🎄12 Days of HPC

Fats Proteins and Salt: The Perfect Christmas Dinner All Inside A Computer

Blog post number 5 in our 12 days of HPC series showing how HPC is used to simulate proteins interacting with biological membranes!

During the month of December we’re featuring blog posts from researchers from across the University of Leeds showcasing the fantastic work they do using our High performance computing system. Follow us @RC_at_Leeds to keep up to date with our 12 days of HPC blog series.

What’s your name?

Alexandra Holmes

What department do you work in?

Faculty of Biological Sciences

What research question are you trying to answer?

I’m interested in proteins (tools cells use to do their jobs), in particular how the ones in the greasy cell membrane, work and do their jobs. To fully understand how something works it is useful to see it in action, which I can achieve using large simulations of the proteins in their fatty membrane and surrounded by salt and water. The proteins I’m studying are Piezo1, an ion channel that activates when poked and membane-integral pyrophosphatases, which are important in some parasites. I’m mainly trying to answer the questions: How does Piezo1 sense poking? How do ions travel through Piezo1? and how do membrane-integral pyrophosphatases interact with their environment?

How does HPC help your research?

I use HPC to perform the very large simulations - often over 500k atoms needing to be kept track of!

What is the potential impact of your research?

Hopefully my research will answer questions about clinically relevant membrane proteins. Increasing our understanding can lead to breakthroughs in treatments for diseases related to them. For example, Piezo1 is associated with various anaemias, and even COVID-19 if you have a certain kind of mutated Piezo1! Membrane-integral pyrophosphatases are essential for certain parasites ability to infect people.

In your personal opinion what’s the coolest thing about your research?

Seeing teeny tiny parts of the body moving around! Things 0.00000001 m big - so small you can’t even see them using visible light, but only using electrons or X-rays. And not only seeing them and getting a picture, but seeing them moving around and doing their jobs - processes that happen in the blink of an eye in the body.

What’s your favourite christmas film?

Gremlins - I even have a Gremlins Christmas jumper I like to wear to the Astbury Christmas quiz!

A video of an ion binding into a membrane protein during simulation
A video of an ion binding into a membrane protein during simulation.
An image of membrane-integral pyrophosphatases being lit up by lipids (or fats) nearby
An image of membrane-integral pyrophosphatases being lit up by lipids (or fats) nearby.