Volume 1, Issue 2
The Cellular Mechanic
In 2001, Carlos Bustamante was selected by Time magazine as one of "America's Best" in science and medicine. He is professor of molecular and cell biology, physics, and chemistry and is affiliated with the California Institute for Quantitative Biomedical Research (QB3). (courtesy Howard Hughes Medical Institute)
Carlos Bustamante is a mechanic. He tinkers with machines to see what makes them tick. He talks a lot about torque and force, compression and tension. Bustamante is not an engineer though. He's a UC Berkeley professor of molecular and cell biology, physics, and chemistry. And the devices he studies are the microscopic machines behind life itself--cells, proteins, molecular motors, and DNA.
Bustamante is a pioneer in the field of mechanochemistry, devising miraculous methods to manipulate and study individual molecules of proteins, DNA, and RNA. By pulling, prodding, and twisting these molecules, Bustamante furthers our understanding of how cells and microorganisms work.
"Until recently, biochemists and biophysicists did not think of cell processes using mechanical terms," says Bustamante, who is also a Howard Hughes Medical Institute researcher and faculty scientist at Lawrence Berkeley National Laboratory. "Now we have the methods to directly detect and measure the mechanical forces of biochemical reactions at the level of individual molecules."
Most recently, Bustamante and his research group showed that certain proteins essential to compacting DNA for cell division work as "molecular Velcro," helping the double helix of DNA stay bunched up in a well-defined structure. Previously, other researchers determined that if the gene for the proteins, called condensins, was knocked out, the chromosomes failed to segregate properly. Still, the actual mechanics of the condensins were a mystery. To see what was happening, Bustamante created an experiment to measure the force required to yank apart a compacted DNA molecule that had been treated with condensins.
The biomolecular portal motor of bacteriophage PHI-29 (yellow) compresses the coiled DNA into the viral capsid at 6,000 times its normal pressure. The Bustamante group made the measurement by pulling on the DNA with optical tweezers while it was being packed. (courtesy the researchers)
"When we pulled the molecule apart, we saw it extend in a sawtooth pattern of force, like the click-click-click of Velcro unzipping," he says.
After the researchers pulled and relaxed the molecule dozens of times, they proposed a theory about how the condensin proteins create the Velcro-like effect. Each condensin protein, Bustamante explains, attaches sequentially to the DNA. But it also binds less strongly to its neighboring condensin protein. With each attachment, the DNA scrunches closer together into a condensed structure.
The work was published in a June issue of Science Express, a Web site that provides rapid electronic publishing of selected papers that will appear in the journal Science. While the results of the experiment were exciting, the science behind the assay is equally innovative.
"All of these measurements are only now possible to measure because we can grab single molecules and play tug-of-war," Bustamante says.
Over the last decade, Bustamante and his colleagues have advanced various methods to manipulate single molecules, from atomic force microscopes to "optical tweezers." The latter, most recently used to measure the dynamics of DNA's compression, involves the attachment of tiny plastic beads to both ends of a molecule. In this case, the bead at one end of the DNA strand was held in place with suction from a micropipette. The other bead was captured in an "optical trap" created from the radiation pressure of a laser beam. Grasping the bead with the optical tweezers enables the researchers to move or tug the molecule with precise and measurable force.
In 2001, the researchers examined the folding of three types of RNA substructures, including this "hairpin."
In previous experiments, Bustamante and his frequent collaborator, chemistry professor Ignacio Tinoco, used optical tweezers to unfold and refold single RNA molecules. The way nucleic acids and proteins fold into three-dimensional shapes is critical to their function, Bustamante says. Later, the researchers measured the power of the molecular motor that packs a virus's DNA so tightly that it can be injected into a hijacked cell at ten times the pressure of a cork shooting out of a champagne bottle.
"The cell is really like a tiny industrial city with many factories that all perform different functions," Bustamante says. "In the future, perhaps we could go into the cell and play around with those components in vivo."