Baku, Azerbaijan
Baku, Azerbaijan
Computer modeling based on the use of the method of theoretical conformational analysis and programs that allow obtaining a graphic image of the spatial structures of biomolecules was performed for a hexapeptide molecule – glyproline H-Phe-Gly-Gly-Phe-Gly-Pro-OH. Glyprolines are short peptides whose amino acid sequences contain glycine and proline residues. Their mechanisms of action are currently poorly understood. Using the method of molecular mechanics, the spatial structure and conformational possibilities of this hexapeptide molecule were determined. Its potential energy was estimated as the sum of non-valente, electrostatic, torsion interactions and the energy of hydrogen bonds. 9 low-energy structures were found for the glyproline hexapeptide, the values of the dihedral angles of the main and side chains of the amino acids included in the molecule. The energy of intra- and interresidual interactions was estimated. The calculation showed that the folded forms of the main chain are low-energy for the hexapeptide. In them, the side chains of amino acids phenylalanine and proline, which are conformationally rigid, carry out effective interactions with all parts of the hexapeptide molecule.
structure, conformation, hexapeptide, molecule
1. Martinova K.V., Andreeva L.A., Klimova P.A. et al. Structure-functional investigation of the glysin and prolin containing peptides, which are neyroprotectors. Bioorg. chim., 2009, vol. 35, no. 2, pp. 165-171 (In Russ.).
2. Falalyeyeva T.M., Samonina G.E., Beregovaya T.V. et al. Effects of glyprolines PGP, PG and GP on homeostasis of gastric mucosa in rats with experimental ethanol-induced gastric ulcers. Bull Exp Biol Med, 2010, vol. 149, no. 6, pp. 699-701.
3. Rogozinskaya E.Ya., Lyapina L.A., Shubina T.A., Myasoedov N.F. et al Trombotlastografic research of arginin-containing, leusine-containing and lysine- containing, peptides. Bullet.of Exper. Biology and Medicine, 2020, vol. 169, pp. 716-719 (In Russ.).
4. Wilson K.R., Cruz M.J., Nicolas C., Belau L., Leone S.R., Ahmad M. Thermal vaporization of biological nanoparticles: fragment - free vacuum ultraviolet photoionization mass spectra of tryptophan, phenylalanine-glycine-glycine and beta-carotene. J. Phys. Chem. A., 2006, vol. 110, no. 6, pp. 2106-2113.
5. Rena D., Valdes H., Vondrasek J., Hobza P. Abu-Riziq Ali, Crews Bridgit, Mattanjahs de Vries. Structure and IR spectrum of phenylalanyl-glycyl-glicine tripeptide in the gas-phass: IR/UV experiments, ab initio quantum chemical calculations, and molecular dynamic simulations. Chemistry 2005, vol. 11, no. 23, pp. 6803-6817.
6. Ivanova E.A., Sarycheva N.Yu., Dubynin V.A., Malyshev A.V. et al. Behavioral of Original Tetrapeptide an Analog of N-Terminal Nociceptin Fragment. Bulletin of Experimantal Biology and Medicine, 2012, vol. 153, no. 2, pp. 177-181.
7. Maksumov I.S., Ismailova L.I., Godjayev N.M. Program of the semi-empirical calculation of the conformations of the molecular complexes on the IBM. Journal of structural chemistry, 1983, vol. 24, no. 4, pp. 147-148 (In Russ.).
8. IUPAC-IUB, Quantity, Units and Symbols in Physical Chemistry, Blackwell Scientific Publications, Oxford, 1988, vol. 39,
9. Akhmedov N.A., Gadjieva Sh.N., Abbasli R.M. Structural organization of Asp-Pro- Lys-Gln-Asp-Phe-Met-Arg-Phe-NH2 molecule. Current Topics in Peptide Protein Research, 2009, vol. 10, pp. 57-62.
10. Akhmedov N.A., Ismailova L.I., Agayeva L.N., Godjaev N.M. The spatial structure of the cardio active peptides. Current Topics in Peptide Protein Research, 2010, vol. 11, pp. 87-93.
11. Akhmedov N.A., Ismailova L.I., Abbasli R.M., Agayeva L.N., Akhmedova S.R. Spatial structure of Octarphin Molecule. IOSR Journal of Applied Physics, 2016, vol. 8, pp. 66-70.
12. Akhmedov N.A., Agayeva L.N., Akhmedova S.R., Abbasli R.M., Ismailova L.I. Spatial structure of the β- Casomorphin-7 Molecule. Journal of Applied Physics (IOSR-JAP), 2021, vol. 13, iss. 5, pp. 62-67.
13. Ismailova L.I., Abbasli R.M., Akhmedov N.A. Computer Modeling of the Spatial Structure of Nonapeptide Molecule. COIA, Baku, Azerbaijan, 2020, vol. I, pp. 218-221.
14. Ismailova L.I., Abbasli R.M., Akhmedov N.A. Structural organization of the Gly-Pro-Arg-Pro molecule. Russian Journal of Biological Physics and Chemisrty, 2021, vol. 6, no. 1, pp. 53-56 (In Russ.).
