Dynamical asymmetry exposes 2019-nCoV prefusion spike

Susmita Roy

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.052290 doi: bioRxiv preprint S1). Inter-chain proline-proline distance measurement shows that the corresponding RBD-NTD domains are far away in the case of SARS-CoV S (Fig. 4B ) and further away in the case of MERS-CoVS (Fig. 4C ). This measurement involves their respective Cryo-EM structures. Despite the relatively high degree of sequence similarity between the SARS-CoV-2 S and the SARS-CoV S and also with the spike protein from the bat coronavirus RaTG13, a single histidine residue at the relevant RBD-NTD domain interface is found unique in the vase of SARS-CoV-2 S (Fig. S5 ) (29) . The imidazole ring of histidine is pointing towards the hydrophobic assembly of aforesaid proline-tyrosine in the juxtaposition of the RBD-S1 hinge region. Such inter-chain RBD-NTD connection is thus found to impact the RBD hinge interaction by upregulating more RBD-up conformation (Fig. 4D ). In the absence of such interchain interaction, the RBD mostly stays in the down conformation allowing RBD to break the symmetry rarely in a stochastic manner (Fig. 4E ). The absence of inter-chain RBD-NTD connection also appears to impact the SARS-CoV RBD hinge interaction. Here, the opening of RBD-S1 cleft is significantly less than that of SARS-CoV-2 S in their respective S1-head-up state (Fig. S6 ). The assistance from the inter-chain RBD-S2-stalk related interfacial contacts are also found to modulate the population dynamics of RBD-down conformation (Fig. S7 ). The influence of this inter-chain RBD-S2-stalk interaction has also been observed in an early Cryo-EM analyses where two proline mutations at the top of S2 stalk (inferring RBD-S2 inter-chain connection) helped to stabilize the 'up' conformers of SARS-CoV S (30) .