RESEARCH: COVID-19
FOLDING PROJECT #17342 PROFILE

The project relates to studying how the SARS-CoV-2 virus attaches to human cells. Researchers are using computer simulations to understand how the virus's protein changes shape when it binds to our cells. This knowledge can help scientists design new drugs to fight COVID-19.

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) 17341-3 are repeats of 17336, 17337, and 17339 (RUN8), where each project has 5 RUNs starting from different equilibrated structures.

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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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receptor binding domain (RBD)

Receptor Binding Domain

The receptor binding domain (RBD) is a part of the SARS-CoV-2 spike protein that attaches to the ACE2 receptor on human cells, allowing the virus to enter and infect.

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ACE2

Angiotensin-Converting Enzyme 2

ACE2 is a protein found on the surface of many human cells. The SARS-CoV-2 virus uses ACE2 as its entry point to infect cells.

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glycosylation

The addition of sugar molecules to proteins.

Glycosylation is a common process where sugar molecules are attached to proteins. This can change the protein's shape, function, and how it interacts with other molecules.

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Markov State Models

Mathematical models used to describe the behavior of complex systems over time.

Markov State Models are a type of computer simulation used to study how molecules move and change shape. They can help researchers understand how proteins interact with each other and their environment.

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metastable states

Temporary, stable configurations of a system.

Metastable states are like temporary resting points for molecules. They are not the most stable state, but they can exist for a while before changing to a more stable form.

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drug design

The process of designing and developing new drugs.

Drug design involves using knowledge about diseases and how molecules interact to create new medications that can treat or prevent illnesses.