Harvard University - Department of Molecular & Cellular Biology


by Charlie Schmidt

January 9th, 2007

David Jeruzalmi

For MCB Associate Professor David Jeruzalmi, the lure of research lies in the minute molecular engines that drive what he calls the "broad strokes" of biology. Most of biology’s big-picture views have been well defined, he says, but they can also be changed by what scientists learn about their internal features. "And that’s what interests me," he says. "I want to understand how the broad strokes can be changed by the details."

Jeruzalmi’s work on DNA replication highlights that approach. As a Rockefeller University post-doc, he revealed the intricate arrangement of a molecule that enables newly formed DNA bases to unite themselves in the right order. Known as the clamp loader, that molecule plays a crucial role in DNA synthesis. And by uncovering its structure, Jeruzalmi was able to change how scientists view this larger process.

At Harvard, Jeruzalmi has broadened that research, by addressing the protein-complexes that propel DNA replication. Today, he’s among a growing number of MCB scientists working on structural biology; a field that investigates what molecules do according to how they’ve been put together.  

The Making of a Structural Biologist

After obtaining a B.S. in chemistry from the University of Cincinnati in 1987, Jeruzalmi headed east to Yale, where his interest in structural biology grew. Yale had outstanding faculty in the field, Jeruzalmi says, and top-notch tools for crystallography—a method that allows scientists to discern molecular structures by how they refract X-rays. "Yale was a great place to do this kind of work," he recalls. "The setup for doing structural biology there was amazing."

Jeruzalmi wound up with both a Masters Degree and Ph.D from Yale, each in molecular biophysics and biochemistry. For his Ph.D, he used X-ray crystallography to solve the 3-D structure of RNA polymerase; a protein that converts DNA to RNA during the making of proteins. His advisor was Tom Steitz, a scientist who had worked on the protein during the 1970s, when methods for structural biology were primitive compared to those used now. Steitz had since abandoned the effort and moved on to other projects. But by the time Jeruzalmi joined his laboratory, other scientists had brought the protein’s structure within reach. With recent advances, it had become possible to make RNA polymerase in large, uniform quantities, using genetically engineered microbes.  Jeruzalmi studied a viral form of RNA polymerase (bacteriophage T7) and ultimately published the structure in 1998.

Decoding the Clamp Loader

After Yale, Jeruzalmi moved on  Rockefeller University for a second post-doc, with John Kuriyan now at the University of California at Berkeley. There, he set his sights on the structure of the clamp loader.

Part of a complex, the clamp loader works with two other proteins to accomplish its mission. These include a core DNA polymerase that actually synthesizes DNA, and a sliding clamp that encircles the budding DNA molecule. The sliding clamp’s job is to help the polymerase add new bases to a growing strand of DNA without letting go of it.

What scientists hadn’t figured out was how DNA, being extremely long, could gain entrance to the sliding clamp, which is a closed ring. "Structurally, very little was known about the complex," Jeruzalmi says. "We didn’t really know what it looked like and there were debates over how many components it had."

But by revealing the clamp loader’s structure , Jeruzalmi had pointed to a solution. Based on his findings, scientists were able to show the sliding clamp could develop spring tension properties under certain conditions. [reference?] And those properties, they argued, might allow the clamp to "relax" and allow DNA access to its inner chamber. Jeruzalmi recognizes that key aspects of how the sliding clamp encircles DNA remain unknown, but the recent work builds around his structural findings.

Arrival at Harvard

In July, 2002, after finishing his Rockefeller post-doc and a subsequent six-month stint at Berkeley, Jeruzalmi came to MCB and began the job the holds today.

Since his arrival, he’s turned his attention to even larger molecular complexes. Among them is the origin recognition complex (ORC); which helps to initiate DNA replication, among other tasks. Measuring roughly 400 kilodaltons, the ORC is twice as large as the clamp loader.

Jeruzalmi stresses that by deciphering large molecular complexes, scientists can better understand how proteins trigger biological activity, which is, he says, the main goal of structural biology. "To understand complicated biology you need to know how fundamental processes like DNA replication are regulated," Jeruzalmi explains. "Cells do that when they divide.  It seems simple, but the cells have to ensure the chromosomes are lined up properly without any mistakes. To understand what happens when there are mistakes, you have to study more complex assemblies, which are generally larger."

At Harvard, Jeruzalmi has continued to press forward on DNA replication. While the main goal is to promote fundamental knowledge, the research could also help to identify new targets for antibiotics and drugs, he suggests. For instance, drugs that target proteins in DNA replication could be potentially stop cancer cells from dividing.

Meanwhile, Jeruzalmi says MCB remains an optimal environment for his research. "The Department has a storied program," he says. "And I like my students and colleagues, the people I see every day who influence my work. In the short-term, we’ve got the structures we’re working on now, and we’d like to finish those. As far as the long term, we know that structural biology has changed a lot in the last ten years and will continue to do so. There will continue to be large and difficult problems in this area and people like me who are working on them."