Computational Insights into the Conformational Dynamics of HIV-1 Vpr in a Lipid Bilayer for Ion Channel Modeling

Satyabrata Majumder, Giuseppe Deganutti, Ludovico Pipitò, Dwaipayan Chaudhuri, Joyeeta Datta, Kalyan Giri

Research output: Contribution to journalArticlepeer-review

Abstract

HIV-1 Vpr is a multifunctional accessory protein consisting of 96 amino acids that play a critical role in viral pathogenesis. Among its diverse range of activities, Vpr can create a cation-selective ion channel within the plasma membrane. However, the oligomeric state of this channel has not yet been elucidated. In this study, we investigated the conformational dynamics of Vpr helices to model the ion channel topology. First, we employed a series of multiscale simulations to investigate the specific structure of monomeric Vpr in a membrane model. During the lipid bilayer self-assembly coarse grain simulation, the C-terminal helix (residues 56–77) effectively formed the transmembrane region, while the N-terminal helix exhibited an amphipathic nature by associating horizontally with a single leaflet. All-atom molecular dynamics (MD) simulations of full-length Vpr inside a phospholipid bilayer show that the C-terminal helix remains very stable inside the bilayer core in a vertical orientation. Subsequently, using the predicted C-terminal helix orientation and conformation, various oligomeric states (ranging from tetramer to heptamer) possibly forming the Vpr ion channel were built and further evaluated. Among these models, the pentameric form exhibited consistent stability in MD simulations and displayed a compatible conformation for a water-assisted ion transport mechanism. This study provides structural insights into the ion channel activity of the Vpr protein and the foundation for developing therapeutics against HIV-1 Vpr-related conditions.
Original languageEnglish
Pages (from-to)(In-Press)
JournalJournal of Chemical Information and Modeling
Volume(In-Press)
Early online date10 Apr 2024
DOIs
Publication statusE-pub ahead of print - 10 Apr 2024

Funder

This study was supported by a project grant from the West Bengal Department of Higher Education, Science & Technology and Biotechnology (243(Sanc.)/ST/P/S&T/9G-60/2017) and DST FIST grant to Department of Life Sciences, Presidency University, Kolkata.

Keywords

  • Conformation
  • Ions
  • Membranes
  • Peptides and proteins
  • Vesicles

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