Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I
Figure 9
A depiction of the residues with backbone dihedrals—Asp680φ (purple), Gly711φ (pink), Val713ψ (green), and Ile716φ (blue)—identified as important in the finger domain opening process of DNA polymerase.
The fingers domain is shown in an ice blue cartoon representation, while the O-helix is shown in yellow cartoon. The times within the black arrows between panels indicate the transition times between the conformations. A) Conformation of the fingers domain in the 1LV5 crystal structure (closed) prior to running MD. B) Representative conformation of the intermediate state observed from ∼100–170 ns (139 ns shown) of simulation time. The red arrow indicates the large-scale motion of the N-helix due to a rotation about the Asp680φ dihedral. C) Representative conformation of the open state observed from ∼290–1000 ns (500 ns shown) of MD caused by a rotation of the Asp680φ and Ile716φ dihedrals. D) A side view of the intermediate state at 139 ns depicting the bend in the O-helix caused by rotations of the Gly711φ and Val713ψ dihedrals.