The other night, I decide to cook mom’s spaghetti. *pause* I’m at the grocery store, and there’s this giant wall of pasta. Spaghetti, fettuccine, fusilli, there’s so  many. And I realized, the pasta’s shape affects how it clings to other ingredients. For example spiral shaped fusilli pasta clings to more sauce than spaghetti. And there’s something else where shape matters a lot too. Nature’s created proteins, shaped like different types of pasta. Proteins are involved in almost all biological processes in every living cell.  And different protein shapes have specific  functions, like how different pastas cling to ingredients differently. 

Here at the Joint Genome Institute, we’re investigating how protein shape affects function.

I’m researching proteins involved in photosynthesis, it’s a complex important biological process all around us. And with global warming, we can apply what we learn to for example create more resilient food crops. Specifically, I focus on proteins in this small green alga. It’s photosynthetic, like plants, and easy to cultivate. I’m using AI tools to predict protein structures of unknown genes in this green alga and investigate how they may be involved in photosynthesis.

Essentially, I compare protein structures to predict function. It’s like comparing spiral fusilli pasta with fusilli which some parts look like that. In the above example, the grey protein is an unknown protein of interest. The yellow protein is a known photosynthesis-related protein and it functions to assemble other known photosynthesis proteins. By aligning and overlapping these two proteins, I’m able to show that this previously unknown grey protein possibly has the same function as this yellow one. We can then validate this experimentally as well.

Combining analyses of protein sequences and structures with experiments allows me to tackle difficult questions. How does shape translate to function? How are these proteins involved in photosynthesis? It’s like asking why does fusilli pasta cling to more sauce? I demonstrate that with the previous example. 

There’s so many useful applications we can obtain from understanding the protein structure-function relationship in photosynthesis and we can apply this in areas such as genetic enhancement of food crops, generation of sustainable biofuels, anything involving proteins, the list goes on. The pastabilities are endless and if you have a bowl of mom’s spaghetti tonight, I hope you think of proteins.