RESEARCH: COVID-19
FOLDING PROJECT #17326 PROFILE

This project uses computer simulations to study how the spike protein of the SARS-CoV-2 virus binds to human cells. By looking at different versions of the proteins, scientists hope to understand how sugar molecules affect the binding process and identify potential drug targets.

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.

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 can cause respiratory illness ranging from mild to severe.

RBD

Receptor Binding Domain

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

ACE2

Angiotensin-Converting Enzyme 2

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

Glycosylation

The process of adding sugar molecules to proteins

Glycosylation is a common process where sugar molecules are attached to proteins. This can change the shape and function of the protein.

Markov State Model

A computational model that describes the transitions between different states of a system over time

Markov State Models are used to understand how molecules move and change shape. They can be used to study proteins, viruses, and other complex systems.