RESEARCH: COVID-19
FOLDING PROJECT #17316 PROFILE

This project studies how the spike protein from the virus that causes COVID-19 (SARS-CoV-2) binds to human cells. By simulating these proteins, scientists hope to understand how sugar molecules on the spike protein affect its shape and binding ability. This knowledge could help in developing 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 the virus that causes COVID-19. It's a type of coronavirus that spreads easily from person to person through respiratory droplets. Understanding SARS-CoV-2 is crucial for developing treatments and vaccines.

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RBD

Receptor binding domain

The receptor-binding domain (RBD) is a part of the SARS-CoV-2 spike protein that allows the virus to attach to and enter human cells. Drugs targeting RBD can prevent infection.

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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 its entry point into 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. In the case of SARS-CoV-2, glycosylation on the RBD protein may influence its ability to bind to ACE2.

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Markov State Models

Mathematical models used to simulate the behavior of complex systems over time

Markov State Models are used in computational biology to study the dynamics of proteins and other molecules. They can help predict how a protein will fold or how it will interact with other molecules.

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Metastable States

Temporary states that are relatively stable but can transition to other states

Metastable states are important in understanding the behavior of molecules. In the case of proteins, metastable states can represent different conformations that the protein can adopt.