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Published on: June 14, 2022
Structural Analysis of the SARS-CoV-2 Spike N-Terminal Domain Across Wild-Type and Recent Variants: A Comparative
Miriana Quaranta1, Allegra Via1, Stefano Pascarella1
1Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.
The SARS-CoV-2 virus N-Terminal Domain (NTD) evolves to evade immune responses, with mutations decreasing its net charge and reducing antibody binding effectiveness over time. This molecular evolution impacts viral transmission and immune evasion strategies.
Area of Science:
- Virology
- Molecular Biology
- Structural Biology
Background:
- The Spike protein of SARS-CoV-2 drives viral transmission and immune evasion.
- The N-Terminal Domain (NTD) of the Spike protein is critical for viral pathogenesis.
- Understanding NTD evolution is key to combating SARS-CoV-2 variants.
Purpose of the Study:
- To comparatively analyze the structural evolution of the SARS-CoV-2 NTD across various variants.
- To investigate the impact of NTD mutations on antibody interactions.
- To elucidate the role of NTD structural changes in viral immune escape.
Main Methods:
- Comparative structural analysis of NTD from wild-type and variant strains (BA.2, XBB.1, XBB.1.5, BA.2.86, JN.1, HV.1, KP.2, KP.3, KP.3.1.1).
- Molecular dynamics simulations.
- Surface electrostatic potential analysis.
- Binding energy predictions using the neutralizing antibody 4A8.
Main Results:
- A decreasing net charge trend was observed in the NTD across evolving SARS-CoV-2 variants, contrasting with the RBD.
- The NTD net charge reached a minimum of -1.84 in the KP.3.1.1 variant.
- Antibody 4A8 showed significantly reduced binding efficacy against newer variants, with interaction energy dropping from -96.28 kcal/mol (WT) to -64.00 kcal/mol (KP.3).
Conclusions:
- SARS-CoV-2 NTD mutations facilitate immune escape by altering structural and electrostatic properties.
- The observed evolutionary trajectory favors viral evasion of host immune surveillance.
- This study highlights the dynamic nature of viral evolution and its implications for therapeutic strategies.
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