Molecular simulations of HIV-­‐1 gp41 protein-­‐membrane interactions Vamshi Gangupomu Advisor: Dr. Cameron Abrams Abstract: Cellular and viral membrane fusion is a critical process during viral infection. The HIV-­‐1 surface envelope glycoprotein (gp41) anchored in the cholesterol-­‐rich host cell derived viral membrane is responsible for mediating membrane fusion between the viral and target-­‐cell membranes. The objective of this thesis is to understand the role of cholesterol and gp41, specifically the membrane spanning domain (MSD) and the two ectodomain heptad repeats (N-­‐terminal heptad repeat and C-­‐terminal heptad repeat), during membrane fusion using all-­‐ atom molecular modeling. The 27-­‐residue membrane-­‐spanning domain (MSD) of the HIV-­‐1 glycoprotein gp41 bears conserved sequence elements crucial to the biological function of the virus, in particular a conserved mid-­‐span arginine Arg694. We found that the MSD assumes a stable α-­‐helical conformation and metastable kinked conformations that differ depending upon whether Arg694 side-­‐chain snorkels towards the exoplasmic or endoplasmic side of the viral membrane. It was observed that when the Arg694 side-­‐chain snorkels towards the endoplasmic headgroups the MSD assumes a kinked conformation that was hypothesized from experimental studies. Moreover, we found significant local thinning of the membrane and penetration of water molecules into the membrane core in the presence of mid-­‐span Arg694. The presence of cholesterol in the lipid membrane was found to assist in better anchoring of a non-­‐ polar structure in the membrane while increasing the free-­‐
energy of membrane destabilization. Mechanically destabilizing a cholesterol-­‐rich lipid membrane also resulted in the formation of a larger rupture pore compared to a pure POPC lipid bilayer. Model built structures of the gp41 ectodomain were then used to simulate folding of the gp41 pre-­‐fusion intermediate into a stable six-­‐helix bundle. These models provided important insights into the mechanism of folding and the specific interactions involved during folding. Membrane fusion requires that the opposing membranes are brought into proximity and destabilized to facilitate lipid mixing. The membrane lipids and fusion proteins in both the membranes play important roles in facilitating membrane fusion. In this work we showed specific roles cholesterol and HIV-­‐1 gp41 play in priming the viral membrane to promote fusion.