The Molecular Dynamics Simulation Study Of Influenza Virus B Proton Channel

Flu is caused by influenza virus inflection, which accompanies a significant level of morbidity and mortality. Influenza virus B is an important constituent of human seasonal flu that accounts for about 50% of all influenza disease in recent years, which causes pandemic disease periodically. Due to willing to control actions in the event of a pandemic, it is very important to do some research on influenza virus B. BM2, the proton channel of influenza virus B, is a single-span membrane protein, which is a homotetramer in its native state. BM2 is responsible for acidizing virus and releasing the vRNA. The HXXXW sequence motif in the transmembrane domain is essential for pH sensing and channel gating.Molecular dynamics simulations is a method establishing a molecular simulation on the basis of Newtonian mechanics. By solving the Newtonian mechanical equations can obtain thermodynamic and kinetic properties changing over time. We simulated BM2 for 25ns respectively under GROMOS87 and OPLS force field by using GROMACS 4.5. By the comparation of the results, we noticed that there are some similarity but also much more discrepancy in the application of the two force field. OPLS force field has better performance in simulation, because of the elavorate characteristcs of protein movements and water distribution. The side chain of PHE5 and TRP23 in BM2 transmembrane block the channel, and near these amino acids, the channel radius is smaller than the radius of the water molecules. PHE5 and TRP23 play the role of gate respectively, for the N-terminal and C-terminal . Potentials of mean force for the water along the z axis of the BM2 pore has shown that it has to pass over a much higher energy barrier, which proves the reason for water absence shown by the water density figure.