RESEARCH: COVID-19
FOLDING PROJECT #17323 PROFILE

This project studies how the spike protein of the virus that causes COVID-19 (SARS-CoV-2) binds to human cells. Scientists are using computer simulations to see how the protein changes shape and how adding sugar molecules affects this process. They hope to learn how these changes affect the spread of the virus and use this knowledge to develop new drugs.

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, the virus that causes COVID-19.

SARS-CoV-2 is the name of the virus responsible for causing the disease known as COVID-19. It is a type of coronavirus, a family of viruses that can cause respiratory illnesses in humans. SARS-CoV-2 spreads through respiratory droplets released when an infected person coughs, sneezes, or talks.

Receptor binding domain (RBD)

The region of a viral protein that binds to the host cell receptor.

The receptor binding domain (RBD) is a crucial part of a virus's spike protein. It is responsible for attaching to and entering host cells. In the case of SARS-CoV-2, the RBD binds to the ACE2 receptor on human cells, allowing the virus to infect them.

ACE2

Angiotensin-converting enzyme 2

ACE2 is a protein found on the surface of many human cells, including those in the lungs and heart. It plays a role in regulating blood pressure and fluid balance. SARS-CoV-2 uses ACE2 as its entry point into human cells.

Glycosylation

The process of adding sugar molecules to proteins.

Glycosylation is a crucial process in which sugar molecules are attached to proteins. This modification can affect a protein's structure, function, and stability. In the case of viruses like SARS-CoV-2, glycosylation can influence how they interact with host cells.

Markov State Models

A statistical method for simulating the dynamics of complex systems.

Markov State Models (MSMs) are powerful computational tools used to understand the behavior of complex systems over time. In the context of protein dynamics, MSMs can be used to identify stable states and transitions between those states.