One Health: Control of protein folding strikes at the root of disease

WEST LAFAYETTE, Ind. — The shared culprit in a slew of diseases — cancers, neurodegenerative diseases, diabetes — is molecules our cells have made incorrectly. Think of them as proteins gone wrong. Whether the cause is genetic or environmental, these proteins are improperly folded, fail to do their job and can accumulate in the body with devastating results. By looking for missteps in the intricate process of folding proteins, a project at Purdue University is paving the way for a new generation of therapeutics that strike at the root of these diseases.

“Protein folding, and how well we maintain this process, is fundamental to pretty much every disease. But so far, we look at these diseases as separate end points, treating the symptoms but not the disease,” said Seema Mattoo, an associate professor of biological sciences in Purdue’s College of Science and a member of the research team. “In Alzheimer’s, for example, misfolded proteins clump into toxic aggregates, and one line of therapy is to develop drugs that break up the aggregates. While useful, what if we could stop that aggregation from happening in the first place?”

Mattoo said she and a group of eight Purdue colleagues will “test the hypothesis that identifying and understanding the most critical players of protein folding is going to be key to developing the next generation of therapeutics, which could be applicable to several diseases.” The project applies machine learning to research results obtained from multidisciplinary science techniques to identify target proteins, develop advanced imaging techniques to observe protein folding, and test the role of custom-made proteins and small molecules, with an initial focus on proteins critical to vision.

Vikki Weake, an associate professor of biochemistry in the College of Agriculture and research team member, studies aging in flies’ retinas. She said flies and humans share many similar proteins involved in vision and the same light-sensing pathways, making it possible to test the outcome of disrupting suspect proteins. Research on proteins in flies can also be done more quickly and easily, generating leads for continued research.

“Many inherited retinal diseases that cause blindness involve accumulation of misfolded proteins,” Weake said. “By improving our understanding of how to deal with these improperly folded proteins using our collaborative approach, I think we can make progress on identifying new treatment options for these diseases.”

Their work is one of four research projects funded by a seed grant awarded through a universitywide life and health sciences initiative in November 2023. “Unlocking a Blueprint for Health: The Endoplasmic Reticulum (ER) as a Disease Safeguard” is part of Purdue’s One Health initiative, a presidential initiative that involves research at the intersection of human, animal and plant health and well-being. 

“The science of protein folding is fundamental to all life, implying broad potential for the applications of this research,” said Kaethe Beck, Purdue assistant vice president for strategic impact in life and health sciences. “Whether we’re addressing neurodegenerative diseases or bioengineering crops for greater drought resilience, the underlying knowledge and technology this project is developing will help us to shepherd the critical process of protein folding.”

Proteins start out as a string of amino acids that our cells assemble based on instructions written in DNA. The human genome contains instructions for around 20,000 proteins. But to do its job, each string must be folded onto itself in a complex process unique to that protein, until it becomes a sort of three-dimensional puzzle piece, with its structure determining its function. As the string passes through a cellular organelle called the endoplasmic reticulum (ER), it is folded with the aid of an untold number of molecules, some of which are aptly known as “chaperones,” and is further “decorated” with the addition of smaller molecules. Each step is essential to the correct structure and function of the finished protein.

Two of the projects’ target proteins, HYPE and BiP, exemplify the delicacy of the folding process.

In a 2015 paper published in the Journal of Biological Chemistry, Mattoo’s lab reported that HYPE can add or remove a small adenosine monophosphate (AMP) molecule to BiP, a chaperone involved in clearing misfolded proteins from the ER. This change to BiP, which is called AMPylation, serves as an on/off switch, regulating the rate at which the ER clears misfolded proteins.

If the ER does not clear misfolded proteins as quickly as they are made, they will accumulate, a dysfunction seen in a variety of diseases. In 2019, Mattoo predicted that HYPE plays a role in neurodegenerative disease, a conclusion that has since been confirmed by other research teams.

In addition to BiP and HYPE, the team has compiled a short list of proteins that are formed based on instructions in genes associated with blindness and genes known to be important in protein folding. The list includes proteins and chaperones the team has found to be associated with inherited and age-related blindness. By making slightly altered or “mutant” forms of these proteins, the team can probe the connection between the suspect proteins and protein folding, how quickly proteins are made and destroyed, downstream proteins that may be impacted, and overall homeostasis in the ER.

Fang Huang, the Reilly Associate Professor in the Weldon School of Biomedical Engineering in the College of Engineering and an expert on advanced microscopy, is working on a specialized super-resolution microscope that can produce crisp images of interactions between proteins inside the ER itself. This is an astounding feat, given that the images must focus inside the membranes of both the cell and the ER. His images, with a resolution as high as one nanometer, can be further enhanced by artificial intelligence algorithms to produce three-dimensional images of interactions in the ER.

“It’s difficult to see the origin of disease at the stage of the endoplasmic reticulum and protein folding, but that’s our goal — to be able to visualize some of the earliest anomalies in protein interactions,” Mattoo said. “And that sets the stage for the next goal, because if we can manipulate protein folding at the earliest stages, potentially we can come up with a therapeutic for blindness and other protein-misfolding diseases.”

In addition to Mattoo, Weake and Huang, the team includes Alex Chortos, assistant professor of mechanical engineering in the College of Engineering; Bryon Drown, assistant professor of chemistry in the College of Science; Christina Ferreira, metabolomics analyst in the Bindley Bioscience Center; Daniel Flaherty, associate professor of medicinal chemistry and molecular pharmacology in the College of Pharmacy; Jonathan Schlebach, associate professor of chemistry in the College of Science; and Ramaswamy Subramanian, the Gerald and Edna Mann Director of the Bindley Bioscience Center and professor of biomedical engineering and biological sciences in the College of Science.

About Purdue University

Purdue University is a public research university leading with excellence at scale. Ranked among top 10 public universities in the United States, Purdue discovers, disseminates and deploys knowledge with a quality and at a scale second to none. More than 107,000 students study at Purdue across multiple campuses, locations and modalities, including more than 58,000 at our main campus in West Lafayette and Indianapolis. Committed to affordability and accessibility, Purdue’s main campus has frozen tuition 13 years in a row. See how Purdue never stops in the persistent pursuit of the next giant leap — including its comprehensive urban expansion, the Mitch Daniels School of Business, Purdue Computes and the One Health initiative — at https://www.purdue.edu/president/strategic-initiatives.