RESEARCH: COVID-19
FOLDING PROJECT #17318 PROFILE

This project looks at how the SARS-CoV-2 virus binds to human cells. We're studying the proteins involved and how sugar molecules affect their shapes and interactions. This could help us understand how the virus works and develop new drugs to fight it.

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.

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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. The virus spreads through respiratory droplets and can lead to a range of symptoms from mild to severe.

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RBD

Receptor binding domain

The receptor binding domain (RBD) is a specific part of the SARS-CoV-2 spike protein. This region binds to the ACE2 receptor on human cells, allowing the virus to attach and enter.

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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 is also the receptor used by SARS-CoV-2 to enter cells.

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Glycosylation

The addition of sugar molecules to proteins

Glycosylation is a common process in which sugar molecules are attached to proteins. This modification can affect protein folding, stability, and function. In the case of SARS-CoV-2, glycosylation of certain proteins may influence its ability to bind to ACE2.

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Markov State Models

Mathematical models that describe the transitions between different states of a system

Markov State Models are computational tools used to simulate and understand complex biological systems. They can be used to predict protein folding pathways, identify metastable states, and explore the dynamics of interactions between molecules.

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Metastable States

States that are stable for a relatively long time but can eventually transition to other states

Metastable states are temporary arrangements of molecules or atoms that exist for a certain period before changing to a more stable configuration. These states play a crucial role in biological processes such as protein folding and enzyme catalysis.

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Drug Design

The process of designing and developing new drugs

Drug design is a complex multidisciplinary field that involves identifying potential drug targets, synthesizing and screening compounds, and optimizing their efficacy and safety. It plays a vital role in the development of new therapies for diseases.