Scientists at George Mason University say they have developed a new technique to discover where proteins interact with each other, which, they add, could possibly lead to new therapies for cancer, arthritis, heart disease, and even lung disease.

Specifically, the researchers used brightly colored dyes to reveal the contact points where proteins touch each other. “One protein interlocks with another protein like adjacent pieces in a jigsaw puzzle, and this sends a signal down the line to the next protein,” says Lance Liotta, M.D., Ph.D., co-director of the Mason-based Center for Applied Proteomics and Molecular Medicine.

The mystery is in the “hot spots” where proteins interlock. Researchers know which proteins connect but couldn't pinpoint where it happens, until now. The team published its study (“Protein painting reveals solvent-excluded drug targets hidden within native protein–protein interfaces”) in Nature Communications.

Dyes—the type used in common copying machines and textiles—are mixed with proteins. The dye paints the proteins everywhere except where the proteins are connected to one another. Then the proteins are disconnected but the dye remains, excluding the blank spot where the proteins were touching.

“We introduce protein painting as a new tool that employs small molecules as molecular paints to tightly coat the surface of protein–protein complexes. The molecular paints, which block trypsin cleavage sites, are excluded from the binding interface. Following mass spectrometry, only peptides hidden in the interface emerge as positive hits, revealing the functional contact regions that are drug targets,” wrote the investigators. “We use protein painting to discover contact regions between the three-way interaction of IL1β ligand, the receptor IL1RI and the accessory protein IL1RAcP. We then use this information to create peptides and monoclonal antibodies that block the interaction and abolish IL1β cell signaling. The technology is broadly applicable to discover protein interaction drug targets.”

Finding ways to break up interlocking proteins could be used to locate new drug targets, says Virginia Espina, Ph.D., a professor with the center. Pharmaceutical companies could use the Mason-developed process to create drugs that break up the protein-to-protein connection or stop it from happening altogether, she says.

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