Computer Simulation of Ferredoxin and Ferredoxin-NADP+ reductase Complex Formation
Diakonova A.N., Kovalenko I.B., Abaturova A.M., Riznichenko G.Yu.
Biophysical Department, Biology Faculty, Moscow State University, Moscow, 119992, Russia, Phone: +74959390289, e-mail: alex-diakonova@yandex.ru
1 pp. (accepted)
Electron transport chain protein ferredoxin serves as the ultimate acceptor from photosystem I. It transfers electrons to protein ferredoxin:NADP+ reductase (FNR). FNR subsequently interacts with two molecules of ferredoxin and catalyses NADP+ reduction for the Calvin cycle. Our work is devoted to direct computer simulation of ferredoxin-FNR initial complex formation. We have studied ferredoxin and FNR from bacteria Anabaena PCC7119.
In the model molecules diffuse in cubic reaction volume due to random Brownian force [1, 2]. We obtain dependence of number of complexes upon time and therefore second-order rate constant.
Using the model we studied kinetic characteristics of ferredoxin-FNR complex formation for the wild type proteins and some mutant forms of FNR. We obtained dependencies of the rate constant upon ionic strength for wild type FNR and some of its charge changing mutants. These results were compared with experimental data [3]: they correspond qualitatively well. Also we created a program for quantitative comparison of protein electrostatic potentials and calculation of similarity index (SI) [4] of potentials of two proteins.
References
1. Kovalenko I.B., Abaturova A.M., Gromov P.A., Ustinin D.M., Grachev E.A., Riznichenko G.Yu., Rubin A.B. Direct simulation of plastocyanin and cytochrome f interactions in solution // Phys. Biol. 3, 2006. P. 121-129.
2. Kovalenko I.B., Diakonova A., Abaturova A., Riznichenko G. Direct simulation of ferredoxin and FNR complex formation in solution // Proceedings of the 16th International Symposium Flavins and Flavoproteins 2008. P. 437-442.
3. Hurley J.K., Hazzard J.T., Martinez-Julvez M., Medina M., Gomez-Moreno C., Tollin G. Electrostatic forces involved in orienting Anabaena ferredoxin during binding to Anabaena ferredoxin:NADP+ reductase: site-specific mutagenesis, transient kinetic measurements, and electrostatic surface potentials // Protein Sci. 8, 1999. P. 1614-1622.
4. Blomberg N., Gabdoulline R.R., Nilges M., Wade R.C. Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity // Proteins: Str., Function and Genetics, 37, 1999. P. 379-387.
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