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Structural and Functional Impacts of SARS-CoV-2 Spike Protein Mutations: Insights From Predictive Modeling and
Edem K Netsey1, Samuel M Naandam2, Joseph Asante Jnr3
1Department of Mathematics and Information Communication Technology, School of Physical Sciences, Dambai College of Education, Dambai, Ghana.
JMIR Bioinformatics and Biotechnology
|December 8, 2025
Summary
The study analyzed SARS-CoV-2 spike mutations using graph theory and simulations. Mutations N501Y and L452R significantly altered the spike receptor-binding domain (RBD) structure and stability, impacting COVID-19 variant development.
Area of Science:
- Virology and Structural Biology
- Computational Biology and Bioinformatics
Background:
- The COVID-19 pandemic necessitates a thorough understanding of SARS-CoV-2, especially how spike receptor-binding domain (RBD) mutations affect its structure and function.
- Existing methods lack comprehensive analysis of these mutations across different structural levels.
Purpose of the Study:
- To analyze the impact of specific SARS-CoV-2 point mutations (N501Y, L452R, N440K, K417N, E484A) on the spike RBD structure and function.
- To employ predictive modeling, including graph-theoretic approaches, protein modeling, and molecular dynamics simulations.
Main Methods:
- Utilized a multitiered graph-theoretic framework to model protein structure at three interconnected levels.
- Employed Iterative Threading Assembly Refinement (I-TASSER) for modeling mutated sequences and molecular dynamics simulations to assess protein folding and stability.
- Applied graph-theoretic molecular descriptors to analyze structural changes at various levels.
Main Results:
- Successfully identified structural and functional changes in the SARS-CoV-2 spike RBD (chain E) due to point mutations using three distinct analytical approaches.
- The graph-theoretic model revealed that N501Y and L452R mutations had the most significant impact on RBD conformation and stability compared to the wildtype.
- K417N and E484A mutations showed less pronounced effects, and findings were corroborated by ab initio modeling and molecular dynamics simulations.
Conclusions:
- Advanced the understanding of SARS-CoV-2 spike RBD mutations and their implications for vaccine development, therapeutic design, and variant monitoring.
- Highlighted the effectiveness of combining multiple predictive analytical approaches for studying viral mutations.
- Provided a framework for future research on viral mutations and their impact on protein structure and function.
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