Finding the form of BRCA1

By Pamela Wyngate
HS News & Community Relations

The Human Genome Project gives a one-dimensional readout of a gene by listing the sequence of bases in a DNA molecule that ultimately gives rise to a protein-as it is translated and decoded. But proteins don’t have their functions as long, linear molecules. They only function when they’re folded into specific complicated three-dimensional structures.

Rachel Klevit with some models of protein forms. Photo by Gavin Sisk

Dr. Rachel Klevit, professor of biochemistry and director of the Interdisciplinary Graduate Program in Biomolecular Structure and Design, has described the three-dimensional structure of the breast cancer susceptibility protein (BRCA1). This gene, originally located by Dr. Mary-Claire King, professor of medical genetics and genetics, is associated with inherited breast cancer. About 10 percent of breast cancer cases are due to an inherited mutation in BRCA1 or another gene (called BRCA2).

“The questions we’re trying to address are what are these gene products doing-what is their function and what function do they lose in women who have mutated versions of the gene,” Klevit explains. “Our approach is to determine the three-dimensional structures and from that try to gain insight into what the function of the molecule might be,” she says.

To the untrained eye, a three-dimensional rendering of a protein looks very much like a piece of confetti on New Year’s Day. Similar to other fields of biology, biochemists look at these shapes and infer that function follows form.

“If you look at a bicycle, you probably have an inkling what it can do,” says Klevit. “The three-dimensional form of a complicated molecule also contains hints about its function-in many instances molecules with similar structures perform similar functions. But molecules that don’t seem similar in their one-dimensional structures can take on very similar three-dimensional structures.”

Is there a specific code to predict the three-dimensional structure a molecule will adapt? Perhaps.

“In a sense, there has to be, because every time a protein molecule is made from the gene it goes to that three-dimensional structure,” says Klevit. “But it’s a complicated and subtle code, which is why it has been so elusive.”

Add to that the fact that BRCA1 is a very large protein. Most of the proteins that biochemists have studied in detail are up to 300-400 amino acids in length. BRCA1 has 1863 amino acids.

“It presents a real challenge at an atomic level when you have something so large,” Klevit says. “Many genes associated with disease-BRCA1 and BRCA2 for breast cancer and Parkin for Parkinson’s disease-turn out to be these enormous proteins.”

Instead of analyzing the entire protein at once, Klevit is taking a “divide and conquer” approach. The piece she’s recently described is 110 amino acids, about 5 percent of the BRCA1 protein. Klevit did not just randomly choose this particular piece called the RING Domain. RING is an acronym for “really interesting new gene.” The first RING has a similar structure and was described over five years ago by researchers working on a completely different gene that is not related to breast cancer.

The Ring Domain of BRCA1, described by Klevit and her colleagues, is where a large percentage of the mutations are found in genes from families with high rates of breast cancer. According to Klevit, this suggests the RING Domain is a critical region of the BRCA1 molecule because so many families and individuals with one mistake-one amino acid change-in the region can ultimately develop the disease.

“It’s as though we are trying to put together a jigsaw puzzle of the Sistine Chapel,” she says. “What I would like to say is that we put together the pieces where God and Adam are just about to touch each other - that’s my hope.”

In 1981 Klevit received her Ph.D. in chemistry from Oxford University as a Rhodes Scholar. She was a postdoctoral fellow in the Department of Microbiology at Duke University from 1981 to 1983. Klevit was an American Cancer Society postdoctoral fellow in the Department of Chemistry at the UW in 1983 and 1984. She joined the UW faculty as an assistant professor of biochemistry in 1986. Among her many awards and honors, in 1988 Klevit received the Margaret Oakley Dayhoff Award from the Biophysical Society and in 1990 the DuPont Young Investigator Award from the Protein Society. She is also a fellow of the American Association for the Advancement of Science.