RESEARCH: COVID-19
FOLDING PROJECT #17315 PROFILE

This project studies how the SARS-CoV-2 virus attaches to human cells. Scientists are using computer simulations to see how proteins on the virus (RBD) and in our bodies (ACE2) interact. They're also looking at how sugar molecules affect these interactions. This research could help scientists design 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 a virus that causes the disease COVID-19. It is a type of coronavirus, which are common viruses that can cause mild to severe respiratory illnesses.

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RBD

Receptor binding domain

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

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Glycosylation

The addition of sugar molecules to proteins.

Glycosylation is a process where 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 understanding how complex systems change over time. They can be used to study biological processes, such as protein folding and drug binding.

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Metastable States

Temporary stable states that are not the lowest energy state of a system.

Metastable states are like temporary resting points in a complex system. They are relatively stable but can easily transition to other states.

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Drug Design

The process of designing and developing new drugs.

Drug design is a complex process that involves identifying potential drug targets, designing molecules that interact with these targets, and testing the effectiveness and safety of the resulting drugs.