The SARS-CoV-2 spike (S) protein is processed by a furin-like protease into the S1 binding fragment and the S2 fusion fragment. Involvement of the receptor binding domain (RBD) in S1 by the viral angiotensin receptor modulates enzyme 2 (ACE2) on the surface of host cells followed by secondary proteolytic cleavage within S2.
As a result, the S protein undergoes major conformal changes, leading to S1 separation and an unstable conversion of S2 to a postfusion structure. This removes the virus and the host cell membrane to start infection.
In the prefusion spike protein structure, the S1 subunit folds into four domains – N-terminal domain, RBD, and two C-terminal domains – and orbits around the S2 prefusion subunit. The RBD can take two distinct conventions: “up” for the receptor-accessible state and “down” for the inaccessible state.
D614G prevents changes in spike shape
A variant of SARS-CoV-2 with single-residue substitution (D614G) in its spike protein has quickly grown to become the largest strain in the world. Since this change occurred, it has evolved into worrying changes, including rapid changes in the UK, South Africa and Brazil.
In the new study, researchers from Boston Children’s Hospital researchers led by Bing Chen, PhD, analyzed how the structure of the SARS-CoV-2 spike proteins altered with the D614G mimic. The team imaged the spike protein of the “original” D614 spike and the G614 variable spike using a cyro-electron microscope to visualize atomic-phase crystal structures.
Chen’s team previously said that D614 spike proteins sometimes alter conformation and breakdown before the virus can bind to cells. When the team compared the eluted proteins of D614 to those of the G614, they found that the original spike was found in all concoctions, including prefusion trimers, postfusion trimers, and monomers. dissociated, but the spike protein G614 was found mainly in the precursor form.
This model shows the structure of the spike protein in its closed arrangement, in its original D614 form (left) and its mutant form (G614). In the mutant spike protein, the 630 loop (in red) stabilizes the spike, preventing premature open wetting and making SARS-CoV-2 more infectious. Image courtesy of Bing Chen, PhD, Boston Children’s Hospital.
“Because the original spike protein would release, it was not good enough to induce a strong neutralizing antibody response,” Chen said.
The team found that the S1 subunit separated more easily from the D614 virus than the G614 virus, suggesting that the D614 viral spike protein is not as stable as the G614 variant. In particular, the G614 trimer was found in the RBD-up (accessible) compact more often than the D614 trimer.
Interestingly, they also found that the G614 variant binds weaker to the ACE2 receptor than the D614 trimmer. The researchers explained that the stability of the G614 spike proteins still makes the virus more contagious.
“Say there are 100 spikes in the original virus,” Chen explained. “Because of shape instability, only 50% of them are probably active. In the G614 variables, you probably have 90% that are functional, so while they don’t connect as well, the chances are greater you will have an infection. “
The researchers confirmed that substitution of D614G removes a salt bridge between D614 in the second terminus C of one subunit and K854 in the proximal peptide (FPPR) region of the adjacent subunit, but the “closed” accessible conformation remains structural, contributing to the stability of the spike protein.
They attributed the stability to the ordered nature of 630 loops (neighboring areas on C fields). This causes the spike trimer to more often form the single-ended RBD concave (subunit S1 is prevented from splitting) as the other two RBDs are still accessible due to the structure of the 630 loops. This reduces the overall ACE2 affinity of the G614 trimers.
Future guidance with version G614: vaccines
In the paper, Chen suggested that reconstituted vaccines would include the code for this mutant spike protein. The SARS-CoV-2 S protein has been a target of most first-generation vaccines, using almost the D614 series alone. However, because the G614 mutation has gone hand in hand, these vaccines are blocked and may not focus on the predictive form of the spike protein.
The authors suggested that the G614 spike trimmer is an advanced immunogen for the development of neutral immune responses. They say it would be an excellent scaffold for designing the next generation of vaccines against new changes.
The Boston children’s team is also applying structural biology to better understand how SARS-CoV-2 binds to the ACE2 receptor, with a view to medical therapy to block the virus. from access to host cells. They are studying “decoy” ACE2 proteins that may bind the virus more strongly than natural ACE2 found in human cells.
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