Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations

Biophys J. 2004 Sep;87(3):1478-97. doi: 10.1529/biophysj.103.039313.

Abstract

Molecular dynamics simulations are presented for a Thermus aquaticus (Taq) DNA polymerase I complex (consisting of the protein, the primer-template DNA strands, and the incoming nucleotide) subjected to external forces. The results obtained with a force applied to the DNA template strand provide insights into the effect of the tension on the activity of the enzyme. At forces below 30 pN a local model based on the parameters determined from the simulations, including the restricted motion of the DNA bases at the active site, yields a replication rate dependence on force in agreement with experiment. Simulations above 40 pN reveal large conformational changes in the enzyme-bound DNA that may have a role in the force-induced exonucleolysis observed experimentally.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Computer Simulation
  • DNA / chemistry
  • DNA Polymerase I
  • DNA Primers / chemistry
  • DNA Replication
  • DNA-Directed DNA Polymerase / chemistry
  • DNA-Directed DNA Polymerase / metabolism*
  • Entropy
  • Hot Temperature
  • Models, Molecular
  • Models, Statistical
  • Models, Theoretical
  • Molecular Conformation
  • Nucleotides / chemistry
  • Protein Conformation
  • Temperature
  • Thermus / enzymology
  • Time Factors
  • Water / chemistry

Substances

  • DNA Primers
  • Nucleotides
  • Water
  • DNA
  • DNA Polymerase I
  • DNA-Directed DNA Polymerase