A snapshot of the virus down to the atom
Scientists have obtained a three-dimensional "atomic" photo of the virus for the first time
Physicists from Germany were able to obtain the first full-fledged "atomic" photo of the virus by developing a technique for ultrafast transmission of three-dimensional biological materials using X-rays, according to an article published in the journal Nature Methods (Roedig et al., High-speed fixed-target serial virus crystallography).
"Understanding how a three-dimensional molecule of a protein or any other substance is arranged allows us to reveal what role it plays in the work of cells and the body. For example, the structure of the protein "grappling hook" of the virus, with which it attaches to the cell membrane, can help us protect the cell from its penetration," says David Stuart from the University of Oxford (in a press release Deutsches Elektronen–Synchrotron (DESY) First atomic structure of an intact virus deciphered with an X-ray laser – VM).
Complex protein molecules in our bodies consist of several thousand amino acids, whose chains are often twisted into a complex shape due to interactions between individual links of these peptide chains. So far, biologists have not fully disclosed the laws by which proteins take a certain shape and which allow us to recognize the shape of a molecule by its formula.
Therefore, scientists have to determine the structure of individual proteins "manually" – either using computer simulations, or freezing protein molecules with liquid nitrogen and helium and "shining through" them with super-powerful X-ray lasers.
According to Stewart, scientists have been trying for a long time to adapt this technique to obtain "atomic" photographs of individual cells, bacteria and viruses. All attempts to obtain such images failed for the reason that it is quite difficult to freeze living organisms without destroying them, and the X-ray itself quickly destroys the molecules on their surface and does not allow to obtain high-quality three-dimensional images of the entire microbe or virus.
To solve this problem, Stewart and his team created a new technique for photographing viruses, which they called serial crystallography. The main difference between it and conventional X-ray crystallography is that it does not require freezing of the studied samples and therefore works at room temperature.
Its key part is a special silicon plate with a large number of pores, the dimensions of which are selected in such a way that the virus particles get stuck in them and lose mobility. By shining through each such trap with an X-ray laser, scientists can obtain data on the atomic structure of the part of the virus that "looks out" from the pore, and combine them to obtain a complete three-dimensional image.
Drawing: Philip Roedig, DESY
Such an approach, as Stewart says, allowed his team to obtain photos of the BEV2 virus that infects cattle and causes miscarriages, spending only 14 minutes of time "shining through" the chip using a super-powerful LCLS X-ray laser installed at the American National Accelerator Center SLAC.
Figure: Jingshan Ren, University of Oxford – VM.
Each pixel in the image obtained by Stewart and his colleagues occupies only 0.23 nanometers, which allows you to see individual atoms and groups of molecules on the surface of the virus shell and inside it.
In the near future, physicists plan to increase the number of pores in the plate tenfold and adapt the technique to work with larger and more complex viruses. In addition, the use of the European XFEL laser, capable of producing up to 27 thousand powerful, but short X-ray pulses per second, will make it possible to obtain such three-dimensional images even faster than before, which will accelerate the search for vaccines and medicines for HIV and other viral diseases.
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20.06.2017