The scientists showed for the first time that when certain parts of a protein molecule are modified ?flexible, randomly structured regions believed to be only minor players in the protein world ?they become important in turning genes on and off, but in a way that resembles a dimmer switch rather than an on-off switch.
Genes carry the code that produces proteins to carry out almost all functions in a living organism. But some of these proteins also help control when and where genes do their jobs. The new study deals with how one such protein, named Ets-1, turns genes on or off.
Huntsman Cancer Institute scientists, led by Barbara Graves, Ph.D., professor and chair of the Department of Oncological Sciences at the University of Utah School of Medicine, and doctoral student Miles Pufall, studied Ets-1, a protein known as a transcription factor that helps read genetic information. This factor serves as a cell's librarian, helping find the right genetic instructions.
How much information the librarian provides, and how accurate that information is, must be tightly controlled. Without the right information, cells can't behave properly, and may, as in the case of cancer, grow out of control. The connection between factors such as Ets-1 and a number of cancers prompted the study of how it works.
One way proteins are controlled occurs after a cell creates a protein. Graves illustrates this process by comparing protein structure with beads on a string. "After the protein is made, it can acquire what we call post-translational modifications, which are like decorations on a beaded necklace. In this analogy, one person creates a necklace using similar beads and then a committee comes along and decorates i t, putting a gold star here and a diamond there. These modifications give the protein different properties."
The "decorations" that were studied were phosphate molecules, which previously had been shown to build up on proteins until a certain number accumulated. The result, according to the study, has been described in the past as a sharp on-off switch of protein activity.
"What we found was that each time we added a phosphate to a particular unstructured region of Ets-1, there was an effect on the protein's ability to bind to a gene. Binding was weakened, but it was a gradual weakening. That isn't typical," Graves says. "Instead of acting like an on-off switch, it behaved the way a dimmer switch does to regulate lighting in a gradual manner."
In studying how this fine-tuning worked, they also discovered that conventional wisdom failed to fully describe how proteins function. It was known that proteins have regions with parts that are fixed in space, with a definite structure, and parts that are randomly positioned in space, like spaghetti strands. It was thought that the structured regions did most of the work, while the unstructured regions served only minor roles, such as tethering parts together.
"Scientists understand how a molecule works in part because we understand the shape or structure," Graves explains. "But what we discovered takes us beyond knowing the structure. Our data were about features that are not fixed in space, but that are flexible and changing."
The team used a nuclear magnetic resonance, or NMR, which allows scientists to observe how the atoms of a molecule behave inside a magnetic field. The Graves team found that unstructured regions of the Ets-1 protein were affecting the structured regions in the work of controlling genes. "In fact," Graves reports, "the region's unstructured nature appears to be an essential requirement." NMR showed that phosphate addition to this unstructured region caused a grad ual decline in DNA binding, gradually turning a gene off.
"One thing we didn't get was why Ets-1 worked differently before and after phosphorylation [the addition of phosphate]," says Pufall, "because as far as we could tell, the overall shape of the molecule didn't change."
"A protein molecule is not like a rock. It's more like Jell-O: it has structure, it has shape, but it jiggles," explains Graves. "We didn't discover jiggling, but we were able to determine that the amount of internal motion within a protein corresponds to the ability of a protein to do its work." Phosphorylation was found to decrease the internal motion of Ets-1, reducing its activity.
According to Pufall, "Ets-1 provides a remarkable illustration of how elegantly proteins are put together ?forming a distinct shape, but with the versatility to respond to the changing needs of the cell, however subtle."
The findings have long-term implications for the study of all proteins, because, according to Graves, any protein has the potential to be organized this way, with structured and unstructured regions that work together.