Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I
Figure 5
The proposed opening mechanism for the fingers domain for DNA polymerase I.
The secondary structure of the relevant polymerase residues including the O-helix are shown in yellow ribbons, while the DNA is shown in orange. The key event in each image is circled. A) The X-ray crystal structure of PDB 1LV5. B). The intermediate state showing the breaking of the Tyr714-Glu658 hydrogen bond, and the formation of the salt bridge between Arg703 and Glu562. C) Depiction of the breaking of the Arg703-Glu562 salt bridge, which is quickly followed by D) the rotation of the N-β-glycosyl bond of the template nucleotide allowing Tyr714 to replace the base in the active site, and resulting in the fully open conformation of DNA polymerase I. Simulation times and O-helix distances correspond to the 1LV5 simulation performed using Desmond and the Charmm27 force field.