Molecular simulations and modeling of HIV-1 gp41 membrane spanning domain (MSD) in a model viral bilayer

HIV-1 envelope protein complexes known as "spikes" are trimers of gp120 and gp41 that mediate fusion and infection to target cell membranes. The membrane spanning domain (MSD) of gp41 contains several highly conserved residues important for fusion, however the structure and function of MSD are only partly understood. All-atom simulations can elucidate how the conserved residues affect MSD structure to provide atomistic insight into HIV-1 fusion.;Extensive molecular dynamics (MD) of monomeric HIV-1 gp41 MSD in model viral bilayers was used to investigate the conserved midspan arginine and the requirement of cholesterol for fusion. All wild-type peptides were alpha-helical, remained membrane-spanning, and solvated their midspan arginines with a water defect that was independent of cholesterol. However, the simulations indicate that cholesterol may allow the spike to localize the water defect and to control the tilt of the helices.;The dynamics of the model viral bilayer with ∼50% cholesterol was explored with 3 systems and simulated for up to 10 mus to explore the phase space of configurations, an order of magnitude greater than previous studies. This timescale allowed observation of diffusive motion and calculated diffusion coefficients agreed with experiments.;Oligomeric forms of the MSD were then created to examine the GXXXG motif, known for helical, transmembrane, dimer interactions, but conserved in the MSD of the trimeric gp41. The lowest-energy trimeric MSD with interacting GXXXG residues could not mediate trimerization in a bilayer on 100 ns timescales. However, the lowest energy MSD dimer remained associated on similar timescales, suggesting a dimer form of the MSD during fusion.;Finally, the trimeric MSD was stabilized by addition of the trimeric crystal structure of the gp41 membrane proximal external region (MPER). Simulation of the MPER-MSD trimer for 11 mus showed relaxation towards a different, stable configuration in which the GXXXG motifs were not interacting but the cholesterol recognition motif (CRAC) sequestered water and cholesterol. This is the first simulation of a model of trimeric MPER-MSD in a cholesterol-containing bilayer and it may represent a point between the prefusion and the prefusion intermediate experimental trimeric structures.