RESEARCH: COVID-19
FOLDING PROJECT #17329 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 lead to better 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 the COVID-19 pandemic. It is a type of coronavirus that affects the respiratory system and can cause severe illness.

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Receptor Binding Domain (RBD)

The Receptor Binding Domain

The receptor binding domain (RBD) is a region on the surface of the SARS-CoV-2 virus that binds 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 other bodily functions. The SARS-CoV-2 virus uses ACE2 as a receptor to enter cells.

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Glycosylation

The process of adding sugar molecules to proteins.

Glycosylation is a common modification of proteins that can affect their function, stability, and interactions with other molecules. It plays a role in many biological processes.

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Markov State Models

Markov State Models

Markov State Models are a type of mathematical model used to simulate the behavior of complex systems over time. In biomolecular simulations, they can be used to predict the conformational changes and dynamics of proteins.

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Metastable States

Temporary and stable states of a system that are not the most energetically favorable.

Metastable states are temporary configurations that molecules can exist in before transitioning to a more stable state. Understanding metastable states is important for understanding protein folding and function.

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Drug Design

The process of identifying and developing new drugs.

Drug design is a complex process that involves understanding the target molecule (e.g., a protein or enzyme), designing molecules that can bind to it effectively, and testing their safety and efficacy.