Geodesic
Computer Simulation of Protein-Protein Association in Photosynthesis
I.B. Kovalenko1 ; A.M. Abaturova1 ; A.N. Diakonova1 ; O.S. Knyazeva2 ; D.M. Ustinin1 ; S.S. Khruschev1 ; G.Yu. Riznichenko1 ; A.B. Rubin1
1 Biological faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
2 Physical faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
Mathematical modelling of natural phenomena, Tome 6 (2011) no. 7 Supplement, pp. 39-54.

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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.
DOI : 10.1051/mmnp/20116704

I.B. Kovalenko 1 ; A.M. Abaturova 1 ; A.N. Diakonova 1 ; O.S. Knyazeva 2 ; D.M. Ustinin 1 ; S.S. Khruschev 1 ; G.Yu. Riznichenko 1 ; A.B. Rubin 1

1 Biological faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
2 Physical faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia 
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     title = {Computer {Simulation} of {Protein-Protein} {Association} in {Photosynthesis}},
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I.B. Kovalenko; A.M. Abaturova; A.N. Diakonova; O.S. Knyazeva; D.M. Ustinin; S.S. Khruschev; G.Yu. Riznichenko; A.B. Rubin. Computer Simulation of Protein-Protein Association in Photosynthesis. Mathematical modelling of natural phenomena, Tome 6 (2011) no. 7 Supplement, pp. 39-54. doi : 10.1051/mmnp/20116704. http://geodesic.mathdoc.fr/articles/10.1051/mmnp/20116704/

[1] V.A. Bloomfield. Survey of biomolecular hydrodynamics. On-Line Biophysics Textbook: Separations and Hydrodynamics, 2000.

[2] M.L. Connolly J. Appl. Crystallogr. 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 Arch. Biochem. Biophys. 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 J. Mol. Recognit. 2002 377 392

[8] Hervas M., De La Rosa M., G. Tollin Eur. J. Biochem. 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 Biochim. Biophys. Acta 2000 5 26

[11] J.K. Hurley, J.T. Hazzard, M. Martinez-Julvez, M. Medina, C. Gomez-Moreno, G. Tollin Protein Sci. 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] Knyazeva O.S., Kovalenko I.B., Abaturova A.M., Riznichenko G.Y., Grachev E.A., Rubin A.B. Biophysics 2010 221 227

[14] I.B. Kovalenko, A.M. Abaturova, P.A. Gromov, D.M. Ustinin, E.A. Grachev, G.Y. Riznichenko, A.B. Rubin Phys. Biol. 2006 121 129

[15] Kovalenko I.B., Abaturova A.M., Gromov P.A., Ustinin D.M., Riznichenko G.Y., Grachev E.A., Rubin A.B. Biophysics 2008 140 146

[16] I.B. Kovalenko, A.M. Abaturova, G.Y. Riznichenko, A.B. Rubin Dokl. Biochem. Biophys. 2009 215 217

[17] I.B. Kovalenko, A.M. Abaturova, G.Y. Riznichenko, A.B. Rubin BioSystems 2010 180 187

[18] Kovalenko I.B., Diakonova A.N., Abaturova A.M., Riznichenko G.Y., Rubin A.B. Phys. Biol. 2010 026001

[19] H. Long, C.H. Chang, P.W. King, M.L. Ghirardi, K. Kim Biophys. J. 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] Medina M., Hervas M., Navarro J.A., De La Rosa M.A., Gomez-Moreno C., Tollin G. FEBS 1992 239 242

[22] Panneton F., L’Ecuyer P. ACM T. Model. Comput. Sci. 2005 346 361

[23] D.C. Pearson, E.L. Gross Biophys. J. 1998 2698 2711

[24] F. Rienzo, R. Gabdoulline, M. Menziani, P. Benedetti, R. Wade Biophys. J. 2001 3090 3104

[25] Riznichenko G.Y., Belyaeva N.E., Kovalenko I.B., Rubin A.B. Biophys. J. 2009 10 22

[26] Riznichenko G.Y., Kovalenko I.B., Abaturova A.M., Diakonova A.N., Ustinin D.M., Grachev E.A., Rubin A.B. Biophys. Rev. 2010 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 Photosynth. Res. 1997 143 153

[30] M. Ubbink, M. Ejdebeck, B.G. Karlsson, D.S. Bendall Structure 1998 323 335

[31] Ullmann G.M., Knapp E.-W. Eur. Biophys. J. 1999 533 551

[32] G.M. Ullmann, E.-W. Knapp, N.M. Kostic J. Amer. Chem. Soc. 1997 42 52

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