Computer Simulation of Protein-Protein Association in Photosynthesis

I.B. Kovalenko; A.M. Abaturova; A.N. Diakonova; O.S. Knyazeva; D.M. Ustinin; S.S. Khruschev; G.Yu. Riznichenko; A.B. Rubin

Mathematical Modelling of Natural Phenomena (2011)

  • Volume: 6, Issue: 7, page 39-54
  • ISSN: 0973-5348

Abstract

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The paper is devoted to the method of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. Using this method we have studied kinetic characteristics of protein-protein complex formation for four pairs of proteins involved in photosynthesis at a variety of ionic strength values. Computer simulations describe non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Calculations confirm that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in “wrong” orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer.

How to cite

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Kovalenko, I.B., et al. "Computer Simulation of Protein-Protein Association in Photosynthesis." Mathematical Modelling of Natural Phenomena 6.7 (2011): 39-54. <http://eudml.org/doc/222344>.

@article{Kovalenko2011,
abstract = {The paper is devoted to the method of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. Using this method we have studied kinetic characteristics of protein-protein complex formation for four pairs of proteins involved in photosynthesis at a variety of ionic strength values. Computer simulations describe non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Calculations confirm that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in “wrong” orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer.},
author = {Kovalenko, I.B., Abaturova, A.M., Diakonova, A.N., Knyazeva, O.S., Ustinin, D.M., Khruschev, S.S., Riznichenko, G.Yu., Rubin, A.B.},
journal = {Mathematical Modelling of Natural Phenomena},
keywords = {Brownian dynamics; computer simulation; protein, photosynthesis; electrostatic interaction},
language = {eng},
month = {6},
number = {7},
pages = {39-54},
publisher = {EDP Sciences},
title = {Computer Simulation of Protein-Protein Association in Photosynthesis},
url = {http://eudml.org/doc/222344},
volume = {6},
year = {2011},
}

TY - JOUR
AU - Kovalenko, I.B.
AU - Abaturova, A.M.
AU - Diakonova, A.N.
AU - Knyazeva, O.S.
AU - Ustinin, D.M.
AU - Khruschev, S.S.
AU - Riznichenko, G.Yu.
AU - Rubin, A.B.
TI - Computer Simulation of Protein-Protein Association in Photosynthesis
JO - Mathematical Modelling of Natural Phenomena
DA - 2011/6//
PB - EDP Sciences
VL - 6
IS - 7
SP - 39
EP - 54
AB - The paper is devoted to the method of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. Using this method we have studied kinetic characteristics of protein-protein complex formation for four pairs of proteins involved in photosynthesis at a variety of ionic strength values. Computer simulations describe non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Calculations confirm that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in “wrong” orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer.
LA - eng
KW - Brownian dynamics; computer simulation; protein, photosynthesis; electrostatic interaction
UR - http://eudml.org/doc/222344
ER -

References

top
  1. V.A. Bloomfield. Survey of biomolecular hydrodynamics. On-Line Biophysics Textbook: Separations and Hydrodynamics, 2000.  
  2. M.L. Connolly. Analytical molecular surface calculation. J. Appl. Crystallogr., 16 (1983), 548–558.  
  3. R.M.C. Dawson, D.C. Elliott, W.H. Elliott, K.M. Jones. Data for biochemical research. Oxford Science Publications, OUP, Oxford, 1986.  
  4. M. Doi, S.F. Edwards. The theory of polymer dynamics. Oxford University Press, New York, 1986.  
  5. S.R. Durell, J.K. Labanowski, E.L. Gross. Modeling of the electrostatic potential field of plastocyanin. Arch. Biochem. Biophys., 277 (1990), 241–254.  
  6. A.V. Finkelstein, O.B. Ptitsyn. Protein physics. A course of lectures. Academic Press, Amsterdam/Boston/London/New York/Oxford/Paris/San Diego/San Francisco/Singapore/Sydney/Tokyo, 2002.  
  7. F. Fogolari, A. Brigo, H. Molinari. The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structural biology. J. Mol. Recognit., 15 (2002), 377–392.  
  8. M. Hervas, M. De la Rosa, G. Tollin. A comparative laser-flash absorption spectroscopy study of algal plastocyanin and cytochrome c552 photooxidation by photosystem I particles from spinach. Eur. J. Biochem., 203 (1992), 115–120.  
  9. M. Hippler, F. Drepper. Electron Transfer Between Photosystem I and Plastocyanin or Cytochrome c6, in Photosystem I: The Light-Driven Plastocyanin:Ferredoxin Oxidoreductase. J. (Ed. H. Golbeck). Springer, 2006, 499–513.  
  10. A.B. Hope. Electron transfers amongst cytochrome f, plastocyanin and photosystem I: kinetics and mechanisms. Biochim. Biophys. Acta, 1456 (2000), 5–26.  
  11. J.K. Hurley, J.T. Hazzard, M. Martinez-Julvez, M. Medina, C. Gomez-Moreno, G. Tollin. Electrostatic forces involved in orienting Anabaena ferredoxin during binding to Anabaena ferredoxin:NADP+ reductase: site-specific mutagenesis, transient kinetic measurements, and electrostatic surface potentials. Protein Sci., 8 (1999), 1614–1622.  
  12. J. Janin. Kinetics and thermodynamics of protein-protein interactions. Protein-protein recognition. (Ed. C. Kleanthous). Oxford University Press, Oxford, 2000, 1–32.  
  13. O.S. Knyazeva, I.B. Kovalenko, A.M. Abaturova, G.Y. Riznichenko, E.A. Grachev, A.B. Rubin. Multiparticle computer simulation of plastocyanin diffusion and interaction with cytochrome f in the electrostatic field of the thylakoid membrane. Biophysics, 55 (2010), No. 2, 221–227.  
  14. I.B. Kovalenko, A.M. Abaturova, P.A. Gromov, D.M. Ustinin, E.A. Grachev, G.Y. Riznichenko, A.B. Rubin. Direct simulation of plastocyanin and cytochrome f interactions in solution. Phys. Biol., 3 (2006), 121–129.  
  15. I.B. Kovalenko, A.M. Abaturova, P.A. Gromov, D.M. Ustinin, G.Y. Riznichenko, E.A. Grachev, A.B. Rubin. Computer simulation of plastocyanin-cytochrome f complex formation in the thylakoid lumen. Biophysics, 53 (2008), No. 2, 140–146.  
  16. I.B. Kovalenko, A.M. Abaturova, G.Y. Riznichenko, A.B. Rubin. A novel approach to computer simulation of protein-protein complex formation. Dokl. Biochem. Biophys., 427 (2009), 215–217.  Zbl1189.92029
  17. I.B. Kovalenko, A.M. Abaturova, G.Y. Riznichenko, A.B. Rubin. Computer simulation of interaction of photosystem 1 with plastocyanin and ferredoxin. BioSystems, 103 (2010), 180–187.  
  18. I.B. Kovalenko, A.N. Diakonova, A.M. Abaturova, G.Y. Riznichenko, A.B. Rubin. Direct computer simulation of ferredoxin and FNR complex formation in solution. Phys. Biol., 7 (2010), No. 2, 026001.  
  19. H. Long, C.H. Chang, P.W. King, M.L. Ghirardi, K. Kim. Brownian dynamics and molecular dynamics study of the association between hydrogenase and ferredoxin from Chlamydomonas reinhardtii. Biophys. J., 95 (2008), 3753-3766.  
  20. F.S. Mathews, A.G. Mauk, G.R. Moore. Protein-protein complexes formed by electron transfer proteins, in Protein-Protein recognition. (Ed. C. Kleanthous). Oxford University Press, Oxford, 2000, 60–101.  
  21. M. Medina, M. Hervas, J.A. Navarro, M.A. De la Rosa, C. Gomez-Moreno, G. Tollin. A laser flash absorption spectroscopy study of Anabaena sp. PCC 7119 flavodoxin photoreduction by photosystem I particles from spinach. FEBS, 313 (1992), No. 3, 239–242.  
  22. F. Panneton, P. L’Ecuyer. On the xorshift random number generators. ACM T. Model. Comput. Sci., 15 (2005), No. 4, 346–361.  
  23. D.C. Pearson, E.L. Gross. Brownian dynamics study of the interaction between plastocyanin and cytochrome f. Biophys. J., 75 (1998), 2698–2711.  
  24. F. Rienzo, R. Gabdoulline, M. Menziani, P. Benedetti, R. Wade. Electrostatic analysis and brownian dynamics simulation of the association of plastocyanin and cytochrome f. Biophys. J., 81 (2001), 3090–3104.  
  25. G.Y. Riznichenko, N.E. Belyaeva, I.B. Kovalenko, A.B. Rubin. Mathematical and computer modeling of primary photosynthetic processes. Biophys. J., 54 (2009), No. 1, 10–22.  
  26. G.Y. Riznichenko, I.B. Kovalenko, A.M. Abaturova, A.N. Diakonova, D.M. Ustinin, E.A. Grachev, A.B. Rubin. New direct dynamic models of protein interactions coupled to photosynthetic electron transport reactions. Biophys. Rev., 2 (2010), No. 3, 101–110.  
  27. A. Rubin, G. Riznichenko. Modeling of the primary processes in a photosynthetic membrane. Photosynthesis in silico: Understanding Complexity from Molecules to Ecosystems. (Eds. A. Laisk, L. Nedbal, and Govindjee). Springer, Dordrecht, 2009, 151–176.  
  28. P. Setif. Electron transfer from the bound Iron-Sulfur clusters to Ferredoxin/Flavodoxin: Kinetic and structural properties of Ferredoxin/Flavodoxin reduction by photosystem I. In: Photosystem I: The Light-Driven Plastocyanin:Ferredoxin Oxidoreductase. (Ed. J.H. Golbeck). Springer, 2006, 439–454.  
  29. K. Sigfridsson. Ionic strength and pH dependence of the reaction between plastocyanin and photosystem 1. Evidence of a rate-limiting conformational change. Photosynth. Res., 54 (1997), 143–153.  
  30. M. Ubbink, M. Ejdebeck, B.G. Karlsson, D.S. Bendall. The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics. Structure, 6 (1998), 323–335.  
  31. G.M. Ullmann, E.-W. Knapp. Electrostatic models for computing protonation and redox equilibria in proteins. Eur. Biophys. J., 28 (1999), No. 7, 533–551.  
  32. G.M. Ullmann, E.-W. Knapp, N.M. Kostic. Computational simulation and analysis of dynamic association between plastocyanin and cytochrome f. Consequences for the electron-transfer reaction. J. Amer. Chem. Soc., 119 (1997), 42–52.  

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