Quantifying the Characteristics of Viruses in the Leviviridae Family Using Icosahedral Point Arrays

Abstract

Point arrays provide a neat method for structural comparison between viruses by highlighting different aspects of the viral capsid. For very structurally similar viruses, using multiple point array fits instead of just the best fitting point array reveals more structural differences, particularly if the best fitting point array is the same for the two viruses. The goal of this work was to add an additional layer of geometric characterization through point arrays, which could be used as another component in determining locations for successful point modifications on these viruses. Point arrays were _t for MS2, GA, fr, and QB, and then were compared to determine structural differences. For MS2, the nearest residues to each point in the point array were found using VMD. The mutability of these residues were looked up in Emily Hartman's 2018 landscape of MS2. Loop residues were isolated for each virus to determine more differences. The results found that some residues near point array elements could be modified. We posit that these residues might be modifiable with structurally similar residues that do not change the structure of the loop of the virus. In the future, looking at a spectrum of point arrays might be able to help predict which points, outside of the loops, would be harder to modify.