A new Hungarian method can help protein research

By: Trademagazin Date: 2024. 05. 22. 11:12

In a study published in the journal Nature Communications, the HUN-REN–ELTE Protein Modeling Research Group laid the foundations of a mathematical method that enables a computerized comparison of the three-dimensional structure of proteins. In addition to the position of the atoms, the LoCoHD (Local Composition Hellinger Distance) technique also takes into account the chemical information of the atoms.

In our body, proteins perform the tasks necessary for the functioning of cells, because as molecular machines they can, among other things, turn each other on and off, transcribe information from DNA, carry out the transport of small and large molecules, and regulate chemical reaction pathways. However, for the success of all this, it is essential that the protein in question takes on the appropriate spatial structure, i.e. its own 3D arrangement. Several experimental methods are available to determine the arrangement of atoms in proteins (X-ray crystallography, nuclear nuclear resonance spectroscopy, cryo-electron microscopy), with which protein researchers have revealed the shape of nearly 220,000 proteins in the last few decades. These results increasingly require the spread and development of computer methods that can analyze these arrangements.

The new LoCoHD algorithm, which compares spatial structures based on the chemical nature of the amino acid environments found in proteins (e.g. elemental composition, charge, water repellency, etc.), is such a method. The method developed by Zsolt Fazekas, a student at the ELTE György Hevesy Doctoral School of Chemistry, who works in András Perczel’s research group, determines how different the structures in question are from each other on a simple scale between 0 and 1. Values ​​close to 0 assume high similarity between atomic arrangements and chemical properties, while values ​​close to 1 indicate that the compared proteins may have completely different properties. By using the obtained numerical value (so-called metric), a new type of information can be obtained about the studied system.

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