From Femtosecond Physics to Yeast Genetics

By Jason Socrates Bardi

Rene Descartes once remarked that as a young man, he read every book he could get his hands on—literally. The absurdity of making such a statement today is a measure of the immense explosion of information in the last few centuries.

This explosion of information has had a paradoxical effect on modern science. The more we know, the less aware we become of what we know. Disciplines have become so specialized that it is difficult to keep abreast of the discoveries in one sub-specialty, let alone several fields.

This is problematic for scientists because sometimes the best answers for the most important questions are already known—but not by the people who ask the question. And the people who know the answers are simply unaware that others are asking.

"Interdisciplinary science encourages you to look at problems in a unique way," says Floyd Romesberg, assistant professor in the Department of Chemistry at The Scripps Research Institute (TSRI), shortly before offering a tour of his lab. "That's what attracts me to science and to Scripps."

TSRI fosters interdisciplinary approaches through formal ties and infrastructure that bring scientists from multiple backgrounds together.

"The same people [in my laboratory] synthesize molecules and biophysically analyze them," says Romesberg.

Antibodies, Shaken Not Stirred

One area of research in Romesberg's laboratory involves studying the flexibility and dynamics of proteins using spectroscopy—a new, specialized application of an old tool.

"This is absolutely standard spectroscopy that people have done on small molecules for years," says Romesberg. For years laboratories have routinely used light spectrometers, say, to measure protein concentration or to follow enzymatic reactions.

However, Romesberg's spectrometer is not the kind you might find in any catalog of equipment lying around the lab. It is a custom-built femtosecond (10-15 second) laser spectrometer that takes up nearly an entire room. Nor is the application he is using it for a routine measurement—he is directly probing the flexibility of proteins in solution.

Protein flexibility is an important area in biology because of the role of flexibility in protein–protein recognition. Flexibility may be an important quality that characterizes the recognition of antigens by antibodies or helps an enzyme catalyze a reaction, for instance. Antibody recognition, says Romesberg, may not be the simple, fixed lock-and-key mechanism introductory texts elude to, but one in which the keys and the locks are vibrating and changing their shape as they come together in solution.

However, this sort of flexibility is difficult to characterize experimentally. In proteins, it involves bond vibrations that ever-so-slightly displace atoms a million times every millionth of a second.

These tiny vibrations are important for understanding how a protein recognizes its target with high affinity. And they are what gave Romesberg the idea to try spectroscopy, even though his own background is largely in bioorganic chemistry.

"If the research leads us to [something like] spectroscopy, we will follow the research," he says.

The Reluctant Spectroscopist

Romesberg has built a femtosecond laser to measure protein flexibility. This laser emits a burst of photons in a roughly 17 femtosecond pulse—which is billions of times faster than the fastest shutter speed on a good camera.

This incredible speed is necessary, though, because just as a fast shutter speed captures a fast movement on film, a fast laser captures a fast movement within a protein.

"[The laser] allows us to take 'photographs' of a protein vibrating," says Romesberg.

The femtosecond pulses excite the molecules in the sample, depositing energy, which is absorbed by vibrating bonds within the protein. The electron distribution in these bonds may then change, depending on how much they vibrate. By comparing an excited, "spectra" readout to a normal spectrum, Romesberg and his colleagues can assess how flexible particular parts of a protein are.

This is not always simple, however, since proteins are large molecules with lots of vibrating bonds—so many bonds that a spectrum may have overlapping vibrations that are impossible to differentiate.

So Romesberg selectively incorporates deuterium—so-called "heavy hydrogen" because it has an extra neutron—in the place of normal hydrogen atoms. This extra neutron changes the physics of the vibration and shifts it to a region where it can be observed distinct from other vibrations. This allows him to discriminate between vibrations without affecting the overall shape of the protein.


Next Page | Expanding the Genetic Code and Searching for Mutagenic Genes

1 | 2 |





Investigator Floyd Romesberg directs a diverse program of research in his laboratory in the Department of Chemistry. Photo by Jason S. Bardi.













This laser emits a burst of photons in a roughly 17 femtosecond pulse—a speed billions of times faster than the fastest shutter speed on a good camera.