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All issues Volume 6 / No 7 (2011) Supplement Math. Model. Nat. Phenom., 6 7 (2011) 39-54 References
Free Access
Issue
Math. Model. Nat. Phenom.
Volume 6, Number 7, 2011
Mathematical modeling in biomedical applications
Page(s) 39 - 54
DOI https://doi.org/10.1051/mmnp/20116704
Published online 15 June 2011
  1. V.A. Bloomfield. Survey of biomolecular hydrodynamics. On-Line Biophysics Textbook: Separations and Hydrodynamics, 2000. [Google Scholar]
  2. M.L. Connolly. Analytical molecular surface calculation. J. Appl. Crystallogr., 16 (1983), 548–558. [CrossRef] [Google Scholar]
  3. R.M.C. Dawson, D.C. Elliott, W.H. Elliott, K.M. Jones. Data for biochemical research. Oxford Science Publications, OUP, Oxford, 1986. [Google Scholar]
  4. M. Doi, S.F. Edwards. The theory of polymer dynamics. Oxford University Press, New York, 1986. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  10. A.B. Hope. Electron transfers amongst cytochrome f, plastocyanin and photosystem I: kinetics and mechanisms. Biochim. Biophys. Acta, 1456 (2000), 5–26. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  12. J. Janin. Kinetics and thermodynamics of protein-protein interactions. Protein-protein recognition. (Ed. C. Kleanthous). Oxford University Press, Oxford, 2000, 1–32. [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [Google Scholar]
  22. F. Panneton, P. L’Ecuyer. On the xorshift random number generators. ACM T. Model. Comput. Sci., 15 (2005), No. 4, 346–361. [Google Scholar]
  23. D.C. Pearson, E.L. Gross. Brownian dynamics study of the interaction between plastocyanin and cytochrome f. Biophys. J., 75 (1998), 2698–2711. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [Google Scholar]

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