Projects > Lazár_2009

Projects

+ Holzwarth_2006
+ Photosynthetic apparatus
+ Thylakoid membrane
+ Photosystem II
+ 'P680'
o P680
o P680+
+ 'Qa'
o Qa
o Qa-
+ 'PhD1'
o PhD1
o PhD1-
+ Core Antenna
o ac
o ac*
+ 'ChlD1'
o ChlD1
o ChlD1*
o ChlD1+
+ Laisk_2009
+ Ontology
+ Photosynthetic apparatus
+ Chloroplast stroma
o ADPGlu
o ATP
o E4P
o EOP
o EP
o EPG
o EPP
o ER
o F6P
o FBP
o G6P
o G1P
o NADPH
o OP
o Ru5P
o R5P
o Xu5P
o PGA
+ Ferredoxin
o Fd-
o RuBP
o S7P
o SBP
o GAP
o DHAP
o TRf_
o TRm_
+ Thylakoid membrane
o Cytochrome b6/f
+ Photosystem I
+ 'P700'
o P700
+ 'Fb'
o Fb-
+ Thylakiod lumen
+ Plastocyanin
o Pc
o Hlt
+ Cytosol
o DHAPc
o F26BPc
o F6Pc
o FBPc
o G1Pc
o G6Pc
o GAPc
o OXAc
o P2GAc
o PEPc
o PGAc
o PYRc
o SuPCc
o UDPGluc
+ Enzymes
o ENf_
o ENm_
o
+ Lazár_2009
+ Photosynthetic apparatus
+ Thylakoid membrane
+ Cytochrome b6/f
+ Heme f
o f
o f-
+ Pair of high-potential heme b and heme c
o bH.c-
o bH.c
o bH.c2-
+ Low-potential heme b
o bL-
o bL
+ Photosystem II
+ 'Qa'
o Qa-
o Qa
+ 'P680'
o P680+
o P680
+ 'Qb'
o Qb
o Qb-
o Qb2-
+ Oxygen Evolving Complex
o S0
o S1
o S2
o S3
+ Photosystem I
+ 'Fb'
o Fb
o Fb-
+ 'P700'
o P700+
o P700
+ PQ Pool
+ Plastoquinon
o PQ
o PQH
+ Chloroplast stroma
+ Ferredoxin
o Fd
o Fd-
+ FNR
o FNRa
o FNRa-
o FNRa2-
o FNRi
+ Thylakiod lumen
+ Plastocyanin
o Pc
o Pc+

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Lazár_2009


Lazár D (2009) Modelling of light-induced chlorophyll a fluorescence rise (O-J-I-P transient) and changes in 820 nm-transmittance signal of photosynthesis. Photosynthetica 47(4):483-498
Annotations
Components
Reactions
Parameters
Simulation
+model:Lazár (2009)

Theoretical modelling is often overlooked in photosynthesis research even if it can significantly help with understanding of explored system. A new model of light-induced photosynthetic reactions occurring in and around thylakoid membrane is introduced here and used for theoretical modelling of not only the light-induced chlorophyll (Chl) a fluorescence rise (FLR; the O-J-I-P transient), reflecting function of photosystem II (PSII), but also of the 820 nm-transmittance signal (I820), reflecting function of photosystem I (PSI) and plastocyanin (PC), paralleling the FLR. Correctness of the model was verified by successful simulations of the FLR and I820 signal as measured with the control (no treatment) sample but also as measured with 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone- (inhibits electron transport in cytochrome b6/f) and methylviologen- (accepts electrons from iron-sulphur cluster of PSI) treated samples and with the control sample upon different intensities of excitation light. From the simulations performed for the control sample, contribution of the oxidised donor of PSI, P700, and oxidised PC to the I820 signal minimum (reflects maximal accumulations of the two components) was estimated to be 75 % and 25 %, respectively. Further in silico experiments showed that PC must be reduced in the dark, cyclic electron transport around PSI must be considered in the model and activation of ferredoxin-NADP+-reductase also affects the FLR. Correct simulations of the FLR and I820 signal demonstrate robustness of the model, confirm that the electron transport reactions occurring beyond PSII affect the shape of the FLR, and show usefulness and perspective of theoretical approach in studying of the light-induced photosynthetic reactions.


The scheme below show the reaction scheme of the model as published in Lazár (2009), however, denotation of particular electron transporter as used in that work and as used in e-photosynthesis is different. Therefore, below is a table which lists the denotations and their equivalences.

Table: Equivalences between denotations as used in Lazár (2009) and in e-photosynthesis.
Lazár (2009) e-photosynthesis
P P680
P+ P680+
A Qa
A- Qa-
B Qb
B- Qb-
B2- Qb2-
S S1
S2 S2
S3 S3
S0 S0
PQ PQ
PQH2 PQH
L bL
L- bL-
(HC) bH.c
(HC)- bH.c-
(HC)2- bH.c2-
F f
F- f-
PC Pc
PC+ Pc+
Fd Fd
Fd- Fd-
R P700
R+ P700+
X Fb
X- Fb-
FNRi FNRi
FNRa FNRa
FNRa- FNRa-
FNRa2- FNRa2-


+publication:Lazár (2009)
Lazár D (2009) Modelling of light-induced chlorophyll a fluorescence rise (O-J-I-P transient) and changes in 820 nm-transmittance signal of photosynthesis. Photosynthetica 47(4):483-498
DOI:10.1007/s11099-009-0074-8
Model components grouped by compartments:
+Thylakoid
Initial value: 1
Simulation type: fixed
+bL-/bH.c-/f
Initial value: 0
Simulation type: reaction
+bL-/bH.c-/f-
Initial value: 0
Simulation type: reaction
+bL-/bH.c/f
Initial value: 0
Simulation type: reaction
+bL-/bH.c/f-
Initial value: 0
Simulation type: reaction
+bL-/bH.c2-/f
Initial value: 0
Simulation type: reaction
+bL-/bH.c2-/f-
Initial value: 0
Simulation type: reaction
+bL/bH.c-/f
Initial value: 0
Simulation type: reaction
+bL/bH.c-/f-
Initial value: 0
Simulation type: reaction
+bL/bH.c/f
Initial value: 1
Simulation type: reaction
+bL/bH.c/f-
Initial value: 0
Simulation type: reaction
+bL/bH.c2-/f
Initial value: 0
Simulation type: reaction
+bL/bH.c2-/f-
Initial value: 0
Simulation type: reaction
+Fd
Initial value: 3
Simulation type: reaction
+Fd-
Initial value: 0
Simulation type: reaction
+FNRa
Initial value: 0
Simulation type: reaction
+FNRa-
Initial value: 0
Simulation type: reaction
+FNRa2-
Initial value: 0
Simulation type: reaction
+FNRi
Initial value: 3
Simulation type: reaction
+P680+/Qa-/N
Initial value: 0
Simulation type: reaction
+P680+/Qa-/Qb
Initial value: 0
Simulation type: reaction
+P680+/Qa-/Qb-
Initial value: 0
Simulation type: reaction
+P680+/Qa-/Qb2-
Initial value: 0
Simulation type: reaction
+P680+/Qa/Qb
Initial value: 0
Simulation type: reaction
+P680+/Qa/Qb-
Initial value: 0
Simulation type: reaction
+P680+/Qa/Qb2-
Initial value: 0
Simulation type: reaction
+P680/Qa-/N
Initial value: 0
Simulation type: reaction
+P680/Qa-/Qb
Initial value: 0
Simulation type: reaction
+P680/Qa-/Qb-
Initial value: 0
Simulation type: reaction
+P680/Qa-/Qb2-
Initial value: 0
Simulation type: reaction
+P680/Qa/N
Initial value: 0
Simulation type: reaction
+P680/Qa/Qb
Initial value: 1
Simulation type: reaction
+P680/Qa/Qb-
Initial value: 0
Simulation type: reaction
+P680/Qa/Qb2-
Initial value: 0
Simulation type: reaction
+P700+/Fb
Initial value: 0
Simulation type: reaction
+P700+/Fb-
Initial value: 0
Simulation type: reaction
+P700/Fb
Initial value: 1
Simulation type: reaction
+P700/Fb-
Initial value: 0
Simulation type: reaction
+Pc
Initial value: 3
Simulation type: reaction
+Pc+
Initial value: 0
Simulation type: reaction
+PQ
Initial value: 2.5
Simulation type: reaction
+PQH
Initial value: 2.5
Simulation type: reaction
+S0
Initial value: 0.25
Simulation type: reaction
+S1
Initial value: 0.75
Simulation type: reaction
+S2
Initial value: 0
Simulation type: reaction
+S3
Initial value: 0
Simulation type: reaction
+Activation of FNR
“Inactive FNR (FNRi) is activated in light to active FNR (FNRa) with rate constant ka.”


Function: Mass Action (irreversible)
Reaction rate: ka*FNRi
Product: FNRa
Kinetic rate constant Value
ka 0.01
+Charge separation in photosystem I
“It occurs in the model between P700 and Fb with rate constant kL1 leading to formation of P700+ and Fb-. Value of kL1 is determined by amount of excitations coming to reaction centre of photosystem I and concentration of chlorophylls in a sample.”


Function: Mass Action (irreversible)
Reaction rate: kL1*P700/Fb
Product: P700+/Fb-
Kinetic rate constant Value
kL1 200
+Charge separation in photosystem II (1)
”It occurs in the model between P680 and Qa with rate constant kL2 leading to formation of P680+ and Qa-. Value of kL2 is determined by amount of excitations coming to reaction centre of photosystem II and concentration of chlorophylls in a sample.”


Function: Mass Action (irreversible)
Reaction rate: kL2*P680/Qa/Qb
Product: P680+/Qa-/Qb
Kinetic rate constant Value
kL2 4000
+Charge separation in photosystem II (2)
”It occurs in the model between P680 and Qa with rate constant kL2 leading to formation of P680+ and Qa-. Value of kL2 is determined by amount of excitations coming to reaction centre of photosystem II and concentration of chlorophylls in a sample.”


Function: Mass Action (irreversible)
Reaction rate: kL2*P680/Qa/Qb-
Product: P680+/Qa-/Qb-
Kinetic rate constant Value
kL2 4000
+Charge separation in photosystem II (3)
”It occurs in the model between P680 and Qa with rate constant kL2 leading to formation of P680+ and Qa-. Value of kL2 is determined by amount of excitations coming to reaction centre of photosystem II and concentration of chlorophylls in a sample.”


Function: Mass Action (irreversible)
Reaction rate: kL2*P680/Qa/Qb2-
Product: P680+/Qa-/Qb2-
Kinetic rate constant Value
kL2 4000
+Electron donation 1_1
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa/Qb
Product: S1, P680/Qa/Qb
Kinetic rate constant Value
k01 20000
+Electron donation 1_2
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa/Qb
Product: S2, P680/Qa/Qb
Kinetic rate constant Value
k12 10000
+Electron donation 1_3
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa/Qb
Product: S3, P680/Qa/Qb
Kinetic rate constant Value
k23 3330
+Electron donation 1_4
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa/Qb
Product: S0, P680/Qa/Qb
Kinetic rate constant Value
k30 1000
+Electron donation 1_5
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa-/N
Product: S1, P680/Qa-/N
Kinetic rate constant Value
k01 20000
+Electron donation 2_1
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa-/Qb
Product: S1, P680/Qa-/Qb
Kinetic rate constant Value
k01 20000
+Electron donation 2_2
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa-/Qb
Product: S2, P680/Qa-/Qb
Kinetic rate constant Value
k12 10000
+Electron donation 2_3
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa-/Qb
Product: S3, P680/Qa-/Qb
Kinetic rate constant Value
k23 3330
+Electron donation 2_4
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa-/Qb
Product: S0, P680/Qa-/Qb
Kinetic rate constant Value
k30 1000
+Electron donation 2_5
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa-/N
Product: S2, P680/Qa/N
Kinetic rate constant Value
k12 10000
+Electron donation 3_1
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa/Qb-
Product: S1, P680/Qa/Qb-
Kinetic rate constant Value
k01 20000
+Electron donation 3_2
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa/Qb-
Product: S2, P680/Qa/Qb-
Kinetic rate constant Value
k12 10000
+Electron donation 3_3
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa/Qb-
Product: S3, P680/Qa/Qb-
Kinetic rate constant Value
k23 3330
+Electron donation 3_4
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa/Qb-
Product: S0, P680/Qa/Qb-
Kinetic rate constant Value
k30 1000
+Electron donation 3_5
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa-/N
Product: S3, P680/Qa-/N
Kinetic rate constant Value
k23 3330
+Electron donation 4_1
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa-/Qb-
Product: S1, P680/Qa-/Qb-
Kinetic rate constant Value
k01 20000
+Electron donation 4_2
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa-/Qb-
Product: S2, P680/Qa-/Qb-
Kinetic rate constant Value
k12 10000
+Electron donation 4_3
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa-/Qb-
Product: S3, P680/Qa-/Qb-
Kinetic rate constant Value
k23 3330
+Electron donation 4_4
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa-/Qb-
Product: S0, P680/Qa-/Qb-
Kinetic rate constant Value
k30 1000
+Electron donation 4_5
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k1*S2 * P680+/Qa-/N
Product: S0, P680/Qa-/N
Kinetic rate constant Value
k1 1000
+Electron donation 5_1
Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa/Qb2-
Product: S1, P680/Qa/Qb2-
Kinetic rate constant Value
k01 20000
+Electron donation 5_2
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa/Qb2-
Product: S2, P680/Qa/Qb2-
Kinetic rate constant Value
k12 10000
+Electron donation 5_3
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa/Qb2-
Product: S3, P680/Qa/Qb2-
Kinetic rate constant Value
k23 3330
+Electron donation 5_4
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa/Qb2-
Product: S0, P680/Qa/Qb2-
Kinetic rate constant Value
k30 1000
+Electron donation 6_1
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa-/Qb2-
Product: S1, P680/Qa-/Qb2-
Kinetic rate constant Value
k01 20000
+Electron donation 6_2
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa-/Qb2-
Product: S2, P680/Qa-/Qb2-
Kinetic rate constant Value
k12 10000
+Electron donation 6_3
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa-/Qb2-
Product: S3, P680/Qa-/Qb2-
Kinetic rate constant Value
k23 3330
+Electron donation 6_4
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa-/Qb2-
Product: S0, P680/Qa-/Qb2-
Kinetic rate constant Value
k30 1000
+Electron donation to P700+ by Pc (1)
“Reduced Pc (Pc) donates electron to oxidized P700 (P700+). This reaction is considered reversible with forward and backward rate constants kfR and kbR, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfR*Pc * P700+/Fb-kbR*Pc+ * P700/Fb
Product: Pc+, P700/Fb
Kinetic rate constant Value
kfR 100
kbR 10
+Electron donation to P700+ by Pc (2)
“Reduced Pc (Pc) donates electron to oxidized P700 (P700+). This reaction is considered reversible with forward and backward rate constants kfR and kbR, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfR*Pc * P700+/Fb--kbR*Pc+ * P700/Fb-
Product: Pc+, P700/Fb-
Kinetic rate constant Value
kbR 10
kfR 100
+Electron transport from Fd to FNR (1)
“Reduced Fd (Fd-) donates its electron to active oxidized (FNRa) or singly reduced (FNRa-) FNR with the same values of the forward and backward rate constants kfFd and kbFd, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfFd*FNRa * Fd--kbFd*FNRa- * Fd
Product: FNRa-, Fd
Kinetic rate constant Value
kfFd 5
kbFd 5
+Electron transport from Fd to FNR (2)
“Reduced Fd (Fd-) donates its electron to active oxidized (FNRa) or singly reduced (FNRa-) FNR with the same values of the forward and backward rate constants kfFd and kbFd, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfFd*FNRa- * Fd--kbFd*Fd * FNRa2-
Product: Fd, FNRa2-
Kinetic rate constant Value
kfFd 5
kbFd 5
+Electron transport from cytochrome b6/f complex to oxidized PQ (1)
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”


Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL/bH.c2-/f-"kb(HC)"*bL/bH.c/f * PQH
Product: bL/bH.c/f, PQH
Kinetic rate constant Value
kf(HC) 100
kb(HC) 10
+Electron transport from cytochrome b6/f complex to oxidized PQ (2)
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”


Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL-/bH.c2-/f-"kb(HC)"*PQH * bL-/bH.c/f
Product: PQH, bL-/bH.c/f
Kinetic rate constant Value
kf(HC) 100
kb(HC) 10
+Electron transport from cytochrome b6/f complex to oxidized PQ (3)
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”


Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL/bH.c2-/f--"kb(HC)"*PQH * bL/bH.c/f-
Product: PQH, bL/bH.c/f-
Kinetic rate constant Value
kf(HC) 100
kb(HC) 10
+Electron transport from cytochrome b6/f complex to oxidized PQ (4)
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”


Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL-/bH.c2-/f--"kb(HC)"*PQH * bL-/bH.c/f-
Product: PQH, bL-/bH.c/f-
Kinetic rate constant Value
kf(HC) 100
kb(HC) 10
+Electron transport from cytochrome b6/f complex to oxidized Pc (1)
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL/bH.c/f- * Pc+-kbF*bL/bH.c/f * Pc
Product: bL/bH.c/f, Pc
Kinetic rate constant Value
kfF 100
kbF 10
+Electron transport from cytochrome b6/f complex to oxidized Pc (2)
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL-/bH.c/f- * Pc+-kbF*bL-/bH.c/f * Pc
Product: bL-/bH.c/f, Pc
Kinetic rate constant Value
kfF 100
kbF 10
+Electron transport from cytochrome b6/f complex to oxidized Pc (3)
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL/bH.c-/f- * Pc+-kbF*bL/bH.c-/f * Pc
Product: bL/bH.c-/f, Pc
Kinetic rate constant Value
kfF 100
kbF 10
+Electron transport from cytochrome b6/f complex to oxidized Pc (4)
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL-/bH.c-/f- * Pc+-kbF*bL-/bH.c-/f * Pc
Product: bL-/bH.c-/f, Pc
Kinetic rate constant Value
kfF 100
kbF 10
+Electron transport from cytochrome b6/f complex to oxidized Pc (5)
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL/bH.c2-/f- * Pc+-kbF*bL/bH.c2-/f * Pc
Product: bL/bH.c2-/f, Pc
Kinetic rate constant Value
kfF 100
kbF 10
+Electron transport from cytochrome b6/f complex to oxidized Pc (6)
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL-/bH.c2-/f- * Pc+-kbF*bL-/bH.c2-/f * Pc
Product: bL-/bH.c2-/f, Pc
Kinetic rate constant Value
kfF 100
kbF 10
+Electron transport from photosystem I to Fd (1)
“Reduced state of the last iron-sulfur cluster in photosystem I (Fb-) donates its electron to oxidized Fd. This reaction is considered reversible with forward and backward rate constants kfX and kbX, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfX*Fd * P700/Fb--kbX*P700/Fb * Fd-
Product: P700/Fb, Fd-
Kinetic rate constant Value
kfX 100
kbX 10
+Electron transport from photosystem I to Fd (2)
“Reduced state of the last iron-sulfur cluster in photosystem I (Fb-) donates its electron to oxidized Fd. This reaction is considered reversible with forward and backward rate constants kfX and kbX, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfX*Fd * P700+/Fb--kbX*P700+/Fb * Fd-
Product: P700+/Fb, Fd-
Kinetic rate constant Value
kfX 100
kbX 10
+Electron transport from reduced Fd to cytochrome b6/f complex (1)
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c/f-kbct*Fd * bL/bH.c-/f
Product: Fd, bL/bH.c-/f
Kinetic rate constant Value
kfct 100
kbct 100
+Electron transport from reduced Fd to cytochrome b6/f complex (2)
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c/f-kbct*Fd * bL-/bH.c-/f
Product: Fd, bL-/bH.c-/f
Kinetic rate constant Value
kfct 100
kbct 100
+Electron transport from reduced Fd to cytochrome b6/f complex (3)
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c/f--kbct*Fd * bL/bH.c-/f-
Product: Fd, bL/bH.c-/f-
Kinetic rate constant Value
kfct 100
kbct 100
+Electron transport from reduced Fd to cytochrome b6/f complex (4)
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c/f--kbct*Fd * bL-/bH.c-/f-
Product: Fd, bL-/bH.c-/f-
Kinetic rate constant Value
kfct 100
kbct 100
+Electron transport from reduced Fd to cytochrome b6/f complex (5)
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c-/f-kbct*Fd * bL/bH.c2-/f
Product: Fd, bL/bH.c2-/f
Kinetic rate constant Value
kfct 100
kbct 100
+Electron transport from reduced Fd to cytochrome b6/f complex (6)
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c-/f-kbct*Fd * bL-/bH.c2-/f
Product: Fd, bL-/bH.c2-/f
Kinetic rate constant Value
kfct 100
kbct 100
+Electron transport from reduced Fd to cytochrome b6/f complex (7)
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c-/f--kbct*Fd * bL/bH.c2-/f-
Product: Fd, bL/bH.c2-/f-
Kinetic rate constant Value
kfct 100
kbct 100
+Electron transport from reduced Fd to cytochrome b6/f complex (8)
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c-/f--kbct*Fd * bL-/bH.c2-/f-
Product: Fd, bL-/bH.c2-/f-
Kinetic rate constant Value
kfct 100
kbct 100
+Electron transport from reduced PQ to cytochrome b6/f complex (1)
“When both haem f (f) and low-potential form of haem b (bL) of cytochrome b6/f are oxidized, they are reduced by reduced and protonated PQ molecule (PQH) from the pool: PQH is oxidized (its deprotonation is assumed implicitely) in lumenal side of cytochrome b6/f leading to transport of one electron to bL and one electron to f. This reaction is considered reversible with forward and backward rate constants kfLF and kbLF respectively.”


Function: Mass Action (reversible)
Reaction rate: "kfL,F"*PQH * bL/bH.c/f-"kbL,F"*PQ * bL-/bH.c/f-
Product: PQ, bL-/bH.c/f-
Kinetic rate constant Value
kfL,F 100
kbL,F 10
+Electron transport from reduced PQ to cytochrome b6/f complex (2)
“When both haem f (f) and low-potential form of haem b (bL) of cytochrome b6/f are oxidized, they are reduced by reduced and protonated PQ molecule (PQH) from the pool: PQH is oxidized (its deprotonation is assumed implicitely) in lumenal side of cytochrome b6/f leading to transport of one electron to bL and one electron to f. This reaction is considered reversible with forward and backward rate constants kfLF and kbLF respectively.”


Function: Mass Action (reversible)
Reaction rate: "kfL,F"*PQH * bL/bH.c-/f-"kbL,F"*PQ * bL-/bH.c-/f-
Product: PQ, bL-/bH.c-/f-
Kinetic rate constant Value
kfL,F 100
kbL,F 10
+Electron transport from reduced PQ to cytochrome b6/f complex (3)
“When both haem f (f) and low-potential form of haem b (bL) of cytochrome b6/f are oxidized, they are reduced by reduced and protonated PQ molecule (PQH) from the pool: PQH is oxidized (its deprotonation is assumed implicitely) in lumenal side of cytochrome b6/f leading to transport of one electron to bL and one electron to f. This reaction is considered reversible with forward and backward rate constants kfLF and kbLF respectively.”


Function: Mass Action (reversible)
Reaction rate: "kfL,F"*PQH * bL/bH.c2-/f-"kbL,F"*PQ * bL-/bH.c2-/f-
Product: PQ, bL-/bH.c2-/f-
Kinetic rate constant Value
kfL,F 100
kbL,F 10
+Electron transport inside cytochrome b6/f complex (1)
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”


Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c/f-"k(HC)L"*bL/bH.c-/f
Product: bL/bH.c-/f
Kinetic rate constant Value
kL(HC) 2300
k(HC)L 7
+Electron transport inside cytochrome b6/f complex (2)
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”


Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c/f--"k(HC)L"*bL/bH.c-/f-
Product: bL/bH.c-/f-
Kinetic rate constant Value
kL(HC) 2300
k(HC)L 7
+Electron transport inside cytochrome b6/f complex (3)
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”


Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c-/f-"k(HC)L"*bL/bH.c2-/f
Product: bL/bH.c2-/f
Kinetic rate constant Value
kL(HC) 2300
k(HC)L 7
+Electron transport inside cytochrome b6/f complex (4)
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”


Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c-/f--"k(HC)L"*bL/bH.c2-/f-
Product: bL/bH.c2-/f-
Kinetic rate constant Value
kL(HC) 2300
k(HC)L 7
+Electron transports from Qa- to Qb (1)
"When Qa is reduced, it donates its electron to oxidized Qb. This reaction occurs with forward rate constant kAB1 and the reaction is considered reversible with backward rate constant kBA1." []

Function: Mass Action (reversible)
Reaction rate: kAB1*P680+/Qa-/Qb-kBA1*P680+/Qa/Qb-
Product: P680+/Qa/Qb-
Kinetic rate constant Value
kBA1 175
kAB1 3500
+Electron transports from Qa- to Qb (2)
"When Qa is reduced, it donates its electron to oxidized Qb. This reaction occurs with forward rate constant kAB1 and the reaction is considered reversible with backward rate constant kBA1." []

Function: Mass Action (reversible)
Reaction rate: kAB1*P680/Qa-/Qb-kBA1*P680/Qa/Qb-
Product: P680/Qa/Qb-
Kinetic rate constant Value
kAB1 3500
kBA1 175
+Electron transports from Qa- to Qb- (1)
”When Qa is reduced, it donates its electron to singly reduced Qb. This reaction occurs with forward rate constant kAB2 and the reaction is considered reversible with backward rate constant kBA2.”


Function: Mass Action (reversible)
Reaction rate: kAB2*P680+/Qa-/Qb--kBA2*P680+/Qa/Qb2-
Product: P680+/Qa/Qb2-
Kinetic rate constant Value
kAB2 1750
kBA2 35
+Electron transports from Qa- to Qb- (2)
”When Qa is reduced, it donates its electron to singly reduced Qb. This reaction occurs with forward rate constant kAB2 and the reaction is considered reversible with backward rate constant kBA2.”


Function: Mass Action (reversible)
Reaction rate: kAB2*P680/Qa-/Qb--kBA2*P680/Qa/Qb2-
Product: P680/Qa/Qb2-
Kinetic rate constant Value
kAB2 1750
kBA2 35
+Qb2-/PQ exchange (1)
“When Qb is doubly reduced and protonated (protonation is assumed implicitly), it exchanges with oxidized PQ molecule from the pool leading to presence of oxidized Qb in photosystem II and doubly reduced and protonated PQ molecule (PQH) in the pool. The exchange is is reversible second order reaction with forward and backward rate constants kfB and kbB, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfB*PQ * P680+/Qa/Qb2--kbB*PQH * P680+/Qa/Qb
Product: PQH, P680+/Qa/Qb
Kinetic rate constant Value
kfB 250
kbB 250
+Qb2-/PQ exchange (2)
“When Qb is doubly reduced and protonated (protonation is assumed implicitly), it exchanges with oxidized PQ molecule from the pool leading to presence of oxidized Qb in photosystem II and doubly reduced and protonated PQ molecule (PQH) in the pool. The exchange is is reversible second order reaction with forward and backward rate constants kfB and kbB, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfB*PQ * P680/Qa/Qb2--kbB*PQH * P680/Qa/Qb
Product: PQH, P680/Qa/Qb
Kinetic rate constant Value
kfB 250
kbB 250
+Qb2-/PQ exchange (3)
“When Qb is doubly reduced and protonated (protonation is assumed implicitly), it exchanges with oxidized PQ molecule from the pool leading to presence of oxidized Qb in photosystem II and doubly reduced and protonated PQ molecule (PQH) in the pool. The exchange is is reversible second order reaction with forward and backward rate constants kfB and kbB, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfB*PQ * P680+/Qa-/Qb2--kbB*PQH * P680+/Qa-/Qb
Product: PQH, P680+/Qa-/Qb
Kinetic rate constant Value
kfB 250
kbB 250
+Qb2-/PQ exchange (4)
“When Qb is doubly reduced and protonated (protonation is assumed implicitly), it exchanges with oxidized PQ molecule from the pool leading to presence of oxidized Qb in photosystem II and doubly reduced and protonated PQ molecule (PQH) in the pool. The exchange is is reversible second order reaction with forward and backward rate constants kfB and kbB, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfB*PQ * P680/Qa-/Qb2--kbB*P680/Qa-/Qb * PQH
Product: P680/Qa-/Qb, PQH
Kinetic rate constant Value
kfB 250
kbB 250
+Turnover of FNR
“Active doubly reduced FNR (FNRa2-) turnovers to its active oxidized state (FNRa) by donation of the two electrons to NADP+ (together with two protons from stroma) leading to formation of one NADPH molecule with rate constant kFNR. NADP+ and protons are considered implicitely and the turnover of FNR is a simple first order reaction.”


Function: Mass Action (irreversible)
Reaction rate: kFNR*FNRa2-
Product: FNRa
Kinetic rate constant Value
kFNR 220

Constant quantities

+k(HC)L
Initial value: 7
Simulation type: fixed
+k01
Initial value: 20000
Simulation type: fixed
+k12
Initial value: 10000
Simulation type: fixed
+k23
Initial value: 3330
Simulation type: fixed
+k30
Initial value: 1000
Simulation type: fixed
+ka
Initial value: 0.01
Simulation type: fixed
+kAB1
Initial value: 3500
Simulation type: fixed
+kAB2
Initial value: 1750
Simulation type: fixed
+kb(HC)
Initial value: 10
Simulation type: fixed
+kBA1
Initial value: 175
Simulation type: fixed
+kBA2
Initial value: 35
Simulation type: fixed
+kbB
Initial value: 250
Simulation type: fixed
+kbct
Initial value: 100
Simulation type: fixed
+kbF
Initial value: 10
Simulation type: fixed
+kbFd
Initial value: 5
Simulation type: fixed
+kbL,F
Initial value: 10
Simulation type: fixed
+kbR
Initial value: 10
Simulation type: fixed
+kbX
Initial value: 10
Simulation type: fixed
+kf(HC)
Initial value: 100
Simulation type: fixed
+kfB
Initial value: 250
Simulation type: fixed
+kfct
Initial value: 100
Simulation type: fixed
+kfF
Initial value: 100
Simulation type: fixed
+kfFd
Initial value: 5
Simulation type: fixed
+kfL,F
Initial value: 100
Simulation type: fixed
+kFNR
Initial value: 220
Simulation type: fixed
+kfR
Initial value: 100
Simulation type: fixed
+kfX
Initial value: 100
Simulation type: fixed
+kL(HC)
Initial value: 2300
Simulation type: fixed
+kL1
Initial value: 200
Simulation type: fixed
+kL2
Initial value: 4000
Simulation type: fixed

Assigned quantities

+Fq(t)
Initial expression: ((1-0.55)*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")/(1-0.55*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")))/(1+((1/45+(("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")*4/63))*"PQ"))
Simulation type: assignment
+Funq(t)
Initial expression: (1-0.55)*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")/(1-0.55*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-"))
Simulation type: assignment
+I820
Initial expression: 10^(-(2.16*10^(-7)*1590*"Pc+" + 2.16*10^(-7)*10300*("P700+/Fb"+"P700+/Fb-")))
Simulation type: assignment
+Initial conditions
Name Value
bL-/bH.c-/f 0
bL-/bH.c-/f- 0
bL-/bH.c/f 0
bL-/bH.c/f- 0
bL-/bH.c2-/f 0
bL-/bH.c2-/f- 0
bL/bH.c-/f 0
bL/bH.c-/f- 0
bL/bH.c/f 1
bL/bH.c/f- 0
bL/bH.c2-/f 0
bL/bH.c2-/f- 0
Fd 3
Fd- 0
FNRa 0
FNRa- 0
FNRa2- 0
FNRi 3
P680+/Qa-/N 0
P680+/Qa-/Qb 0
P680+/Qa-/Qb- 0
P680+/Qa-/Qb2- 0
P680+/Qa/Qb 0
P680+/Qa/Qb- 0
P680+/Qa/Qb2- 0
P680/Qa-/N 0
P680/Qa-/Qb 0
P680/Qa-/Qb- 0
P680/Qa-/Qb2- 0
P680/Qa/N 0
P680/Qa/Qb 1
P680/Qa/Qb- 0
P680/Qa/Qb2- 0
P700+/Fb 0
P700+/Fb- 0
P700/Fb 1
P700/Fb- 0
Pc 3
Pc+ 0
PQ 2.5
PQH 2.5
S0 0.25
S1 0.75
S2 0
S3 0
+Parameters

Constant quantities

Name Value
k(HC)L 7
k01 20000
k12 10000
k23 3330
k30 1000
ka 0.01
kAB1 3500
kAB2 1750
kb(HC) 10
kBA1 175
kBA2 35
kbB 250
kbct 100
kbF 10
kbFd 5
kbL,F 10
kbR 10
kbX 10
kf(HC) 100
kfB 250
kfct 100
kfF 100
kfFd 5
kfL,F 100
kFNR 220
kfR 100
kfX 100
kL(HC) 2300
kL1 200
kL2 4000

Assigned quantities

Name Value
Fq(t)
Funq(t)
I820
+Options
Name Value
Simulation end 1
Use log time scale 1
Multiplication of time scale 1
Simulation start 0.000001
Number of steps 200
Simulation tolerance 0.01
Label x-axis time [s]

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