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Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

Computer Simulation of Plastocyanin Diffusion and Interaction with Its Reaction Partners

We present a Langevin dynamics computer model of limited diffusion of protein plastocyanin and its interaction with transmembrane protein complexes photosystem 1 and cytochrome bf in the narrow chloroplast thylakoid lumen. The model is multiparticle, it considers many plastocyanin molecules that compete to form complexes with numerous photosystem 1 and cytochrome bf complexes embedded in the photosynthetic membranes. The model takes into account the geometry of the luminal space packed with many protein molecules and considers electrostatic interactions of plastocyanin with its reaction partners in the thylakoid membrane. The model uses a continuum electrostatic approach that describes molecules at the atomic level using a macroscopic description. The Poisson-Boltzmann formalism was used to determine the electrostatic potentials of the electron carrier proteins and the thylakoid membrane at different ionic strengths. This work uses the model parameters of protein-protein association estimated in our papers (1-4).

Calculations correctly reproduce the experimentally registered kinetic curves of redox changes of the reaction center P700 of photosystem 1 and cytochrome f. The model demonstrates non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. The simulation method presented in this work can be applied for the description of diffusion and functioning of many macromolecules that interact in the heterogeneous interior of subcellular systems.

References

  1. I. B. Kovalenko, A. M. Abaturova, P. A. Gromov, D. M. Ustinin, E. A. Grachev, G. Y. Riznichenko, A. B. Rubin, Phys. Biol. 3, 121–129 (2006).
  2. I. B. Kovalenko, A. M. Abaturova, P. A. Gromov, D. M. Ustinin, G. Y. Riznichenko, E. A. Grachev, A. B. Rubin, Biophysics 53, 140–146 (2008).
  3. I. B. Kovalenko, A. M. Abaturova, G. Y. Riznichenko, A. B. Rubin, BioSystems, doi: 10.1016/j.biosystems.2010.09.013 (2010).
  4. O. S. Knyazeva, I. B. Kovalenko, A. M. Abaturova, G. Y. Riznichenko, E. A. Grachev, A. B. Rubin, Biophysics 55, 221–227 (2010).

Ilya Kovalenko*
Alexandra Diakonova
Olga Knyazeva
Anna Abaturova
Galina Riznichenko
Andrei Rubin

Biophysics Department
Biological Faculty
Moscow State University
Leninskie Gory, Moscow 119992 Russia

ph: +7-495-9390289
fx +7-495-9391115
E-mail:ikovalenko78@gmail.com