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

In order to explore the most dominant features of the protein dynamics in the closed and open states, PCA was performed using all conformations of protomer A, B and C sampled in the closed state MD simulations and all protomer B conformations sampled in the open state MD simulations. PCA is an effective and proven method used to dissect the most prominent motions of a protein along a given MD trajectory (Please refer to Sec. II D for details) (Gur et al. 2018) . For a MD trajectory of a system comprised of N atoms, PCA provides 3xN modes of motions, among which PC1 and PC2 represent the first and second most prominent motion observed in the MD trajectory. PC1 and PC2 obtained from the combined MD trajectory of down . 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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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 conformation of protomer in closed state and up conformation of protomer in open state is shown in Fig. 6(a) . The ratio of the variances between PC1 and PC2 are 1 2 ⁄ = 69.35, and cumulatively they account for 98.6% of the total motion in the MD trajectory; i.e. the first two PCs account for 98.6% of the total variance. As can be seen in Fig. 6(a) , PC1 describes a rigid body like motion of RBD. PC1 alone is able to describe 98% of the structural transition between the protomer in its down an up conformation (Loop regions and NTD were not included in this calculation). PC2 is also characterized by predominant movement of RBD.