Analysis of the SARS-CoV-2 nucleocapsid protein suggests multiple structures suitable for use in vaccine design

SARS-CoV-2 is the virus that causes the Covid-19 respiratory disease. Recently, we developed an aerosol based vaccine strategy using the Spike protein as the main antigen. However, the nucleocapsid protein (N-protein) of this virus is also highly immunogenic and has potential for use as part of a vaccine strategy. Here, we use a combination of Structure-Based Epitope Predictions and Molecular Dynamics Simulations to find and investigate the stability of N-protein epitopes. We observed that the N-protein contains structures that are stable, and thus have potential for use in our new vaccine strategy. ***This project was completed with contributions from Esteban Dodero-Rojas and José N. Onuchic from Rice University.