HIV-1 Env gp41 Transmembrane Domain Dynamics are Modulated by Lipid, Water, and Ion Interactions

Abstract

The gp41 transmembrane domain (TMD) of the envelope glycoprotein (Env) of the human immunodeficiency virus (HIV) modulates the conformation of the viral envelope spike, the only druggable target on the surface of the virion. Understanding of TMD dynamics is needed to better probe and target Env with small molecule and antibody therapies. However, little is known about TMD dynamics due to difficulties in describing native membrane properties. Here, we performed atomistic molecular dynamics simulations of a trimeric, prefusion TMD in a model, asymmetric viral membrane that mimics the native viral envelope. We found that water and chloride ions permeated the membrane and interacted with the highly conserved arginine bundle, (R696) 3 , at the center of the membrane and influenced TMD stability by creating a network of hydrogen bonds and electrostatic interactions. We propose that this (R696) 3 -water -anion network plays an important role in viral fusion with the host cell by modulating protein conformational changes within the membrane. Additionally, R683 and R707 at the exofacial and cytofacial membrane-water interfaces, respectively, are anchored in the lipid headgroup region and serve as a junction point for stabilization of the termini. The membrane thins as a result of the tilting of the TMD trimer, with nearby lipids increasing in volume, leading to an entropic driving force for TMD conformational change. These results provide additional detail and perspective on the influence of certain lipid types on TMD dynamics and rationale for targeting key residues of the TMD for therapeutic design. These insights into the molecular details of TMD membrane anchoring will build towards a greater understanding of dynamics that lead to viral fusion with the host cell.

HIV-1 Envelope and MPER antibody structures in lipid assemblies

“…Influenza hemagglutinin was shown to have similar TMD dynamics with tilted and straight orientations, suggesting that these could be common type I viral fusion proteins TMD topologies (Benton et al, 2018). The arrangement of helices shown here for HIV Env is different than the three-helix bundle topology observed in NMR structures of the TM helices alone (Chen and Chou, 2017;Chiliveri et al, 2018;Dev et al, 2016;Hollingsworth et al, 2018;Kwon et al, 2018a). Thus, the compact three-helix bundle conformation likely represents the low-energy post-fusion conformation of the TMD and its formation is preferred in the minimal constructs used in the NMR and MD studies.…”

“…75 ° angle ( Figure 3B). The helices crossed in the micelle at the conserved R696, a residue previously shown to be important for modulating conformational changes of the TMD (Cooper et al, 2018;Hollingsworth et al, 2018;Wang et al, 2019).…”

HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies

“…Interestingly, the individual transmembrane (TM) helices crossed the micelle in a tilted fashion forming an X shape with TMDs from adjacent protomers crossing at an $75 angle and at $50 in relation to the postulated membrane plane (Figure 3B). The helices crossed in the micelle at the conserved R696, a residue previously shown to be important for modulating conformational changes of the TMD (Cooper et al, 2018;Hollingsworth et al, 2018;Wang et al, 2019).…”

The Conserved Positive Charge in the Transmembrane Domain of HIV Gp41 Contributes to Its Intrinsic Preference for Trimerization

“…Arg 696 has been suggested to play a structural role in trimerization by forming polar contacts within the membrane, either alone or in combination with a GxxxG motif, and computational studies on the gp41 TM domain support this claim. 9,[12][13][14] Biophysical studies on the HIV TM have yielded inconsistent results on the oligomeric state of this domain. An NMR analysis of a TM peptide in a DMPC/DHPC mixed micelle showed no evidence of trimerization, but the specific transmembrane peptide used in that study contained significant portions of the MPER and cytoplasmic tail.…”