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The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is amajor worldwide public health emergency that has infected over $1.5$ millionpeople. The partially open state of S1 subunit in spike glycoprotein isconsidered vital for its infection with host cell and is represented as a keytarget for neutralizing antibodies. However, the mechanism elucidating thetransition from the closed state to the partially open state still remainsunclear. Here, we applied a combination of Markov state model, transition paththeory and random forest to analyze the S1 motion. Our results explored apromising complete conformational movement of receptor-binding domain, fromburied, partially open, to detached states. We also numerically confirmed thetransition probability between those states. Based on the asymmetry in both thedynamics behavior and backbone C$\alpha$ importance, we further suggested arelation between chains in the trimer spike protein, which may help in thevaccine design and antibody neutralization.

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