An Investigation of the Influenza Hemagglutinin Membrane Fusion Process using Microsecond-Level MD Simulations

Abstract

Influenza virus hemagglutinin (HA) is a homotrimeric envelope protein that undergoes pH-triggered conformational changes in order to facilitate the fusion of the viral envelope with the endosomal membrane of the infected host cell. Previous experimental studies have outlined a mechanism for the conformational transitions that lead to membrane fusion. At low pH, the HA1 chains move away from the HA2 chains, which then undergo a series of conformational changes to expose the N-terminal fusion peptide. The HA2 chains then bend at a hinge region to form a hairpin shaped structure, thus bringing the viral envelope into contact with the endosomal membrane. While this model is well established, the conformational changes have never been observed in all-atom equilibrium MD simulations. Using a combination of equilibrium MD simulations and non-equilibrium SMD simulations, we have characterized the conformational dynamics of the membrane fusion process. Six models were simulated for 2.4 microseconds each. By modifying the protonation state of a conserved histidine in the HA2 hinge region, we have successfully simulated the pH-mediated conformational changes that occur when HA1 moves away from HA2. Our atomistic MD simulations confirmed that the HA1 chain associated with an HA2 chain moves away only when the histidine is protonated. Using non-equilibrium pulling simulations, we have also modeled the complex conformational and secondary-structural transitions that lead to the uncoiling of HA2 and the exposure of the fusion peptide. In addition to the conformational changes that occur within hemagglutinin, we have independently modeled the fusion of the viral envelope with the host cell endosomal membrane. For the very first time, we have studied the conformational dynamics of the entire HA-membrane complex using microsecond-level atomistic MD simulations and non-equilibrium simulations.