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arnold10

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AGPase

AGPase

HeP + ATP = ADPG + PiPi

ATP_S

ATP synthase

ADP + Pi = ATP

F26BPc_P

F26BPc phosphatase

F26BPc > HePc + Pic

F6P_TK

Transketolase (F6P)

HeP + TP = E4P + PeP

F6Pc_K

F6Pc kinase

HePc > F26BPc + ADPc

FBP_A

Aldolase (FBP)

{2.0}TP = FBP

FBPase

FBPase

FBP = HeP + Pi

FBPc_A

cyt. Aldolase (FBP)

{2.0}TPc = FBPc

FBPcase

cyt. FBPase

FBPc = HePc + Pic

PGA_K

PGA kinase

PGA + ATP = TP + ADP + Pi

Ru5P_K

Ru5P kinase

PeP + ATP = RuBP + ADP

RuBisCO_1

RuBisCO (1)

RuBP + E = ER

RuBisCO_2_CO2

RuBisCO (2) - V(CO2)

ER + CO2 > EPP

RuBisCO_4

RuBisCO (4)

EPP = PGA + EP

RuBisCO_5_EOP

RuBisCO (5) - EOP

EOP = ∅

RuBisCO_5_EP

RuBisCO (5) - EP

EP = PGA + E

RuBisCO_6_O2

RuBisCO (6) - V(O2)

ER + O2 + {0.5}ATP > EPG + {0.5}PGA + {0.5}ADP

RuBisCO_7

RuBisCO (7)

EPG > EP

S7P_TK

Transketolase (S7P)

S7P + TP = {2.0}PeP

SBP_A

Aldolase (SBP)

E4P + TP = SBP

SBPase

SBPase

SBP = S7P + Pi

StS

Starch synthase

ADPG = ADP

SucPc_P

Sucrose phosphatase

SucPc = Succ + Pic

SucPc_S

Sucrose synthase

HePc + UDPGc = UDPc + SucPc + Hc

TPT_PGA

TPT (PGA)

PGA = PGAc

TPT_TP

TPT (TP)

TP = TPc

UGPase

UGPase

HePc + UTPc = UDPGc + PiPic

Parameters

Global parameters
AGPase
ATP_S
F26BPc_P
F6P_TK
F6Pc_K
FBP_A
FBPase
FBPc_A
FBPcase
PGA_K
Ru5P_K
RuBisCO_1
RuBisCO_2_CO2
RuBisCO_4
RuBisCO_5_EP
RuBisCO_6_O2
RuBisCO_7
S7P_TK
SBP_A
SBPase
StS
SucPc_P
SucPc_S
TPT_PGA
TPT_TP
UGPase

Fixed species

Initial values

Functions and Rules

Assignment rules

Pic = PiTc - 2.0 * (FBPc + UTPc + ATPc + PiPic) - (PGAc + TPc + HePc + SucPc + UDPGc + UDPc + ADPc)

F6P = HeP * 0.999837 / (1.0 + 0.999837 + 0.999308)

Ru5P = PeP * 0.99974 / (1.0 + 0.99974 + 0.99974 / 1.000053)

GAP = TP / (1.0 + 1.0007329)

ADPc = ADTc - ATPc

W4 = 6.0 * EOP - 70000.0 * Pi * E

E = Et - (ER + EPP + EPG + EP + EOP)

CO2 = (1.200000e-05 / (0.38 + 0.015) + 8.0 * 4.0 * 0.00055 * 3030.3 * ER * O2 / 2.0) / (1.0 / (0.38 + 0.015) + 8.0 * 4.0 * 0.00055 * 300000.0 * ER)

DHAPc = 1.0007329 * TPc / (1.0 + 1.0007329)

GAPc = TPc / (1.0 + 1.0007329)

Pi = PiT - 2.0 * (EPP + EPG + RuBP + FBP + SBP + ATP + PiPi) - (EP + PGA + TP + HeP + E4P + S7P + PeP + ADP + ADPG)

ADP = ADT - ATP

R5P = PeP / (1.0 + 0.99974 + 0.99974 / 1.000053)

F6Pc = HePc * 0.999837 / (1.0 + 0.999837 + 0.999308)

G6Pc = HePc / (1.0 + 0.999837 + 0.999308)

DHAP = 1.0007329 * TP / (1.0 + 1.0007329)

G1Pc = HePc * 0.999308 / (1.0 + 0.999837 + 0.999308)

G1P = HeP * 0.999308 / (1.0 + 0.999837 + 0.999308)

G6P = HeP / (1.0 + 0.999837 + 0.999308)

X5P = PeP * (0.99974 / 1.000053) / (1.0 + 0.99974 + 0.99974 / 1.000053)

Function definitions

function_28(Vm, r1, r2, s1, s2, p1, p2, q, Ks1, Ks2, Kp1, Kp2) = Vm * pow(r1 / r2, 2) * (s1 * s2 - p1 * p2 / q) / (Ks1 * Ks2 * ((1 + s1 / Ks1) * (1 + s2 / Ks2) + (1 + p1 / Kp1) * (1 + p2 / Kp2) - 1))

function_25(Vm, s1, p1, p2, q, Ks1, Kp1, Kp2) = Vm * (s1 - p1 * p2 / q) / (Ks1 * (1 + s1 / Ks1 + p1 / Kp1 + p1 * p2 / (Kp1 * Kp2)))

function_31(Vm, s1, s2, p1, p2, p3, q, Ks1, r1, Kr11, Ks2, Kp1, Kp2, Kr12) = Vm * s1 * (s1 * s2 - p1 * p2 * p3 / q) / (pow(Ks1 * (1 + r1 / Kr11), 2) * Ks2 * ((1 + pow(s1 / (Ks1 * (1 + r1 / Kr11)), 2)) * (1 + s2 / Ks2) + (1 + p1 / Kp1) * (1 + p2 / Kp2) - 1 + r1 / Kr12))

function_33(Vm, s1, Ks1, r1, r2, Kr1, r3, Kr3, r4, Kr4) = Vm * s1 / Ks1 * (1 + (r1 + r2) / Kr1) / (1 + r3 / Kr3 + r4 / Kr4)

function_26(Vm, s1, p1, p2, q, Ks1, Kp1, Kp2) = Vm * (s1 - p1 * p2 / q) / (Ks1 * (s1 / Ks1 + (1 + p1 / Kp1) * (1 + p2 / Kp2)))

function_24(s1, s2, p1, q, Ks1, Ks2, Kp1, Vm) = Vm * (s1 * s2 - p1 / q) / (Ks1 * Ks2 * ((1 + s1 / Ks1) * (1 + s2 / Ks2) + p1 / Kp1))

Transketolase(Vm, q, s1, s2, p1, p2, K1, K2, K1s2, K2s1, r1, K2r1, K2s2, r2) = Vm * (q * s1 * s2 - p1 * p2) / (K1 * K2 * (1 + (1 + s2 / K1s2) * (s1 / K2s1 + r1 / K2r1) + s2 / K2s2 + 1 / K2 * (p2 * (1 + p1 * r2 / K1) + p1 + r2)))

function_23(Vm, s1, s2, p1, p2, p3, q, Ks1, Ks2, Kp1, Kp2, Kp3) = Vm * (s1 * s2 - p1 * p2 * p3 / q) / (Ks1 * Ks2 * ((1 + s1 / Ks1) * (1 + s2 / Ks2) + p1 / Kp1 + p2 / Kp2 + p3 / Kp3 + p1 * p2 * p3 / (Kp1 * Kp2 * Kp3)))

function_27(s1, s2, p1, p2, q, Ks1, Ks2, Kp1, Kp2, Vm) = Vm * (s1 * s2 - p1 * p2 / q) / (Ks1 * Ks2 * ((1 + s1 / Ks1) * (1 + s2 / Ks2) + (1 + p1 / Kp1) * (1 + p2 / Kp2) - 1))

function_32(Vm, s1, Ks1, r1, Kr1, r2, r3, Kr2) = Vm * s1 / Ks1 * (1 + r1 / Kr1) / (1 + (r2 + r3) / Kr2)

function_29(Vm, s1, p1, q, Ks1, Kp1) = Vm * (s1 - p1 / q) / (Ks1 * (1 + s1 / Ks1 + p1 / Kp1))

TPTout(Vm, s, Ks, r1, Kr1, r2, Kr2, p, Kp, r3, Kr3, r4, Kr4) = Vm / (s / Ks + r1 / Kr1 + r2 / Kr2 + p / Kp + r3 / Kr3 + r4 / Kr4 + (s / Ks + r1 / Kr1 + r2 / Kr2) * (p / Kp + r3 / Kr3 + r4 / Kr4)) * (s * (p / Kp + r3 / Kr3 + r4 / Kr4) / Ks - p * (s / Ks + r1 / Kr1 + r2 / Kr2) / Kp)

function_30(Vm, s1, p1, p2, q, Ks1, r1, Kr1, Kp1, Kp2) = Vm * s1 * (s1 - p1 * p2 / q) / (pow(Ks1 * (1 + r1 / Kr1), 2) * (pow(s1 / (Ks1 * (1 + r1 / Kr1)), 2) + (1 + p1 / Kp1) * (1 + p2 / Kp2)))

function_34(v) = v

Events

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.


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A quantitative comparison of Calvin-Benson cycle models.

  • Anne Arnold
  • Zoran Nikoloski
Trends Plant Sci. 2011; 16 (12): 676-683
Abstract
The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering.
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000392) Biomodels notes: The steady state concentration of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Laisk 2006) of the reference (supp. material) publication. The simulation was done using Copasi v4.7 (Build 34). JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.