Figure_4.tif (887.08 kB)
Time evolution of the DhaA p1 tunnel.
figure
posted on 2012-10-18, 01:58 authored by Eva Chovancova, Antonin Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlikova, Artur Gora, Vilem Sustr, Martin Klvana, Petr Medek, Lada Biedermannova, Jiri Sochor, Jiri Damborsky(A) Evolution of the p1 tunnel bottleneck radius over time. The dotted orange lines indicate bottleneck radii of the p1 tunnel in DhaA crystal structures with added hydrogen atoms: PDB-IDs 1BN6 and 1BN7 (bottleneck radius 1.2 Å) and 1CQW (1.3 Å). The four green circles indicate bottleneck radii of the p1 tunnel from the 2.76 ns (bottleneck radius 1.4 Å), 5.85 ns (2.3 Å), 7.57 ns (0.9 Å) and the 7.72 ns (0.9 Å) snapshots from the molecular dynamics simulation of DhaA. (B) The p1 tunnel identified in DhaA crystal structures with added hydrogen atoms (PDB-IDs 1CQW, 1BN6, 1BN7). (C) The p1 tunnel identified in the 2.76 ns, 5.85 ns, 7.57 ns and 7.72 ns snapshots of the MD trajectory of DhaA.
