RESEARCH: COVID-19
FOLDING PROJECT #17335 PROFILE

The project relates to using computer simulations to study how the protein pieces of the COVID-19 virus bind to human cells. By looking at different versions of these proteins, scientists hope to understand how sugar molecules on the virus affect its ability to infect cells and how binding to human cells changes the virus's structure. This information could help in designing 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 respiratory illnesses in humans and animals.

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Receptor binding domain (RBD)

Region on the spike protein of a virus that binds to receptors on host cells

The receptor binding domain (RBD) is a crucial part of the SARS-CoV-2 spike protein. It's responsible for attaching 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, including those in the lungs and heart. It plays a role in regulating blood pressure and other bodily functions.

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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 and stability. In the case of SARS-CoV-2, glycosylation can influence how well the virus binds to human cells.

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Markov State Models

Mathematical models that describe the transition between different states of a system over time

Markov State Models are used in computational biology to simulate the behavior of complex systems, such as proteins. They can help us understand how molecules move and interact at the atomic level.

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Metastable States

Temporary states that a molecule can occupy for an extended period of time before transitioning to another state

Metastable states are important in understanding how proteins function. They represent transient configurations that can influence the protein's overall behavior and interactions.