Shedding light on chemistry with a biological twist

Mar 15, 2013 by David Bradley
Shedding light on chemistry with a biological twist
The isomerization of a small molecule caged inside a photoactive protein recorded by time-resolved x-ray crystallography reveals a detailed sequence of events (represented by dominos) composed of a short-lived intermediate (red) whose reaction trajectory bifurcates along bicycle-pedal (left) and hula-twist (right) pathways.

( —Many of life's processes rely on light to trigger a chemical change. Photosynthesis, vision, the movement of light-seeking or light-avoiding bacteria, for instance, all exploit photochemistry. Discovering exactly how living things absorb and convert light energy into a form that can change the molecules involved in such processes would not only help scientists understand them but could lead to ways to mimic such processes for more efficient solar energy conversion, for instance. A clearer understanding of how light can drive biological processes has emerged from x-ray diffraction studies carried out on beamlines at the U.S. Department of Energy Office of Science's Advanced Photon Source (APS) at Argonne, and the European Synchrotron Radiation Facility (ESRF). This work will help science shed a brighter light on some of life's most critical processes.

At the heart of these processes are photoactive . Under the right conditions, when shines on them, specific within the light-absorbing part of the protein can undergo a chemical change called isomerization.

For example, photoactive yellow protein (PYP) is a in the bacterium Halorhodospira halophila. When PYP is activated by light it triggers a cascade of that allow the bacterium to move away from the light, a process known as negative phototaxis. At the heart of PYP is a color center, or chromophore, that absorbs the required photons of light and in so doing undergoes a —a trans to cis isomerization. This chemical flip in turn changes the behavior of PYP itself and signals the start of that cascade.

The use of the word "flip" belies a much more complicated process than a straightforward transformation of the chromophore, as the researchers from the Institute for Basic Science (Republic of Korea), KAIST (Republic of Korea), The University of Wisconsin–Milwaukee, and The University of Chicago discovered. They point out that the complexity of any protein discounts the simplistic one-bond flip of the kind that might take place in simple laboratory chemicals. Instead, they suggest that sophisticated chemical choreography must take place to allow the flip to occur without disrupting the overall shape and volume of the protein.

The team utilized time-resolved Laue diffraction x-ray crystallography at the BioCARS 14-ID-B beamline at the APS and the ESRF ID09B beamline to build up a frame-by-frame picture of the changes occurring every 100 ps, at 1.6-Å resolution, as the chromophore absorbs light and the photochemical reactions in PYP begin.

The PYP chromophore is p-coumaric acid, a molecule widespread in nature and present in several edible plants including tomatoes and garlic, as well as the bacterium on which the research team has focused. This molecule contains a between two central carbon atoms in its structure. Such bonds are usually amenable to the kind of transformation that involves a flip from a trans to a cis state where chemical groups linked by the double bond shift from both being on opposite sides to both being on the same side. In the trans state, p-coumaric acid gives rise to the yellow color of PYP, but when it changes to cis, having absorbed a photon, its color is lost and the light energy is transformed into the required physical change in the protein.

Whereas in the laboratory the trans-to-cis flip can occur in a straightforward manner, the team's crystallographic studies of the transformation as it occurs within the protein reveal that an intermediate is involved. This intermediate is a highly strained molecule in which the chemical groups on either side of the double bond in p-coumaric acid are forced to align from their original positions on either side before the molecule releases its pent up energy to generate the cis form with both groups on the same side.

Even this apparently simple release is complicated by the existence of two reaction paths: the "hula-twist" and the "bicycle-pedal." These distinct reaction routes allow the groups adjacent to the double bond either to squirm into the cis position, in the former case, or to rotate around the bond like rotating bicycle pedals. The team has used a mutant version of the protein to control which of these two pathways is taken. A mutation in PYP known as E46Q weakens the connection between p-coumaric acid and the protein itself and this seems to preclude the process from taking the bicycle pedal route.

These findings will help scientists better interpret spectroscopic data from this and similar systems as well as improving their computational models all shedding more light on some of life's most critical processes.

Explore further: Protein secrets of Ebola virus

More information: Jung, Y. et al. Volume-conserving trans–cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography, Nat. Chem. 5, 212 (March 2013). DOI:10.1038/NCHEM.1565

Related Stories

Watching a protein as it functions

Mar 15, 2013

( —When it comes to understanding how proteins perform their amazing cellular feats, it is often the case that the more one knows the less one realizes they know. For decades, biochemists and biophysicists ...

Scientists solve mystery of the eye

Nov 17, 2011

( -- Scientists have a good overall understanding of human vision: when light enters our eyes, it is focused by the lens and strikes the retina in the back of the eye. The light causes some of ...

Unique close-up of the dynamics of photosynthesis

May 10, 2010

Researchers at the University of Gothenburg, Sweden, have managed, with the help of an advanced X-ray flash, to photograph the movement of atoms during photosynthesis - an achievement that has been recognised ...

Discovery alters conventional understanding of sight

Jun 23, 2011

A discovery by a team of researchers led by a Syracuse University physicist sheds new light on how the vision process is initiated. For almost 50 years, scientists have believed that light signals could not be initiated unless ...

Recommended for you

Chemical biologists find new halogenation enzyme

15 hours ago

Molecules containing carbon-halogen bonds are produced naturally across all kingdoms of life and constitute a large family of natural products with a broad range of biological activities. The presence of halogen substituents ...

Protein secrets of Ebola virus

20 hours ago

The current Ebola virus outbreak in West Africa, which has claimed more than 2000 lives, has highlighted the need for a deeper understanding of the molecular biology of the virus that could be critical in ...

Protein courtship revealed through chemist's lens

20 hours ago

Staying clear of diseases requires that the proteins in our cells cooperate with one another. But, it has been a well-guarded secret how tens of thousands of different proteins find the correct dancing partners ...

Decoding 'sweet codes' that determine protein fates

23 hours ago

We often experience difficulties in identifying the accurate shape of dynamic and fluctuating objects. This is especially the case in the nanoscale world of biomolecules. The research group lead by Professor Koichi Kato of ...

Conjecture on the lateral growth of Type I collagen fibrils

Sep 12, 2014

Whatever the origin and condition of extraction of type I collagen fibrils, in vitro as well as in vivo, the radii of their circular circular cross sections stay distributed in a range going from 50 to 100 nm for the most ...

User comments : 1

Adjust slider to filter visible comments by rank

Display comments: newest first

not rated yet Mar 15, 2013
They point out that the complexity of any protein discounts the simplistic one-bond flip of the kind that might take place in simple laboratory chemicals. Instead, they suggest that sophisticated chemical choreography must take place to allow the flip to occur without disrupting the overall shape and volume of the protein.


The 'flip' is at least the one phase state in common to structures that have coupled. Position shaping outcomes so to speak. The point is predictability.