RESEARCH: COVID-19
FOLDING PROJECT #17337 PROFILE

The project relates to simulating how the spike protein of the COVID-19 virus (SARS-CoV-2) binds to human cells. Scientists are studying how sugar molecules on these proteins affect their shape and binding. This information can help 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. 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

Severe Acute Respiratory Syndrome Coronavirus 2

SARS-CoV-2 is the virus that causes COVID-19. It's a type of coronavirus that spreads easily from person to person through respiratory droplets.

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Receptor Binding Domain (RBD)

Receptor Binding Domain

The RBD is a part of the SARS-CoV-2 spike protein that attaches 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 acts as the receptor for the SARS-CoV-2 virus.

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Glycosylation

The process of attaching sugar molecules to proteins

Glycosylation is a common process in which sugar molecules are added to proteins. This can change the protein's shape, function, and stability.

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Markov State Models

Mathematical models that describe the transitions between different states of a system

Markov State Models are used to study the dynamics of complex systems, such as proteins. They can help us understand how proteins move and change shape over time.

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Metastable States

States of a system that are not stable but persist for a long time

Metastable states are like temporary resting places for molecules. They can exist for a while before changing into a more stable state.