Molecular Dynamics of Influenza Hemagglutinin Fusion Peptide

We considered a 23-residue long HAfps: wt GLFGAIAGFIEGGWQGMVDGWYG and E11A and and W14A mutants. The N-terminus was modeled as a charged amino group, and the C-terminus was amidated. For most cases, we simulated E11 in protonated (neutral) state; however, a peptide with its charged version, denoted as wt ${}^{-}$ , was considered as well for membrane-spanning configurations. Simulated systems included one peptide, 162 POPC molecules (81 per leaflet) and 9337 TIP3P [32 (link)] water molecules together with sodium and chloride ions necessary to construct a neutral system consisting of a membrane slab with ∼20 Å of 0.15 mol/L NaCl solution margins on both sides. Peptides and lipids were modeled with Amber99SB-ILDNP* [33 (link)] and Amber Lipid14 [34 (link)] force fields, respectively. In addition, we considered wt HAfp simulations in transmembrane hairpin configuration using Charmm36 force field [35 (link)]. Starting geometries for surface bound and transmembrane peptides were taken from our previous runs [20 (link)]. Necessary mutations were introduced with Discovery Studio Visualiser (Biovia).