Phosphomimetic S207D Lysyl-tRNA Synthetase Binds HIV-1 5'UTR in an Open Conformation and Increases RNA Dynamics

Structural and computational studies of HIV-1 RNA

Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.

Sequestering the 5′‐cap for viral RNA packaging

Many viruses evolved mechanisms for capping the 5'-ends of their plus-strand RNAs as a means of hijacking the eukaryotic messenger RNA (mRNA) splicing/translation machinery. Although capping is critical for replication, the RNAs of these viruses have other essential functions including their requirement to be packaged as either genomes or pre-genomes into progeny viruses. Recent studies indicate that human immunodeficiency virus type-1 (HIV-1) RNAs are segregated between splicing/translation and packaging functions by a mechanism that involves structural sequestration of the 5'-cap. Here, we examined studies reported for other viruses and retrotransposons that require both selective packaging of their RNAs and 5'-RNA capping for host-mediated translation. Our findings suggest that viruses and retrotransposons have evolved multiple mechanisms to control 5'-cap accessibility, consistent with the hypothesis that removal or sequestration of the 5' cap enables packageable RNAs to avoid capture by the cellular RNA processing and translation machinery.