SARS-CoV-2 Spike Protein Glycan Shield Role and Ancestors

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike protein Class I fusion Glycoprotein It interacts with the angiotensin converting enzyme 2 (ACE2) receptor on the surface of human cells, allowing them to enter the cell.This is a major target for both natural and vaccination Neutralizing antibody..

Peplomers are coated with a thick glycan shield that plays a role in target site recognition and conformational stability towards both ACE2 receptors and neutralizing antibodies, between closed and open forms. An open prefusion foam that regulates the state of peplomers in and enhances their affinity for ACE2 receptors by presenting receptor binding domains.

In recent studies, the occupancy and structure of the peplomer glycan shield plays an important role in host cell invasion and immune function, and various factors regulate the rate and order in which glycans coat proteins, resulting in different glycoforms. It has been suggested that there is a possibility.

Multiple N-glycans are strategically placed around the opening of the receptor binding domain to prevent water molecules from entering the crevice when in the open position, providing a peplomer structure and affinity for ACE2. It may weaken.

Specifically, the N-glycan at position N234 fills the cavity and supports the open conformation of the protein. On the other hand, N-glycans at positions N165 and N343 are thought to be involved in stabilizing open conformations and mediating transitions between states. These functions are facilitated by contact with adjacent protein residues. Therefore, altering the sequence, length, and branching of glycans at these sites affects the conformational variation and stability of the peplomer and alters the affinity of SARS-CoV-2 for the ACE2 receptor. There is a possibility.

Research papers recently uploaded to the preprint server bioRxiv* Harbison et al.. (April 1st^st 2021) A set of molecular dynamics simulations with a length of several microseconds studied the effects of glycosylation changes at sites N234, N165, N343, and the newly identified ancestral site N370, and these sites for infectivity. Clarify the impact of.

Panel a) Fully glycosylated SARS-CoV-2 S (PDBid 6VYB) 6 external domain structure. The proteins are shown in gray and the RBDs in chains B and C are highlighted in orange and white, respectively. The glycan shield is highlighted in blue. Panel b) Close up the open pocket with the N-type sugar chains at strategic positions N234, N165, and N343 highlighted in green, cyan, and purple, respectively. Panel c) N-glycans examined in various models studied in this work, represented by SNFG23 and drawn by DrawGlycan24 (http://www.virtualglycome.org/DrawGlycan/). Molecular rendering done with VMD25.

Conformation stability and ACE2 affinity

This group began by replacing the N234 glycans with shorter oligomannose structures (Man5). Note that in the open state, the cavity of the receptor binding domain was not completely occupied and the conformation was somewhat flexible. The open conformation was still considered stable. Slightly longer, more branched glycans (Man9) are also tested in this position, which can fill the space more effectively, promote interaction with proteins on the other side of the crevice, and further stabilize the open conformation. It’s done. Replacing glycans N165 and N343 with shorter glycans Man5 was found to reduce the conformational stability of the receptor-binding domain at the open position, but the presence of a large Man9 at position N234 was found to be open by occupying it. I was able to stabilize the position sufficiently. An open rift. Replacing N234 with Man5 or Man9 maintained the affinity for the ACE2 receptor because the open conformation was relatively stable.

The glycan N234 was then replaced by the shorter oligomannose still (Man3), and the group noted that at this length the glycans were unable to form functional interactions with proteins adjacent to the crevices that contributed to stability. I am. In this case, the N-type sugar chains of N165 and N343 predominate in conformational interactions, forcing the receptor-binding domain into an intermediate conformation between fully open and closed states.This conformational change via Decreased open conformational stability reduced affinity for the ACE2 receptor.

SARS-CoV-2 Glycan ancestors

This group also performed an ancestral reordering of the SARS peplomer sequence, and compared to recent ancestors, SARS-CoV-2 lacks a seek-on (the amino acid chain that anchors N-glycans) at position N370. I found that. This group added this position to the SARS-CoV-2 sequence and re-run the molecular dynamics simulation at position N234 using Man9. The open conformation was found to have equal stability and affinity for the previously tested Man9-N234 model and ACE2. However, in this case, most of the receptor binding domain crevices are filled with N370 and Man9-N234 is pushed into the pocket entrance.

Similarly, in the closed state, N370 was found to pass two halves of the peplomer receptor binding domain together to improve stability. However, improved closed stability reduces the likelihood of interacting with the ACE2 receptor and reduces the virulence of the virus. This group proposes that the loss of glycosylation at N370 contributed more strongly to the increased toxicity observed at SARS-CoV-2 than at SARS-CoV-1. Analysis of this ancestor suggests that the role of glycans at position N234 evolved relatively recently at SARS-CoV-2 and may have grown in lieu of loss of N370. This substitution may have played an evolutionary role in lowering the energy cost of receptor-binding domains that enter an open conformational state.

*Important Notices

bioRxiv Publish preliminary scientific reports that should not be considered definitive as they are not peer-reviewed, guide clinical practice / health-related behaviors, and should not be treated as established information.