Determining the confromational ensemble of the HIV-1 LTR G-quadruplexes through gaussian-accelerated molecular dynamics using the drude polarizable force field.

Abstract

Human immunodeficiency virus (HIV) impacts nearly 37.6 million people globally, but there is no effective cure for the infections it causes. HIV-1 is a retrovirus containing a single-stranded RNA genome. After reverse transcription, the 5’ long terminal repeat (LTR) acts as a promoter for viral replication. Two DNA G-quadruplexes (GQs), known as LTR-III and LTR-IV, form within this promoter and inversely regulate viral gene expression. The LTR-III GQ downregulates viral expression and is a quadruplex: duplex hybrid whereas LTR-IV upregulates viral expression and is a parallel GQ containing a single-nucleotide bulge. Their distinct topologies and functional roles suggest their potential to act as selective drug targets for HIV-1.To gain a greater understanding of structure and dynamics of the LTR-III and LTR-IV GQs, we performed conventional molecular dynamics simulations using the Drude polarizable force field. The loop nucleotides in both structures were highly flexible, sampling a variety of conformational states. The LTR-IV loop also formed base pair interactions that limited ion access to its loop cavity and further highlighted two distinct ion binding sites near the backbone tetrad guanines. Within the LTR-III duplex loop, an additional Watson-Crick base pair formed between Ade4:Thy14 and persisted for 40% of the snapshots collected in the total 4-μs simulation time. Analysis of the electric field exerted on Thy14 indicates a preference for base pairing with Ade4 compared to being unpaired as in the NMR ensemble. Gaussian-accelerated molecular dynamics simulations were also performed to identify high and low energy conformational states for subsequent drug targeting. Our results emphasize the importance of electronic polarization in GQ dynamics and can guide future development of antiviral therapeutics.