Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics
Category
Published on
Type
journal-article
Author
Weiwei He and Josue San Emeterio and Michael T Woodside and Serdal Kirmizialtin and Lois Pollack
Citation
He, W., San Emeterio, J., Woodside, M. T., Kirmizialtin, S., & Pollack, L. (2023). Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics. Nucleic Acids Research, 51(20), 11332–11344. https://doi.org/10.1093/nar/gkad809
Abstract
Abstract
SARS-CoV-2 depends on −1 programmed ribosomal frameshifting (−1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating −1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing −1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.
