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Computer Simulation of Protein-Protein Association in Photosynthesis

Published online by Cambridge University Press:  15 June 2011

I.B. Kovalenko ,
A.M. Abaturova ,
A.N. Diakonova ,
O.S. Knyazeva ,
D.M. Ustinin ,
S.S. Khruschev ,
G.Yu. Riznichenko  and
A.B. Rubin
I.B. Kovalenko*
Affiliation:
Biological faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
A.M. Abaturova
Affiliation:
Biological faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
A.N. Diakonova
Affiliation:
Biological faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
O.S. Knyazeva
Affiliation:
Physical faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
D.M. Ustinin
Affiliation:
Biological faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
S.S. Khruschev
Affiliation:
Biological faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
G.Yu. Riznichenko
Affiliation:
Biological faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
A.B. Rubin
Affiliation:
Biological faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
*
⋆ Corresponding author. E-mail: ikovalenko78@gmail.com
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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.

Keywords

Brownian dynamicscomputer simulationprotein, photosynthesiselectrostatic interaction
Type
Research Article
Information
Mathematical Modelling of Natural Phenomena , Volume 6 , Issue 7: Mathematical modeling in biomedical applications , 2011 , pp. 39 - 54
Copyright
© EDP Sciences, 2011

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