JMB-S-21-00552

Molecular dynamics simulation files for in-review JMB-S-21-00552 manuscript: topologies, initial coordinates and indices, simulation parameters, downsampled trajectories, raw results (RMSD, RMSF).

Abstract:

The coronaviral pandemic is exerting a tremendously detrimental impact on global
health. The Spike proteins of coronaviruses, responsible for cell receptor binding and
viral internalization, possess multiple and frequently conservative disulfide bonds
raising the question about their role in the antigen function. Here, we present a detailed
structural and functional investigation of the disulfide bonds of the SARS-CoV-2 Spike
receptor-binding domain (RBD). Molecular dynamics simulations of the RBD predict
increased domain flexibility when the four disulfide bonds of the domain are reduced.
This flexibility is particularly prominent for the S-S bond-containing surface loop
(residues 456-490) that participates in the formation of the interaction surface with the
Spike cell receptor ACE2. In vitro the disulfide bond reducing agents affect the RBD
secondary structure, lower its melting temperature from 52°C to 36-39°C and decrease
its binding affinity to ACE2 by two orders of magnitude at 37°C. Consistent with these
in vitro findings, the reducing agents tris (2-carboxyethyl)phosphine (TCEP) and
dithiothreitol (DTT) were able to inhibit viral replication at low mM levels in cell-based
assays. Our research demonstrates the mechanism by which the disulfide bonds are
contributing to the molecular structure of the Spike protein, allowing the latter to
execute its viral function.