Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies
| Autor: | Sang-Jun Park, Wonpil Im, Hyeonuk Woo, Martin Frank, Yiwei Cao, Yeol Kyo Choi, Chaok Seok, Min Sun Yeom |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Glycan
Glycosylation Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Plasma protein binding Computational biology Molecular Dynamics Simulation medicine.disease_cause Article Antigen-Antibody Reactions chemistry.chemical_compound Viral envelope Polysaccharides medicine Humans Computer Simulation Physical and Theoretical Chemistry Receptor chemistry.chemical_classification Mutation Molecular Structure biology Chemistry Spike Protein COVID-19 Antibodies Neutralizing Computer Science Applications Enzyme Spike Glycoprotein Coronavirus biology.protein Antibody Protein Binding |
| Zdroj: | Journal of Chemical Theory and Computation bioRxiv article-version (status) pre article-version (number) 1 |
| ISSN: | 1549-9626 1549-9618 |
| Popis: | The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a public health crisis, and the vaccines that can induce highly potent neutralizing antibodies are essential for ending the pandemic. The spike (S) protein on the viral envelope mediates human angiotensin-converting enzyme 2 (ACE2) binding and thus is the target of a variety of neutralizing antibodies. In this work, we built various S trimer-antibody complex structures on the basis of the fully glycosylated S protein models described in our previous work, and performed all-atom molecular dynamics simulations to get insight into the structural dynamics and interactions between S protein and antibodies. Investigation of the residues critical for S-antibody binding allows us to predict the potential influence of mutations in SARS-CoV-2 variants. Comparison of the glycan conformations between S-only and S-antibody systems reveals the roles of glycans in S-antibody binding. In addition, we explored the antibody binding modes, and the influences of antibody on the motion of S protein receptor binding domains. Overall, our analyses provide a better understanding of S-antibody interactions, and the simulation-based S-antibody interaction maps could be used to predict the influences of S mutation on S-antibody interactions, which will be useful for the development of vaccine and antibody-based therapy. |
| Databáze: | OpenAIRE |
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