Multiscale Dynamics of Flavivirus Fusion Peptides - Membrane Interactions via Simulation and Experiments

Abstract

A primary causative agent of infectious disease is the positive single-stranded RNA flavivirus genus. Members of this family include Dengue (DENV), tick-borne encephalitis, west nile virus (WNV), japanese encephalitis, yellow fever and zika virus (ZIKV). During receptor-mediated endocytosis and exposure to lowered pH, the envelope (E) proteins undergo major structural changes and a dimeric-to-trimeric transition. This structural rearrangement leads to exposure of the hydrophobic tips - fusion peptides (FPs) which interact with the endosomal bilayer, subsequently initiating fusion of the viral and host membranes. The FP sequence is highly conserved among all known flaviviruses. Here, a multiscale molecular dynamics (MD) simulation approach has been employed to investigate the interaction of all FP sequences with lipid membranes, the results of which were compared with biophysical experiments. Following extensive validation using all-atom simulations with a range of sampling methods and force fields, coarse-grained models of the FP were derived in order to follow the long-timescale process of FP/lipid bilayer assembly. Atomic-resolution free energy profiles were calculated as a function of insertion depth within lipid bilayers composed of a physiologically realistic endosomal membrane model. These profiles were correlated with peptide structural and lipid-interaction data, and validated by comparison with fluorescence spectroscopy and NMR data. A mutant (W101A) previously shown to abolish flavivirus membrane fusion was found to possess twice as low affinity towards host lipid bilayers in comparison with the wild-type FP. The binding affinity was similarly reduced for wild-type FP interaction with pure zwitterionic membranes in comparison with realistic endosomal membrane models containing anionic lipids. Novel insights into the structural and thermodynamic basis for flavivirus virus infection process obtained here should prove useful in future rational antiviral therapeutic development.