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Home » March 8, 2010 Issue » Cover Story » Nifty At Fifty » Ultrafast Structural Dynamics Of
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March 8, 2010
Volume 88, Number 10
p. 15

Ultrafast Structural Dynamics Of Biomolecules

Lauren Wolf

Renee Frontiera & Chong Fang/UC Berkeley

STRUCTURAL SNAPSHOTS Using femtosecond stimulated Raman spectroscopy, Mathies and coworkers
found that a wagging motion of the phenoxy group in green fluorescent protein's chromophore is vital to its
proton transfer mechanism.
T he ability to create stable femtosecond pulses of laser light has giv en chemists access to the reaction
and structural dy namics of a host of biomolecules that were formerly off-limits.

"The real challenge is study ing biomolecular structure in the 1 0-femtosecond to 1 -picosecond time
domain," say s Richard A. Mathies, dean of the College of Chemistry at the Univ ersity of California,
Berkeley . "That's the intrinsic time ov er which chemical reactions occur."

In the past four decades, in particular, say s phy sics professor Paul M. Champion of Northeastern
Univ ersity , "the laser has allowed v ibrational modes of biomolecules to be observ ed in their natural
aqueous env ironments with both static and time-resolv ed Raman spectroscopies." A nd ultrafast
techniques hav e enabled research groups like his to study coherent reaction dy namics in complex es such
as heme proteins (Science 1994, 266, 629).

Mathies and coworkers hav e used time-resolv ed techniques such as femtosecond absorption spectroscopy
and, more recently , femtosecond stimulated Raman spectroscopy (FSRS) to interrogate photochemical
reaction dy namics in v isual pigments, including rhodopsin. For ex ample, Mathies' group measured the
photoisomerization of rhodopsin's chromophore, an important step in v ision (Science 1991, 254, 41 2).
A nd last y ear, the same group analy zed ex cited-state structural changes in green fluorescent protein, a
common fluorescent tag, during proton transfer (Nature 2009, 462, 200).

A nother "hot field" in which scientists are using lasers to observ e biochemical reaction dy namics in the
condensed phase is two-dimensional infrared spectroscopy , Champion say s. The concept of 2-D IR
spectroscopy was dreamed up in the 1 97 0s, when nuclear magnetic resonance spectroscopists were
learning to do 2-D NMR, say s Martin T. Zanni, a chemistry professor at the Univ ersity of Wisconsin,

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Madison. "It just couldn't be implemented" without femtosecond infrared laser pulses, he adds.

But within the past 1 0 y ears, the technology and know-how hav e become av ailable, and scientists such as
field pioneer Robin M. Hochstrasser of the Univ ersity of Pennsy lv ania are now creating 2-D time-resolv ed
structural maps of sy stems that include peptides and small proteins. Zanni's group recently elucidated an
amino-acid-resolv ed mechanism for the aggregation of amy loid peptides, complex es that are the hallmark
of diseases such as A lzheimer's and ty pe 2 diabetes (Proc. Natl. A cad. Sci. USA 2009, 1 06, 661 4).

By apply ing v isible, rather than infrared, femtosecond laser pulses in sequence, researchers can also study
biological chromophores and photochemical sy stems. Graham R. Fleming and his group at UC Berkeley
use 2-D electronic spectroscopy to study molecular energy transfer in photosy nthesis. These studies,
Zanni say s, "hav e shed a lot of light, so to speak, on how plants conv ert solar energy into chemical energy ."

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