Computer Simulation of Protein-Protein Association in Photosynthesis

Abstract

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.

Influence of pH and ionic strength on electrostatic properties of ferredoxin, FNR, and hydrogenase and the rate constants of their interaction

“…If x-ray diffraction or NMR 3D structure of the complex is available, this distance can be estimated from experimental data. Additionally, approximation of the protein surface adds several Angstrom to the molecule surface, therefore the model distance r is higher than in the experimentally obtained structure (Kovalenko et al 2006(Kovalenko et al , 2010(Kovalenko et al , 2011). In the model the docking distance for ferredoxin and FNR was the distance between Fe1 atom of the ferredoxin iron-sulfur cluster and C8M atom of FNR's FAD; for ferredoxin and hydrogenase it was the distance between Fe1 atom of the iron-sulfur cluster of ferredoxin and Fe1 atom of the iron-sulfur cluster of hydrogenase.…”

Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling

“…To simulate the interactions of mobile electron carriers with multi-enzyme complexes in photosynthetic membrane the method of 'direct multi-particle modeling' was developed at the Lomonosov Moscow State University by the Department of Biophysics of the Biological Faculty together with the Department of Computer Methods in Physics of the Physics Faculty. The main idea of this approach and the results obtained are presented in the papers [4,[6][7][8][9][10][11][12].…”

“…With the help of the multi-particle Brownian dynamics, the interaction of the Pc molecule with the cytochrome f cofactor in a solution [7,18] and in the lumen of the thylakoid [14,16], the interaction of Pc with the PSI donor part and the interaction of Fd with the PSI acceptor part [9] and Fd with subsequent electron acceptors, FNR [8], and hydrogenase [19][20][21]) were simulated ( Fig. 2.)…”

Multi-particle Brownian Dynamics software ProKSim for protein-protein interactions modeling

“…Разработана компьютерная программа ProKSim (Protein Kinetics Simulator), предназначенная для моделирования взаимодействия макромолекул в растворе и в клетке методом многочастичной броуновской динамики (БД) с учетом электростатических взаимодействий [Kovalenko et al, 2006;Kovalenko et al, 2011;Коваленко и др., 2009]. В модели молекулы белка рассматриваются как броуновские частицы, совершающие поступательное и вращательное движения в вязкой среде.…”