The study of glycine conformations in the polypeptide chain of a protein by the method of building networks

Savin D.O., Savin D.O.1

Department of Theoretical and Mathematical Physics, Ural Federal University, Kuibysheva 48,

1Ekaterinburg, 620002, Russia, 89326076527,

Proteins are the regulators of a large number of physiological processes in the cell, and their properties depend on their conformations.Amino acid residues are the “vertebrae” of protein conformation - protein movement consists of amino acid movements and in order to better understand the dynamics of protein conformation, it is necessary to understand what can be static in protein and what is mobile.The simplest types of protein subsets are the amino acid residues of glycine, and this work is devoted to the conformations of glycine residues in a protein.

Let each glycine according to the data of nuclear magnetic resonance be assigned a complete simple graph [1,2,3] with the weights of the edges equal to the interatomic distances between the vertices (a network with the Euclidean metric as the function of the edges`s weights), then [4], for the 12–217 part of the ryanodine-sensitive mouse channel type 2, kits from the 21st weight can be obtained, which characterize glycine conformations up to the enantiomer, which in the case of glycine coincides with one of its possible conformations.

I have isolated glycine residues from a file with the NMR structure of a portion of the ryanodine-sensitive channel of the cardiac isoform and calculated their weight from the data available in the structure (see Fig. 1.). Fig. 1. - Graphs of ordered sets of independent weights of glycine residue networks in the graph of the protein section 12 - 217 mRyR2 (isoforms of the heart muscle of the ryanodine-sensitive mouse channel).

For all weights according to the Student's T-criterion, the average values ​​and the confidence intervals of these components of glycine conformations with a confidence probability of 95% on a sample of 13 selected samples were calculated. And from the analysis of the confidence intervals the components of glycine conformations in the polypeptide, we can conclude that many components of glycine conformations remain with high accuracy constant during conformational changes in glycine in the polypeptide chain, and other significant changes in the presence of conformation isolate the glycine motion invariants and components, the variation of which is largely the conformation of the molecule, since their variation is necessary for conformability.

The average value and margin of error, that characterize the scatter of the values ​​of the components were 0.979166 ± 1.96695e-006, 2.11529 ± 7.03267e-006, 2.94086 ± 0.0280611, 3.60831 ± 0.46099, 2.60395 ± 0.0654937, 2.70481 ± 0.0822327, 1.44921 ± 1.1558e-004, 281.2281. , 2.06841 ± 6.55914e-006, 2.06849 ± 7.30576e-006, 1.51478 ± 1.45213e-005, 2.3876 ± 3.07523e-005 1.07979 ± 3.3965e-007, 1.07984 ± 5.0834e-007, 1.23088 ± 1.17125e-006, 2.12597 ± 1.12648e-005, 2.12556 ± 8.44272e-006, 2.77738 ± 0.0346298, 2.93385 ± 0.0556492, 1.75736 ± 1.33879e-006 angstrom for components 0 - 20, respectively.

The work was supported by the project PPK-5-100-2020.


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