12/28/2023 0 Comments X ray diffraction definition chemistry![]() ![]() The physical principle of crystallography is based on X-ray diffraction by all the electrons constituting the atoms of all the macromolecules contained in the crystal ( Figure 2). The protein Data Bank (PDB) is a databank that contains 120,262 entries of macromolecules structures (protein, nucleic acids, complexes), 107,455 have been solved by X-ray crystallography (July 2016). Currently, more than 25 crystal structures are deposited daily in the Protein Data Bank () 1 Today, crystallography is able to address the determination of three-dimensional structures of macromolecules more and more complex, more and more quickly. In only 50 years, crystallography has become the technique of choice for the determination of structures of biological macromolecules at atomic scale, taking advantage of the major advances in the scientific fields as diverse as molecular biology, biochemistry, computer science, physics and more recently robotics. ![]() Using a crystal, that contains about 10 15 identical macromolecules periodically arranged in the three directions of space, overcomes these obstacles. First, the signal from a single macromolecule is too low, second, a device, such as lenses, generating a direct image of a macromolecules, does not exist for X-rays. Why using a crystal? To date, the conception of an X-ray microscope encounters two obstacles. Why using X-rays? Their wavelength is of the order of the angström and thus corresponds to the distance between two bound atoms. The length of a 60 base pairs DNA double helix is 204 Å. ĭimension of biological macromolecules represented at the same scale (picture provided by Dr Jérémie Piton). To reach atomic details, the method of choice is crystallography, whose principle is based on the bombardment by X-ray of crystals composed of biological macromolecules. “Seeing” proteins or nucleic acids in three dimensions, a dream or a reality? Could microscopy, a technic known since more than 350 years that allows to visualize biological cells, be the right approach? Of course, the dimensions of these two objects, macromolecules and cells are very different: The cell size ranges generally from 10 to 100 microns (10 −6 m), the dimensions of biological macromolecules, proteins or nucleic acids, are of the order of tens of angstroms (10 −10 m) ( Figure 1). “Seeing” the structure of biological macromolecules, such as proteins or nucleic acids (RNA or DNA), allows researchers to elucidate the mechanisms of live in all organisms, and among many other applications, allows them to design new drugs. During their synthesis, proteins adopt a specific three-dimensional structure that allows them to perform their functions within the cell. Proteins, the nanomachines essential to living organisms, have their “manufacturing plan” encoded in their DNA gene sequence. In 1953, James Watson and Francis Crick revealed the double helical structure of DNA using the results of Rosalyn Franklin obtained by X-ray scattering on natural filaments formed by DNA molecules.
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