RESEARCH: COVID-19
FOLDING PROJECT #17319 PROFILE

This project uses computer simulations to study how the SARS-CoV-2 virus attaches to human cells. Researchers are looking at how sugar molecules (glycosylation) affect the shape of the virus and its ability to bind to a protein called ACE2 on our cells. Understanding this could help scientists 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.

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SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2

SARS-CoV-2 is the virus responsible for causing COVID-19. It's a type of coronavirus that primarily affects the respiratory system.

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Receptor Binding Domain (RBD)

Region of the SARS-CoV-2 spike protein that binds to ACE2 receptors.

The RBD is a crucial part of the SARS-CoV-2 virus. It allows the virus to attach itself to human cells by binding to the ACE2 receptor.

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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.

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Glycosylation

The process of adding sugar molecules to proteins.

Glycosylation is a common modification of proteins that can affect their structure, function, and interactions with other molecules.

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Markov State Models

Mathematical models used to predict the future 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 simulate protein folding, drug binding, and other biological processes.

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Metastable States

Transient states that a system can exist in before transitioning to another 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 medications.

Drug design is a complex process that involves identifying potential drug targets, screening for promising compounds, and optimizing their properties.