User:Rachael Vavul/Sandbox 1
From Proteopedia
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LCB1 is a fully computationally designed mini protein with a compact, optimized interface. A de novo design approach was taken to design LCB1, incorporating the helical structure of the binding alpha helix in ACE2, but with modifications of residues to make more interactions and have a higher affinity for the spike protein than the ACE2 receptor. | LCB1 is a fully computationally designed mini protein with a compact, optimized interface. A de novo design approach was taken to design LCB1, incorporating the helical structure of the binding alpha helix in ACE2, but with modifications of residues to make more interactions and have a higher affinity for the spike protein than the ACE2 receptor. | ||
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| + | <scene name='10/1076042/Lcb3-spike_protein_interaction/1'>TextToBeDisplayed</scene> | ||
Revision as of 13:04, 8 April 2025
Contents |
Introduction
Overview of SARS-CoV-2
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is a RNA virus that is responsible for the highly infectious respiratory disease, COVID-19. It is made up of four key proteins: the spike protein, the envelope protein, the membrane protein, and the nucleocapsid protein. The envelope protein is responsible for ...
Function
The spike protein lies on the surface of SARS-CoV-2 to facilitate entry of the virus into human cells. More specifically, after SARS-CoV-2 has entered the respiratory system, its spike protein binds to the ACE2 receptor (Angiotensin Converting Enzyme Receptor 2) in the lungs. The spike protein contains two functional subunits: S1 and S2. S1 contains the RBDs (receptor binding domains), which is where it binds to the ACE2 receptor. S2 facilitates membrane fusion between the virus and host cell, allowing viral RNA to enter and replicate.
Structure
The spike protein is a homotrimer with three RBDs which contains the active site on the protein. The majority of interface residues in ACE2 is found on its alpha helix in the active site.
- Add image of ACE2 binding with Spike + pic of binding site#
Spike Protein Inhibitors
LCB1
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LCB3
Conformations
- gray closed conf: SARS-CoV-2 Spike protein in closed conformation. Interface residues (in open conformation) are colored gray 6ZP0" (ref#:Xiong, X., Qu, K., Ciazynska, K.A. et al 2020).
The spike protein is unable to bind when in the closed conformation. Binding requires at least two of the RBDs to be in the "up" or "open" conformation.
Key features
This is a default text for your page Rachael Vavul/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.
=== Disease ===
Relevance
Structural highlights
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.
</StructureSection>
References
Xiong, X., Qu, K., Ciazynska, K.A. et al. A thermostable, closed SARS-CoV-2 spike protein trimer. Nat Struct Mol Biol 27, 934–941 (2020). https://doi.org/10.1038/s41594-020-0478-5
