RESEARCH: COVID-19
FOLDING PROJECT #17333 PROFILE

This project uses computer simulations to study how the SARS-CoV-2 virus attaches to human cells. Researchers are looking at how sugars on the virus and human cell proteins affect this attachment process. By understanding these interactions, scientists hope to develop 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).

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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 and MERS.

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RBD

Receptor Binding Domain

The 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 a doorway to enter and infect these cells.

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Glycosylation

The process of attaching sugar molecules to proteins

Glycosylation is a common modification of proteins that can affect their shape, function, and interactions with other molecules. In the case of SARS-CoV-2, glycosylation on the spike protein can influence its ability to bind to the ACE2 receptor.

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Markov State Models

Mathematical models that describe the probabilities of different states a system can be in over time.

Markov State Models are used to simulate the behavior of complex systems, such as proteins. By analyzing these simulations, researchers can gain insights into how proteins move and interact.

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Metastable States

Stable states that a system can exist in for a prolonged period but are not the most stable state.

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

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Drug Design

The process of designing and developing new drugs.

Drug design involves identifying molecules that can interact with specific targets in the body to treat diseases. This often requires a deep understanding of how proteins and other biomolecules function.