Transformation of AA to PGH2

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The COX enzyme possesses two isoforms, COX-1 and COX-2, of which both produce bioactive eicosanoids. The two isoforms have nearly identical active site residues (Simmons et al. 2004), but COX-1 is a constitutive enzyme, whereas COX-2 is an inducible enzyme. Both enzymes add molecular oxygen to arachidonic acid, generating an endoperoxide species, PGH2, by catalysing the two-step reaction of cycloooxygenation and oxygenation, followed by a hydroperoxide reduction.

PGH2 possesses a short life time due to the formation of a reactive functional group. The endoperoxide undergoes rapid isomerisation reactions, catalysed by a series of synthase enzymes (PGES, PGDS, PGIS, PGFS and TXAS). The resultant species of the isomerisation reactions are PGs (PGE2, PGD2, PGJ2, deoxy-PGJ2 and PGF2α), TXs (TXA2 and TXB2) and prostacyclin (PGI2), all of which have varying effects on the immune system.

Reaction

Chemical equation

$AA \rightleftharpoons PGH2$

Rate equation

Enzyme Parameters

K_eq

Gibbs Free Energy Change

Value	Units	Species	Notes	Weight	Reference
(-30)	kcal/mol	Unspecified	Calculations with a Gaussian98 suite of programs Enzyme: COX (Unspecific) Substrate: Arachidonate Temperature: 298.15 K Pressure: 1 bar	64

Description of the COX-2 Keq distribution

Mode	Confidence Interval	Location parameter (µ)	Scale parameter (σ)
4.18E+28	1.00E+01	6.67E+01	8.90E-01

The estimated probability distribution for COX-2 Keq. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.

K_ms

Literature Information

Value	Units	Species	Notes	Weight	Reference
1.62E-02 ± 0.22E-02	$mM$	Human	Expression Vector: Embryonic kidney cells Enzyme: Cyclooxygenase-2 pH: Not specified Temperature: Not specified	128
5.14E-03 ± 2.90E-04	mM	Mouse	Expression Vector: Baculovirus (Insect Cell) Enzyme: COX-2 pH: 8.0 Temperature: 37 °C 1–200 µM of substrate.	128
2.1E-03 ± 4.00E-04	mM	Human	Expression Vector: E. Coli Enzyme: Wild Type Cyclooxygenase-2 Enzyme pH: 8.5 Temperature:30 °C	64
2.1E-03 ± 4.00E-04	mM	Human	Expression Vector: Baculuvirus Enzyme: Wild Type Cycloxygenase-2 pH: 7.2 Temperature: 30 °C 100 uM arachidonate substrate,	128

Description of the COX-2 Kms distribution

Mode (mM)	Confidence Interval	Location parameter (μ)	Scale parameter (σ)
4.90E-03	5.70E+00	-4.72E+00	7.77E-01

The estimated probability distribution for COX-2 Kms. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.

K_mp (Dependent parameter)

This is a “Dependent parameter”, meaning that the log-normal distribution for this parameter was calculated using multivariate distributions (discussed in Protocol for defining informative priors for ensemble modelling in systems biology). As a result, no confidence interval factor or literature values were cited for this parameter.

Description of the COX-2 Kmp distribution

Mode	Location parameter (µ)	Scale parameter (σ)
4.70E-03	-4.75E+00	7.87E-01

The estimated probability distribution for COX-2 Kmp. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.

k_cat

Literature Information

Value	Units	Species	Notes	Weight	Reference
1620 ± 24	per minute	Mouse	Expression Vector: Baculovirus (Insect Cell) Enzyme: COX-2 pH: 8.0 Temperature: 37 °C 1–200 µM of substrate.	128

Description of the COX-2 k_cat distribution

Mode (min-1)	Confidence Interval	Location parameter (µ)	Scale parameter (σ)
1.62E+03	1.01E+00	7.39E+00	1.48E-02

The estimated probability distribution for COX-2 kcat. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.

Enzyme concentration

Literature Information

Value	Units	Species	Notes	Weight	Reference
13.7	$ppm$	Human	Expression Vector: Platlet Enzyme: Cyclooxygenase-2 (PGTS2) pH: 7.5 Temperature: 37 °C	1024
4.11	$ppm$	Human	Expression Vector: Stomach Enzyme: Cyclooxygenase-2 (PGTS2) pH: 7.5 Temperature: 37 °C	1024
1.49	$ppm$	Human	Expression Vector: Oral Cavity Enzyme: Cyclooxygenase-2 (PGTS2) pH: 7.5 Temperature: 37 °C	1024

The abundance of COX-2 (ppm) was converted to COX-2 (mM). As a result, the concentration of COX-2 in unstimulated tissue was estimated as 2.27 x10-5 mM. The upregulation of COX-2 in HaCaT keratinocytes was estimated using western blotting in (Kiezel-Tsugunova, 2017), figure * shows an example. Using this information, in silico experiments which included an upregulation of COX-2, included the concentration of COX-2 reaching 100 times higher concentration than the estimated unstimulated concentration. Therefore, the COX-2 induction event includes the concentration of COX-2 eventually reaching a concentration of 2.27 x10-3 mM after 6h post irradiation.

The relative expression of COX-2 protein in HaCaT keratinocytes (Kiezel-Tsugunova, 2017).

COX Enzyme Parameters with other substrates

Michaelis-Menten Constants (When EPA is the substrate)

Value	Units	Species	Notes	Reference
9.45E-03 ± 7.30E-04	mM	Mouse	Expression Vector: Baculovirus (Insect Cell) Enzyme: COX-2 pH: 8.0 Temperature: 37 °C 1–200 µM of substrate.

Enzyme Turnover Numbers (When EPA is the substrate)

Value	Units	Species	Notes	Reference
522 ± 12.6	per minute	Mouse	Expression Vector: Baculovirus (Insect Cell) Enzyme: COX-2 pH: 8.0 Temperature: 37 °C 1–200 µM of substrate.

Michaelis-Menten Constants (When DHA is the substrate)

Value	Units	Species	Notes	Reference
3.68E-02 ± 4.25E-03	mM	Mouse	Expression Vector: Baculovirus (Insect Cell) Enzyme: COX-2 pH: 8.0 Temperature: 37 °C 1–200 µM of substrate.

Enzyme Turnover Numbers (When DHA is the substrate)

Value	Units	Species	Notes	Reference
207 ± 9	per minute	Mouse	Expression Vector: Baculovirus (Insect Cell) Enzyme: COX-2 pH: 8.0 Temperature: 37 °C 1–200 µM of substrate.

Related Reactions

• Transformation of PL to AA
• Transformation of PGH2 to PGF2α
• Transformation of PGH2 to TXA2
• Transformation of PGH2 to PGI2
• Transformation of PGH2 to PGD2
• Transformation of PGH2 to PGE2