Advertisement

Method of Direct Multiparticle Simulation of Protein Interactions

  • Andrew Rubin
  • Galina Riznichenko
Chapter
Part of the Biological and Medical Physics, Biomedical Engineering book series (BIOMEDICAL)

Abstract

Electron transport processes in the photosynthetic and mitochondrial membranes of a cell are mediated by protein–protein complexes and mobile carriers. For a general kinetic description of these reactions mathematical models have been developed where some modifications of the mass action law are used. The rate constants of biochemical reactions of protein–protein association and concentrations of donor and acceptor protein molecules serve as parameters in these kinetic models. Rate constant values are determined under various conditions (e.g., different pH, ionic strength) and evaluated according to experimental data; therefore, the corresponding kinetic models are essentially phenomenological since their rate constants have effective values.

Keywords

Thylakoid Membrane Mobile Carrier Brownian Dynamic Cyclic Electron Flow Cyclic Electron Transport 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Albertsson P-A (2000) The domain structure and function of the thylakoid membrane. Recent Res Dev Bioener 1:143–171Google Scholar
  2. Albertsson P-A (2001) A quantitative model of the domain structure of the photosynthetic membrane. Trends Plant Sci 6:349–354CrossRefGoogle Scholar
  3. Belyaeva NE, Schmitt F-J, Paschenko VZ et al (2008) PSII model-based simulations of single turnover flash-induced transients of fluorescence yield monitored within the time domain of 100ns-10 s on dark-adapted Chlorella pyrenoidosa cells. Photosynth Res 98:105–119CrossRefGoogle Scholar
  4. Belyaeva NE, Schmitt F-J, Paschenko VZ et al (2011) PS II model based analysis of transient fluorescence yield measured on whole leaves of Arabidopsis thaliana after excitation with light flashes of different energies. Biosystems 103(2):188–195CrossRefGoogle Scholar
  5. Bendall DS, Manasse RS (1995) Cyclic photophosphorylation and electron transport. Biochim Biophys Acta 1229:23–38CrossRefGoogle Scholar
  6. Chow WS, Hope AB (2004) Electron fluxes through photosystem I in cucumber leaf discs probed by far-red light. Photosynth Res 81:77–89CrossRefGoogle Scholar
  7. Cleland RE, Bendall DS (1992) Photosystem I cyclic electron transport: measurement of ferredoxin-plastoquinone reductase activity. Photosynth Res 34:409–418CrossRefGoogle Scholar
  8. Cruz JA, Salbilla BA, Kanazawa A et al (2001) Inhibition of plastocyanin to P700 + electron transfer in Chlamydomonas reinhardtii by hyperosmotic stress. Plant Physiol 127:1167–1179CrossRefGoogle Scholar
  9. Dekker JP, Boekema EJ (2005) Supramolecular organization of thylakoid membrane proteins in green plants. Biochim Biophys Acta 1706:12–39CrossRefGoogle Scholar
  10. Fan D-Y, Nie Q, Hope AB et al (2007) Quantification of cyclic electron flow around Photosystem I in spinach leaves during photosynthetic induction. Photosynth Res 94:347–357CrossRefGoogle Scholar
  11. Gross EL, Pearson DC (2003) Brownian dynamics simulations of the interaction of Chlamydomonas cytochrome f with plastocyanin and cytochrome c6. Biophys J 85:2055–2068CrossRefGoogle Scholar
  12. Gross EL, Rosenberg I (2006) A Brownian dynamics study of the interaction of Phormidium cytochrome f with various cyanobacterial plastocyanins. Biophys J 90:366–380CrossRefGoogle Scholar
  13. Haddadian EJ, Gross EL (2005) Brownian dynamics study of cytochrome f interactions with cytochrome c6 and plastocyanin in Chlamydomonas reinhardtii plastocyanin, and cytochrome c6 mutants. Biophys J 88:2323–2339CrossRefGoogle Scholar
  14. Haddadian EJ, Gross EL (2006) A Brownian dynamics study of the interactions of the luminal domains of the cytochrome b 6 f complex with plastocyanin and cytochrome c 6: the effects of the Rieske FeS protein on the interactions. Biophys J 91:2589–2600CrossRefGoogle Scholar
  15. Haehnel W, Propper A, Krause H (1980) Evidence for complexed plastocyanin as the immediate electron donor of P-700. Biochim Biophys Acta 593:384–399CrossRefGoogle Scholar
  16. Haehnel W, Ratajczak R, Robenek H (1989) Lateral distribution and diffusion of plastocyanin in chloroplast thylakoids. J Cell Biol 108:1397–1405CrossRefGoogle Scholar
  17. Hope AB (2000) Electron transfers amongst cytochrome f, plastocyanin and photosystem I: kinetics and mechanisms. Biochim Biophys Acta 1456:5–26CrossRefGoogle Scholar
  18. Joliot P, Lavergne J, Beal D et al (1992) Plastoquinone compartmentation in chloroplasts. I. Evidence for domains with different rates of photo-reduction. Biochim Biophys Acta 1101:1–12CrossRefGoogle Scholar
  19. Kirchhoff H, Horstmann S, Weis E (2000) Control of the photosynthetic electron transport by PQ diffusion microdomains in thylakoids of higher plants. Biochim Biophys Acta 1459:148–168CrossRefGoogle Scholar
  20. Kirchhoff H, Mukherjee U, Galla H-J (2002) Molecular architecture of the thylakoid membrane: lipid diffusion space for plastoquinone. Biochemistry 41:4872–4882CrossRefGoogle Scholar
  21. Kovalenko IB, Ustinin DM, Grachev NE et al (2003) Experimental and theoretical investigation of cyclic electron transport around photosystem I. Biofizika 48(4):656–665Google Scholar
  22. Kovalenko IB, Abaturova AM, Gromov PA et al (2006) Direct simulation of plastocyanin and cytochrome f interactions in solution. Phys Biol 3:121–129ADSCrossRefGoogle Scholar
  23. Kovalenko IB, Abaturova AM, Ustinin DM et al (2007) Multiparticle computer simulation of photosynthetic electron transport in a thylakoid membrane. Biofizika 52(3):492–502Google Scholar
  24. Kovalenko IB, Abaturova AM, Gromov PA et al (2008) Computer simulation of plastocyanin–cytochrome f complex formation in the thylakoid lumen. Biophysics 53:140–146CrossRefGoogle Scholar
  25. Kovalenko IB, Abaturova AM, Riznichenko GY et al (2009) A novel approach to computer simulation of protein–protein complex formation. Dokl Biochem Biophys 427:215–217CrossRefGoogle Scholar
  26. Kovalenko IB, Knyazeva OS, Riznichenko GY et al (2011a) Mechanisms of interaction of electron transport proteins in photosynthetic membranes of cyanobacteria. Dokl Biochem Biophys 440:272–274CrossRefGoogle Scholar
  27. Kovalenko IB, Abaturova AM, Diakonova AN et al (2011b) Computer simulation of protein-protein association in photosynthesis. Math Model Nat Phenom 6:39–54CrossRefMathSciNetGoogle Scholar
  28. Kovalenko IB, Abaturova AM, Riznichenko GY et al (2011c) Computer simulation of interaction of photosystem 1 with plastocyanin and ferredoxin. Biosystems 103:180–187CrossRefGoogle Scholar
  29. Krendeleva TE, Kukarskikh GP, Timofeev KN et al (2001) Ferredoxin-dependent cyclic electron transport in isolated thylakoids occurs with the participation of ferredoxin-NADP-reductase. Dokl Ross Akad Nauk 379:1–4 (Rus)Google Scholar
  30. Kruger GHJ, Tsimilli-Michael M, Strasser RJ (1997) Light stress provokes plastic and elastic modification in structure and function of Photosystem II in camellia leaves. Physiol Plantarum 101:265–287CrossRefGoogle Scholar
  31. Kubo R (1966) The fluctuation-dissipation theorem. Rep Prog Phys 29(I):255–284ADSCrossRefGoogle Scholar
  32. Lazar D (2003) Chlorophyll a fluorescence rise induced by high light illumination of dark-adapted plant tissue studied by means of a model of photosystem II and considering photosystem II heterogeneity. J Theor Biol 220:469–503CrossRefGoogle Scholar
  33. Lazar D (2006) The polyphasic chlorophyll a fluorescence rise measured under high intensity of exciting light. Funct Plant Biol 33:9–30CrossRefMathSciNetGoogle Scholar
  34. Malkin R, Niyogi K (2000) Photosynthesis. In: Buchanan BB, Gruissem W, Jones R (eds) Biochemistry and molecular biology of plants. American Society of Plant Physiologists, Rockville, MDGoogle Scholar
  35. Nelson N, Yocum CF (2006) Structure and function of photosystems I and II. Annu Rev Plant Biol 57:521–565CrossRefGoogle Scholar
  36. Pearson DC Jr, Gross EL (1998) Brownian dynamics study of the interaction between plastocyanin and cytochrome f. Biophys J 75:2698–2711CrossRefGoogle Scholar
  37. Pearson DC, Gross EL, David ES (1996) Electrostatic properties of cytochrome f: implications for docking with plastocyanin. Biophys J 71:64–76CrossRefGoogle Scholar
  38. Rienzo FR, Gabdoulline M, Menziani P et al (2001) Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f. Biophys J 81:3090–3104CrossRefGoogle Scholar
  39. Riznichenko GY, Belyaeva NE, Kovalenko IB et al (2009) Mathematical and computer modeling of primary photosynthetic processes. Biophysics 54:10–22CrossRefGoogle Scholar
  40. Riznichenko GY, Kovalenko IB, Abaturova AM et al (2010) New direct dynamic models of protein interactions coupled to photosynthetic electron transport reactions. Biophys Rev 2:101–110CrossRefGoogle Scholar
  41. Rubin A, Riznichenko G (2009) Modeling of the primary processes in a photosynthetic membrane. In: Laisk A, Nedbal L, Govindjee (eds) Photosynthesis in silico: understanding complexity from molecules to ecosystems. Springer, DordrechtGoogle Scholar
  42. Scheller HV (1996) In vitro cyclic electron transport in barley thylakoids follows two independent pathways. Plant Physiol 110:187–194Google Scholar
  43. Shimoni EO, Rav-Hon O, Ohad I et al (2005) Three-dimensional organization of higher-plant chloroplast thylakoid membranes revealed by electron tomography. Plant Cell 17:2580–2586CrossRefGoogle Scholar
  44. Staehelin AL, van der Staay GWM (1996) Structure, composition, functional organization and dynamic properties of thylakoid membranes. In: Govindjee (ed) Advances in photosynthesis and respiration, vol 4. Springer, Dordrecht, p 11Google Scholar
  45. Stirbet A, Govindjee, Strasser BJ et al (1998) Chlorophyll a fluorescence induction in higher plants: modeling and numerical simulation. J Theor Biol 193:131–151Google Scholar
  46. Strasser RJ, Tsimilli-Michael M, Srivastava A (2004) Analysis of the chlorophyll a fluorescence transient. In: Papageorgiou GC, Govindjee (eds) Chlorophyll fluorescence: a signature of photosynthesis. Springer, DordrechtGoogle Scholar
  47. Ullmann GM, Knapp E-W, Kostic NM (1997) Computational simulation and analysis of dynamic association between plastocyanin and cytochrome f. Consequences for the electron-transfer reaction. J Am Chem Soc 119:42–52CrossRefGoogle Scholar
  48. Yamashita E, Zhang H, Cramer WA (2007) Structure of the cytochrome b6f complex: quinone analogue inhibitors as ligands of heme cn. J Mol Biol 370:39–52CrossRefGoogle Scholar
  49. Zhu X-G, Govindjee, Baker NR, deSturler E et al (2005) Chlorophyll a fluorescence induction kinetics in leaves predicted from a model describing each discrete step of excitation energy and electron transfer associated with Photosystem II. Planta 223:114–133Google Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Andrew Rubin
    • 1
  • Galina Riznichenko
    • 1
  1. 1.Department of BiophysicsLomonosov Moscow State UniversityMoscowRussia

Personalised recommendations