Novel device can add or eliminate sugar from proteins

Overview

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• Source: Harvard University


• Date: 12 Mar,2021

Sugar has been called “evil,” “toxic,” and “poison.” But the body needs sugars, also. Sugar molecules help cells recognize and fight germs and viruses, shuttle proteins from cell to cell, and make sure those proteins function.

Too much or too small can give rise to a range of maladies, including neurodegenerative diseases like Alzheimer’s, diabetes, inflammation, and even cancer.

About 85 percent of proteins, including those associated with Alzheimer’s and Parkinson’s, are beyond the reach of current drugs. One significant and abundant sugar (O-GlcNAc, pronounced o-glick-nack) is found on over 5,000 proteins, often those considered”undruggable.”

Now, however, researchers at Harvard University have designed a new highly-selective O-GlcNAc pencil and eraser–tools that can add or remove the sugar from a protein with no off-target effects–to examine exactly what these sugars are doing and, finally, engineer them to new treatments for the”undruggable.”

“We can now begin studying particular proteins and see what happens when you remove or add the sugar,” explained Daniel Ramirez, a co-author on the newspaper printed in Nature Chemical Biology and a Ph.D. candidate in biological and biomedical sciences at the Graduate School of Arts and Sciences. “This is turning out to be very important for a lot of chronic diseases like cancer and diabetes and Alzheimer’s.”

Ramirez designed the first O-GlcNAc pencil, which was reported in ACS Chemical Biology.

All cells carry a multitude of sugars (called glycans), but they’re notoriously tough to study. Current tools either provide a wide-lens view (turning off or on all of the O-GlcNAc in a cell) or an ultra-zoomed in opinion (turning off or on a single sugar on one amino acid on one protein).

Once you have any protein of interest, you can apply this tool on that protein and look at the outcomes directly.”

Yun Ge, Study First Author and Postdoctoral Scholar, Harvard University

Neither of these perspectives can show what O-GlcNAc molecules do to a protein as a whole, the vital insight that would enable researchers to connect the dots from O-GlcNAc to disorder.

“With the protein-level approach, we’re filling in a significant piece that has been missing,” said Christina Woo, an associate professor of chemistry and chemical biology, who headed the study. Her lab’s tool is like Goldilocks’ lukewarm bowl of porridge: Not too broad, not too specific. Just perfect.

Ge engineered the O-GlcNAc eraser, which, like the pencil, uses a nanobody as a protein homing device. The tool is adaptable, too; provided that a nanobody exists for a protein of choice, the tool can be altered to target any protein for which a homing nanobody exists.

The nanobody is a crucial part, but it has limits: Whether or not it stays stuck to the target protein remains in question, and the molecule could change the structure or function of the protein once stuck. If cellular changes can’t be definitively linked to the sugar on the protein, that muddies the information.

To skirt these possible limitations, the team engineered their pens and erasers to be”catalytically dead,” said Woo. The neutered enzymes will not make unwanted changes along the way to their target protein.

And, they can both add and remove sugars, unlike previous tools, which cause irreversible alterations. Of course, once they connect a specific protein function to O-GlcNAc, they could then use those tools to zoom in and locate precisely where those sugars are latching onto and changing the protein.

Already, some of the Woo lab’s collaborators are using the pencil/eraser combo to research O-GlcNAc in live animals. One, for instance, is using fruit flies to study how the sugar impacts a protein associated with Alzheimer’s disease.

The glucose can also be associated with Parkinson’s disease progression:”If you are taking in less glucose,” said co-author Ramirez,”then you’re not able to create this sugar inside the cells.” That means the body can not attach the sugars to the proteins, which induces wide-reaching changes to the cells, aggravating the illness.

In diabetes, excessive sugars cause similar worldwide disruption; and cancer cells have a tendency to eat lots of sugars. Now, with the Woo laboratory’s pencil/eraser pair, researchers can identify exactly how these sugars impact various proteins and start to design drugs to reverse negative outcomes.

Next, the team plans to tweak their tool to achieve even greater control. With optogenetics, for example, they could switch sugars on or off with just a flash of light.

They’re also designing an eraser for the eraser–a tool with a kill switch–and plan to incorporate nanobodies that may target a naturally-occurring protein (for this study, they tagged proteins so the nanobody could find them). “We are basically trying to make the system more natural and function how the cell does,” said Ramirez.

Woo also plans to research how O-GlcNAc may influence traditionally”undruggable” proteins called transcription factors, which turn genes off and on. If O-GlcNAc plays a part in that process, the sugars could be designed to study and regulate gene function, also.

“We really do not know what people are going to find once we give them these tools,” said Ramirez. The tool could be fresh, but the possibility is great:”We are on the iPhone one, basically,” he continued,”but we’re already working on the next couple generations.”