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

Area of Science:

• Virology
• Structural Biology
• Biophysics

Background:

• SARS-CoV-2 utilizes -1 programmed ribosomal frameshifting (-1 PRF) for essential protein expression.
• The RNA pseudoknot is crucial for -1 PRF and a potential antiviral drug target.
• Existing structural models from cryo-EM and crystallography present discrepancies.

Purpose of the Study:

• To determine the solution structure of the SARS-CoV-2 RNA pseudoknot.
• To reconcile conflicting structural data and clarify the pseudoknot's dynamic conformation.

Main Methods:

• Small-angle X-ray scattering (SAXS) was employed to measure the pseudoknot's solution structure.
• All-atom molecular dynamics (MD) simulations were guided by SAXS data for structural refinement.
• Analysis included a point mutant that abolishes -1 PRF.

Main Results:

• SAXS data revealed discrepancies with previously solved pseudoknot structures.
• MD simulations refined structures towards a bent conformation, aligning better with cryo-EM models.
• A pseudoknot mutant exhibited a significantly more bent structure with altered helix orientation.

Conclusions:

• This study clarifies the dynamic solution structures of the SARS-CoV-2 RNA pseudoknot.
• Refined structural models provide a clearer understanding of pseudoknot function in -1 PRF.
• The findings offer insights for the rational design of antiviral therapies targeting the pseudoknot.