D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction

• Published in: Cell Reports Vol. 34; no. 2; p. 108630
• Main Authors: Gobeil, Sophie M.-C., Janowska, Katarzyna, McDowell, Shana, Mansouri, Katayoun, Parks, Robert, Manne, Kartik, Stalls, Victoria, Kopp, Megan F., Henderson, Rory, Edwards, Robert J., Haynes, Barton F., Acharya, Priyamvada
• Format: Journal Article Web Resource
• Language: English
• Published: United States Elsevier Inc 12.01.2021; Elsevier BV; The Author(s); Elsevier
• Subjects: allostery; COVID-19; COVID-19 - pathology; COVID-19 - virology; cryo-EM; Cryoelectron Microscopy; D614G; furin cleavage; Humans; Immunogenicity, Vaccine; Molecular Dynamics Simulation; Mutation; Peptide Hydrolases - metabolism; Protein Domains; Protein Stability; Protein Structure, Quaternary; Protein Subunits - metabolism; Proteolysis; SARS-CoV-2; SARS-CoV-2 - isolation & purification; SARS-CoV-2 - metabolism; spike; Spike Glycoprotein, Coronavirus - chemistry; Spike Glycoprotein, Coronavirus - genetics; Spike Glycoprotein, Coronavirus - metabolism; COVID-19; SARS-CoV-2; furin cleavage; D614G; cryo-EM; 2P; spike; allostery
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2020.108630

The severe acute respiratory coronavirus 2 (SARS-CoV-2) spike (S) protein is the target of vaccine design efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Despite a low mutation rate, isolates with the D614G substitution in the S protein appeared early during the pandemic and are now the dominant form worldwide. Here, we explore S conformational changes and the effects of the D614G mutation on a soluble S ectodomain construct. Cryoelectron microscopy (cryo-EM) structures reveal altered receptor binding domain (RBD) disposition; antigenicity and proteolysis experiments reveal structural changes and enhanced furin cleavage efficiency of the G614 variant. Furthermore, furin cleavage alters the up/down ratio of the RBDs in the G614 S ectodomain, demonstrating an allosteric effect on RBD positioning triggered by changes in the SD2 region, which harbors residue 614 and the furin cleavage site. Our results elucidate SARS-CoV-2 S conformational landscape and allostery and have implications for vaccine design. [Display omitted] •SARS-CoV-2 S 2P mutations do not impact its structure, stability, or antigenicity•D614G mutation increases RBD “up” state and enhances S1/S2 junction proteolysis•Structure and antigenicity reveal allostery between the S1/S2 junction and RBD•SD2 anchors the mobile RBD and NTD, separating large S1 subunit motions from S2 SARS-CoV-2 spike undergoes large conformational changes during cell fusion. Gobeil et al. identify a subdomain anchor that limits large motions in the receptor binding subunit of the pre-fusion spike from propagating to its fusion subunit. They demonstrate that the D614G mutation increases the rate of furin cleavage, which may impact infectivity.