File:An-Induced-Pocket-for-the-Binding-of-Potent-Fusion-Inhibitor-CL-385319-with-H5N1-Influenza-Virus-pone.0041956.s001.ogv

English: The video showing the “induced fit” mechanism of CL-385319 binding to the hemagglutinin. This video composed hundreds of snapshots through the whole MD simulation, which provides straight-forward information of the distance between F1102 and M241 during MD simulation. In the crystal structure of the protein (PDB: 2IBX), the distance between F1102 and M241 is 4.235 Å. The first 1200 ps of simulation shown in this video is the MD simulation of hemaggutinin in aqueous solution without CL-385319. At 1200 ps, the distance between F1102 and M241 is 5.370 Å, a little larger than that observed from CL-385319-HA complex after energy minimization (5.330 Å), which means the benzene ring of CL-385319 can enter the pocket between F1102 and M241. Along with the total 100 ns MD simulation, the distance between F1102 and M241 had been increasing, as well as the distance between trifluorophenyl group of CL-385319 and V482. Finally, the average distance between F1102 and M241 residues increased to 8.950 Å. Other significant conformation changes of residues could not be observed during MD simulation.