bakker1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000071) Biomodels notes: The paper refers to the model equations present in Bakker et al's " Glycolysis in bloodstream from Trypanosoma brucei can be understood in terms of the kinetics of glycolytic enzymes" (Pubmed ID: 9013556), also, the authors claim that some of the modifications in these equations were made based on the experimental results from the paper "Contribution of glucose transport in the control of glycolytic flux in Trypanosoma brucei" (Pubmed ID: 10468568). The model reproduces the various flux values in Fig 3 for 100% TPI activity. It also matches with the values provided in Table 2 of the paper. The model was successfully tested with Copasi and SBML ODE Solver. The volumes are set to the values containing 1 mg of total protein per microlitre total cell volume. To change the protein concentration use Vt , the total cell volume in micro litre per mg protein. To change the TPI activity use the global parameter TPIact. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

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Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei.

  • S Helfert
  • AM Estévez
  • B Bakker
  • P Michels
  • Christine Clayton
Biochem. J. 2001; 357 : 117-125
Abstract
Kinetoplastid protozoa compartmentalize the first seven enzymes of glycolysis and two enzymes of glycerol metabolism in a microbody, the glycosome. While in its mammalian host, Trypanosoma brucei depends entirely on glucose for ATP generation. Under aerobic conditions, most of the glucose is metabolized to pyruvate. Aerobic metabolism depends on the activities of glycosomal triosephosphate isomerase and a mitochondrial glycerophosphate oxidase, and on glycerophosphate<-->dihydroxyacetone phosphate exchange across the glycosomal membrane. Using a combination of genetics and computer modelling, we show that triosephosphate isomerase is probably essential for bloodstream trypanosome survival, but not for the insect-dwelling procyclics, which preferentially use amino acids as an energy source. When the enzyme level decreased to about 15% of that of the wild-type, the growth rate was halved. Below this level, a lethal rise in dihydroxyacetone phosphate was predicted. Expression of cytosolic triosephosphate isomerase inhibited cell growth. Attempts to knockout the trypanosome alternative oxidase genes (which are needed for glycerophosphate oxidase activity) were unsuccessful, but when we lowered the level of the corresponding mRNA by expressing a homologous double-stranded RNA, oxygen consumption was reduced fourfold and the rate of trypanosome growth was halved.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
Id Name Spatial dimensions Size
default_compartment 3.0 1.0
Id Name Initial quantity Compartment Fixed
BPGA13 0.0 default_compartment
DHAP 1.0 default_compartment
Fru16BP 10.0 default_compartment
Fru6P 1.0 default_compartment
GAP 0.0 default_compartment
Glc6P 1.0 default_compartment
GlcE 5.0 default_compartment
GlcI 0.0 default_compartment
Gly 0.0 default_compartment
Gly3P 0.0 default_compartment
NAD 4.0 default_compartment
NADH 0.0 default_compartment
Nb 1.0 default_compartment
Pc 1.0 default_compartment
Pg 1.0 default_compartment
Pyr 1.0 default_compartment
PyrE 0.0 default_compartment
X 0.0 default_compartment

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
v_1 GlcE = {0.175439}GlcI

Vm1*(GlcE - GlcI)/(K1Glc + GlcE + GlcI + afac*GlcE*GlcI/K1Glc)
v_10 {0.183306}Pyr = PyrE

Vm10*Pyr/K10Pyr/(1 + Pyr/K10Pyr)
v_11 {4.087719}BPGA13 = {0.175439}Nb + {4.087719}Pg

(Vm11*(Vm11f*(BPGA13*ADPg/K11BPGA13/K11ADPg - Vm11r/Vm11f*PGA3*ATPg/K11PGA3/K11ATPg)/((1 + BPGA13/K11BPGA13 + PGA3/K11PGA3)*(1 + ADPg/K11ADPg + ATPg/K11ATPg))))
v_12 {0.175439}Nb = {0.183306}Pc + {0.183306}Pyr

(Vm12*((PEP/K12PEP)^n12 * ADPc/K12ADP/(1+(PEP/K12PEP)^n12)/(1+ADPc/K12ADP)))
v_13 {0.183306}Pc = X

(K13*ATPc/ADPc)
v_14 X = Gly + {4.087719}Pg

(Vm14*(Vm14f*(Gly3Pg*ADPg/K14Gly3Pg/K14ADPg) - (Vm14r*(Gly*ATPg/K14Gly/K14ATPg)))/((1 + Gly3Pg/K14Gly3Pg + Gly/K14Gly)*(1+ADPg/K14ADPg+ATPg/K14ATPg)))
v_2 {0.175439}GlcI + {4.087719}Pg = {4.087719}Glc6P

(Vm2*ATPg*GlcI/K2GlcI/K2ATPg/(1 + ATPg/K2ATPg + ADPg/K2ADPg)/(1 + GlcI/K2GlcI + Glc6P/K2Glc6P))
v_3 {4.087719}Glc6P = {4.087719}Fru6P

Vm3*(Glc6P/K3Glc6P - Fru6P/K3Fru6P)/(1 + Glc6P/K3Glc6P + Fru6P/K3Fru6P)
v_4 {4.087719}Fru6P + {4.087719}Pg = {4.087719}Fru16BP

(Vm4*(K4i1Fru16BP/(K4i1Fru16BP + Fru16BP)*Fru6P/K4Fru6P*ATPg/K4ATPg/(1 + Fru6P/K4Fru6P + Fru16BP/K4i2Fru16BP)/(1 + ATPg/K4ATPg)))
v_5 {4.087719}Fru16BP = {0.175439}DHAP + {4.087719}GAP

(Vm5*(Vm5f*Fru16BP/K5Fru16BP - Vm5r*GAP*DHAPg/K5GAP/K5DHAP)/(1+Fru16BP/K5Fru16BP+GAP/K5GAP+DHAPg/K5DHAP+Fru16BP/K5Fru16BP*GAP/K5i+GAP*DHAPg/K5GAP/K5DHAP))
v_6 {0.175439}DHAP = {4.087719}GAP

(Vm6*(DHAPg/K6DHAPg - 5.7*GAP/K6GAP)/(1 + DHAPg/K6DHAPg + GAP/K6GAP))
v_7 {4.087719}GAP + {4.087719}NAD = {4.087719}BPGA13 + {4.087719}NADH

Vm7*(Vm7f*(GAP*(NAD/K7GAP/K7NAD) - (Vm7r/Vm7f)*(BPGA13*NADH/K7BPGA13/K7NADH))/((1 + GAP/K7GAP + BPGA13/K7BPGA13)*(1 + NAD/K7NAD + NADH/K7NADH)))
v_8 {0.175439}DHAP + {4.087719}NADH = Gly3P + {4.087719}NAD

(Vm8*(Vm8f*((DHAPg*NADH/K8DHAPg/K8NADH) - (Vm8r/Vm8f)*(NAD*Gly3Pg/K8NAD/K8Gly3Pg))/((1 + DHAPg/K8DHAPg + Gly3Pg/K8Gly3Pg)*(1 + NADH/K8NADH + NAD/K8NAD))))
v_9 Gly3P = {0.175439}DHAP

(Vm9*(Gly3Pc/K9Gly3Pc)/(1+Gly3Pc/K9Gly3Pc))

Global parameters

Id Value
ADPc 0.0
ADPg 0.0
AMPg 0.0
ATPc 0.0
ATPg 0.0
DHAPc 0.0
DHAPct0 4.01536
DHAPg 0.0
Gly3Pc 0.0
Gly3Pg 0.0
K10Pyr 1.96
K11ADPg 0.1
K11ATPg 0.29
K11BPGA13 0.05
K11PGA3 1.62
K12ADP 0.114
K12PEP 0.0
K13 50.0
K14ADPg 0.12
K14ATPg 0.19
K14Gly 0.12
K14Gly3Pg 5.1
K1Glc 2.0
K2ADPg 0.126
K2ATPg 0.116
K2Glc6P 12.0
K2GlcI 0.1
K3Fru6P 0.12
K3Glc6P 0.4
K4ATPg 0.026
K4Fru6P 0.82
K4i1Fru16BP 15.8
K4i2Fru16BP 10.7
K5DHAP 0.015
K5Fru16BP 0.0
K5GAP 0.067
K5i 0.098
K6DHAPg 1.2
K6GAP 0.25
K7BPGA13 0.1
K7GAP 0.15
K7NAD 0.45
K7NADH 0.02
K8DHAPg 0.1
K8Gly3Pg 2.0
K8NAD 0.4
K8NADH 0.01
K9Gly3Pc 1.7
KeqAK 0.442
KeqENO 6.7
KeqPGM 0.187
PEP 0.0
PGA3 0.0
Vc 5.4549
Vg 0.2451
Vm1 106.2
Vm10 200.0
Vm11 1.0
Vm11f 640.0
Vm11r 18.56
Vm12 2600.0
Vm14 1.0
Vm14f 200.0
Vm14r 33400.0
Vm2 625.0
Vm3 848.0
Vm4 780.0
Vm5 1.0
Vm5f 184.5
Vm5r 219.555
Vm6 842.0
Vm7 1.0
Vm7f 1470.0
Vm7r 984.9
Vm8 1.0
Vm8f 533.0
Vm8r 149.24
Vm9 368.0
Vt 5.7
ac 0.0
afac 0.75
ag 0.0
n12 2.5
rsum 0.0
sumAc 3.9
sumAg 6.0
sumc4 45.0
sumc5 5.0

Local parameters

Id Value Reaction

Assignment rules

Definition
ADPg = Pg-2*ATPg
Gly3Pc = sumc5 - DHAPc
Gly3Pg = sumc4 - DHAPg - Glc6P - Fru6P - 2*Fru16BP - GAP - BPGA13 - Pg
AMPg = sumAg-ATPg-ADPg
ag = 1-4*KeqAK
ADPc = Pc-2*ATPc
PEP = PGA3*KeqPGM*KeqENO
ac = 1-4*KeqAK
DHAPg = (DHAP*Vt - DHAPc*Vc)/Vg
K12PEP = 0.34*(1 + ATPc/0.57 + ADPc/0.64)
K5Fru16BP = 0.009*(1+ATPg/0.68+ADPg/1.51+AMPg/3.65)
PGA3 = Nb*(1 + Vc/Vg)/(1 + Vc/Vg*(1 + KeqPGM + KeqPGM*KeqENO))
ATPg = (-(sumAg-Pg*ag)+((sumAg-Pg*ag)*(sumAg-Pg*ag)-4*ag*(-KeqAK*Pg*Pg))^0.5)/2/ag
DHAPc = sumc5*DHAP*(Vc/Vg+1)/(sumc5*Vc/Vg + rsum)
rsum = sumc4 - Glc6P - Fru6P - 2*Fru16BP - GAP - BPGA13 - Pg
ATPc = (-(sumAc-Pc*ac)+((sumAc-Pc*ac)*(sumAc-Pc*ac)-4*ac*(-KeqAK*Pc*Pc))^0.5)/2/ac

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments