Ukr.Biochem.J. 2021; Volume 93, Issue 3, May-Jun, pp. 101-110

doi: https://doi.org/10.15407/ubj93.03.101

Application of petri nets methodology to determine biophysicochemical parameters of mitochondria functioning

01.07.2021   Uncategorized   No comments

H. V. Danylovych*, A. Yu. Chunikhin, Yu. V. Danylovych, S. O. Kosterin

Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
*e-mail: danylovych@biochem.kiev.ua

Received: 01 Nobember 2020; Accepted: 17 May 2021

With the use of Petri net methodology a mathematical simulation model able to predict simultaneous changes in biophysicochemical parameters of mitochondria functioning was developed. The model allowed to interconnect in time the changes in mitochondria hydrodynamic diameter, electronic transport chain functioning, endogenous fluorescence of adenine nucleotides, DCF fluorescence signal of ROS production and NaN3 effects. It was shown that the calculated values of the studied biophysicalchemical parameters correspond to those obtained experimentally. The model permit to link mitochondrial functional changes and their  structural representation and to optimize significantly experimental procedures.

Keywords: , , , ,

References:

  1. Bernardi P, Rasola A. Calcium and cell death: the mitochondrial connection. Subcell Biochem. 2007;45:481-506. PubMed, CrossRef
  2. Graier WF, Frieden M, Malli R. Mitochondria and Ca(2+) signaling: old guests, new functions.  Eur J Physiol. 2007;455(3):375-396. PubMed, PubMedCentral, CrossRef
  3. Orrenius S, Packer L, Cadenas E. (Eds.). Mitochondrial signaling in health and disease. N.Y.: CRC Press, 2012. 493 p.  CrossRef
  4. Csordás G, Várnai P, Golenár T, Sheu SS, Hajnóczky G. Calcium transport across the inner mitochondrial membrane: molecular mechanisms and pharmacology. Mol Cell Endocrinol. 2012;353(1-2):109-113. PubMed, PubMedCentral, CrossRef
  5. Szabadkai G, Duchen MR. Mitochondria: the hub of cellular Ca2+ signaling. Physiology (Bethesda). 2008;23(2):84-94. PubMed, CrossRef
  6. Danylovych YuV, Karakhim SA, Danylovych GV, Kolomiets OV, Kosterin SO. Electrochemical potential of the inner mitochondrial membrane and Ca2+ homeostasis of myometrium cells. Ukr Biochem J. 2015;87(5):61-71. PubMed, CrossRef
  7. Wang HW, Wei YH, Guo HW. Reduced nicotinamide adenine dinucleotide (NADH) fluorescence for the detection of cell death. Anticancer Agents Med Chem. 2009;9(9):1012-1017. PubMed, CrossRef
  8. Heikal AA. Intracellular coenzymes as natural biomarkers for metabolic activities and mitochondrial anomalies. Biomark Med. 2010;4(2):241-263. PubMed, PubMedCentral, CrossRef
  9. Brocard JB, Rintoul GL, Reynolds IJ. New perspectives on mitochondrial morphology in cell function. Biol Cell. 2003;95(5):239-242. PubMed, CrossRef
  10. Kaasik A, Safiulina D, Zharkovsky A, Veksler V. Regulation of mitochondrial matrix volume. Am J Physiol Cell Physiol. 2007;292(1):C157-C163. PubMed, CrossRef
  11. Nowikovsky K, Schweyen RJ, Bernardi P. Pathophysiology of mitochondrial volume homeostasis: potassium transport and permeability transition. Biochim Biophys Acta. 2009;1787(5):345-350. PubMed, CrossRef
  12. Iakovenko IN, Zhirnov VV. Sodium azide as indirect nitric oxide donor: researches on the rat aorta isolated segments. Ukr Biokhim Zhurn. 2005;77(4):120-123. (In Russia). PubMed
  13. Wingender E. (Ed.). Biological Petri Nets. IOS Press; 2011. 316 p.
  14. Kosterin SA, Bratkova NF, Кursky MD. The role of sarcolemma and mitochondria in calcium-dependent control of myometrium relaxation. Biokhimiia. 1985;50(8):1350-1361. (In Russian). PubMed
  15. Bradfor dMM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976;72(1-2):248-254. PubMed, CrossRef
  16. Merkus HG. Particle size measurements. Fundamentals, practice, quality. Springer; 2009.
  17. Nagasaki M, Saito A, Doi A, Matsuno H, Miyano S. Foundations of Systems Biology. Using Cell Illustrator and Pathway Databases. Springer; 2009.
  18. Kolomiets OV, Danylovych YuV, Danylovych GV, Kosterin SO. Ca2+ accumulation study in isolated smooth muscle mitochondria using Fluo-4 AM. Ukr Biokhim Zhurn. 2013;85(4):30-39. (In Ukrainian). PubMed, CrossRef
  19. Chang S, Lamm SH. Human health effects of sodium azide exposure: a literature review and analysis. Int J Toxicol. 2003;22(3):175-186. PubMed, CrossRef
  20. Ji D, Kamalden TA, del Olmo-Aguado S, Osborne NN. Light- and sodium azide-induced death of RGC-5 cells in culture occurs via different mechanisms. Apoptosis. 2011;16(4):425-437. PubMed, CrossRef
  21. Feissner RF, Skalska J, Gaum WE, Sheu SS. Crosstalk signaling between mitochondrial Ca(2+) and ROS. Front Biosci (Landmark Ed). 2009;14:1197-1218. PubMed, PubMedCentral, CrossRef
  22. Santo-Domingo J, Wiederkehr A, De Marchi U. Modulation of the matrix redox signaling by mitochondrial Ca(2+). World J Biol Chem. 2015;6(4):310-323. PubMed, PubMedCentral, CrossRef
  23. Bernardi P, von Stockum S. The permeability transition pore as a Ca(2+) release channel: new answers to an old question. Cell Calcium. 2012;52(1):22-27. PubMed, PubMedCentral, CrossRef
  24. Trumpower BL. The protonmotive Q cycle. Energy transduction by coupling of proton translocation to electron transfer by the cytochrome bc1 complex. J Biol Chem. 1990;265(20):11409-11412. PubMed, CrossRef
  25. Bringold U, Ghafourifar P, Richter C. Peroxynitrite formed by mitochondrial NO synthase promotes mitochondrial Ca(2+) release. Free Radic Biol Med. 2000;29(3-4):343-348. PubMed, CrossRef
  26. 26. Gellerich FN, Gizatullina Z, Trumbeckaite S, Nguyen HP, Pallas T, Arandarcikaite O, Vielhaber S, Seppet E, Striggow F. The regulation of OXPHOS by extramitochondrial calcium. Biochim Biophys Acta. 2010;1797(6-7):1018-1027. PubMed, CrossRef
  27.  Elfering SL, Haynes VL, Traaseth NJ, Ettl A, Giulivi C. Aspects, mechanism, and biological relevance of mitochondrial protein nitration sustained by mitochondrial nitric oxide synthase. Am J Physiol Heart Circ Physiol. 2004;286(1):H22-H29. PubMed, CrossRef
  28. Rasola A, Bernardi P. Mitochondrial permeability transition in Ca(2+)-dependent apoptosis and necrosis. Cell Calcium. 2011;50(3):222-233. PubMed, CrossRef
  29. Chance B, Williams GR. Respiratory enzymes in oxidative phosphorylation. III. The steady state. J Biol Chem. 1955;217(1):409-427. PubMed, CrossRef
  30. Danylovych H, Chunikhin A, Danylovych Yu, Kosterin S. Methodology of Petri networks for simultaneous evaluation of the impact of different modifiers on the fluorescence of nucleotides from electron transport chain in isolated mitochondria and on the process of swelling. J Biotech Comput Biol Bionanotech. 2018;99(1):37-48.  CrossRef
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