RESEARCH: COVID-19
FOLDING PROJECT #17338 PROFILE

This project studies how the SARS-CoV-2 virus attaches to human cells. Scientists are using computer simulations to see how the virus protein (RBD) and the human receptor (ACE2) interact, both alone and together. They're also looking at the effects of sugar molecules (glycosylation) on these interactions. This research could help scientists develop 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 responsible for causing COVID-19. It's a type of coronavirus that spreads through respiratory droplets. Understanding its structure and how it interacts with human cells is crucial for developing treatments and vaccines.

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Receptor binding domain (RBD)

Region of the SARS-CoV-2 spike protein that binds to the ACE2 receptor.

The RBD is a crucial part of the SARS-CoV-2 virus. It's the part of the virus that attaches to human cells, allowing it to infect them. Scientists are studying the RBD to understand how the virus works and to develop treatments.

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ACE2

Angiotensin-converting enzyme 2

ACE2 is a protein found on the surface of human cells. The SARS-CoV-2 virus uses ACE2 as a receptor to enter cells. Understanding ACE2 helps researchers develop treatments that block viral entry.

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Glycosylation

The process of adding sugar molecules to proteins.

Glycosylation is a common process in cells that modifies proteins. It can affect how proteins function and interact with other molecules. In the case of viruses like SARS-CoV-2, glycosylation can influence their ability to bind to cells.

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Markov State Models

Mathematical models used to simulate the dynamics of complex systems.

Markov State Models are a powerful tool for studying biological systems. They allow researchers to simulate how molecules move and interact over time. This helps us understand how proteins fold, how viruses infect cells, and more.

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Metastable states

Transient, relatively stable configurations of a system.

Metastable states are temporary arrangements of molecules that are more stable than some states but less stable than the most stable state. Understanding metastable states helps us understand how systems like proteins transition between different shapes and functions.