Helicase Mutations in United States Isolates of SARS-CoV-2 Altered Protein Stability and Binding Dynamics
TL;DR
The concurrent occurrence of reduced predicted protein stability and more favorable docking-derived nucleic acid interface scores suggests that these mutations may influence helicase–nucleic acid recognition; however, direct effects on viral replication kinetics require experimental validation.
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2, which causes Coronavirus 2019, has resulted in the deaths of more than 7 million people. The helicase, encoded by non-structural protein-13 in the virus genome, plays a critical role in the virus's life cycle and is at the heart of treatment approaches. The study revealed the impact of helicase protein mutations on protein stability and nucleic acid binding dynamics in United States SARS-CoV-2 isolates. Nine recurrent mutations exceeding the predefined occurrence threshold were identified and subjected to structural modeling, protein stability prediction, and helicase–nucleic acid docking analysis. Utilizing data from nine mutations (Ser36Pro, Thr127Asn, His164Tyr, Met233Ile, Tyr324Cys, Ala368Val, Ala389Val, Arg392Cys, Thr599Ile) identified from isolates, mutant protein models were generated using deep learning algorithms. Protein stability alterations were assessed using SDM2, mCSM, DUET, and DynaMut2 tools. The helicase-nucleic acid interaction was evaluated through molecular docking analysis. Consensus-based stability prediction indicated that several mutations were predicted to reduce nsp13 stability, whereas His164Tyr was consistently predicted to have a stabilizing effect across all four tools. Some substitutions, including Met233Ile and Thr599Ile, showed method-dependent effects. Molecular docking analysis suggested that the recurrent mutation set may alter helicase–RNA interface energetics and spatial arrangement. However, these docking-derived changes should be interpreted as computational estimates rather than direct evidence of increased nucleic acid-binding affinity. The concurrent occurrence of reduced predicted protein stability and more favorable docking-derived nucleic acid interface scores suggests that these mutations may influence helicase–nucleic acid recognition; however, direct effects on viral replication kinetics require experimental validation.