This work, illuminating the highest resolution structure ever of a protein of its class, will help drug designers understand Src in atomic detail. Since Src closely resembles eight other members of its family, this long-sought structure establishes general principles for how these complex proteins fold up their amino acid chain to regulate their important but dangerous biochemical work in the cell. Indeed, a structure of a second family member published by other researchers in the same issue of Nature confirms these principles.
Rational drug design has been much touted as the smart, new way to find drugs more quickly, but the driving force behind it is really structural biology. Without a 3-D view of how the atoms of a protein implicated in disease arrange themselves in molecular space, rational drug designers are poking in the dark, trying to shoot bullets at a target they can't see.
Many researchers in academia and industry have tried to elucidate the structure of Src, and several pharmaceutical companies are searching for inhibitors for tyrosine kinases, the class of enzymes of which Src is a flagship member. These still elusive inhibitors could treat not only cancer, but potentially transplant rejection and autoimmune diseases, as well.
The protein Src comes as a Dr. Jeckyll-Mr. Hyde pair. Its benevolent form helps control growth and division, but mutations can turn it into an oncogene. This villain often enters cells via a virus, the context in which it was discovered in 1970. Since this Nobel-prize-winning research, Src has become a household name among bioscientsts. "Src is a granddaddy of famous proteins," says Eck, assistant professor of biological chemistry and molecular pharmacology. In hundreds of studies, researchers have zoomed in on its normal and subverted functions in ever greater detail.
Normal Src conveys growth signals from the cell's outside to its inside. It does so by tacking phosphate groups onto tyrosine amino acids in other proteins, in a process called phosphorylation. Previous research suggested that Src, much like a switch, occurs in the "off" state most of the time and that stimulation flips it to the "on" state. Scientists also have known that cancer-causing mutations lock Src in the "on" position, sending it into a growth-promoting frenzy.
But how exactly does this work? Src must be a sort of multiplex switch, for it receives different types of input and, in response, turns on or off. More than scientific curiosity, this question is key to attempts to interfere therapeutically, says Harrison. "Now at least we have a first view of this class of switch," says Harrison, who is also professor at Harvard.
Most people think of proteins simply as tiny blobs. But when Eck, Harrison, and postdoc Wenquin Xu scrutinized the structure of Src, they realized that it is a formidable product of nano-engineering. "Src is a fancy little machine. It has an incredible amount of information technology built into a tiny package, where every bit matters and is used creatively," says Eck.
Src consists of four lobes: Two lobes make up the kinase performing the protein's ultimate function, and two others, dubbed SH2 and SH3, regulate the kinase and help Src travel to its site of action within the cell. Previous research had visualized parts of Src, but this is the first study that puts them together into a broader vista of how the parts interact. To their surprise, the researchers found that several mechanisms are at work simultaneously to keep Src idle, says Eck.
For one, the four lobes are connected by short "linker" stretches, like pearls on a string. The crystal structure reveals that when Src is in the "off" state, the string is curled up into a compact ball, with the molecule's tail end wrapped around the SH2 lobe in a tight embrace. This crunched conformation pulls shut the cleft between the two kinase lobes, the site where the enzyme--when active--engulfs and phosphorylates its target.
For another, the SH3 domain turns its binding surface inward and snuggles up against the surface of one of the stretches linking two lobes. This atomic interaction in effect hides SH3 from the proteins it would bind in the active state of Src, preventing SH3 from facing outward, where it could encounter those proteins. The tail reaching around SH2 similarly locks away this lobe. Thirdly, a crucial stretch of protein helix, located above the active site, is squeezed out of position.
Together, these and more mechanisms serve to keep a lid on Src. At the same time, they keep it poised to spring into action, much like a Jack-in-the-box. That is because these intramolecular ties are weak, says Eck. When a growth signal comes along, it probably offers stronger, more attractive binding surfaces for one of Src's many sensitive spots, unraveling and activating the protein.
The details of how Src gets turned on require still more research, Eck adds. But the structure has already shown that some of the known mutations making Src cancerous disturb this web of inhibitory ties, letting the Jack permanently out of the box. Says Eck: "Src looks like an oncogene product waiting to happen. Because everything is so interdependent, you can imagine that disrupting any of its internal ties might cause the house of cards to fall."
Editors, please note: a four-color print or electronic file of the Src structure are available on request.
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