RESEARCH: COVID-19
FOLDING PROJECT #17332 PROFILE

The project relates to studying how the SARS-CoV-2 virus attaches to human cells. Scientists are using computer simulations to understand how proteins on the virus and in our bodies interact. This research could 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).

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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 spreads through respiratory droplets and can lead to severe respiratory illness.

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Receptor Binding Domain (RBD)

Receptor Binding Domain

The RBD is a part of the SARS-CoV-2 spike protein responsible for attaching to and entering human cells. It binds to the ACE2 receptor.

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ACE2

Angiotensin-Converting Enzyme 2

ACE2 is a protein found on the surface of human cells. The SARS-CoV-2 RBD binds to ACE2, allowing the virus to enter and infect cells.

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Markov State Models

Mathematical models used to simulate the dynamics of complex systems.

Markov State Models are used to predict the behavior of molecules over time. In this case, they will help understand how proteins interact and change shape.

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Glycosylation

The addition of sugar molecules to proteins.

Glycosylation is a common modification of proteins that can affect their structure and function. This research will investigate how glycosylation impacts the interaction between SARS-CoV-2 proteins.

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Metastable States

Stable but transient states of a system.

Metastable states are temporary configurations that molecules can exist in. Understanding these states can reveal how proteins change shape and function.

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Drug Design

The process of identifying and developing new medications.

Drug design aims to create drugs that target specific molecules or pathways involved in diseases. The insights gained from this research can inform the development of antiviral therapies against SARS-CoV-2.