Coarse Grained Molecular Dynamics Simulation of Interaction between Hemagglutinin Fusion Peptides and Lipid Bilayer Membranes

Microscopic level interaction between fusion-peptides and lipid bilayer membranes plays a crucial role in membrane fusion, a key step of viral infection. In this paper, we use coarse-grained molecular dynamics (CGMD) simulations to study the interaction between hemagglutinin fusion-peptides and phospholipid bilayer membranes. With CGMD, we are able to simulate the interaction of fusion peptides with a relatively large piece of membrane for a sufficiently long time period, which is necessary for a detailed understanding of the fusion process. A conformation of the peptide with a kink at the level of phosphate group is obtained, consistent with NMR and EPR studies. Our results show that the N-terminal segment of the peptide inserts more deeply into the membrane bilayer compared to the C-terminal segment, as observed in previous experiments. Our simulations also show that the presence of fusion peptides inside the membrane may cause bilayer thinning and lipid molecule disorder. Finally, our results reveal that peptides tend to aggregate, indicating cluster formation as seen in many experiments. AMS subject classifications: 52B10, 65D18, 68U05, 68U07