New direct dynamic models of protein interactions coupled to photosynthetic electron transport reactions.

Autor: Riznichenko GY; Dept. of Biophysics, Biology Faculty, M.V. Lomonosov Moscow State University, 119992, Moscow, Russia. riznich@biophys.msu.ru., Kovalenko IB; Dept. of Biophysics, Biology Faculty, M.V. Lomonosov Moscow State University, 119992, Moscow, Russia., Abaturova AM; Dept. of Biophysics, Biology Faculty, M.V. Lomonosov Moscow State University, 119992, Moscow, Russia., Diakonova AN; Dept. of Biophysics, Biology Faculty, M.V. Lomonosov Moscow State University, 119992, Moscow, Russia., Ustinin DM; Dept. of Biophysics, Biology Faculty, M.V. Lomonosov Moscow State University, 119992, Moscow, Russia., Grachev EA; Dept. of Computer Methods in Physics, Physical Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia., Rubin AB; Dept. of Biophysics, Biology Faculty, M.V. Lomonosov Moscow State University, 119992, Moscow, Russia.
Jazyk: angličtina
Zdroj: Biophysical reviews [Biophys Rev] 2010 Aug; Vol. 2 (3), pp. 101-110. Date of Electronic Publication: 2010 Jun 10.
DOI: 10.1007/s12551-010-0033-4
Abstrakt: This review covers the methods of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. A direct multiparticle simulation method that simulates reactions describing interactions of ensembles of molecules in the heterogeneous interior of a cell is developed. In the models, protein molecules move according to the laws of Brownian dynamics, mutually orient themselves in the electrical field, and form complexes in the 3D scene. The method allows us to visualize the processes of molecule interactions and to calculate the rate constants for protein complex formation reactions in the solution and in the photosynthetic membrane. Three-dimensional multiparticle computer models for simulating the complex formation kinetics for plastocyanin with photosystem I and cytochrome bf complex, and ferredoxin with photosystem I and ferredoxin:NADP + -reductase are considered. Effects of ionic strength are featured for wild type and mutant proteins. The computer multiparticle models describe nonmonotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions.
Databáze: MEDLINE
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