RESEARCH: COVID-19
FOLDING PROJECT #17331 PROFILE

This project studies how the spike protein of the COVID-19 virus (SARS-CoV-2) attaches to human cells. Scientists are using computer simulations to see how the virus's spike protein changes shape when it binds to a receptor on our cells called ACE2. They will also look at how sugar molecules attached to the spike protein affect this process. Understanding these interactions can help scientists develop new drugs to treat 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. 17329-331 replace 17316-8 (change from rectangular to truncated octahedron box) 17332-5 replace 17325-8 ((change from rectangular to truncated octahedron box).

---

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 spreads easily from person to person through respiratory droplets. Symptoms can range from mild (like a cold) to severe, including pneumonia and difficulty breathing.

---

receptor binding domain (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. This binding allows the virus to enter and infect cells.

---

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 a receptor to enter human cells.

---

glycosylation

The process of attaching sugar molecules to proteins.

Glycosylation is a common process that occurs in cells where sugar molecules are added to proteins. This can change the protein's shape, function, and stability.

---

Markov State Models

Mathematical models used to study the dynamics of complex systems.

Markov State Models are used in computational biology to simulate how molecules move and change over time. This can help researchers understand protein folding, drug interactions, and other biological processes.

---

metastable states

Temporary, stable configurations of a molecule.

Metastable states are like temporary resting points for molecules. They are relatively stable but can eventually transition to other states.

---

drug design

The process of designing and developing new drugs.

Drug design is a complex process that involves understanding how diseases work and designing molecules that can target specific proteins or pathways involved in those diseases.