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.
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