The SARS 2 coronavirus virus (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19). The “peak” or protein S facilitates the entry of the virus into the host’s cells.
Now, a group of researchers from the National University of Seoul in South Korea, the University of Cambridge in the United Kingdom, and Lehigh University in the United States, have collaborated to produce the first open-source of all protein atoms of a full length S of the protein. Researchers say this is of particular importance because protein S plays a central role in the entry of the virus into cells, making it a primary target for vaccine and development of antiviral drugs.
Details can be found in a book, “The Development of a Full-Length Glycosylated SARS-CoV-2 Spicle Protein Model of a Viral Membrane”, published online in The Journal of physical Chemistry B.
This demonstration video shows how to build this membrane system from their SARS-CoV-2 S protein models. The reinforcement program model is open access and can be found from the CHARMM-GUI home page by clicking on the COVID-19 Archive link or by clicking on the archives link in the header, then COVID-19 Proteins link in the left sidebar.
Developed by Wonpil Im, professor at Lehigh University, in the Department of Biological Sciences and Bioengineering Department, CHARMM-GUI (GUI = graphical user interface) is a program that simulates complex biomolecular systems simply, precisely and quickly. I’m describing it as a “microscope calculus” that allows scientists to understand at the molecular level the interactions that can’t be observed any other way. More information on CHARMM-GUI can be found in this video.
“Our models are the first fully glycosylated full-length SARS-CoV-2 peak (S) protein models that are available to other scientists,” said the cat. “I was fortunate to collaborate with Dr. Chaok Seok of the National University of Seoul in Korea, and Mr. Tristan Croll of the University of Cambridge in the United Kingdom, Our team spent days and nights at the construction of these models very carefully from the known cryo-EM structure of the parts. Modeling was very difficult, as there were many areas where modeling failed to provide high quality models. ”
Scientists can use innovative research simulation driving models for the prevention and treatment of COVID-19, according to Gi.
The S of protein structure was determined with cryo-EM with RBD up (PDB ID: 6VSB), and with low RBD (PDB ID: 6VXX). But, this model has a lot of residue. So they first modeled the lack of amino acid residues, and then others lacking domains. In addition, they modeled the potential for all glycans (or carbohydrates) attached to protein S. These glycans prevent the recognition of antibodies, making it difficult to develop a vaccine. They also built a viral membrane of the protein S system for the simulation of molecular dynamics.