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arXiv · 2004.05256

Deciphering the Protein Motion of S1 Subunit in SARS-CoV-2 Spike Glycoprotein Through Integrated Computational Methods

Hao Tian·Peng Tao
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Abstract

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major worldwide public health emergency that has infected over $1.5$ million people. The partially open state of S1 subunit in spike glycoprotein is considered vital for its infection with host cell and is represented as a key target for neutralizing antibodies. However, the mechanism elucidating the transition from the closed state to the partially open state still remains unclear. Here, we applied a combination of Markov state model, transition path theory and random forest to analyze the S1 motion. Our results explored a promising complete conformational movement of receptor-binding domain, from buried, partially open, to detached states. We also numerically confirmed the transition probability between those states. Based on the asymmetry in both the dynamics behavior and backbone C$\alpha$ importance, we further suggested a relation between chains in the trimer spike protein, which may help in the vaccine design and antibody neutralization.

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Hao Tian, Peng Tao. 2020-04-10. Deciphering the Protein Motion of S1 Subunit in SARS-CoV-2 Spike Glycoprotein Through Integrated Computational Methods. https://arxiv.org/abs/2004.05256

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