Biologists and chefs alike know that oil and water don’t mix. So several years ago, when researchers first discovered intramembrane proteases—a class of hydrophilic (“water-loving”) enzymes that inexplicably appeared to function smack in the middle of the oily membrane that surrounds cells—many scientists were perplexed. Some were downright skeptical.

By publishing the first-ever crystal structure of one such enzyme, Ya Ha, Ph.D., assistant professor of pharmacology, and colleagues may have revealed the intramembrane proteases’ recipe for success.

In addition to providing a solution to a slippery biological mystery, Ha’s work could shed light on the mechanisms underlying Alzheimer’s disease.

Chewing up proteins, a process known as proteolysis, is the job of proteases. But protein-splitting reactions require water, a substance that is normally excluded from the greasy interior of cell membranes.

In 1997, Nobel laureates Joseph L. Goldstein, Ph.D., and Michael S. Brown, Ph.D., published intriguing data in Cell suggesting that a protease involved in regulating cholesterol somehow did its work within the cell membrane. Goldstein and Brown acknowledged that this protease must be “unusual,” but they proposed that gamma-secretase, the enzyme that cleaves amyloid protein into the toxic fragments seen in the brains of Alzheimer’s patients, might operate in the same manner.

When structural biologist Ha came to the School of Medicine from Harvard University five years ago, he first set his sights on gamma-secretase to try to crack the paradox of intramembrane proteases. Ha was convinced that obtaining structural information through X-ray crystallography was the key to understanding how these controversial enzymes worked.

But despite the Ha research team’s best efforts, gamma-secretase could not be coaxed into forming crystals, the first step in determining a protein’s molecular structure. Without a crystal, there was little chance of grant support from the National Institutes of Health, so Ha scraped together funds from the Department of Pharmacology and private foundations to continue his work.

When a family of bacterial enzymes with similar activity known as rhomboid proteins was discovered, Ha seized on those as an alternative. From there, he and postdocs Yongcheng Wang, Ph.D., and Yingjiu Zhang, Ph.D., worked for four more years before they successfully formed a rhomboid protein crystal and obtained the first X-ray data.

At last, they saw how an intramembrane enzyme is built: in the middle of a sea of fat, the rhomboid protease creates a protective bubble to shelter water molecules in its active site. The protein is serpentine, crisscrossing the cell membrane six times. Five of these segments bundle together to create a water-filled chamber within the membrane.

Ha says his lab’s first picture of the rhomboid protease is merely a snapshot. A small dent in the protein facing outward from the cell might be an entryway for water molecules, and a protein flap just outside the central chamber could be a gate that controls the entry of proteins to be cleaved. He wants to capture more views of the protein to find out how this gate might work and how the enzyme’s activity is regulated.

However improbable this enzyme’s mechanics, they are medically important. The rhomboid proteases are part of the family that includes human gamma-secretase, which cleaves a large transmembrane protein in the brain to release the amyloid fragments thought to cause Alzheimer’s disease.

“Compounds that inhibit the production of toxic amyloid peptides are now believed to be one of the most promising approaches to the development of drugs for Alzheimer’s disease,” says Vincent T. Marchesi, M.D., Ph.D., Anthony N. Brady Professor of Pathology and an expert on both membrane protein structure and Alzheimer’s disease. “Ha’s findings are an important contribution to this effort.”

Ha says that the rhomboid protease is a good model system for intramembrane proteases in general, but he confesses that he still has his eye on gamma-secretase. “I would love to see it,” he says.

While the two enzymes are not related by their protein sequence or by evolution, Ha believes that they share common features because they face the same challenge of mixing water with oil. “Once you have a few structures, you’ll see a pattern start to emerge,” Ha explains. “That will give us a better understanding of how inhibitors might work, and then maybe we can design better inhibitors, and maybe those inhibitors can be used as drugs.”

Now that a protein structure that proves that intramembrane proteolysis is possible is in hand, Ha says, “the doubters can be satisfied.” And other researchers, doubters or not, are certainly taking note: the Ha lab’s paper was published in the online version of the journal Nature at 1 p.m. on October 11; four hours later, scientists were ringing Ha’s phone requesting his raw data to apply to their own studies.