New Insights into Proteins Linked to Neurodegeneration

Researchers at Yale School of Medicine have conducted the first comprehensive structural analyses of a class of proteins whose dysfunction is associated with neurodegenerative diseases.

In two new studies published in Cell and Molecular Cell, researchers investigated, at the atomic level, two very similar proteins whose mutations result in chorea-acanthocytosis (a Huntington-like condition) and Parkinson’s disease. Collectively, the findings provide a foundation to understand how these proteins function and are regulated and how their mutations result in disease.

The findings represent a new step in a long-term collaboration between the laboratories of Karin Reinisch, PhD, David W. Wallace Professor of Cell Biology, and Pietro De Camilli, MD, John Klingenstein Professor of Neuroscience and professor of cell biology. The research team included Bodan Hu, PhD, and Dazhi Li, PhD, from the Reinisch group and Xinbo Wang, PhD; Hongyan Hao, PhD; and Jessica Eden, PhD, from the De Camilli group.

The membranes of cells and the organelles within them are made up of molecules called lipids, most of which are created in the cell’s endoplasmic reticulum (ER). Scientists once thought that transport of lipids from the ER to other organelles occurred either in bulk via bubble-like structures called vesicles, or piecemeal via lipid-transport proteins that shuttle back and forth between the ER and other membranes.

But over the last decade, structural studies by the Reinisch lab together with cell biology studies by the De Camilli lab, have found that lipid transport also occurs through rod-like proteins, such as members of the VPS13 protein family. These rod-like proteins act as bridges enabling the bulk movement of lipid molecules directly from the ER to organelle membranes.

The two new studies represent the first complete molecular characterization of two VPS13 proteins and provide insight into their regulation.

The first study, published in Cell and led by Reinisch, focused on the protein VPS13A, mutations in which are associated with chorea-acanthocytosis (now renamed VPS13A disease), a neurodegenerative disorder that causes involuntary movement and abnormally-shaped blood cells.

The researchers used a technique called single-particle cryo-electron microscopy (cryo-EM) to visualize the atomic structure of VPS13A while it was bound to a membrane. The team of collaborator and co-senior author Stefano Vanni, PhD, a professor at University of Fribourg, Switzerland, also conducted simulations that showed how lipids were moving from VPS13A to a membrane.

Membranes are made up of two layers of lipids. VPS13A is anchored to one layer by a protein known as XK. As VPS13A delivers lipids to that layer, XK then helps evenly distribute those lipids between both membrane lipid layers, the researchers found.

“This is essential—you can’t deliver lipids just to one layer because then you would have two unequally-sized layers in the membrane,” Reinisch explains.

Interestingly, mutations in XK are also associated with a neurodegenerative condition very similar to chorea-acanthocytosis, called McLeod syndrome.

This is also the first time researchers have gotten insight into how lipids can be delivered en masse to a membrane, De Camilli, a coauthor of the study, adds.

In the second study, published in Molecular Cell, researchers also used cryo-EM to analyze the structure of VPS13C, whose dysfunction is associated with Parkinson’s disease. Last year, De Camilli’s lab discovered that when the membranes of lysosomes, the trash cans of cells, are damaged, VPS13 proteins rush to contacts between the ER and these organelles to repair them by delivering new lipids.

In the new study, the researchers found that when VPS13C is not attached to a lysosome, there is a crown-shaped structure blocking the tube that lipids travel through that prevents the protein from attaching to a membrane. This suggests that the protein is in an inactive state and needs to undergo a conformational change to be able to deliver lipids, the scientists say.

This crown-shaped structure also exists on VPS13A, as shown in the Cell study. Because the team had analyzed VPS13A when it was bound to a membrane, they were able to capture this protein in its active state. In this conformation, the crown-like structure had moved to the side, unblocking the tube.

The findings from both studies highlight that VPS13 proteins may exist in active and inactive states. More research will be needed to understand how these proteins transition between the two states. “But this is a really big step in terms of understanding how the VPS13 proteins are regulated,” Reinisch says.

Understanding how these proteins function and are regulated can help scientists elucidate the mechanisms underlying neurodegenerative diseases, and, therefore, develop therapies. Growing evidence suggests, for example, that leaky lysosome membranes may be a cause of Parkinson’s disease. Because lysosomes act as the cell’s garbage disposal, if their membranes break down, the toxic material they contain leaks into the cell. Scientists think this might contribute to the onset of neurodegenerative diseases.

Enhancing the function of VPS13C could help in cases of Parkinson’s disease where dysfunction of lysosomes is implicated.

“There are now data suggesting that in fact this protein can be made more efficient,” De Camilli says. “That is something for the future, but it’s a promising avenue.”