Fig. 7.

MD simulation of the HIV-1 gp41 trimer. Molecular modeling and MD simulation of the extracellular portion of the HIV-1 JR-FL gp41 trimer with and without a I37K mutation were performed using modules in the Molecular Operating Environment and the AMBER 11 program package [46]. a The distribution of the RMSFs of three protomers consisting of the gp41 trimer. Double-arrow heads indicate regions between positions 20 and 65 in protomers 1, 2, and 3. b Structures of the extracellular portion of the HIV-1 JR-FL gp41 trimer with and without a I37K mutation. The structures at 100 ns of MD simulations are shown. The amino acid residues between positions 20 and 65 in protomers 1 (red), 2 (blue), and 3 (green) are highlighted