Homology Modeling and Evaluation of Sars-Cov-2 Spike Protein Mutant: D614G

Introduction

COVID 19 pandemic has spread across 180 countries from its source country China where the first human to human transmission was reported in December 2019 (Li et al., 2020; Wu et al., 2020). The pandemic agent is a coronavirus, named as “severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)” by the International Committee on Taxonomy of Viruses (ICTV) on 11 February 2020 (Lauxmann et al., 2020). SARS-Cov-2 infects the host cell with a positive single stranded RNA which is comparatively a large genome of ~30kb consisting of 9860 amino acids, 29891 nucleotides and 10 open reading frames (Wang et al., 2020). The viral genome codes for polyprotein 1a, polyprotein 1b, 16 non- structural proteins, and 4 main structural proteins: an envelope protein (E), spike protein (S), nucleocapsid protein (N) and membrane protein (M) (Guo et al., 2020; Hussain et al., 2005). Spike protein is the largest surface protein of SARS-Cov-2 virus and is a type1 membrane protein (Hoffmann et al., 2020). The attachment and entry of the SARS-Cov-2 virus to the host is mediated through S protein (Wu et al., 2020). S protein consists of an ecto-domain element, having 2 subunits, S1 and S2 (Shajahan et al., 2020). The S1 subunit has two subunits subdomains 1 and 2 (SD1 and SD2) and a Receptor Binding Domain (RBD) which will recognize and bind to the Angiotensin-Converting Enzyme 2 (ACE2) receptor (Wan et al., 2020) revealing the furin cleavage site on the S2 domain (Yan et al., 2020; Walls et al., 2020). Host cell proteases like TMPRSS2 initiate viral entry by acting upon the exposed cleavage site of the S2 domain (Li et al., 2020) by priming and activation cleavage mechanisms (Belouzard et al., 2009). The activation cleavage brings the viral membrane and host cell membrane in close proximity for viral fusion and entry (Li et al., 2020).

The rate and duration of infection within a selected population can alter the SARS-CoV-2 RNA genome with mutations that could potentially impact on its virulence and transmission (Timofeeva et al., 2020). A novel SARS-CoV-2 variant with a non-synonymous mutation D614G (aspartate to glycine at 614^th position) at the Carboxyl terminal region of SD2 (Becerra‐Flores & Cardozo, 2020; Cortey et al., 2020) had enhanced the spike protein cleavage by proteases which increased transmission efficiency by limiting the shedding of S1 domain from the virion (Becerra‐Flores & Cardozo, 2020; Zhang et al., 2020). It was observed that D614G mutation will lead to a change in the structure as well as type of interaction between the amino acids present in 613, 614, 615 positions and is followed by change in 3D structure of the protein, its orientation, finally resulting in functional changes. Due to this mutation, critical interprotomer hydrogen bonding from the S2 domain is disrupted and a shift is observed in the equilibrium between the open and closed states of S protein ectodomain (Johnson et al., 2020; Korber et al., 2020; Weissman et al., 2021). SD2 acts as an anchor that demarcates the movement of RBD as well as events like ACE2 receptor engagement and TMPRSS2 protease cleavage (Gobeil et al., 2021). In the evolution of coronaviruses to invade the host’s immune system, spike proteins play a crucial role.