Researchers decode targets for hundreds of signaling enzymes

When cells in the human body sense a change in the environment, molecules called kinases can help them respond: these specialized enzymes activate proteins, propagating signals within a cell that ultimately change their function. But if scientists want to understand the role of a particular kinase—and there are hundreds of them—they must first understand which protein it targets. In most cases, this is not known.

In a new analysis of more than 300 kinases in the human body, Yale researchers have revealed new insights into the proteins these enzymes are most likely to target. Their findings will lead to a deeper understanding of human biology, they say, and identify targets for disease treatment.

The results were published in nature.

Kinases are enzymes that facilitate a process called phosphorylation. Essentially, a kinase recruits a small piece of a molecule called a phosphate group, which consists of a phosphorus atom and four oxygen atoms, and helps bind it to a specific area of ​​a protein called a phosphorylation site.

“When a protein gets phosphorylated by a kinase, it flips a switch that can change the activity of the protein or when it goes into the cell. It can change the function of the protein in any number of ways,” said Benjamin Turk, associate professor with pharmacology. at the Yale School of Medicine and co-senior author of the study. Other co-senior authors are Michael Yaffe at the Massachusetts Institute of Technology and Lewis Cantley at Weill Cornell Medicine.

There are more than 500 kinases in the human body that act on hundreds of thousands of phosphorylation sites. That diversity, Turk said, speaks to how essential phosphorylation is to cellular processes.

“But it’s a huge knowledge gap not knowing which kinases go with which phosphorylation sites,” he said.

To fill that gap, Turk and his colleagues focused on how kinases recognize their targets. Proteins are made up of amino acids, of which there are 20; Kinases recognize short strings of amino acids surrounding the phosphorylation site. For the study, the researchers put together different amino acid strings, using all possible amino acid combinations, and measured how quickly different kinases phosphorylated each of the amino acid strings .

“By looking at the fastest and slowest phosphorylated chains, it tells you which sequences of amino acids are best or disappeared by a particular kinase,” said Turk.

In an interesting finding, Turk said, the researchers found that some phosphorylation sites scored poorly for their known kinases. But they scored much worse for the other kinases.

“We think in cases like this the phosphorylation site may have evolved to evade the wrong kinases rather than increasing recognition by the right kinase,” he said. “This tells us more about how specificity emerges in these systems.”

The new study provided an online resource that other researchers can now use. Those who want to know what their kinase of interest might phosphorylate – or which kinase their protein of interest is phosphorylated by – can use a search engine that produces a ranked list of possible options based on the results of the study.

The findings also informed another project in Turk’s lab where researchers are exploring a small group of kinases called mitogen-activated protein kinases, or MAP kinases. Each of these kinases has a very different role in the human body despite being molecularly quite similar.

In a second study published in Scientific Signage, Turk and his colleagues—including lead author Guangda Shi, who conducted the research as a graduate student in Turk’s lab and is now at the University of Pennsylvania—described how different MAP kinases target their proteins and various effects. The work, they say, helps clarify how signaling pathways in cells can be as specific as they are and may have implications for understanding and treating diseases such as cancer.

“Certain MAP kinases are often hyperactivated in cancer and become drug targets for treatment,” explained Turk. “Understanding how and where kinases act will help us understand their signaling pathways more deeply. And that will give us insight into all kinds of biological functions and where they go wrong in disease.”