RESEARCH: COVID-19
FOLDING PROJECT #17334 PROFILE

This project studies how the spike protein of the COVID-19 virus (SARS-CoV-2) binds to human cells. By simulating these proteins, scientists hope to understand how sugars on the virus affect its shape and how it attaches to our cells. This knowledge can help in designing new drugs to fight 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).

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SARS-CoV-2

Severe Acute Respiratory Syndrome Coronavirus 2

SARS-CoV-2 is the virus responsible for COVID-19. It is a type of coronavirus that causes respiratory illness in humans.

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Receptor binding domain (RBD)

The region of a viral protein that binds to a host cell receptor

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, 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 addition of sugar molecules to proteins

Glycosylation is a common process that can affect the structure and function of proteins. In the case of SARS-CoV-2, glycosylation can influence how the virus interacts with host cells.

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Markov State Models

Mathematical models used to describe the dynamic behavior of complex systems

Markov State Models are a powerful tool for understanding how molecules move and interact over time. They can be used to study protein folding, drug binding, and other biological processes.

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Metastable States

Intermediate states between different energy levels in a system

Metastable states are temporary configurations that molecules can exist in. They play an important role in biological processes such as protein folding and enzyme catalysis.

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Drug Design

The process of discovering and developing new drugs

Drug design is a complex and multidisciplinary field that involves using various techniques to identify and optimize molecules with therapeutic properties.