Measuring the protein-metabolite interactome

As our bodies run multiple parallel processes, they shuttle a flurry of messages around inside—often as protein-metabolite interactions (PMIs), where small molecules bind to a protein and initiate or modify the protein’s functions. But analyzing these PMIs is tough. So Jared Rutter’s group at the University of Utah has developed a platform to systematically detect them (Science 2023, DOI: 10.1126/science.abm3452).

The team calls the platform mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically—or MIDAS, which is less of a mouthful. “The technology itself is based on this classical biochemical technique called equilibrium dialysis,” says Kevin Hicks, who led the work in Rutter’s lab. “We took that technique and made it more high throughput and multiplexed.”

The new method runs with small well plates filled simultaneously. In each well, the team loads purified proteins and metabolites on opposite sides of a protein-impermeable membrane. After the metabolite mix equilibrates across the membrane, the researchers remove the proteins and load the solutions from each side into a mass spectrometer. Differences across the membrane suggest a PMI at play.

The team investigated carbohydrate metabolism as proof of principle and uncovered many previously unknown PMIs.

While the peer-reviewed paper is newly published, Rutter has presented the work as a non-peer-reviewed preprint and in talks. The University of Arizona’s James Galligan says MIDAS is a “cool application” and that he’s seen people lining up after presentations to ask questions about the technique.

Rutter hopes to partner with researchers to build a complete interactome. He and Hicks are also involved in a company using a modified version of the platform to discover novel allosteric sites for drug discovery. “We hope both of those go full speed,” he says.