RESEARCH: COVID-19
FOLDING PROJECT #17339 PROFILE

This project studies how the protein parts of the COVID-19 virus bind to human cells. Scientists are using computer simulations to see how these proteins change shape and interact with each other. This research will help us understand how the virus works and could lead to new drugs.

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) 17336-40 replace 17330, 32-35 (fix glycan stereoisomer).

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SARS-CoV-2

A coronavirus strain that causes COVID-19.

SARS-CoV-2 is the virus responsible for the global COVID-19 pandemic. It's a type of coronavirus that can infect humans and cause severe respiratory illness.

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receptor binding domain (RBD)

The portion of a protein that binds to receptors.

The receptor binding domain (RBD) is the part of a virus protein that attaches to specific receptors on host cells. This allows the virus to enter and infect the cell.

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ACE2

Angiotensin-converting enzyme 2.

ACE2 is a protein found on the surface of many human cells. The SARS-CoV-2 virus uses ACE2 as a receptor to enter and infect cells.

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glycosylation

The process of adding sugar molecules to proteins.

Glycosylation is a crucial process where sugar molecules are attached to proteins. This modification can affect protein folding, stability, and function.

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Markov State Models

A type of computational model used to simulate the dynamics of complex systems.

Markov State Models are powerful tools used in bioinformatics to understand how molecules and systems change over time. They help researchers predict protein folding and other biological processes.

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metastable states

Intermediate energy states that are stable for a certain period.

Metastable states are like temporary resting points in the journey of molecules. They represent stable configurations but can transition to other states under specific conditions.