This week I spoke with Sarah Yorke, a first year PhD student at the NanoDTC in Cambridge. Originally from West Yorkshire, Sarah is a part of the Knowles Lab in Cambridge and focuses on the assembly behaviour of peptides. In her spare time, she likes to row, cycle and bake. Hello Sarah!
So to begin, could you tell me about yourself and how you ended up in Cambridge?
Hello! I’m Sarah and I studied chemistry in Nottingham for my undergraduate degree. I come from West Yorkshire, although I might not sound like that! I initially applied to the NanoDTC, thinking it was a long shot and I thought the interview went awful. During interviews, they usually ask you questions until you don’t know the answer anymore, so everyone reaches the stage where they don't know what they're talking about. And because of that, it's easy to reflect on it negatively when actually it went quite well!
But it’s clear it went very, very well because you’re here and you're in second year now at the NanoDTC!
Yes, I'm in my second year of the NanoDTC and the first year of my PhD. The first year, the MRes Year, was very much a whistle stop tour of lots of physics, which wasn't necessarily my strong suit, but it was a really good opportunity to explore new areas. In particular, we did short projects which are eight weeks long in different research groups. It really allows you to kind of explore different fields that you may not have considered before. And I think that definitely helped me to inform my choice about what sort of PhD I wanted to do.
So when you came here, did you know exactly what you wanted to do?
No, I had no idea! I thought of doing something in Chemistry. Throughout my master's in Nottingham, I did heterogeneous catalysis which involved using metals to catalyse photo-active reactions. I thought I'd probably do something along the lines of physical chemistry, but without a biological focus. After all, I didn't do any biology in my degree!
However, I found both my short projects in my MRes year, which were both focused on biology, very interesting! They showed me the complexity of biological systems and how powerful they can be.
That’s super cool Sarah! Do you think your background in Chemistry is useful in this different field?
Yeah, I think so. Afterall, it’s the chemistry that governs the behaviour of all of these biological systems and given my background, I have the ability to see it in a deeper way that a biologist may not see. There’s also a lot of similarities practically, especially the lab work!
I think that is what is special about the NanoDTC! It brings all our different backgrounds under the same roof! Can you tell me a bit about you PhD project?
Specifically, I look at peptides, which are really small proteins made up of only a couple of amino acids. A protein chain is a sequence of hundreds and thousands of amino acids, which are the building blocks that our body makes to make proteins, and these govern the behaviour of the cell.
And what I look at are really, really small proteins, called peptides, which are only a couple of amino acids long. In particular, I look at how they can interact with one another and assemble to form materials.
A polymer chain is simply lots of monomers bonded together through a condensation reaction. These are really long and flexible chains that can interact with each other to make the plastic surfaces that we know, and the same principles can be applied in biology to biopolymers.
That reminds me a lot about plastics! Are they similar?
Yes, there's lots of examples of where biological molecules use plastic-like behaviour, so carbohydrates and starches for example. There’s actually a spin out in my research group, called Xampla, which make materials from pea protein. In particular, they make films which can be used, for example, as a sandwich packet. As well as that, then they also make smaller things to think, for example, to encapsulate nutrients and preservatives within different foods.
That sounds a lot better for the environment! Is that true?
Exactly! Even using synthetic biomolecules to make a protein in the lab instead of getting it from an animal, that protein is still biocompatible. Our body can digest it and it is nontoxic to animals. They’re also biodegradable because they're just organic matter and they can break down in the environment in a way that synthetic polymers can’t. So, there’s clearly a huge amount of potential and they have a huge advantage of being safe and friendly to natural life.
One of the advantages of using peptides for this is that they have really tuneable functionality. They’re small molecules so even making a single change to the molecule has a really, really big impact on the behaviour. It's very easy to change the properties of your peptide to give a material that you want, and you can therefore control the assembly behaviour in a specific way. This means that they have potential to be effective in lots of different applications, not just to make plastic. They can also be used in optics, to make photonic crystals.
And what projects and experiments are you focusing on now?
At the moment, I'm looking at how I can manipulate phase changes in peptide systems. Biological systems have a property called liquid-liquid phase separation. This is where proteins or biological molecules form a condensed liquid phase, which is discrete and separate from the surrounding liquid phase.
This is something that happens in cells and it's powerful because you can trap molecules in these discrete phases and form organelles. For example, if your cell is stressed, it forms these stress granules which are condensed proteins. Within them are different biomolecules, which the cell doesn't have time to use because it's responding to the stress instead of functioning normally. And then once the cell is no longer stressed, these stress granules will become miscible again in the surrounding cytoplasm, and then the important molecules will be released, and they can be used.
So, it’s like you have a bubble inside a liquid almost?
Yes, you have a liquid bubble inside of it. Sort of like an oil in water.
And how do you measure these phase changes and separations?
I usually image and measure the peptides using capillaries or microfluidic devices, which involves confining liquid in smooth channels so you can remove the laminar flow, and allows these liquids to flow without mixing. Usually, the channels are about 50 x 100 microns.
That sounds super complicated! Are there many issues with this technique?
One of the issues when you're looking at these changes is it could evaporate, and that will change the concentration of your solution. But if we load our liquid into a small micro-diameter capillary tube, we can seal the ends and that means there's no evaporation occurring in the system. We can also eliminate the flow of the liquid which means we can look at a specific point for a really long period of time.
And as a final question, do you have any advice you incoming PhD students?
I think it's important to focus on the environment that you will be studying in. It's something that you're going to be doing every single day and people you're going to be spending every single day with for at least 3 years. I think if you're comfortable and happy with your environment, you'll be able to weather the ups and downs of the actual research much better.
Thanks Sarah!
References for Diagrams:
Shen, Y., et al. (2021). "From Protein Building Blocks to Functional Materials." ACS Nano 15(4): 5819-5837.
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