ABSTRACT:
This is a kinetic model of the monomeric photosystem II (PSII).
The model is partially based on the earlier model used for simulation of the flash-induced period-four damped oscillation of oxygen evolution and chlorophyll fluorescence (Jablonsky J and Lazar D (2008) Biophys J, 94: 2725-2736 pubmedID: 18178650
). For short description of reactions and initial concentrations, see the notes in the model file. For explanation of the value of the rate constants, see: Lazar D (2003) J. theor. Biol. 220:469-503 pubmedID: 12623282
; Jablonsky J and Lazar D, 2008 Biophys J, 94: 2725-2736 pubmedID: 18178650
and Jablonsky, Susila and Lazar, 2008, DOI: 10.1093/bioinformatics/btn530
pubmedID: 18845578
).
The oxygen signal in the model is defined as a maximum of the sum of concentrations of the model forms in the iS3Yp-state (handled in MATLAB). This version of model cannot be used for simulation of the chlorophyll fluorescence because for simplicity the reactions behind the loss of excited state are not considered.
The meaning of the particular letters in the model is as follows: P – P680 (special chlorophyll pair), H – pheophytin, A – QA (the first quinone electron acceptor), B – QB (the second quinone electron acceptor), PQ – oxidized plastoquinone molecules in the PQ pool, PQH – reduced and protonated PQ molecules in the PQ pool, Y/Yp – reduced/oxidized state of tyrosine 161-D1, YD/YDox – reduced/oxidized state of tyrosine 160-D2, Sn (n = 0, 1, 2, 3) – the S-states of oxygen evolving complex (OEC), iSn (n = 0, 1, 2, 3) – the intermediate S-states of OEC.
All reactions describing electron transport through PSII entered into the model are assumed to be first order reactions with respect to one reactant and are defined as mass action reactions. This approach enables to consider D1-Y161 (YZ) and oxygen evolving complex (OEC) as the integral parts of the PSII, in contrary of the multi-units PSII model (Jablonsky and Lazar, 2008, Biophys J, 94: 2725-2736 pubmedID: 18178650
) or model of dimeric PSII (Jablonsky, Susila and Lazar, 2008, DOI: 10.1093/bioinformatics/btn530).
initial conditions:
S1=100%,
YDox=89%
PHABm = 0.25
PHAB = 0.75
list of reactions:
R1-R144 ... excitation
R145- R180... charge separation_open
R181- R216... charge separation_closed
R217-R324 ... charge stabilisation
R325-R360 ... recombination PpHm (P680+pheophytin-)
R361-R396... recombination PpAm (P680+QA-)
R397-R399 ... recombination S2Am (S2-state of OEC and QA-)
R400-R471 ... electron transfer from QA to QB
R472-R543 ... electron transfer from QA to QB-
R544-R687 ... exchange of double reduced QB by free plastoquinone molecule from the PQ pool
R688 ... Ox/red PQ and PQH
R689-R700 ... reduction of Pp by Yz in S0
R701-R712 ... reduction of Pp by Yz in S1
R713-R724 ... reduction of Pp by Yz in S2
R725-R736 ... reduction of Pp by Yz in S3
R737-R784 ... formation of the intermediated S-states iS0,1,2, 3
R785-R832 ... electron donation from OEC to YZox during the S0->S1, S1->S2, S2->S3, S3->S0 transitions (Kok cycle)
R833-R850 ... YD oxidation by S3/S2 state of OEC; YDox reduction by S0 state of OEC
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
Jiri Jablonsky 
