Solving the Mystery of a Protein’s Shape

Many of us can recall looking through a microscope in biology class, examining stained slides that revealed the inner workings of cells. Those microscopes sat within easy reach and were straightforward to use. Cryogenic electron microscopes, like those used by Simons Fellow Rosemary Cater, are different. Rather than using light, these microscopes harness the power of electrons to illuminate the structure of biological molecules at the atomic level, offering a higher resolution than other microscopes provide.

Few people are experts in this microscopic technique, which is known as single-particle cryo-electron microscopy, or, more simply, cryo-EM. Cater, a third-year member of the Simons Society of Fellows, is one such expert. She is a structural biologist who completed her undergraduate and graduate studies at the University of Sydney in Australia and currently holds a postdoctoral appointment in Filippo Mancia’s lab at Columbia University Irving Medical Center. In her work, Cater uses cryo-EM to study proteins that transport substances across the cellular membrane, an envelope mostly made up of lipids that surrounds each cell.

Cater’s focus is on MFSD2A, a protein that transports nutritious omega-3 fatty acids, found in foods such as fish, eggs, nuts and seeds, from the bloodstream into our brains. (Omega-3’s are formed by double bonds between chains of fatty acids.) By harnessing the power of cryo-EM, Cater aims to create a three-dimensional model showing what this protein looks like. This could ultimately help scientists design new drugs that can be shuttled efficiently into the brain, just like the omega-3 fatty acids.

Cater and I recently discussed the implications of her work, how cryo-EM has revolutionized the field of structural biology, and how the Simons fellowship has helped her career and broadened her scientific horizons. Our conversation has been edited for clarity.

First things first: What are lipids, and why are they important? I usually equate lipids with fats, but that’s probably too simplistic.

Lipids are a class of molecules that are critical for all forms of life. You’re right that they are fatty, but this essentially just means that they aren’t soluble in water. Olive oil is a great example of this. In biology, one of the most important roles that lipids serve is forming cell membranes: no lipids, no cell membranes, no cells, no life! In addition to lipids, cell membranes also contain proteins, the main workhorses of our bodies. Proteins perform a variety of duties in the cell, from shuttling molecules across the membrane itself, to mediating communication between cells. I’m interested in understanding how MFSD2A, a protein that resides in the cell membrane, transports lipids themselves across the membrane. To do so requires a deep understanding of MFSD2A’s three-dimensional structure.

Why is it important to know a protein’s shape?

Proteins carry out many of our body’s main functions. Their specific shapes are custom-built to fulfill specific tasks. If we know the three-dimensional shape of a protein, we can use this information to determine how it works — and how it stops working properly in certain diseases. This information can then help researchers design drugs that interact with these proteins to rectify disease states. This important area of biology is called structural biology.

What is Cryo-EM?

Cryo-EM is Nobel Prize-winning technology that has an unmatched ability to reveal some of the innermost secrets of microscopic life. Before cryo-EM, scientists typically used a technique called X-ray crystallography to reconstruct three-dimensional structures of proteins. While powerful, this technique comes with several challenges, namely a requirement that the protein of interest be transformed into an ordered crystal structure in order to study its structure. In many cases, this crystal formation process is difficult or even impossible to achieve.

Cryo-EM completely avoids this crystal formation step. While cryo-EM has been used for a long time, there have recently been some very exciting developments in the hardware of the microscopes and the software used to analyze the data.

With cryo-EM, we can suspend a protein of interest — in my case, MFSD2A — in a very thin layer of ice. We use powerful cameras to take millions of photos of the protein from countless angles. We then use computer algorithms to analyze the photos and deduce the protein’s three-dimensional shape.

This has truly revolutionized the field of structural biology, allowing us to determine the shapes of more proteins than ever before.

Let’s turn now to your research. I understand that MFSD2A transports omega-3 fatty acids into the brain when we eat foods like fish or nuts. Why did you choose to study the structure of this particular protein?

Omega-3 fatty acids regulate many processes that are essential for proper neuronal development, both in early stages of life and during aging. However, the brain itself can’t make these omega-3 fatty acids; they need to be shuttled into the brain from the blood vessels that surround it. This delivery method involves crossing the ‘blood-brain barrier,’ which actually serves to protect the brain from exposure to harmful molecules. Proteins like MFSD2A act like a backstage pass; only molecules that are shuttled across this barrier by these proteins can enter the brain.

Cryo-EM has allowed me to visualize the three-dimensional shape of MFSD2A, giving me greater insight as to how this whole fascinating process works.

With that knowledge, could MFSD2A be used to deliver a neuro-therapeutic drug into the brain, the way it delivers omega-3s?

Potentially, yes! If we know what this protein looks like and how omega-3s bind to it, then we can design drugs that look like omega-3s and can therefore be transported by the same protein into the brain.

The blood-brain barrier has long served as a roadblock to life-saving drugs to treat a whole host of neurological disorders. By knowing the three-dimensional shape of MFSD2A, we are closer to removing that roadblock.

Your Simons fellowship is scheduled to end in 2021, although it may be extended in light of slowdowns caused by the pandemic. Besides your deeper expertise in protein structure, how have you benefited from the fellowship?

One of the most rewarding aspects of the Simons Society of Fellows is that we meet regularly with other fellows from a vast array of scientific fields, some of them very far removed from my own. I have been truly humbled by an atmosphere that encourages me to think outside the box, and to not be afraid to ask what may seem like naive questions. Science is meant to be curiosity-driven — plus, it’s way more fun to ask the naive question than to shy away! I feel lucky to be part of a community that has nurtured this culture, and I can see the impact that it’s had on the way I conduct and communicate my science.