Scientists at Scripps Research Institute say that they have figured out the workings of the molecular motor inside a DNA repair complex called MRN complex. The complex’ motor molecule, known as Rad50, is a surprisingly flexible protein that can change shape and even rotate depending on the task at hand, they explain.
The finding solves the long-standing mystery of how this single protein complex can repair DNA in a number of different ways that seem impossible for standard issue proteins to do, the research team remarks. They say that their work also provides critical insight into the ABC-ATPase superfamily of molecular motors, of which Rad50 is a member.
"Rad50 and its brethren proteins in this superfamily are biology's general motors, and if we know how they work, we might be able to control biological outcomes when we need to," comments John Tainer, Ph.D., of Scripps and co-leader of the study.
Details are published in an advance online edition of Nature Structural and Molecular Biology from March 27. The paper is titled “ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair.”
Knowing that Rad50 changes its contour to perform a function suggests it might be possible to therapeutically target unique elements in that specific conformation, the investigators note. "There could be a new generation of drugs that are designed not against an active site, like most drugs now—an approach that can cause side effects—but against the shape the protein needs to be in to work," Dr. Tainer explains.
Paul Russell, Ph.D., of Scripps, who was the second co-leader, adds, "Proteins are often viewed as static, but we are showing the moving parts in this complex. They are dynamic. They move about and change shape when engaging with other molecules."
The MRN complex is known as a first-responder molecule that rushes in to repair serious double-strand breaks in the DNA helix. When MRN senses a break, it activates an alarm telling the cell to shut down division until repairs are made. Then it binds to ATP and repairs DNA in three different ways, depending on whether two ends of strands need to be joined together or if DNA sequences need to be replicated.
"The same complex has to decide the extent of damage and be able to do multiple things," Dr. Tainer points out. "The mystery was how can it do it all."
To find out, Dr. Tainer, head of a structural biology group, and Dr. Russell, who leads a yeast genetics laboratory, began collaborating five years ago. With the additional help of team members at Lawrence Berkeley National Laboratory and its advanced light source beamline, called SIBYLS, the partnership produced a series of high-resolution images of the crystal structure of parts of all three proteins (rad50, Mre11, and Nbs1) taken from fission yeast and archaea. The scientists also used the lab's x-ray scattering tool to determine the proteins' overall architecture in solution, which approximates how a protein appears in a natural state.
Drs. Tainer and Russell were able to produce crystal and x-ray scattering images of parts of where Rad50 and Mre11 touched each other, what happened when ATP bound to this complex, and what it looked like when it didn't.
In these four new structures they showed that ATP binding allows Rad50 to drastically change its shape. When not bound to ATP, Rad50 is flexible and floppy, but bound to ATP, Rad50 snaps into a ring that presumably closes around DNA to repair it.
"We saw a lot of big movement on a molecular scale," notes Dr. Tainer. "Rad50 is like a rope that can pull. It appears to be a dynamic system of communicating with other molecules, and so we can now see how flexibly linked proteins can alter their physical states to control outcomes in biology."
Rad50 and ATP provide energy for a number of biological processes that operate across species. These processes are also linked to disorders such as cystic fibrosis. It is caused by a defect in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which is a member of the ABC ATPase superfamily.
"Our study suggests that ABC ATPase proteins are used so often in biology because they can flexibly hook up to so many different things and produce a specific biological outcome," Dr. Tainer states.
Drs. Tainer and Russell thus envision a future in which therapies might be designed that target Rad50 when it changes into a shape that promotes a disease. For example, chemotherapy could be coupled with an agent that prevents the MRN complex from repairing DNA damage, promoting death of cancer cells.