Difference between revisions of "Transformation of AA to PGH2"

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(COX-2 Enzyme Parameters)
(Kms)
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[[Image:5.jpg|center|thumb|500px|Figure 1: 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.  ]]
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[[Image:5.jpg|thumb|500px|Figure 1: 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<sub>mp</sub> (Dependent parameter) ===
 
=== K<sub>mp</sub> (Dependent parameter) ===

Revision as of 14:30, 14 May 2019

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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

R2 AA-PGH2.jpg

Chemical equation

 AA \rightleftharpoons PGH2

Rate equation

R02.PNG

COX-1/-2 Enzyme Parameters

Gibbs Free Energy Change
Value Units Species Notes Reference
(-30) kcal/mol Unspecified Calculations with a Gaussian98 suite of programs

Enzyme: COX (Unspecific) Substrate: Arachidonate Temperature: 298.15 K Pressure: 1 bar

[1]

COX-1 Enzyme Parameters

COX-1 Michaelis-Menten Constants
Value Units Species Notes Reference
0.0088 ± 0.0022  mM Human Expression Vector: Human

Enzyme: Cyclooxygenase-1 pH: 7.6 - 8.4 Temperature: 37 °C

[2]
0.0019 ± 0.0002  mM Ram Expression Vector: Ram

Enzyme: Cyclooxygenase-1 pH: 8 Temperature: 30 ± 0.2 °C

[3]
COX-1 Turnover Number
Value Units Species Notes Reference
8820 ± 360  per minute Ram Expression Vector: Ram

Enzyme: Cyclooxygenase-1 pH: 8 Temperature: 30 ± 0.2 °C

[3]


COX-1 Abundance
Value Units Species Notes Reference
1176  ppm Human Expression Vector: Urinary Bladder

Enzyme: Cyclooxygenase-1 (PGTS1) pH: 7.5 Temperature: 37 °C

[4]
849  ppm Human Expression Vector: Platlet

Enzyme: Cyclooxygenase-1 (PGTS1) pH: 7.5 Temperature: 37 °C

[4]
208  ppm Human Expression Vector: Stomach

Enzyme: Cyclooxygenase-1 (PGTS1) pH: 7.5 Temperature: 37 °C

[5]
130  ppm Human Expression Vector: Esophagus

Enzyme: Cyclooxygenase-1 (PGTS1) pH: 7.5 Temperature: 37 °C

[5]
70.8  ppm Human Expression Vector: Oral Cavity

Enzyme: Cyclooxygenase-1 (PGTS1) pH: 7.5 Temperature: 37 °C

[5]
19.1  ppm Human Expression Vector: Lung

Enzyme: Cyclooxygenase-1 (PGTS1) pH: 7.5 Temperature: 37 °C

[4]

COX-2 Enzyme Parameters

Kms

Literature COX-2 Michaelis-Menten Constant (When AA is the substrate)
Value Units Species Notes Reference
1.62E-02 ± 0.22E-02  mM Human Expression Vector: Embryonic kidney cells

Enzyme: Cyclooxygenase-2 pH: Not specified Temperature: Not specified

[6]
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.

[7]
2.1E-03 ± 4.00E-04 mM Human Expression Vector: E. Coli

Enzyme: Wild Type Cyclooxygenase-2 Enzyme pH: 8.5 Temperature:30 °C

[8]
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,

[9]


Summary 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


Figure 1: 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.

Kmp (Dependent parameter)

Summary of the COX-2 Kmp distribution
Mode Location parameter (µ) Scale parameter (σ)
4.70E-03 -4.75E+00 7.87E-01
6.jpg

kcat

|+ style="text-align: left;" | Literature COX-2 kcat
Value Units Species Notes 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.

[7]
|+ style="text-align: left;" | Summary of the COX-2 kcat distribution
Mode (min-1) Confidence Interval Location parameter (µ) Scale parameter (σ)
1.62E+03 1.01E+00 7.39E+00 1.48E-02
Cox2 kcat.jpg


Enzyme concentration

|+ style="text-align: left;" | Literature COX-2 concentration
Value Units Species Notes Reference
13.7  ppm Human Expression Vector: Platlet

Enzyme: Cyclooxygenase-2 (PGTS2) pH: 7.5 Temperature: 37 °C

[4]
4.11  ppm Human Expression Vector: Stomach

Enzyme: Cyclooxygenase-2 (PGTS2) pH: 7.5 Temperature: 37 °C

[5]
1.49  ppm Human Expression Vector: Oral Cavity

Enzyme: Cyclooxygenase-2 (PGTS2) pH: 7.5 Temperature: 37 °C

[5]

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.

MKT COX-2.png

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.

[7]
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.

[7]
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.

[7]
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.

[7]

References

  1. P. Silva, "A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase" Theor Chem Acc (2003) 110: 345
  2. Y. Noreen Development of a Radiochemical Cyclooxygenase-1 and -2 in Vitro Assay for Identification of Natural Products as Inhibitors of Prostaglandin BiosynthesisJ. Nat. Prod., 1998, 61 (1), pp 2–7)
  3. 3.0 3.1 Mukherjee Molecular Oxygen Dependent Steps in Fatty Acid Oxidation by Cyclooxygenase-1 Biochemistry, 2007, 46 (13), pp 3975–3989
  4. 4.0 4.1 4.2 4.3 M. Kim A draft map of the human proteome Nature, 2014 509, 575–581
  5. 5.0 5.1 5.2 5.3 5.4 [http://www.nature.com/nature/journal/v509/n7502/pdf/nature13319.pdf M. Wilhelm Mass-spectrometry-based draft of the human proteome Nature, 2014 509, 582–587]
  6. S.F. Kim Inducible nitric oxide synthase binds, S-nitrosylates, and activates cyclooxygenase-2. Science 2005,310(5756):1966-70)
  7. 7.0 7.1 7.2 7.3 7.4 7.5 [www.ncbi.nlm.nih.gov/pubmed/20463020 Vecchio A. J. "Structural basis of fatty acid substrate binding to cyclooxygenase-2." J. Biol. Chem. 285 22152-63 (2010)]
  8. [http://pubs.acs.org/doi/pdf/10.1021/bi035717o Rogge C. "Identification of Tyr504 as an Alternative Tyrosyl Radical Site in Human Prostaglandin H Synthase-2" Biochemistry 2004, 43, 1560-1568]
  9. [http://www.jbc.org/content/279/6/4084.full.pdf Bambai B. "Role of Asn-382 and Thr-383 in Activation and Inactivation of Human Prostaglandin H Synthase Cyclooxygenase Catalysis" February 6, 2004 The Journal of Biological Chemistry, 279, 4084-4092.]

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