Mathematical model of search of the active centers in structure of interaction of proteins with small molecules SO2, H2S, NO2, NH3

Zolotareva N. V., Evsina E. M.

A mathematical model of the search of active centers involved in the interaction with small molecules is proposed on the basis of the static method with the introduction of energy, structural and charge characteristics into the calculation. The result of this simulation is the preparation of molecular diagrams of the active centers of the surface exposed to the toxicant. In the formulation of the mathematical model, the following assumptions are made: 1) the complex geometry of the cell membrane is presented as separate structural components – protein, carbohydrate, lipid/phospholipid; 2) as a molecular model of the protein system we used n-peptide, consisting of a sequence of amino acid residues and recorded as a z-matrix in the internal coordinates (or a set of Cartesian coordinates); 3) intermolecular interaction is carried out by the formation of multiparticle hydrogen bonds by type of bimolecular reaction. The results of mathematical modeling can be presented in the form of graphic diagrams of a specific area of the protein system exposed to the toxicant (molecular diagram of the active centers of the surface). The calculated parameters – the bond length, the charge (under the atom) and the value of π-electron density (indicated by an arrow) were chosen for the diagram. The developed mathematical model of the search for the active centers of protein systems allows to localize the area exposed to the toxicant molecule. On the basis of the obtained results, we can form a data bank on the prevalence, toxicity of small molecules such as SO2, H2S, NO2, NH3, CO and their ionized forms, on specific functional groups of the protein system exposed to the greatest impact.

Keywords:mathematical model, toxicants, structural components, centers of protein systems, ionized forms.