User:Andre Wu Le Chun/Sandbox 1

This is a default text for your page Andre Wu Le Chun/Sandbox 1. Click above on edit this page to modify. Be careful with the < and > signs.

You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Structural highlights

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, which contains the receptor binding domain (RBD), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that start from a metastable pre-fusion conformation to a stable post-fusion conformation, in which the receptor-binding domain assumes a up conformation.

This protein also shares amino acid sequence identity of 76% with SARS-CoV Urbani, however it has amino acid insertions that indicate a furin like cleavage site, that must be primed in order to enable the viral pathogenicity. In the Receptor binding domain, units of beta-sheets, alpha-helices and loops can be observed.

Function

The spike glycoprotein recognizes the hosts cell's angiotensin-converting enzime 2 (1r42) and binds itself on it, allowing the fusion of viral and cellular membrane, therefore enabling the viral infection.

Disease

6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale epidemics in 2020. The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense. The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

Relevance

Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domains of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future

Interaction with angiotensin-converting enzime 2

The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, which is a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that determinants for the virus-cell binding. Due to the conformational movements, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name. It binds itself to the ACE2 with high affinity (15nM). In order to activate infection, the spike protein is cleaved by TMPRSS2, a host's serine protease, also fundamental for the viral infection. Furine cleavage site

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.