Repository > Lazár_2009 > Thylakoid membrane > Photosystem II > 'P680' > P680

Repository

+ 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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P680

Annotations
Components
Reactions
Parameters
Simulation
+species:chlorophyll a reduced
“Reduced state of homodimer of chlorophyll a (PD1-PD2) originally thought to be the primary electron donor in photosystem II. However, later studies showed that the primary electron donor in photosystem II is the accessory chlorophyll in D1 protein of photosystem II (ChD1) and not P680. Therefore, P680 is the secondary electron donor in photosystem II, reducing oxidized ChD1.”

P680
Model states corresponding to the currently selected level:
+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
+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
+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
+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 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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+Electron donation 5_1
Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa/Qb2-
Product: S1, P680/Qa/Qb2-
Kinetic rate constant Value
+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
+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
+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

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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