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

The starting and end conformations of the SMD simulations were selected from our MD simulations of the closed and open states at time instances 20 ns and 40 ns. Cα atoms of RBD residues P337-A344, F347-V350, W353-S371, S375-Y380, V390-I410, G416-Y423, T430-S438, G447-R454, L492-Q498, Q506-L517, T523-G526 of protomer B were selected as SMD atoms, since they show minimal deformation upon superposition of up and down RBD conformations. In the first 20 ns of closed state MD simulations residues K986, D985 of protomer A and K113, D985, E988 of protomer C interacted with RBD of protomer B. Thus, their Cα atoms were kept fixed during our SMD simulations. Pulling vector was constructed by first aligning closed and open state conformations via S2 of protomer B and subsequently constructing a vector pointing from the center of SMD atoms in the closed state conformation to the open state conformation. A pulling velocity of 1 Å/ns was selected and spring constant is selected as 50 / /Å 2 . These conditions satisfy stiff-spring approximation (i.e. dummy atom followed the center of mass of SMD atoms closely), while the spring constant was soft enough to allow small deviations (Isralewitz, Gao et al. 2001) .