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Enhanced-Sampling Simulations Reveal Distinct Intermediates in SARS-CoV-2 FSE Pseudoknot Interconversion.

Karim Malekzadeh¹, Mangesh Bhendale¹, Gül H Zerze²

¹William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, 4226 Martin Luther King Boulevard, Houston, Texas, 77204, USA.

Biophysical Journal

|July 3, 2026

Summary

This summary is machine-generated.

The SARS-CoV-2 frameshifting stimulatory element (FSE) can adopt multiple structures, influencing viral protein synthesis. This study reveals the pathways and intermediates involved in transitions between these FSE structures.

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Area of Science:

Molecular Biology
Virology
Computational Biology

Background:

The SARS-CoV-2 frameshifting stimulatory element (FSE) is crucial for viral protein synthesis via programmed -1 ribosomal frameshifting.
The FSE is a known target for antiviral therapies.
The FSE is structurally heterogeneous, adopting alternative conformations that influence frameshifting efficiency.

Purpose of the Study:

To investigate the transition pathways between alternative structures of the SARS-CoV-2 FSE.
To understand the role of conformational plasticity in FSE function.
To identify structural intermediates during FSE structural rearrangements.

Main Methods:

Atomistic resolution molecular dynamics simulations using the Multithermal-Multiumbrella On-the-Fly Probability Enhanced Sampling (MM-OPES) technique.
Sampling interconversions between two H-type 3-stem pseudoknots (motifs 3_3 and 3_6) of the SARS-CoV-2 FSE.
Free-energy calculations and trajectory analysis to identify transition pathways and intermediates.

Main Results:

Well-defined free-energy basins for motifs 3_3 and 3_6 were identified, along with intermediate regions.
Distinct terminal-segment-mediated contacts were observed during interconversions.
Trajectories revealed stepwise and concurrent transition routes, including transient triplex-like interactions and metastable intermediates stabilized by non-native contacts.

Conclusions:

The study elucidates the molecular mechanisms underlying SARS-CoV-2 FSE conformational plasticity.
Identified structural intermediates and contact rearrangements provide insights into frameshifting efficiency modulation.
Understanding these pathways can inform the design of novel antiviral strategies targeting FSE structure.