Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis.

Chaoyi Xu,Alan N Engelman,Roman Zadorozhnyi,Robert A Dick,Zandrea Ambrose,Sanela Rankovic,Wen Li,Itay Rousso,Juan R Perilla,Tatyana Polenova,Brent Runge,Christopher Aiken,Douglas K Fischer,Jinwoo Ahn,Edward M Campbell

doi:10.1371/journal.pbio.3001015

Abstract

Reverse transcription, an essential event in the HIV-1 life cycle, requires deoxynucleotide triphosphates (dNTPs) to fuel DNA synthesis, thus requiring penetration of dNTPs into the viral capsid. The central cavity of the capsid protein (CA) hexamer reveals itself as a plausible channel that allows the passage of dNTPs into assembled capsids. Nevertheless, the molecular mechanism of nucleotide import into the capsid remains unknown. Employing all-atom molecular dynamics (MD) simulations, we established that cooperative binding between nucleotides inside a CA hexamer cavity results in energetically favorable conditions for passive translocation of dNTPs into the HIV-1 capsid. Furthermore, binding of the host cell metabolite inositol hexakisphosphate (IP6) enhances dNTP import, while binding of synthesized molecules like benzenehexacarboxylic acid (BHC) inhibits it. The enhancing effect on reverse transcription by IP6 and the consequences of interactions between CA and nucleotides were corroborated using atomic force microscopy, transmission electron microscopy, and virological assays. Collectively, our results provide an atomistic description of the permeability of the HIV-1 capsid to small molecules and reveal a novel mechanism for the involvement of metabolites in HIV-1 capsid stabilization, nucleotide import, and reverse transcription.

Highlights

Fusion between HIV-1 virions and target cells engenders the release of the viral capsid into the host cell cytoplasm
To explore the effects of the dynamic behavior of capsid protein (CA) hexamers on the permeability of molecules through assembled HIV-1 capsids, we employed free-energy molecular dynamics (MD) simulations to determine the free energy landscapes of deoxynucleotide triphosphate (dNTP) and inositol hexakisphosphate (IP6) interacting with the central cavity (Fig 1D, S1 Fig, S1 Table)
The prediction of impaired dNTP translocation suggested that reverse transcription should likewise be impaired for K25A and K25N HIV-1, leading to decreased infectivity

Summary

Introduction

Fusion between HIV-1 virions and target cells engenders the release of the viral capsid into the host cell cytoplasm. To explore the effects of the dynamic behavior of CA hexamers on the permeability of molecules through assembled HIV-1 capsids, we employed free-energy MD simulations to determine the free energy landscapes of dNTPs and IP6 interacting with the central cavity (Fig 1D, S1 Fig, S1 Table).

Results

Conclusion