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

Biophysical Reviews

Volumn 2, Issue 3, 2010, Pages 101-110

  Riznichenko, Galina Yu ^a   Kovalenko, Ilya B ^a   Abaturova, Anna M ^a   Diakonova, Alexandra N ^a   Ustinin, Dmitry M ^a   Grachev, Eugene A ^a   Rubin, Andrew B ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

Complex formation; Computer model; Electrostatic interaction; Photosynthesis; Protein interaction

Indexed keywords

EID: 78751701128     PISSN: 18672450     EISSN: 18672469     Source Type: Journal    
DOI: 10.1007/s12551-010-0033-4     Document Type: Review

References (43)

1. Abaturova AM, Kovalenko IB, Riznichenko GY, Rubin AB (2008) Direct multiparticle computer simulation of ionic strength dependence of the association rate constant for flavodoxin and photosystem I. Mathematics (in Russian). Comput Educ 15(3): 925-933.
2. Albertsson P-Å (2001) A quantitative model of the domain structure of the photosynthetic membrane. Trends Plant Sci 6(8): 349-358. doi: 10. 1016/S1360-1385(01)02021-0.
3. Belyaeva NE, Schmitt F-J, Steffen R, Paschenko VZ, Riznichenko GY, Chemeris YK, Renger G, Rubin AB (2008) PSII model-based simulations of single turnover flash-induced transients of fluorescence yield monitored within the time domain of 100 ns-10 s on dark-adapted Chlorella pyrenoidosa cells. Photosynth Res 98: 105-119. doi: 10. 1007/s11120-008-9374-2.
4. Crowley PB, Hunter DM, Sato K, McFarlane W, Dennison C (2004) The parsley plastocyanin-turnip cytochrome f complex: a structurally distorted but kinetically functional acidic patch. Biochem J 378: 45-51. doi: 10. 1042/BJ20031423.
5. + electron transfer in Chlamydomonas reinhardtii by hyperosmotic stress. Plant Physiol 127: 1167-1179.
6. Dekker JP, Boekema EJ (2005) Supramolecular organization of thylakoid membrane proteins in green plants. Biochim Biophys Acta 1706(1-2): 12-39. doi: 10. 1016/j. bbabio. 2004. 09. 009.
7. Fogolari F, Brigo A, Molinari H (2002) The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J Mol Recognit 15(6): 377-392. doi: 10. 1002/jmr. 577.
8. Fromme P, Jordan P, Krauss N (2001) Structure of photosystem I. Biochim Biophys Acta 1507: 5-31. doi: 10. 1016/S0005-2728(01)00195-5.
9. Gabdoulline RR, Wade RC (1997) Simulation of the diffusional association of barnase and barstar. Biophys J 72(5): 1917-1929. doi: 10. 1016/S0006-3495(97)78838-6.
10. Gabdoulline RR, Wade RC (1998) Brownian dynamics simulation of protein-protein diffusional encounter. Methods 14(3): 329-341. doi: 10. 1006/meth. 1998. 0588.
11. Gross EL, Pearson DC Jr (2003) Brownian dynamics simulations of the interaction of Chlamydomonas cytochrome f with plastocyanin and cytochrome c6. Biophys J 85(3): 2055-2068. doi: 10. 1016/S0006-3495(03)74633-5.
12. Gross EL, Rosenberg I (2006) A Brownian dynamics study of cytochrome f interactions with cytochrome c6 and plastocyanin in Chlamydomonas reinhardtii plastocyanin, and cytochrome c6 mutants. Biophys J 88(3): 2323-2339. doi: 10. 1529/biophysj. 104. 053561.
13. Hope AB (2000) Electron transfers amongst cytochrome f, plastocyanin and photosystem I: kinetics and mechanisms. Biochim Biophys Acta 1456: 5-26. doi: 10. 1016/S0005-2728(99)00101-2.
14. Janin J (2000) Kinetics and thermodynamics of protein-protein interactions. In: Kleanthous C (ed) Protein-protein recognition. Oxford University Press, Oxford, pp 1-32.
15. Kannt A, Young S, Bendall DS (1996) The role of acidic residues of plastocyanin in its interaction with cytochrome f. Biochim Biophys Acta 1277(1-2): 115-126. doi: 10. 1016/S0005-2728(96)00090-4.
16. Karavaev VA, Kukushkin AK (1993) Theoretical model of light and dark processes of photosynthesis: the problem of regulation. Biophysics 38: 987-1003.
17. Kovalenko IB, Riznichenko GY (2007) Multiparticle direct simulation of photosynthetic electron transport processes. In: Deutsch A, Brusch L, Byrne H, de Vries G, Herzel H (eds) Mathematical modeling of biological systems. Birkhäuser, Boston, pp 3-11.
18. Kovalenko IB, Ustinin DM, Grachev NE, Krendeleva TE, Kukarskih GP, Timofeev KN, Riznichenko GY, Grachev EA, Rubin AB (2003) Cyclic electron transport around photosystem I: an experimental and theoretical study. Biophysics 48(4): 614-623.
19. Kovalenko IB, Abaturova AM, Gromov PA, Ustinin DM, Grachev EA, Riznichenko GY, Rubin AB (2006) Direct simulation of plastocyanin and cytochrome f interactions in solution. Phys Biol 3: 121-129. doi: 10. 1088/1478-3975/3/2/004.
20. Kovalenko IB, Abaturova AM, Ustinin DM, Grachev EA, Riznichenko GY, Rubin AB (2007) Multiparticle computer simulation of photosynthetic electron transport in the thylakoid membrane. Biophysics 52(5): 492-502. doi: 10. 1134/S0006350907050053.
21. Kovalenko IB, Abaturova AM, Gromov PA, Ustinin DM, Riznichenko GYu, Grachev EA, Rubin AB (2008a) Computer simulation of plastocyanin-cytochrome f complex formation in the thylakoid lumen. Biophysics 53(2): 140-146. doi: 10. 1134/S0006350908020048.
22. Kovalenko IB, Diakonova AN, Abaturova AM, Riznichenko GY (2008b) Direct computer simulation of ferredoxin and FNR complex formation in solution. In: 16th International Symposium on Flavins and Flavoproteins, 8-13 June 2008, Prensas Universitarias de Zaragoza, Zaragoza, pp 437-442.
23. Kovalenko IB, Abaturova AM, Riznichenko GY, Rubin AB (2009) A novel approach to computer simulation of protein-protein complex formation. Dokl Biochem Biophys 427(1): 215-217. doi: 10. 1134/S1607672909040127.
24. Kukushkin A, Poltev S, Khuznetsova S (2002) Coupling of electron and proton transport in photosynthetic membranes: molecular mechanism. Bioelectrochemistry 56(1): 9-12. doi: 10. 1016/S1567-5394(02)00021-X.
25. Kuznetsova SA, Kukushkin AK (1999) A new theoretical approach to studies of regulatory links in photosynthesis. Biophysics 44: 448-454.
26. Laisk F, Nedbal L, Govindjee (2009) Photosynthesis in silico. Understanding complexity from molecules to ecosystems. Springer, Dordrecht.
27. Lazar D (2003) Chlorophyll a fluorescence rise induced by high light illumination of dark-adapted plant tissue studied by means of a model of photosystem II and considering photosystem II heterogeneity. J Theor Biol 220(4): 469-503. doi: 10. 1006/jtbi. 2003. 3140.
28. Malkin R, Niyogi K (2000) Photosynthesis. In: Buchanan B, Gruissem W, Jones R (eds) Biochemistry and molecular biology of plants. Kluwer Academic, Dordrecht, pp 413-429.
29. Mathews FS, Mauk AG, Moore GR (2000) Protein-protein complexes formed by electron transfer proteins. In: Kleanthous C (ed) Protein-protein recognition. Oxford University Press, Oxford, pp 60-101.
30. Medina M, Hervas M, Navarro JA, De la Rosa MA, Gomez-Moreno C, Tollin G (1992) A laser flash absorption spectroscopy study of Anabaena sp. PCC 7119 flavodoxin photoreduction by photosystem I particles from spinach. FEBS 313(3): 239-242. doi: 10. 1016/0014-5793(92)81200-6.
31. Nelson N, Yocum CF (2006) Structure and function of photosystems I and II. Annu Rev Plant Biol 57: 521-565. doi: 10. 1146/annurev. arplant. 57. 032905. 105350.
32. Pearson DC Jr, Gross EL (1998) Brownian dynamics study of the interaction between plastocyanin and cytochrome f. Biophys J 75(6): 2698-2711. doi: 10. 1016/S0006-3495(98)77714-8.
33. Rienzo F, Gabdoulline R, Menziani M, Benedetti P, Wade R (2001) Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f. Biophys J 81: 3090-3104. doi: 10. 1016/S0006-3495(01)75947-4.
34. Riznichenko GY, Lebedeva GV, Demin OV, Belyaeva NE, Rubin AB (1999) Kinetic mechanisms of biological regulation in photosynthetic organisms. J Biol Phys 25(2-3): 177-192. doi: 10. 1023/A: 1005101703188.
35. Riznichenko GY, Beljaeva NE, Kovalenko IB, Rubin AB (2009) Mathematical and computer modeling of primary photosynthetic processes. Biophysics 54(1): 10-22. doi: 10. 1134/S0006350909010035.
36. Rubin AB, Riznichenko GY (2009) Modeling of the primary processes in a photosynthetic membrane. In: Laisk A, Nedbal L, Govindjee R (eds) Photosynthesis in silico: understanding complexity from molecules to ecosystems. Springer, Dordrecht, pp 151-176.
37. Staehelin LA, van der Staay GWM (1996) Structure, composition, functional organization and dynamic properties of thylakoid membranes. In: Ort DR, Yocum CF (eds) Oxygenic photosynthesis. The lght reactions. Kluwer Academic, Dordrecht, pp 11-30.
38. Stirbet A, Govindjee SBJ, Strasser RJ (1998) Chlorophyll a fluorescence induction in higher plants: modelling and numerical simulation. J Theor Biol 193: 131-151. doi: 10. 1006/jtbi. 1998. 0692.
39. Strasser RJ, Tsimilli-Michael M, Srivastava A (2004) Analysis of the chlorophyll a fluorescence transient. In: Papageorgiou GC (ed) Chlorophyll a fluorescence: a signature of photosynthesis. Springer, Dordrecht, pp 321-362.
40. Ubbink M, Ejdeback M, Karlsson BG, Bendall DS (1998) The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics. Structure 6(3): 323-335. doi: 10. 1016/S0969-2126(98)00035-5.
41. Ullmann GM, Knapp E-W (1999) Electrostatic models for computing protonation and redox equilibria in proteins. Eur Biophys J 28(7): 533-551. doi: 10. 1007/s002490050236.
42. Ullmann GM, Knapp E-W, Kostic NM (1997) Computational simulation and analysis of dynamic association between plastocyanin and cytochrome f. Consequences for the electron-transfer reaction. J Am Chem Soc 119(1): 42-52. doi: 10. 1021/ja962237u.
43. Zhu XG, Govinjee BNR, de Sturler E, Ort DR, Long SP (2005) Chlorophyll a fluorescence induction kinetics in leaves predicted from a model describing each discrete step of excitation energy and electron transfer associated with photosystem II. Planta 223: 114-133. doi: 10. 1007/s00425-005-0064-4.