Molecular dynamics simulations of anchored viral peptide interactions

The authors use molecular dynamics simulations to investigate viral peptide interactions as the cause of pH-dependent fusion in liposomal drug delivery. Viral peptides (LEFN) are composed of a linker peptide (LELELELE) connected to a synthetic viral peptide (DRGWGNGCGLFGKGSI). Rather than being anchored in a lipid bilayer, the viral peptides are anchored to a neutral surface by the amino termini of the linker peptide (anchor atoms are mobile in the xy-plane). Atomistic-level peptide pair arrangement on a surface depends on pH; however, the overall propensity to cluster is independent of pH, indicating that pH-sensitive liposome fusion is not due to peptide clustering. To further investigate a molecular cause of pH-sensitive fusion, the authors treat the linker peptides as ectodomains, with the assumption that the viral peptides are already inserted into a target membrane. In these simulations, the linker peptides are elongated to encourage them to bundle. At both high and low pH, the peptides readily bundle. At high pH, however, bundling was constrained by long-range order induced by sodium ions bridging negatively charged glutamic acid residues on neighboring peptides. The authors hypothesize that this constraint hinders the ability of the linker peptides to support viral peptide insertion, resulting in decreased levels of fusion observed experimentally.