RESEARCH: COVID-19
FOLDING PROJECT #17324 PROFILE

This project studies how the SARS-CoV-2 virus attaches to human cells. They are using computer simulations to see how the virus protein (RBD) changes shape when it binds to a receptor on our cells (ACE2). This helps scientists understand how viruses work and design new drugs to stop them.

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.

---

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 spreads easily from person to person through respiratory droplets.

---

Receptor Binding Domain (RBD)

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

The RBD is a crucial part of the SARS-CoV-2 spike protein. It's responsible for attaching to ACE2 receptors on human cells, allowing the virus to enter and infect them.

---

ACE2

Angiotensin-converting enzyme 2

ACE2 is a protein found on the surface of many human cells, including those in the lungs. It plays a role in regulating blood pressure and other bodily functions.

---

Glycosylation

The process of attaching sugar molecules to proteins.

Glycosylation is a common modification that affects protein function. In the case of SARS-CoV-2, glycosylation on the RBD can influence how it binds to ACE2 receptors.

---

Markov State Models

Mathematical models used to simulate the behavior of complex systems over time.

Markov State Models are used to study protein dynamics and identify different states that a protein can adopt. This can help understand how proteins function and interact with other molecules.

---

Metastable States

Intermediate states that a protein can occupy before reaching its final folded conformation.

Metastable states are important for understanding how proteins fold and function. Proteins can spend time in these intermediate states before settling into their stable, functional form.

---

Drug Design

The process of discovering and developing new drugs.

Drug design involves identifying potential drug targets, designing molecules that interact with these targets, and testing the effectiveness and safety of these drug candidates.