Exploring Conformational Transition of 2019 Novel Coronavirus Spike Glycoprotein Between Its Closed and Open States Using Molecular Dynamics Simulations

Mert Gur; Elhan Taka; Sema Zeynep Yilmaz; Ceren Kilinc; Umut Aktas; Mert Golcuk

Coronavirus S protein structures having PDB IDs 6VYB (Walls, Park et al. 2020 ) and 6VXX (Walls, Park et al. 2020) , which are in the closed and open states respectively, were used as starting structures in our MD simulations. As shown in Fig. 1 , these crystal structures comprise most of the S protein domains; S1 subunit (NTD and RBD) and S2 (FP and HR1). Furthermore, S trimers are extensively decorated with N-linked glycans ( Fig. 1) , which are important for proper folding (Rossen et al. 1998 ) and for modulating accessibility to host proteases and neutralizing antibodies (Walls et al. 2016 , Yang et al. 2016 , Xiong et al. 2018 , Walls et al. 2019 . Closed and open state crystal structures of the S protein were obtained by performing the following mutation: (i) R682S, R683G, and R685G, which were performed to abrogate furin S1/S2 cleavage site, and (ii) K986P and V987P, which were performed for stabilization (stabilizing structure). The trimeric crystal structures comprise the sequence A27-S1147 of each protomer. However, out of these 1121 residues there are structural information missing for 149 of them in the closed state: V70-F79, Y144-N164, Q173-N185, R246-A262, V445-G446, L455-C488, G502, P621-S640, Q677-A688, L828-Q853. For the open state, on the other hand, there are 155, 172 and 161 residues missing for its three protomers (denoted by A, B and C) as follows: V70-N81, T114-Q115, Y144-N165, Q173-N185, A243-A262, S443-G447, E471-Y489, G502, P621-S640, Q677-S689, P812, L828-L854 of protomer A, A67-D80, L141-A163, Q173-N185, I197-G199, L212-R214, A243-A262, L455-L461, D467-F490, E516-P521, P621-S640, Q677-A688, P812, L828-Q853 of protomer B, and A67-D80, Y144-N165, Q173-N185, . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.17.047324 doi: bioRxiv preprint A243-A263, V445-G447, L455-L461, E471-F490, P621-S640, Q677-S689, P812, L828-F855 of protomer C. In order to model the missing residue stretches and add them to the protein structures, the three-dimensional structures of the closed and open states were modeled using SWISS-MODEL web server (Waterhouse et al. 2018 ) using 6VXX and 6VYB structures, respectively, as templates. For both closed and open states, the FASTA sequence spanning residues A27-S1147 for each S protein protomer is taken from NCBI having RefSeq: YP_009724390 (O'Leary et al. 2016 ). Prior to submission to SWISS-MODEL, all mutations in the crystal structures were reversed in the sequence. Using VMD (Humphrey et al. 1996) , both closed and open crystal structures were separately solvated in water boxes each having at least 12 Ã… cushion of water in each direction. Ions were added to neutralize the system and NaCl concentrations were set to 0.150 M to represent a more typical biological environment. The size of the solvated S protein systems in the closed and open states were of ~410000 and ~415000 atoms in size, respectively.