Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

Weiwei He, Josue San Emeterio, Michael T. Woodside, Serdal Kirmizialtin, Lois Pollack

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)11332-11344
Number of pages13
JournalNucleic acids research
Issue number20
StatePublished - Nov 10 2023

ASJC Scopus subject areas

  • Genetics


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