RESEARCH: COVID-19
FOLDING PROJECT #17336 PROFILE

This project uses computer simulations to study how the SARS-CoV-2 virus attaches to human cells. They're looking at how sugars attached to the virus and the cell receptor affect how they bind. This could help scientists design new drugs to stop the virus.

Note: This TLDR is a simplication and may not be 100% accurate.

These projects involve the SARS-CoV-2 receptor binding domain (RBD) and its target receptor in humans, ACE2.

We are simulating these proteins alone and in complex with each other (and with and without glycosylation).

We will build Markov State Models using the Fah simulation data, which will help us identify the metastable states of each protein/protein complex.

Given these experiments, we hope to be able to explain the impact of glycosylation on RBD conformational dynamics as well as identify whether there are shifts in metastable states upon RBD:ACE2 binding.

Ultimately, the knowledge gained here will help infom drug design efforts. Note: 17313-6 replace 17307-9, as 17307-9 used a different, less stable integrator. 17329-331 replace 17316-8 (change from rectangular to truncated octahedron box) 17332-5 replace 17325-8 (change from rectangular to truncated octahedron box) 17336-40 replace 17330, 32-35 (fix glycan stereoisomer).

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SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2

SARS-CoV-2 is the virus that causes COVID-19. It's a type of coronavirus, which are common viruses that can cause illnesses ranging from the common cold to more severe diseases like SARS.

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RBD

Receptor binding domain

The RBD is a part of the SARS-CoV-2 spike protein that binds to human cells. This binding is essential for the virus to infect cells and cause disease.

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ACE2

Angiotensin-converting enzyme 2

ACE2 is a protein found on the surface of human cells. The SARS-CoV-2 RBD binds to ACE2, allowing the virus to enter and infect cells.

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Glycosylation

The process of adding sugar molecules to proteins

Glycosylation is a common modification of proteins that can affect their function. In the case of SARS-CoV-2, glycosylation of the spike protein can influence its ability to bind to human cells.

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Markov State Models

A type of model used to simulate the dynamics of complex systems

Markov State Models are used to study how molecules move and change over time. In this case, they will be used to understand the behavior of SARS-CoV-2 proteins and their complexes.

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Metastable States

States that are relatively stable but can transition to other states over time

Metastable states are like temporary resting points for molecules. Understanding these states can help us predict how proteins will behave and interact.