Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis

Biochemistry. 2017 Mar 7;56(9):1227-1238. doi: 10.1021/acs.biochem.6b00934. Epub 2017 Feb 23.

Abstract

DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform in the "intrinsic processivity" subdomain of the enzyme. Our data indicate that noncatalytic mutations may disrupt replisomal interactions, thereby causing Pol γ-associated neurodegenerative disorders.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • DNA / metabolism
  • DNA Polymerase gamma
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism*
  • Humans
  • Mitochondria / enzymology*
  • Molecular Dynamics Simulation*
  • Mutation
  • Neurodegenerative Diseases / enzymology
  • Neurodegenerative Diseases / genetics
  • Protein Structure, Secondary
  • Rotation

Substances

  • DNA
  • DNA Polymerase gamma
  • DNA-Directed DNA Polymerase