Functional implications of hexameric dynamics in SARS-CoV-2 Nsp15

SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has undergone continuous evolution, leading to the emergence of variants with altered transmissibility and immune evasion. For the non-structural proteins (Nsps) of SARS-CoV-2, there are limited structural analyses of their naturally occurring mutations. Here, we identified four non-synonymous single-nucleotide polymorphisms (nsSNPs) in the Epsilon lineage of SARS-CoV-2 within Nsp15, an endoribonuclease critical for immune evasion. Of these Epsilon nsSNPs, E266Q is in the catalytic domain. This study investigates the effects of this on enzymatic activity, structural stability, and oligomeric assembly by serial crystallography. By solving the structure of the Nsp15 hexamer at room temperature of both Nsp15-E266Q and WT in the P2₁ space group to 3 Å, we observed asymmetric motions within its trimer subunits, a feature not visible in previously reported higher-symmetry space groups. These asymmetric motions resemble substrate-induced conformational changes reported in RNA-bound Nsp15 structures, suggesting functional relevance. Biochemical analyses further reveal that Nsp15-E266Q exhibited significantly higher enzymatic activity and thermal stability compared to the wild-type protein. These findings highlight how mutations in Nsp15 contribute to viral replication and immune evasion, offering insights into the molecular mechanisms underlying SARS-CoV-2 variant evolution and potential therapeutic strategies.