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Posted: Nov 04, 2014

Photosynthesis in X-ray vision

(Nanowerk News) Photosynthesis is one of the most important processes in nature. The complex method with which all green plants harvest sunlight and thereby produce the oxygen in our air is, however, still not fully understood. Researchers using DESY's X-ray light source PETRA III have examined a photosynthesis subsystem in a near-natural state. According to the scientists led by Privatdozentin Dr. Athina Zouni from the Humboldt University (HU) Berlin, the X-ray experiments on what is known as photosystem II reveal, for example, yet unknown structures. Their results are published in the scientific journal Structure ("Native-like Photosystem II Superstructure at 2.44 Å Resolution through Detergent Extraction from the Protein Crystal"). The technology utilised could also be of interest for analysing other biomolecules.
Molecular structure of photosystem II, which arranges itself in rows
Molecular structure of photosystem II, which arranges itself in rows. (Image: Martin Bommer/HU Berlin)
Photosystem II forms part of the photosynthetic machinery where water, with the help of sunlight, is split into hydrogen and oxygen. As one of the membrane proteins, it sits in the cell membrane. Membrane proteins are a large and vital group of biomolecules that are, for example, important in addressing a variety of medical issues. In order to decode the protein structure and reveal details on how biomolecules function, researchers use the very bright and short-wave X-rays of PETRA III and other similar facilities. Small crystals, however, must initially be grown from these biomolecules.
“The structure of single molecules cannot be directly seen even with the brightest X-rays,” explains co-author and DESY researcher Dr. Anja Burkhardt of Measuring Station P11, where the experiments were carried out. “In a crystal, however, a multitude of these molecules are arranged in a highly symmetrical fashion. Thus the signal, resulting from X-ray diffraction of these molecules, is amplified. The molecular structure can then be calculated from the diffraction images.”
Biomolecules – and especially membrane proteins – cannot easily be compelled into crystal form as it is contrary to their natural state. Preparing suitable samples is therefore a crucial step in the whole analysis process. For instance, photosystem II must be first separated from the membrane, where it is bound to numerous small fat molecules (lipids). Researchers use special detergents for this purpose, such as those also principally found in soap. The catch: instead of lipids, the biomolecules are now surrounded by detergents, which may make the crystals spongy under certain conditions, thus exacerbating the analysis.
“What we want is to come as close as possible to nature,” stresses Zouni. The closer the proteins in the crystal are to their natural state, the better the results.
The group led by Zouni has now managed to produce photosystem II crystals, which no longer contain detergents so that the biomolecules are frozen in a near-natural state.
“The trick was to use a detergent that strongly differs from the lipids in composition and structure,” explains the researcher.
Before examining the biomolecular crystals using X-rays, a portion of the water is extracted and replaced by an anti-freeze. The crystals are usually frozen for the experiments because the high-energy X-ray doesn’t damage them so quickly in the frozen state. During this process, the researchers would like to avoid ice formation.
“The dehydration process removed not only the water in our samples, but also completely removed the detergent, something we didn’t expect,” says Zouni.“Our samples are closer to the natural state than what has been reported before.”
Consequently, the investigation’s spatial resolution increased from about 0.6 nanometres (a millionth of a millimetre) to 0.244 nanometres. This is not, in fact, the highest resolution ever achieved in a photosystem II study, but the analysis shows that the photosystem II proteins are arranged within the crystals as pairs of rows, something that also occurs in the natural environment.
Electron microscope investigations by Professor Egbert Boekema’s group at the University of Groningen in the Netherlands had already shown the photosystems’ crystal like arrangement in the natural membrane — a kind of tiny solar cell. Electron microscopy could better recognize connections using direct observation of the native membrane while X-ray crystallography could reveal the smallest details.
“We placed the structural data over the electron microscope images – they matched precisely,” says Zouni. The investigation also revealed structures that were invisible before. “We can see exactly where the bonds to the lipids are located,” the scientist explains. The more the researchers discover about photosystem II, the better they understand exactly how it functions.
The procedure of using a new detergent, however, is not only interesting in terms of photosystem II. “The method can potentially be applied to many membrane proteins,” stresses Zouni. In the future, many biomolecules could maybe examined in a more natural state than ever before.
Source: Deutsches Elektronen-Synchrotron
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