RESEARCH: COVID-19
FOLDING PROJECT #17308 PROFILE

This project studies how the SARS-CoV-2 virus attaches to human cells. Scientists are using computer simulations to understand how proteins on the virus and in our bodies interact. They hope this will lead to better 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: these projects are replacing 17304-6, as 17304-6 had to be stopped due to work server issues.

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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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Receptor binding domain (RBD)

Region of the SARS-CoV-2 spike protein that binds to host cell receptors

The receptor binding domain (RBD) is a part of the spike protein found on the surface of the SARS-CoV-2 virus. This domain is responsible for attaching the virus to human cells, allowing it to infect them.

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ACE2

Angiotensin-converting enzyme 2

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

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Glycosylation

The process of adding sugar molecules to proteins

Glycosylation is a common process in which sugar molecules are attached to proteins. This process can affect the function and stability of proteins.

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Markov State Models

Mathematical models used to simulate the dynamics of complex systems

Markov state models are a powerful tool for studying the behavior of complex systems over time. They can be used to predict how systems will evolve and to understand the underlying mechanisms that govern their behavior.

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Metastable states

States that are relatively stable but can transition to other states over time

Metastable states are temporary configurations that molecules can exist in. These states are more stable than highly unstable configurations, but they can eventually transform into a different state.