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Table 1 Model parameters for convenience kinetics

From: Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

Parameter

Symbol

unit

item in graph

energy interpretation

Energy constant

k i G MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemyAaKgabaacbaGae83raCeaaaaa@30AF@

1

metabolite

metabolite formation

Velocity constant

k l V MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemiBaWgabaacbaGae8Nvayfaaaaa@30D3@

1/s

reaction

transition state

Michaelis-Menten constant

k l i M MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemiBaWMaemyAaKgabaacbaGae8xta0eaaaaa@321C@

mM

arrow reaction – substrate

substrate binding

Activation constant

k l i A MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemiBaWMaemyAaKgabaacbaGae8xqaeeaaaaa@3204@

mM

arrow reaction – activator

activator binding

Inhibition constant

k l i I MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemiBaWMaemyAaKgabaacbaGae8xsaKeaaaaa@3214@

mM

arrow reaction – inhibitor

inhibitor binding

Metabolite concentration

c i

mM

metabolite

 

Enzyme concentration

E l

mM

reaction

 
  1. The system parameters (top) are thermodynamically independent. Their numerical values can be written as exp(G/RT) where G denotes either a Gibbs free energy or a difference of Gibbs free energies. The corresponding molecular processes are listed in the last column. In contrast to the system parameters, enzyme and metabolite concentrations (bottom) can easily fluctuate over time; we call them state parameters.