Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I
Figure 2
The dynamics of the fingers domain illustrated by A) the α-C distance between Pro699-Arg629 of DNA polymerase simulated with B) Desmond using the Charmm27 force field, C) Desmond using the Amber ff99Sb force field, and D) Amber using the Amber ff99SB force field.
The simulations are named according to their PDB codes and initial starting conformations where 1L3S (red) began in the open conformation, 3HP6 (green) began in the ajar conformation, and 1LV5 (blue) was started from the closed conformation. The black horizontal lines represent the distances corresponding to the three major observed conformations: open (O), closed (C), and the newly observed intermediate (I) state. The inset in B) displays a close-up of the distances from 0–5 ns (highlighted by the vertical orange dashed line) to more clearly depict the relatively quick opening of the simulation started from the 3HP6 ajar conformation.