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An improved method for protein crystal structure visualization

January 20, 2020

The X-ray crystal structure visualization technique has been known for over a hundred years. It keeps improving, but it is extremely difficult to focus the rays on the objects that are invisible with a naked eye, such as proteins. However, to get a clear image and effectively visualize the structure of a crystal, a sample should be positioned correctly. An international team of scientists suggested an optic system to help see a protein crystal in X-rays and place it in the center of a beam. The results of the study were published in the Structural Biology journal.

During crystallization atoms are arranged in a 3D lattice structured in a specific way. The distances between the atoms in that lattice are determined by the atoms themselves. The X-ray wavelength is comparable to interatomic distances, so the rays can be refracted on the planes. Due to this effect one can analyze crystal structure. The X-ray images show the distances between the planes. Based on this information it is possible to determine what atoms are in the lattice and how they interact with each other. In proteins studying, for example in the search of new drugs, their structure can be determined on the level of basic atom groups (amino acids).

The main issue of X-ray crystallography is that microscopic protein crystals are very difficult to be positioned in the center of an X-ray beam so that X-ray diffraction image may be blurry. Moreover, if the exact position of a crystal is unknown, one has to scan the whole sample. This increases the time of exposure to very intensive X-rays. Biological molecules start to denature under that exposure.

An international team of scientists developed an optic system allowing one to see a sample in X-rays and learn its position and orientation relative to the beam. Just like with a regular optical microscope it can move the sample, adjust rays intensity and focus the beam. Such a system can significantly reduce the time of analysis and thus preserve the integrity of the molecules. Scientists have demonstrated how the system works on the example of a crystal of antibacterial protein lysozyme. The quality of X-ray diffraction images turned out to be much higher after the positioning of the sample in the X-ray beam.

"Our system is now successfully used in the international research center by the DESY synchrotron in Hamburg, where the laboratories of the world's leading universities carry out their crystal structure studies. In the future, we plan to automate the crystal positioning process using neural networks," said Prof. Anatoly Snigirev, the head of the Science and Research Center "Coherent X-Ray Optics for Megascience Installations" at Kant Baltic Federal University.
-end-
The participants of the work also represented the European Molecular Biology Laboratory (Hamburg, Germany), European Synchrotron Radiation Facility (Grenoble, France), and Biological Research Center of the Hungarian Academy of Sciences (Szeged, Hungary).

Immanuel Kant Baltic Federal University

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