Molecular Dynamics Simulations Reveal the HIV-1 Vpu Transmembrane Protein to Form Stable Pentamers

Abstract

The human immunodeficiency virus type I (HIV-1) Vpu protein is 81 residues long and has two cytoplasmic and one transmembrane (TM) helical domains. The TM domain oligomerizes to form a monovalent cation selective ion channel and facilitates viral release from host cells. Exactly how many TM domains oligomerize to form the pore is still not understood, with experimental studies indicating the existence of a variety of oligomerization states. In this study, molecular dynamics (MD) simulations were performed to investigate the propensity of the Vpu TM domain to exist in tetrameric, pentameric, and hexameric forms. Starting with an idealized α-helical representation of the TM domain, a thorough search for the possible orientations of the monomer units within each oligomeric form was carried out using replica-exchange MD simulations in an implicit membrane environment. Extensive simulations in a fully hydrated lipid bilayer environment on representative structures obtained from the above approach showed the pentamer to be the most stable oligomeric state, with interhelical van der Waals interactions being critical for stability of the pentamer. Atomic details of the factors responsible for stable pentamer structures are presented. The structural features of the pentamer models are consistent with existing experimental information on the ion channel activity, existence of a kink around the Ile17, and the location of tetherin binding residues. Ser23 is proposed to play an important role in ion channel activity of Vpu and possibly in virus propagation.

The HIV-1 Vpu transmembrane domain topology and formation of a hydrophobic interface with BST-2 are critical for Vpu-mediated BST-2 downregulation

“…The sequences of the TMDs of the peptides used in the study are shown in Table 2. As described previously [55,56], extra residues have been considered on both sides of the TMD to ensure that there are no destabilizing effects due to abrupt termination of the TMD.…”

Viral channel forming proteins — How to assemble and depolarize lipid membranes in silico

“…The principles of prepositioning ideal helices around a central axis to generate a bundle based on known architectures are generally used if knowledge-based architectural constraints allow to do so as in the case of Vpu [90,91]. These bundle models are then used in classical [90] or REMD simulations [91] to address mechanical features. In other studies, e.g.…”

“…In another study, the number of monomers forming a functional bundle is estimated to be five on symmetry considerations and energy estimates using classical and replica exchange MD simulations of tetra-to hexameric bundle architectures [91]. Dimer and trimer have not assembled in REMD simulations while the tetra-to hexamer bundles did so.…”

Prediction of the structures of helical membrane proteins based on a minimum unfavorable contacts approach

“…Using REMD with an implicit membrane environment, Brooks and coworkers have been able to predict the structures of homo‐oligomers, given that the number of monomeric subunits in the oligomer is known. It has also been possible to predict the oligomeric state of the protein Vpu from HIV‐1 by initially sampling possible conformations of different oligomeric states of the protein using REMD, and then subjecting a few representative conformations to extensive simulations in an explicit lipid bilayer environment . The study shows that the pentameric form of Vpu is the preferred oligomeric state, and thereby proposes a structural model for the pentameric channel.…”