title: A model of chlorophyll a fluorescence induction kinetics with explicit description of structural constraints of individual photosystem II units.
abstract: Chlorophyll a fluorescence induction (FI) kinetics, in the microseconds to the second range, reflects the overall performance of the photosynthetic apparatus. In this paper, we have developed a novel FI model, using a rule-based kinetic Monte Carlo method, which incorporates not only structural and kinetic information on PSII, but also a simplified photosystem I. This model has allowed us to successfully simulate the FI under normal or different treatment conditions, i.e., with different levels of measuring light, under 3-(3',4'-dichlorophenyl)-1,1-dimethylurea treatment, under 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone treatment, and under methyl viologen treatment. Further, using this model, we have systematically studied the mechanistic basis and factors influencing the FI kinetics. The results of our simulations suggest that (1) the J step is caused by the two-electron gate at the Q B site; (2) the I step is caused by the rate limitation of the plastoquinol re-oxidation in the plastoquinone pool. This new model provides a framework for exploring impacts of modifying not only kinetic but also structural parameters on the FI kinetics.
authors.affiliation: CAS Key Laboratory of Computational Biology, CAS-MPG (Chinese Academy of Sciences-German Max Planck Society) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
authors.forename: Chang-Peng
authors.initials: CP
authors.lastname: Xin
authors.forename: Jin
authors.initials: J
authors.lastname: Yang
authors.forename: Xin-Guang
authors.initials: XG
authors.lastname: Zhu
mesh_terms: D002734:Chlorophyll / Q000378:metabolism*; D000077194:Chlorophyll A; D003198:Computer Simulation; D007700:Kinetics; D008954:Models, Biological; D009010:Monte Carlo Method; D045332:Photosystem II Protein Complex / Q000378:metabolism*; D013050:Spectrometry, Fluorescence
chemical_list: D045332:Photosystem II Protein Complex; D002734:Chlorophyll; D000077194:Chlorophyll A
references.citation: Biochemistry. 1997 Jan 7;36(1):86-92
references.pmid: 8993321
references.citation: Photosynth Res. 1989 Dec;22(3):257-75
references.pmid: 24424815
references.citation: Biochim Biophys Acta. 2005 Jun 30;1708(2):275-82
references.pmid: 15869738
references.citation: Biophys J. 1969 Jan;9(1):1-21
references.pmid: 5782892
references.citation: Eur Biophys J. 1999;28(6):468-77
references.pmid: 10460340
references.citation: J Exp Bot. 2000 Apr;51(345):659-68
references.pmid: 10938857
references.citation: Biochim Biophys Acta. 1976 Aug 13;440(2):346-55
references.pmid: 8123
references.citation: Biophys J. 1972 Jul;12(7):815-31
references.pmid: 5037337
references.citation: J Photochem Photobiol B. 2011 Jul-Aug;104(1-2):258-70
references.pmid: 21530301
references.citation: Biochim Biophys Acta. 1999 May 26;1412(1):1-28
references.pmid: 10354490
references.citation: Biochim Biophys Acta. 2012 Aug;1817(8):1134-51
references.pmid: 22521596
references.citation: Arch Biochem Biophys. 1984 Jun;231(2):378-89
references.pmid: 6375572
references.citation: J Theor Biol. 2009 Mar 21;257(2):260-9
references.pmid: 19108782
references.citation: Planta. 2005 Dec;223(1):114-133
references.pmid: 16411287
references.citation: Biochim Biophys Acta. 1974 Jan 18;333(1):85-94
references.pmid: 19396996
references.citation: Biochemistry. 1993 Sep 14;32(36):9379-86
references.pmid: 8369309
references.citation: Photochem Photobiol. 1970 Jun;11(6):457-75
references.pmid: 5456273
references.citation: Photosynth Res. 2012 Sep;113(1-3):15-61
references.pmid: 22810945
references.citation: Plant Physiol. 1989 Jun;90(2):765-72
references.pmid: 16666841
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep;78(3 Pt 1):031910
references.pmid: 18851068
references.citation: Photosynth Res. 1993 Mar;35(3):323-43
references.pmid: 24318762
references.citation: Biophys J. 1995 Jun;68(6):2474-92
references.pmid: 7647250
references.citation: J Theor Biol. 2003 Feb 21;220(4):469-503
references.pmid: 12623282
references.citation: Biochim Biophys Acta. 2011 Sep;1807(9):1032-43
references.pmid: 21669182
references.citation: Photosynth Res. 2000;63(2):171-82
references.pmid: 16228427
references.citation: Photosynth Res. 2013 Mar;114(3):143-54
references.pmid: 23188059
references.citation: Biochim Biophys Acta. 1973 Aug 31;314(2):250-6
references.pmid: 4747068
references.citation: Biophys J. 1992 May;61(5):1147-63
references.pmid: 19431828
references.citation: Photosynth Res. 1986 Jan;10(3):381-92
references.pmid: 24435386
references.citation: Biophys J. 1988 Sep;54(3):397-405
references.pmid: 19431730
references.citation: Biochim Biophys Acta. 1976 Mar 12;423(3):610-4
references.pmid: 1259962
references.citation: Biochim Biophys Acta. 2007 Apr;1767(4):295-305
references.pmid: 17412308
references.citation: Photosynth Res. 2014 May;120(1-2):43-58
references.pmid: 23456268
references.citation: J Photochem Photobiol B. 2011 Jul-Aug;104(1-2):236-57
references.pmid: 21295993
references.citation: C R Hebd Seances Acad Sci. 1964 May 4;258:4622-5
references.pmid: 14146826
references.citation: Biochim Biophys Acta. 2005 Feb 17;1706(3):250-61
references.pmid: 15694353
references.citation: J Biol Chem. 1984 Nov 25;259(22):14003-10
references.pmid: 6389539
references.citation: Proc Natl Acad Sci U S A. 2006 May 2;103(18):6895-900
references.pmid: 16641109
references.citation: Biochem Z. 1960;332:277-92
references.pmid: 14404931
references.citation: Photosynth Res. 1990 Jul;25(1):39-48
references.pmid: 24420169
references.citation: Biochim Biophys Acta. 1979 Mar 15;545(3):519-27
references.pmid: 427143
references.citation: Photosynth Res. 1986 Jan;9(1-2):273-83
references.pmid: 24442303
references.citation: Photosynth Res. 2007 May;92(2):217-24
references.pmid: 17647089
references.citation: Photosynth Res. 1990 Jan;23(1):105-9
references.pmid: 24420999
references.citation: FEBS Lett. 1994 Jun 20;347(1):45-50
references.pmid: 8013659