Computational study of the force dependence of phosphoryl transfer during DNA synthesis by a high fidelity polymerase.
High fidelity polymerases are efficient catalysts of phosphodiester bond formation during DNA replication or repair. We interpret molecular dynamics simulations of a polymerase bound to its substrate DNA and incoming nucleotide using a quasiharmonic model to study the effect of external forces applied to the bound DNA on the kinetics of phosphoryl transfer. The origin of the force dependence is shown to be an intriguing coupling between slow, delocalized polymerase-DNA modes and fast catalytic site motions. Using noncognate DNA substrates we show that the force dependence is context specific.
Venkatramani
Ravindra
R
Department of Bioengineering , University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Radhakrishnan
Ravi
R
D003198:Computer Simulation; D004261:DNA Replication; D004269:DNA, Bacterial / Q000096:biosynthesis* / Q000737:chemistry*; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000378:metabolism*; D001411:Geobacillus stearothermophilus / Q000235:genetics / Q000378:metabolism; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D013816:Thermodynamics
D004269:DNA, Bacterial; D004259:DNA-Directed DNA Polymerase