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McArdle Laboratory researchers collaborate with local start-up to elucidate super-weak protein interactions

miyamoto, burgess, and berryMcArdle Laboratory faculty members Dr. Shigeki Miyamoto and Dr. Richard Burgess, collaborators on the NIH SBIR, and Dr. Scott Berry of Salus Discovery.

Dr. Shigeki Miyamoto and Dr. Richard Burgess, faculty in the McArdle Laboratory, are a part of a two-year NIH Small Business Innovation Research (SBIR) grant awarded to the Madison biotech start-up Salus Discovery. Scott Berry, at Salus, is the PI of the grant and is a former scientist from the lab of Dave Beebe, Prof. of Biomedical Engineering and the founder of Salus. 

This two-year grant, entitled “Seeing the Unseen”, will allow the researchers to continue to improve and validate a novel method of identifying previously undetectable weak binding components of important protein complexes.  Some proteins in a protein complex are tightly bound and co-purify through many steps of a protein purification procedure.  However, proteins that are weakly bound, with dissociation half times of a minute or less, are likely to dissociate and be lost during purification. Thus, much of the crucial information is lost using existing technologies.

“One of the problems with the conventional methods of protein purification is that many protein-protein interactions can be relatively weak,” says Dr. Miyamoto. “When trying to isolate them, it takes time and they fall apart, so we miss some potentially key interactions, or we may significantly underestimate the quantity of those interactions.”

It is now clear that there are important regulatory components of protein complexes that are involved in writing, reading or erasing protein post-translational modifications. Many of these regulatory components are specific to the complex, but only weakly or transiently bound.  Establishing and refining methods for identifying these otherwise invisible components has the potential to revolutionize the fields of biochemistry and cancer biology. 

Salus’s new method uses small magnetic beads with bound antibodies specific to one of the proteins in the complex.  The beads are mixed with a crude samples of cell extract, serum, or urine so that the antibodies can link the protein complex to the bead.  Unlike conventional protein complex purification techniques that involve several iterative, time-consuming precipitation and washing steps, in the Salus system the bead is removed from the crude sample very rapidly using a magnet, with the protein complexes pulled through a single wash solution before being directly denatured for analysis.  The entire process takes only a few seconds and is thus able to capture, better than any prior method, both tightly and weakly bound proteins associated with the complex of interest.

“The idea is to minimize protein-protein disassembly while we’re purifying, and the hope is that we can capture more different types of proteins, and also do it more quantitatively,” says Dr. Miyamoto.

Weak binding proteins that regulate cell signaling complexes represent desirable drug discovery targets, since weak protein-protein interactions may be easier to inhibit by potential therapeutic chemicals. Dr. Burgess’s lab, particularly senior scientist Nancy Thompson, is working with scientists at Salus to improve and validate the system by using engineered model proteins to better characterize the specificity and precision of the technology. Dr. Miyamoto’s lab is testing the method to identify new proteins that are involved in the regulation of the NF-κB system, a key player in the cellular inflammatory and cancer cell survival responses.

“My lab is looking at endogenous proteins in mouse, and evaluating the system in an actual physiological context,” says Dr. Miyamoto. “Once we purify and identify weakly-interacting proteins, we can then knockdown the protein in cell lines and observe if the signaling cascade we are interested in is disturbed.”

Small Business Innovation Research (SBIR) grants are sponsored by the NIH and are designed to support research into cutting-edge biomedical technologies. By providing seed money to companies with innovative ideas and products, these grants help bring new technologies that will benefit the public to market.

SBIR grants are structured to encourage collaboration between the worlds of industry and academic research, bridging the gap in order to deliver solutions faster and to maximize the impact of new technologies. Approximately two-thirds of the funding for Salus Discovery’s SBIR will go to the company, with one-third going to the research collaborators at the McArdle Laboratory.

Over the last several decades, Madison has become a hub for biomedical and biotechnology innovation. There are currently over 200 biotech companies operating in Madison, including Promega and Aldevron, compared to just 3 companies 35 years ago. This is thanks in no small part to the exceptional quality of life sciences research at UW-Madison. Programs such as the UW Biotechnology Center have actively fostered this growth, and many UW-Madison graduate students have gone on to form companies of their own.

“Collaboration between the university and local and nation-wide companies is essential to bring new inventions and discoveries to the point where there is a product or a service made available for the benefit of the general public,” says Dr. Burgess.

Right now, Dr. Miyamoto is excited to apply this new technology to his laboratory’s research, and study key interactions that would otherwise be unobservable.

“Our ultimate goal is to add to the knowledge of discovering unknowns, that’s our main motivation. We might be able to see something no one has seen before, and that potential for discovery is very cool.”

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