Ultrafast Structural Dynamics Of Biomolecules

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.

The ability to create stable femtosecond pulses of laser light has given chemists access to the reaction and structural dynamics of a host of biomolecules that were formerly off-limits.

"The real challenge is studying biomolecular structure in the 10-femtosecond to 1-picosecond time domain," says Richard A. Mathies, dean of the College of Chemistry at the University of California, Berkeley. "That's the intrinsic time over which chemical reactions occur."

In the past four decades, in particular, says physics professor Paul M. Champion of Northeastern University, "the laser has allowed vibrational modes of biomolecules to be observed in their natural aqueous environments with both static and time-resolved Raman spectroscopies." And ultrafast techniques have enabled research groups like his to study coherent reaction dynamics in complexes such as heme proteins (Science 1994, 266, 629).

Mathies and coworkers have used time-resolved techniques such as femtosecond absorption spectroscopy and, more recently, femtosecond stimulated Raman spectroscopy (FSRS) to interrogate photochemical reaction dynamics in visual pigments, including rhodopsin. For example, Mathies' group measured the photoisomerization of rhodopsin's chromophore, an important step in vision (Science 1991, 254, 412). And last year, the same group analyzed excited-state structural changes in green fluorescent protein, a common fluorescent tag, during proton transfer (Nature 2009, 462, 200).

Another "hot field" in which scientists are using lasers to observe biochemical reaction dynamics in the condensed phase is two-dimensional infrared spectroscopy, Champion says. The concept of 2-D IR spectroscopy was dreamed up in the 1970s, when nuclear magnetic resonance spectroscopists were learning to do 2-D NMR, says Martin T. Zanni, a chemistry professor at the University of Wisconsin, Madison. "It just couldn't be implemented" without femtosecond infrared laser pulses, he adds.

But within the past 10 years, the technology and know-how have become available, and scientists such as field pioneer Robin M. Hochstrasser of the University of Pennsylvania are now creating 2-D time-resolved structural maps of systems that include peptides and small proteins. Zanni's group recently elucidated an amino-acid-resolved mechanism for the aggregation of amyloid peptides, complexes that are the hallmark of diseases such as Alzheimer's and type 2 diabetes (Proc. Natl. Acad. Sci. USA 2009, 106, 6614).

By applying visible, rather than infrared, femtosecond laser pulses in sequence, researchers can also study biological chromophores and photochemical systems. Graham R. Fleming and his group at UC Berkeley use 2-D electronic spectroscopy to study molecular energy transfer in photosynthesis. These studies, Zanni says, "have shed a lot of light, so to speak, on how plants convert solar energy into chemical energy."

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