In a new study in PNAS, researchers at the University of California, San Diego, and Rice University present an algorithm they wrote to search for "knots" in the 74,200 proteins in the Protein Data Bank, reports Wired Science's Dave Mosher. Knotted proteins were discovered almost 20 years ago, and researchers are beginning to realize that that these shapes may play an important role in cellular activity, Mosher says.
But deciphering the actual shape of the knot is difficult. "The major challenge of working with any protein is verifying its actual structure," Mosher adds. "Computer models can hint at a functional form, but until a protein is isolated and scanned, it's educated guesswork." The researchers created an algorithm to find knots and tested it on the Protein Data Bank — they found 398 proteins with complex knots and 222 proteins with simple knots. "What's more, the knotted structures they discovered appeared in a wide array of life forms, from bacteria and plants to yeast and humans," Mosher says. "Each branch of life seems to have found some way to make specific knots." Now, the team adds, research can be done to determine the purpose of these knots in the proteins of various life forms, and whether they play a role in diseases like Alzheimer's.