A University of Limerick scientist has discovered a way to extract hidden proteins from the cell that could become important new targets for drug therapies, writes Claire O'Connell.
IT'S HARD TO FIGHT an enemy you can't see. So when you are designing a drug, it helps to know what the target molecule looks like. But many proteins in the body that could be valuable drug targets lie tucked away in cell membranes, making it difficult for scientists to take them out and see what they look like.
Now researchers based at the University of Limerick have come up with a gloopy, toothpaste-like substance that can help coax tricky membrane proteins out of hiding so their structures may be examined. It could open the way to screening thousands of potential new targets for therapeutic drugs.
"Really what we are after is understanding how the proteins work at a molecular level. To do that we need to get the molecular structure, and ideally we want that at or close to atomic resolution," says Martin Caffrey, professor of membrane structural and functional biology at UL.
Getting that close-up information requires X-ray crystallography, a tried-and-tested method for working out the structure of many water-soluble proteins that are easy to put into a crystal. But the proteins that normally live in cell membranes are more awkward to deal with, explains Prof Caffrey.
"They have an oily part and a water-soluble part that allows them to orient properly in the membrane. But the problem is that when you take them out of the membrane to put them into a crystal there's an intermediate step and often the protein aggregates, it comes out of solution and then it's gone, you can't do anything with it," he says. "So really the major advantage in this field is around the methods for getting the protein out of the biological membrane and into the ordered crystal."
Now his group has come up with a way to keep the sensitive proteins onside. They smash the membrane open with a soapy detergent, and then move the proteins into a thick substance called a "cubic mesophase", through which the proteins can happily march up to join the crystal face.
"It's quite a fascinating structure, extremely viscous, akin to a thick toothpaste," says Prof Caffrey, who returned to Ireland from the United States five years ago. He has developed a robot to dispense the gloopy liquid in tiny, picolitre quantities, and the system is attracting the attention of scientists around the world who want to crack the structures of hard-to-handle membrane proteins. And it's of particular interest to the pharmaceutical industry, because many membrane proteins act as gatekeepers or triggers for processes associated with disease.
PROF CAFFREY'S GROUP is now using the approach to look at membrane proteins in the superbug Pseudomonas to find out more about the signals the bacteria send to each other when they want to attack their human host.
"If you can intercept that process and essentially block it then the bacteria no longer go into that pathogenic mode and we hope they could live in a peaceful co-existence with the host," explains Prof Caffrey, whose work is funded by Science Foundation Ireland and the US National Institutes of Health.
Prof Caffrey spoke about his protein extraction method at the recent Keystone Symposium on GPCRs, which was hosted in Killarney, in collaboration with Science Foundation Ireland.