The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State.

BioRxiv : the Preprint Server for Biology
Rachael A MansbachS Gnanakaran

Abstract

The COVID-19 pandemic underwent a rapid transition with the emergence of a SARS-CoV-2 variant that carried the amino acid substitution D614G in the Spike protein that became globally prevalent. The G-form is both more infectious in vitro and associated with increased viral loads in infected people. To gain insight into the mechanism underlying these distinctive characteristics, we employed multiple replicas of microsecond all-atom simulations to probe the molecular-level impact of this substitution on Spike closed and open states. The open state enables Spike interactions with its human cellular receptor, ACE2. Here we show that changes in the inter-protomer energetics due to the D614G substitution favor a higher population of infection-capable (open) states. The inter-protomer interactions between S1 and S2 subunits in the open state of the D-form are asymmetric. This asymmetry is resolved in the G-form due to the release of tensile hydrogen bonds resulting in an increased population of open conformations. Thus, the increased infectivity of the G-form is likely due to a higher rate of profitable binding encounters with the host receptor. It is also predicted to be more neutralization sensitive due to enhanced exposure of the r...Continue Reading

Citations

Sep 10, 2020·Nature·Ewen Callaway
Dec 12, 2020·Emerging Microbes & Infections·Victoria ElizondoRalf Duerr
Apr 6, 2021·Frontiers in Immunology·Jaime Fergie, Amit Srivastava
May 11, 2021·Computational and Structural Biotechnology Journal·Zachariah P SchuursNeha S Gandhi
Jun 11, 2021·Frontiers in Molecular Biosciences·Sonia Beeckmans, Edilbert Van Driessche

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