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Understanding glucose transport by the bacterial phosphoenolpyruvate:glycose phosphotransferase system on the basis of kinetic measurements in vitro.

  • Johann M Rohwer
  • ND Meadow
  • S Roseman
  • Hans V Westerhoff
  • PW Postma
J. Biol. Chem. 2000; 275 (45): 34909-34921
Abstract
The kinetic parameters in vitro of the components of the phosphoenolpyruvate:glycose phosphotransferase system (PTS) in enteric bacteria were collected. To address the issue of whether the behavior in vivo of the PTS can be understood in terms of these enzyme kinetics, a detailed kinetic model was constructed. Each overall phosphotransfer reaction was separated into two elementary reactions, the first entailing association of the phosphoryl donor and acceptor into a complex and the second entailing dissociation of the complex into dephosphorylated donor and phosphorylated acceptor. Literature data on the K(m) values and association constants of PTS proteins for their substrates, as well as equilibrium and rate constants for the overall phosphotransfer reactions, were related to the rate constants of the elementary steps in a set of equations; the rate constants could be calculated by solving these equations simultaneously. No kinetic parameters were fitted. As calculated by the model, the kinetic parameter values in vitro could describe experimental results in vivo when varying each of the PTS protein concentrations individually while keeping the other protein concentrations constant. Using the same kinetic constants, but adjusting the protein concentrations in the model to those present in cell-free extracts, the model could reproduce experiments in vitro analyzing the dependence of the flux on the total PTS protein concentration. For modeling conditions in vivo it was crucial that the PTS protein concentrations be implemented at their high in vivo values. The model suggests a new interpretation of results hitherto not understood; in vivo, the major fraction of the PTS proteins may exist as complexes with other PTS proteins or boundary metabolites, whereas in vitro, the fraction of complexed proteins is much smaller.

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
60.0 second
1e-06 mole litre^(-1.0)
Id Name Spatial dimensions Size
default_compartment 3.0 1.0
Id Name Initial quantity Compartment Fixed
EI 3.0 uM/<compartment size units> default_compartment
EIIA 20.0 uM/<compartment size units> default_compartment
EIIAP 20.0 uM/<compartment size units> default_compartment
EIIAPIICB 0.0 uM/<compartment size units> default_compartment
EIICB 5.0 uM/<compartment size units> default_compartment
EIICBP 5.0 uM/<compartment size units> default_compartment
EIICBPGlc 0.0 uM/<compartment size units> default_compartment
EIP 2.0 uM/<compartment size units> default_compartment
EIPHPr 0.0 uM/<compartment size units> default_compartment
Glc 500.0 uM/<compartment size units> default_compartment
GlcP 50.0 uM/<compartment size units> default_compartment
HPr 25.0 uM/<compartment size units> default_compartment
HPrP 25.0 uM/<compartment size units> default_compartment
HPrPIIA 0.0 uM/<compartment size units> default_compartment
PEP 2800.0 uM/<compartment size units> default_compartment
Pyr 900.0 uM/<compartment size units> default_compartment
PyrPI 0.0 uM/<compartment size units> 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 PEP + EI = PyrPI

k1f*PEP*EI - k1r*PyrPI
v_10 EIICBPGlc = EIICB + GlcP

k10f*EIICBPGlc - k10r*EIICB*GlcP
v_2 PyrPI = Pyr + EIP

k2f*PyrPI - k2r*Pyr*EIP
v_3 EIP + HPr = EIPHPr

k3f*EIP*HPr - k3r*EIPHPr
v_4 EIPHPr = EI + HPrP

k4f*EIPHPr - k4r*EI*HPrP
v_5 HPrP + EIIA = HPrPIIA

k5f*HPrP*EIIA - k5r*HPrPIIA
v_6 HPrPIIA = HPr + EIIAP

k6f*HPrPIIA - k6r*HPr*EIIAP
v_7 EIIAP + EIICB = EIIAPIICB

k7f*EIIAP*EIICB - k7r*EIIAPIICB
v_8 EIIAPIICB = EIIA + EIICBP

k8f*EIIAPIICB - k8r*EIIA*EIICBP
v_9 EIICBP + Glc = EIICBPGlc

k9f*EIICBP*Glc - k9r*EIICBPGlc

Global parameters

Id Value
k10f 4800.0
k10r 0.0054
k1f 1960.0
k1r 480000.0
k2f 108000.0
k2r 294.0
k3f 14000.0
k3r 14000.0
k4f 84000.0
k4r 3360.0
k5f 21960.0
k5r 21960.0
k6f 4392.0
k6r 3384.0
k7f 880.0
k7r 880.0
k8f 2640.0
k8r 960.0
k9f 260.0
k9r 389.0

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments