ABSTRACT
The Brownian dynamics method is used for qualitative analysis of events leading to formation of a functionally active plastocyanin-cytochrome f complex. Intermediate states of this process are identified by density-based hierarchical clustering. Diffusive entrapment of plastocyanin by cytochrome f is a key point of the suggested putative scenario of protein-protein approaching. Mobility of plastocyanin is characterized for different values of protein-protein electrostatic interaction energy.
Subject(s)
Cytochromes f/chemistry , Electrons , Molecular Dynamics Simulation , Plastocyanin/chemistry , Binding Sites , Brassica rapa/chemistry , Cluster Analysis , Diffusion , Electron Transport , Oxidation-Reduction , Protein Binding , Protein Structure, Secondary , Protein Structure, Tertiary , Spinacia oleracea/chemistry , Static Electricity , ThermodynamicsABSTRACT
The application of Brownian dynamics for simulation of transient protein-protein interactions is reviewed. The review focuses on theoretical basics of Brownian dynamics method, its particular implementations, advantages and drawbacks of the method. The outlook for future development of Brownian dynamics-based simulation techniques is discussed. Special attention is given to analysis of Brownian dynamics trajectories. The second part of the review is dedicated to the role of Brownian dynamics simulations in studying photosynthetic electron transport. Interactions of mobile electron carriers (plastocyanin, cytochrome c6, and ferredoxin) with their reaction partners (cytochrome b6f complex, photosystem I, ferredoxin:NADP-reductase, and hydrogenase) are considered.
Subject(s)
Biophysical Phenomena , Cytochromes c6/chemistry , Photosynthesis , Plastocyanin/chemistry , Cytochromes f , Electron Transport , Ferredoxins/chemistry , Kinetics , Models, Molecular , Molecular Dynamics Simulation , Photosystem I Protein Complex , Protein ConformationABSTRACT
The basic principles of the design of direct multiparticle models and the results of multiparticle computer simulation of electron transfer by mobile protein carriers in the photosynthetic membrane of a chloroplast thylakoid are presented. The reactions of complex formation of the protein plastocyanin with the protein cytochrome f and the pigment-protein complex of photosystem I, as well as of the protein ferredoxin with the protein FNR and photosystem 1 are considered. The role of diffusion and electrostatic interactions is discussed, and the effect of the shape of the reaction volume and ionic strength on the rate of electron transport are discussed.
Subject(s)
Computer Simulation , Cytochromes f/chemistry , Ferredoxins/chemistry , Models, Biological , Photosystem I Protein Complex/chemistry , Thylakoids/chemistry , Electron Transport , Ferredoxin-NADP Reductase/chemistry , Plastocyanin/chemistry , Protein Binding , Static ElectricityABSTRACT
Ferredoxin reduced by Photosystem I in light serves as an electron donor for the reduction of NADP(+) to NADPH, and this reaction is catalyzed by enzyme ferredoxin:NADP(+)-reductase (FNR). Kinetics and mechanisms of this reaction have been extensively studied experimentally by site-specific mutagenesis, laser flash photolysis and stopped-flow methods. We have applied a method of multiparticle computer simulation to study the effects of electrostatic interactions upon the reaction rate of Fd-FNR complex formation. Using the model we calculated rate constants of Fd-FNR complex formation for the wild-type proteins and some mutant forms of FNR at different values of ionic strength. Simulation revealed that electrostatic interactions play an important role in Fd-FNR complex formation and define its specificity.
Subject(s)
Anabaena/metabolism , Bacterial Proteins/metabolism , Ferredoxin-NADP Reductase/metabolism , Ferredoxins/metabolism , Anabaena/chemistry , Anabaena/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Computer Simulation , Ferredoxin-NADP Reductase/chemistry , Ferredoxin-NADP Reductase/genetics , Ferredoxins/chemistry , Ferredoxins/genetics , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Static ElectricityABSTRACT
A multiparticle computer model of plastocyanin-cytochrome f complex formation in the thylakoid lumen has been designed, which takes electrostatic interactions of proteins and the thylakoid membrane into account. The Poisson-Boltzmann formalism was used to determine the electrostatic potential field generated by the electrical charges of the proteins and the thylakoid membrane for different ionic strength values. The role of electrostatic field of the thylakoid membrane in plastocyanin-cytochrome f complex formation was determined. Using the model, the rate constant of plastocyanin-cytochrome f reaction for different values of ionic strength and membrane surface charge were calculated.
Subject(s)
Computer Simulation , Cytochromes f/chemistry , Models, Biological , Plastocyanin/chemistry , Thylakoids/chemistry , Protein Binding , Static ElectricitySubject(s)
Models, Molecular , Proteins/chemistry , Proteins/metabolism , Computer Simulation , Diffusion , Probability , Protein Binding , Static ElectricityABSTRACT
The diffusion of the protein plastocyanine and complex formation between plastocyanine and cytochrome f (a subunit of a cytochrome b6/f complex) in the chloroplast thylakoid lumen has been studied. A 3D computer simulation model of diffusion and binding of plastocyanine and cytochrome f has been constructed, which considers their electrostatic interaction. Based on the experimental data, the parameters of the model for complex formation between plastocyanine and cytochrome f in solution have been estimated. The dependence of the rate of plastocyanine-cytochrome f reaction on the size of the luminal space has been studied. It was shown that the contraction of the luminal space leads to a decrease in the reaction rate, which is in agreement with the experimental data on the inhibition of the reaction under hyperosmotic stress.
Subject(s)
Cytochromes f/chemistry , Plastocyanin/chemistry , Thylakoids/chemistry , Computer Simulation , Diffusion , Protein Binding , Static ElectricityABSTRACT
Most biological functions, including photosynthetic activity, are mediated by protein interactions. The proteins plastocyanin and cytochrome f are reaction partners in a photosynthetic electron transport chain. We designed a 3D computer simulation model of diffusion and interaction of spinach plastocyanin and turnip cytochrome f in solution. It is the first step in simulating the electron transfer from cytochrome f to photosystem 1 in the lumen of thylakoid. The model is multiparticle and it can describe the interaction of several hundreds of proteins. In our model the interacting proteins are represented as rigid bodies with spatial fixed charges. Translational and rotational motion of proteins is the result of the effect of stochastic Brownian force and electrostatic force. The Poisson-Boltzmann formalism is used to determine the electrostatic potential field generated around the proteins. Using this model we studied the kinetic characteristics of plastocyanin-cytochrome f complex formation for plastocyanin mutants at pH 7 and a variety of ionic strength values.
