Ribonucleic acid (RNA) is a central biomolecule for encoding and transmitting genetic information. A large class of viruses, which includes highly infectious pathogens [e.g., severe acute respiratory syndrome, Zika, Ebola, and human immunodeficiency virus 1 (HIV-1)], also possesses viral RNA genomes with structurally well-organized elements crucial to viral growth and replication. Because RNA viruses cause seasonal epidemics (e.g., influenza) and diseases with high fatality rates (e.g., COVID-19), it is becoming increasingly necessary to develop approaches to probe structures of viral RNAs and their interaction partners.

The cover image for the November 16 issue of Biophysical Journal is a molecular-scale depiction of key interactions between a viral RNA element from HIV-1 and a small peptide molecule that binds to it, which we studied in our work. The RNA and peptide molecules are highlighted in yellow and red cartoons, respectively, along with the space-filling representations of those nucleotide–amino acid pairs (yellow and red spheres, respectively) that we identified as playing a crucial role in formation of the RNA-peptide complex.

Because our work involves the most detailed atomic-scale models and simulations of the RNA-peptide complex, the cover image reflects our aim of studying these atomic details in complex biomolecular systems. These computational approaches, especially the non-equilibrium simulations used in our work, allow us to fill in the gaps in dynamics that are often hidden in biomolecular structures determined via experimental techniques. We hope that our fundamental structure-function studies will inspire future work on the design of inhibitory molecules targeting viral RNA.

- Lev Levintov and Harish Vashisth