# Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes

## TL;DR

This paper predicts the 3D structures of RNA complexes in coronaviruses, helping explain their stability and offering insights for antiviral drug design.

## Contribution

The study validates and applies a new pipeline for predicting RNA dimer structures, revealing structural differences in SARS-CoV and SARS-CoV-2.

## Key findings

- VFold3D/LA-IsRNA pipeline accurately predicts RNA dimer structures with RMSD of 3.28 Å compared to crystal structures.
- SARS-CoV s2m kissing complexes are more kinked than linear extended duplexes, explaining differences in gel electrophoresis migration.
- SARS-CoV-2 and Delta s2m form canonical basepairs, leading to less stable dimers compared to SARS-CoV.

## Abstract

The three-dimensional (3D) atomistic-resolution structure
and dynamics
of RNA kissing complexes (KCs) and extended duplexes (EDs), homodimers
formed through palindromic base pairing, are crucial for understanding
viral replication and structure-informed therapeutic design. Polyacrylamide
gel electrophoresis (PAGE) evidence suggests KC and ED dimer formation
between stem-loop II motif (s2m) elements in SARS-CoV, SARS-CoV-2,
and Delta SARS-CoV-2, which may regulate host immune response. However,
the absence of 3D structural data on s2m dimers limits structural
interpretation needed to explain differences in stability indicated
by native PAGE and biophysical implications. In this work, we evaluate
the VFold3D/LA-IsRNA pipeline for resolving 3D structures of s2m KCs
and EDs by validating its accuracy with blind and referenced predictions
against experimental HIV-1 DIS KC and ED structures. Engendering confidence
in the approach for blind prediction of KC and ED structures, HIV-1
DIS predictions achieved an average RMSD of 3.28 Å relative to
crystal structures, while local interactions, such as palindrome-flanking
purine stack orientations in the terminal loops, were in closer agreement
with reported solution-phase NMR (RMSD ∼ 2.5 Å), cryo-EM
maps, and previous molecular dynamics (MD) simulations. We find that
the predicted 3D dimer structures of s2m resulted in kinked or linear
shapes of s2m KC complexes that provide an interpretation consistent
with native PAGE migration differences, where KCs are more kinked
(63° to 133°) than linear ED dimers (127° to 156°).
Following MD refinement, the SARS-CoV s2m KC adopts stacking palindromic
basepair triplets, whereas SARS-CoV-2 and Delta s2m only form canonical
palindrome basepairs, explaining their relative dimer instability
suggested by PAGE band intensity. Ultimately, our results support
the use of the VFold3D/LA-IsRNA pipeline for KC and ED generation,
yielding predictions consistent with experimental data and providing
an atomistic foundation for data-driven design of antiviral therapies
to disrupt the lifecycle or immune response of viruses.