RESEARCH: COVID-19
FOLDING PROJECT #17314 PROFILE

This project looks at how the spike protein of the coronavirus (SARS-CoV-2) binds to human cells. Scientists are using computer simulations to understand how this binding changes when sugars (glycosylation) are present. This could help in designing 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 that can spread from person to person through respiratory droplets.

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Receptor Binding Domain (RBD)

Region of a viral protein that binds to a cellular receptor

The RBD is a part of the spike protein on the SARS-CoV-2 virus. It's responsible for attaching to ACE2 receptors on human cells, allowing the virus to enter and infect.

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ACE2

Angiotensin-converting enzyme 2

ACE2 is a protein found on the surface of many human cells. It's involved in regulating blood pressure and plays a role in the entry of SARS-CoV-2 into cells.

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Glycosylation

The addition of sugar molecules to proteins or other molecules

Glycosylation is a common process in cells where sugars are attached to proteins. It can affect how proteins function and interact with other molecules.

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Markov State Models

Mathematical models used to simulate the dynamics of complex systems

Markov State Models are used in biophysics and computational biology to study how molecules change over time. They can help predict protein folding and other biological processes.

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Metastable States

Transient states that are relatively stable but can eventually transition to other states

Metastable states are like temporary resting points for molecules. They are not completely stable, but they can last for a long time before changing to another state.

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Drug Design

The process of designing and developing new drugs

Drug design involves using scientific knowledge to create molecules that can treat diseases. It's a complex process that requires expertise in chemistry, biology, and pharmacology.