RESEARCH: COVID-19
FOLDING PROJECT #17313 PROFILE

This project studies how the SARS-CoV-2 virus attaches to human cells. Researchers are simulating proteins involved in this process, with and without sugar molecules (glycosylation). They aim to understand how glycosylation affects protein shape and binding, potentially leading to new drug design strategies.

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.

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SARS-CoV-2

Severe Acute Respiratory Syndrome Coronavirus 2

SARS-CoV-2 is a virus that causes COVID-19. It's a type of coronavirus that was first identified in Wuhan, China in late 2019. The virus spreads through respiratory droplets and can cause a range of symptoms from mild to severe.

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receptor binding domain (RBD)

Receptor Binding Domain

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

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ACE2

Angiotensin-converting enzyme 2

ACE2 is a protein found on the surface of many human cells. It plays a role in regulating blood pressure and other bodily functions. The SARS-CoV-2 virus uses ACE2 as a receptor to enter and infect cells.

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glycosylation

The process of attaching sugar molecules to proteins or lipids.

Glycosylation is a common modification that affects the function and structure of many proteins. In the case of SARS-CoV-2, glycosylation can impact how the virus binds to human cells and evades the immune system.

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Markov State Models

Mathematical models used to simulate the dynamic behavior of molecules.

Markov State Models are used to understand how proteins change shape and interact with other molecules over time. In this case, they will be used to study how glycosylation affects the binding between SARS-CoV-2 RBD and ACE2.

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metastable states

States that are relatively stable but can transition to other states.

Metastable states represent temporary configurations that molecules can occupy. Understanding these states is important for understanding how proteins function and interact.