RESEARCH: COVID-19
FOLDING PROJECT #17341 PROFILE

This project studies how the SARS-CoV-2 spike protein (RBD) binds to human cells (ACE2). Scientists are using computer simulations to see how RBD changes shape with and without sugars attached. This helps understand how the virus attaches and could lead to better drug designs.

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) 17341-3 are repeats of 17336, 17337, and 17339 (RUN8), where each project has 5 RUNs starting from different equilibrated structures.

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 primarily affects the respiratory system.

receptor binding domain (RBD)

Receptor Binding Domain

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

ACE2

Angiotensin-Converting Enzyme 2

ACE2 is a protein found on the surface of human cells that acts as the receptor for the SARS-CoV-2 virus. When the virus binds to ACE2, it can enter and infect the cell.

glycosylation

The process of adding sugar molecules to proteins or lipids.

Glycosylation is a common modification that occurs in cells. It can affect the function and stability of proteins.

Markov State Models

A type of statistical model used to simulate the behavior of complex systems over time.

Markov State Models are used in biophysics and other fields to study how molecules and systems evolve.

metastable states

Stable states that are not the lowest energy state but can persist for a long time.

Metastable states are temporary configurations that molecules can occupy. Understanding them is important for understanding how proteins function.