Modeling of Protein Complex Formation in Solution with Diffusion and Electrostatic Interactions

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

Abstract

In the first versions of the direct multiparticle simulation method, protein interactions were treated as simple collisions, as described in Chap. 13. However, electron-carrying proteins have rather complicated shapes. To perform electron transfer, donor and acceptor carriers should form a complex in which the distance between the active sites must be small enough to support electron tunneling from the donor molecule to the acceptor molecule. Therefore, their proper mutual orientation in a complex stabilized by means of van der Waals and hydrophobic interactions, hydrogen bonds, and other biochemical interactions is necessary.

Keywords

Magnesium Chlorophyll Photosynthesis Luminal Tryptophan 

References

  1. Abaturova AV, Kovalenko IB Riznichenko GY et al (2008) Direct computer modeling of the ionic strength effect on the rate constant of interaction of flavodocsin with Photosystem 1. In: Mathematics, computer, education, vol 15(3). ICS-RCD, Moscow-Izhevsk, p 71 (Rus)Google Scholar
  2. Abaturova AV, Kovalenko IB, Riznichenko GY et al (2009) Investigation of complex formation of flavodoxin and Photosystem I by means of direct multiparticle computer simulation. Comput Res Model 1(1):85–91 (Rus)Google Scholar
  3. Bloomfield P (2000) Fourier analysis of time series. An introduction. Wiley, New YorkCrossRefMATHGoogle Scholar
  4. de la Cerda B, Navarro JA, Hervas M et al (1997) Changes in the reaction mechanism of electron transfer from plastocyanin to photosystem I in the Cyanobacterium Synechocystis sp. PCC 6803 as induced by site-directed mutagenesis of the copper protein. Biochemistry 36:10125–10130CrossRefGoogle Scholar
  5. Diakonova AN, Abaturova AV, Kovalenko IB et al (2008) Direct computer modeling of ferredocsin-FNR complex formation. In: Mathematics, computer, education, vol 15(3). ICR-RCD, Moscow-Izhevsk, p 263 (Rus)Google Scholar
  6. Finkelstein AV, Ptitsyn OB (2002) Protein physics. A course of lectures. Academic, AmsterdamGoogle Scholar
  7. Gabdoulline RR, Wade RC (1997) Simulation of the diffusional association of barnase and barstar. Biophys J 72(5):1917–1929CrossRefGoogle Scholar
  8. Gabdoulline RR, Wade RC (1998) Brownian dynamics simulation of protein-protein diffusional encounter. Methods 14:329–341CrossRefGoogle Scholar
  9. 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
  10. 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
  11. 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
  12. 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
  13. Hall DO (1976) The coupling of photophosphorylation to electron transport in isolated chloroplasts. In: Barber J (ed) The intact chloroplast. Elsevier North-Holland Biomedical, Amsterdam, p 135Google Scholar
  14. Jolley C, Ben-Shem A, Nelson N et al (2005) Structure of plant photosystem I revealed by theoretical modeling. J Biol Chem 280:33627–33636CrossRefGoogle Scholar
  15. 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
  16. 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
  17. 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
  18. 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
  19. Medina M, Hervas M, Navarro JA et al (1992) A laser flash absorption spectroscopy study of Anabaena sp. PCC 7119 flavodoxin photoreduction by photosystem I particles from spinach. FEBS Lett 313(3):239–242CrossRefGoogle Scholar
  20. Myshkin E, Bullerjahn GS (2002) Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to photosystem I: modeling the electron transfer complex. Biophys J 82:3305–3313CrossRefGoogle Scholar
  21. Schlarb-Ridley BG, Bendall DS, Howe CJ (2002) The role of electrostatics in the interaction between cytochrome f and plastocyanin of the cyanobacterium Phormidium laminosum. Biochemistry 21:3279–3285CrossRefGoogle Scholar
  22. Ubbink M, Ejdebeck M, Karlsson BG et al (1998) The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics. Structure 6:323–335CrossRefGoogle Scholar
  23. 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

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