Dynamical asymmetry exposes 2019-nCoV prefusion spike

Susmita Roy

movement that generates the 'up' and 'down' conformations (7, 8, 10) . Other betacoronaviruses, like SARS-CoV, MERS-CoV and distantly related alphacoronavirus porcine epidemic diarrhea virus (PEDV) also have this apparently stochastic RBD movement (11, 12) . The combination of RBD up-down rearrangement may lead each S1-head of the trimeric prefusion spike protein of coronavirus to adopt different possible conformations: (i) 3down, (ii) 1up-2down, (iii) 2up-1down, and (iv) 3up (Fig. 1C) . Among them 3down, 3up are symmetric conformers and 1up-2down, 2up-1down are asymmetric conformers. Single-particle cryo-electron microscopy (Cryo-EM) determined few such symmetric and asymmetric structures referred to as the receptorbinding inactive state and receptor-binding active state, respectively (8) . The asymmetric structure where one of the RBDs rotates up was thought to be less stable for SARS-CoV S (10) . In comparison, the recent Cryo-EM study found three RBDs in 1up-2down conformation as a predominant arrangement in the prefusion state of 2019-nCoV S trimer (7) . This arrangement apparently appears legitimate for SARS-CoV-2 S in order to explain the higher affinity of 1up-2down for ACE2 receptor than that of SARS-CoV S. However, we cannot rule out the possibility of 2up-1down conformation as a functional state, which may provide even stronger binding with ACE2 considering the fact that ACE2 is a dimeric receptor (9, 13) . This hypothesis is consistent with a recent crystallographic study demonstrating that CR3022, a neutralizing antibody isolated from convalescent SARS patients targets the RBD when at least two RBD on the trimeric spike protein are in the up conformation (14) . Assembling all these experimental results it is high time to understand the molecular mechanism of S1-head coordination of trimeric SAR-CoV-2 S and to identify important interaction in regulating spike up-down conformations. A schematic of receptor-bound spike protein including the receptor-binding subunit S1, the membrane-fusion subunit S2 of a coronavirus is shown. B. Side and top views of the homo-trimeric structure of SARS-CoV-2 spike protein with one RBD of the S1 subunit head rotated in the up conformation. C. RBD up-down movement expected to lead S1 heads of the trimeric spike protein to attain the following possible conformers: (i) 3 down (ii) 1up-2down (iii) 2up-1down, and (iv) 3up. These are an analogue demonstration of the spike protein top-view where NTDs are represented by colored ovals, RBDs are represented by flexible sticks and S2 domains are represented by filled circles.