate whether an open-to-closed transition before the chemical step and induced-fit mechanism exist in DNA polymerase μ (pol μ), we analyze a series of molecular-dynamics simulations with and without the incoming nucleotide in various forms, including mutant systems, based on pol μ's crystal ternary structure. Our simulations capture no significant large-scale motion in either the DNA or the protein domains of pol μ. However, subtle residue motions can be distinguished, specifically of His329 and Asp330 to assemble in pol μ's active site, and of Gln 440 and Glu443 to help accommodate the incoming nucleotide. Mutant simulations capture a DNA frameshift pairing and indicate the importance of Arg444 and Arg447 in stacking with the DNA template, and of Arg448 and Gln440 in helping to stabilize the position of both the DNA template and the incoming nucleotide. Although limited sampling in the molecular-dynamics simulations cannot be ruled out, our studies suggest an absence of a largescale motion in pol μ. Together with the known crystallization difficulties of capturing the open form of pol μ, our studies also raise the possibility that a well-defined open form may not exist. Moreover, we suggest that residues Arg448 and Gln440 may be crucial for preventing insertion frameshift errors in pol μ.

Original languageEnglish (US)
Pages (from-to)3463-3472
Number of pages10
JournalBiophysical journal
Volume99
Issue number10
DOIs
StatePublished - Nov 17 2010

ASJC Scopus subject areas

  • Biophysics

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