ArticleBiophysical journal2010
Modeling DNA polymerase μ motions: subtle transitions before chemistry.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Insights into DNA polymerase δ's mechanism for accurate DNA replication.Journal of molecular modeling · 2019Article
- Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.Nature communications · 2017Article
- Article
- Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair.The EMBO journal · 2015Article
- Molecular dynamics study of the opening mechanism for DNA polymerase I.PLoS computational biology · 2014Article
- Decision-making during NHEJ: a network of interactions in human Polμ implicated in substrate recognition and end-bridging.Nucleic acids research · 2014Article
- Structures of the Leishmania infantum polymerase beta.DNA repair · 2014Article
- C(α) torsion angles as a flexible criterion to extract secrets from a molecular dynamics simulation.Journal of molecular modeling · 2014Article
- Sustained active site rigidity during synthesis by human DNA polymerase μ.Nature structural & molecular biology · 2014Article
- A specific N-terminal extension of the 8 kDa domain is required for DNA end-bridging by human Polμ and Polλ.Nucleic acids research · 2013Article
- "Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides.PLoS computational biology · 2013Article
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2 authors.
Funding
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 His(329) and Asp(330) to assemble in pol μ's active site, and of Gln(440) and Glu(443) to help accommodate the incoming nucleotide. Mutant simulations capture a DNA frameshift pairing and indicate the importance of Arg(444) and Arg(447) in stacking with the DNA template, and of Arg(448) and Gln(440) 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 large-scale 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 Arg(448) and Gln(440) may be crucial for preventing insertion frameshift errors in pol μ.
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