RESEARCH: COVID-19
FOLDING PROJECT #17317 PROFILE

The project relates to understanding how the virus protein (RBD) attaches to human cells using simulations. Researchers will study RBD alone and with a human receptor (ACE2), with and without added sugars. This helps understand how sugars affect the virus's shape and how it binds to cells. The goal is to use this knowledge to design better drugs.

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, which are common in animals but can sometimes infect humans. This particular virus emerged in late 2019 and spread rapidly worldwide.

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Receptor Binding Domain (RBD)

Receptor binding domain

The receptor binding domain (RBD) is a specific part of the SARS-CoV-2 spike protein. This region binds to the ACE2 receptor on human cells, allowing the virus to enter and infect them.

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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 its entry point into human cells.

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Glycosylation

The addition of sugar molecules to proteins or lipids

Glycosylation is a common process where sugar molecules are attached to proteins. This can affect the protein's shape, function, and stability. In the case of viruses like SARS-CoV-2, glycosylation can influence how they interact with human cells.

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Markov State Model

A statistical model used to describe the dynamics of a system over time

Markov State Models are used in computational biology to simulate how molecules move and interact. They can help researchers understand complex biological processes like protein folding and virus binding.

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Metastable States

States of a system that are stable for a certain period but can transition to other states over time

Metastable states are like temporary resting points in a system. They might seem stable for a while, but eventually, the system will move on to a different state. Understanding metastable states is important in fields like drug design because it can help explain how molecules interact and behave.