Difference between revisions of "Transformation of 12-HPETE to 12-HETE"

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[[Welcome to the In-Silico Model of Cutaneous Lipids Wiki | Return to overview]]
 
[[Welcome to the In-Silico Model of Cutaneous Lipids Wiki | Return to overview]]
 +
 +
Upon being generated, 12-HPETE can be reduced by an oxidoreductase enzyme, phospholipid hydroperoxide glutathione peroxidase (PHGPx), to form 12-HETE respectively.
 +
 
== Reaction ==
 
== Reaction ==
  
Line 6: Line 9:
 
==Chemical equation==
 
==Chemical equation==
  
−
<center><math> AA \rightleftharpoons PGH2 </math></center>
+
<center><math> 12-HPETE \rightleftharpoons 12-HETE </math></center>
  
 
== Rate equation ==
 
== Rate equation ==
  
 +
[[File:R20.PNG |center|500px]]
  
 
== Parameters ==
 
== Parameters ==
 +
Note that the literature values are the same as [[Transformation of 5-HPETE to 5-HETE |reaction 12]].
 +
 +
=== K<sub>ms</sub> ===
 +
{|class="wikitable sortable"
 +
|+  style="text-align: left;" | Literature values
 +
|-
 +
! Value
 +
! Units
 +
! Species
 +
! Notes
 +
! Weight
 +
! Reference
 +
|-
 +
|3.00E-01
 +
|<math> mM </math>
 +
|Human
 +
|Expression Vector: Bioimprited Enzyme - Selenosubtilisin
 +
Enzyme: Glutathione Peroxidase
 +
pH: 7
 +
Temperature: 37
 +
|512
 +
|<ref name="Liu2008"> [http://www.ncbi.nlm.nih.gov/pubmed/18163571 Liu L. "Functional mimicry of the active site of glutathione peroxidase by glutathione imprinted selenium-containing protein.'' Biomacromolecules. 2008 Jan;9(1):363-8. doi: 10.1021/bm7008312. Epub 2007 Dec 29.]</ref>
 +
|-
 +
|11.1 ± 2.90E-01
 +
|<math> mM </math>
 +
|Human
 +
|Expression Vector: E Coli
 +
Enzyme: Wild Type Glutathione Peroxidase Enzyme (Se-hGSTZ1-1)
 +
pH: 7
 +
Temperature: 37
 +
|1024
 +
|<ref name="Zheng2008"> [http://www.ncbi.nlm.nih.gov/pubmed/18373941 Zheng K. "A novel selenium-containing glutathione transferase zeta1-1, the activity of which surpasses the level of some native glutathione peroxidases.'' Int J Biochem Cell Biol. 2008;40(10):2090-7. doi: 10.1016/j.biocel.2008.02.006. Epub 2008 Feb 15.]</ref>
 +
|-
 +
|4.00E-03
 +
|<math> mM </math>
 +
|Rat
 +
|Expression Vector: Rat Liver Cells
 +
Enzyme: Glutathione Peroxidase
 +
pH: 7.4
 +
Temperature: 37
 +
|768
 +
|<ref name="Hirat1997"> [http://www.ncbi.nlm.nih.gov/pubmed/9030530 Hiratsuka A. "Subunit Ya-specific glutathione peroxidase activity toward cholesterol 7-hydroperoxides of glutathione S-transferases in cytosols from rat liver and skin.'' J Biol Chem. 1997 Feb 21;272(8):4763-9.]</ref>
 +
|-
 +
|}
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PHGPx Kms distribution
 +
! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 3.19E-01 || 1.02E+03 || 2.54E+00 || 1.92E+00
 +
|}
 +
 +
[[Image:37.jpg|none|thumb|500px|The estimated probability distribution for PHGPx 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> ===
 +
This is a “Dependent parameter”, meaning that the log-normal distribution for this parameter was calculated using multivariate distributions  (this is discussed in detail[[Quantification of parameter uncertainty | here]]). As a result, no confidence interval factor or literature values were cited for this parameter. 
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PHGPx Kmp distribution
 +
! Mode (mM) !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 3.15E-01 || 2.53E+00 || 1.92E+00
 +
|}
 +
 +
[[Image:38.jpg|none|thumb|500px|The estimated probability distribution for PHGPx 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<sub>cat</sub> ===
 +
{|class="wikitable sortable"
 +
|+  style="text-align: left;" | Literature values
 +
|-
 +
! Value
 +
! Units
 +
! Species
 +
! Notes
 +
! Weight
 +
! Reference
 +
|-
 +
|1170 ± 50
 +
|<math> min^{-1} </math>
 +
|Human
 +
|Expression Vector: Bioimprited Enzyme - Selenosubtilisin
 +
Enzyme: Glutathione Peroxidase
 +
pH: 7
 +
Temperature: 37
 +
| 512
 +
|<ref name="Liu2008"> [http://www.ncbi.nlm.nih.gov/pubmed/18163571 Liu L. "Functional mimicry of the active site of glutathione peroxidase by glutathione imprinted selenium-containing protein.'' Biomacromolecules. 2008 Jan;9(1):363-8. doi: 10.1021/bm7008312. Epub 2007 Dec 29.]</ref>
 +
|-
 +
|24500 ± 150
 +
|<math> min^{-1} </math>
 +
|Human
 +
|Expression Vector: E Coli
 +
Enzyme: Wild Type Glutathione Peroxidase Enzyme (Se-hGSTZ1-1)
 +
pH: 7
 +
Temperature: 37
 +
|1024
 +
|<ref name="Zheng2008"> [http://www.ncbi.nlm.nih.gov/pubmed/18373941 Zheng K. "A novel selenium-containing glutathione transferase zeta1-1, the activity of which surpasses the level of some native glutathione peroxidases.'' Int J Biochem Cell Biol. 2008;40(10):2090-7. doi: 10.1016/j.biocel.2008.02.006. Epub 2008 Feb 15.]</ref>
 +
|-
 +
|}
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PHGPx kcat distribution
 +
! Mode (min-1) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 2.44E+04 || 4.20E+00 || 1.11E+01 || 9.75E-01
 +
|}
 +
 +
[[Image:39.jpg|none|thumb|500px|The estimated probability distribution for PHGPx 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.  ]]
  
−
* [[Transformation of 5-HPETE to 5-HETE |See PHGPx parameters here. ]]
+
=== Enzyme concentration ===
  
−
{|class="wikitable"  
+
To convert the enzyme concentration from ppm to mM, the following [[Common equations#Enzyme concentration (mM)|equation]] was used.
−
! Name
+
 
 +
{|class="wikitable sortable"
 +
|+  style="text-align: left;" | Literature values
 +
|-
 
! Value
 
! Value
 
! Units
 
! Units
 
! Species
 
! Species
 +
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
−
| X
+
|459
−
| Y
+
|<math> ppm </math>
−
| Z
+
|Human
−
| A
+
|Expression Vector: Skin
−
| B
+
Enzyme: PHGPx
 +
pH: 7.5
 +
Temperature: 37 °C
 +
|2048
 +
|<ref name="Wilhelm2014"> [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]</ref>
 +
|-
 +
|307
 +
|<math> ppm </math>
 +
|Human
 +
|Expression Vector: Lung
 +
Enzyme: PHGPx
 +
pH: 7.5
 +
Temperature: 37 °C
 +
|1024
 +
|<ref name="Wilhelm2014"> [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]</ref>
 +
|-
 +
|282
 +
|<math> ppm </math>
 +
|Human
 +
|Expression Vector: Esophagus
 +
Enzyme: PHGPx
 +
pH: 7.5
 +
Temperature: 37 °C
 +
|1024
 +
|<ref name="Wilhelm2014"> [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]</ref>
 +
|-
 +
|204
 +
|<math> ppm </math>
 +
|Human
 +
|Expression Vector: Gut
 +
Enzyme: PHGPx
 +
pH: 7.5
 +
Temperature: 37 °C
 +
|1024
 +
|<ref name="Kim2014"> [http://www.nature.com/nature/journal/v509/n7502/pdf/nature13302.pdf M. Kim ''A draft map of the human proteome'' Nature, 2014 509, 575–581]</ref>
 +
|-
 
|}
 
|}
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PHGPx concentration distribution
 +
! Mode (ppm) !! Mode (mM) !!  Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 3.14E+02 ||1.74E-03|| 1.38E+00 || 5.85E+00 || 3.09E-01
 +
|}
 +
 +
[[Image:166.jpg|none|thumb|500px|The estimated probability distribution for PHGPx concentration. 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>eq</sub> ===
 +
 +
{|class="wikitable sortable"
 +
|+  style="text-align: left;" | Literature values
 +
|-
 +
! Gibbs Free Energy Change
 +
! Units
 +
! Species
 +
! Notes
 +
! Weight
 +
! Reference
 +
|-
 +
|(-26.941177)
 +
|kcal/mol
 +
|Not stated
 +
|Estimated
 +
Enzyme: PHGPx
 +
Substrate:a hydroperoxy-fatty-acyl-[lipid]
 +
Product: a hydroxy-fatty-acyl-[lipid]
 +
pH: 7.3
 +
ionic strength: 0.25
 +
|64
 +
|<ref name="MetaCyc”>[http://metacyc.org/META/NEW-IMAGE?type=REACTION&object=1.11.1.12-RXN Caspi et al 2014, "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases," Nucleic Acids Research 42:D459-D471]</ref>
 +
|}
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PHGPx Keq distribution
 +
! Mode !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 5.90E+19 || 1.00E+01 || 4.63E+01 || 8.90E-01
 +
|}
 +
 +
[[Image:40.jpg|none|thumb|500px|The estimated probability distribution for PHGPx 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.  ]]
  
 
== Related Reactions ==
 
== Related Reactions ==

Latest revision as of 08:20, 21 August 2019

Return to overview

Upon being generated, 12-HPETE can be reduced by an oxidoreductase enzyme, phospholipid hydroperoxide glutathione peroxidase (PHGPx), to form 12-HETE respectively.

Reaction

R20 HPETE12 - HETE12.jpg

Chemical equation

12-HPETE \rightleftharpoons 12-HETE

Rate equation

R20.PNG

Parameters

Note that the literature values are the same as reaction 12.

Kms

Literature values
Value Units Species Notes Weight Reference
3.00E-01 mM Human Expression Vector: Bioimprited Enzyme - Selenosubtilisin

Enzyme: Glutathione Peroxidase pH: 7 Temperature: 37

512 [1]
11.1 ± 2.90E-01 mM Human Expression Vector: E Coli

Enzyme: Wild Type Glutathione Peroxidase Enzyme (Se-hGSTZ1-1) pH: 7 Temperature: 37

1024 [2]
4.00E-03 mM Rat Expression Vector: Rat Liver Cells

Enzyme: Glutathione Peroxidase pH: 7.4 Temperature: 37

768 [3]
Description of the PHGPx Kms distribution
Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
3.19E-01 1.02E+03 2.54E+00 1.92E+00
The estimated probability distribution for PHGPx 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

This is a “Dependent parameter”, meaning that the log-normal distribution for this parameter was calculated using multivariate distributions (this is discussed in detail here). As a result, no confidence interval factor or literature values were cited for this parameter.

Description of the PHGPx Kmp distribution
Mode (mM) Location parameter (µ) Scale parameter (σ)
3.15E-01 2.53E+00 1.92E+00
The estimated probability distribution for PHGPx 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.

kcat

Literature values
Value Units Species Notes Weight Reference
1170 ± 50 min^{-1} Human Expression Vector: Bioimprited Enzyme - Selenosubtilisin

Enzyme: Glutathione Peroxidase pH: 7 Temperature: 37

512 [1]
24500 ± 150 min^{-1} Human Expression Vector: E Coli

Enzyme: Wild Type Glutathione Peroxidase Enzyme (Se-hGSTZ1-1) pH: 7 Temperature: 37

1024 [2]
Description of the PHGPx kcat distribution
Mode (min-1) Confidence Interval Location parameter (µ) Scale parameter (σ)
2.44E+04 4.20E+00 1.11E+01 9.75E-01
The estimated probability distribution for PHGPx 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

To convert the enzyme concentration from ppm to mM, the following equation was used.

Literature values
Value Units Species Notes Weight Reference
459 ppm Human Expression Vector: Skin

Enzyme: PHGPx pH: 7.5 Temperature: 37 °C

2048 [4]
307 ppm Human Expression Vector: Lung

Enzyme: PHGPx pH: 7.5 Temperature: 37 °C

1024 [4]
282 ppm Human Expression Vector: Esophagus

Enzyme: PHGPx pH: 7.5 Temperature: 37 °C

1024 [4]
204 ppm Human Expression Vector: Gut

Enzyme: PHGPx pH: 7.5 Temperature: 37 °C

1024 [5]
Description of the PHGPx concentration distribution
Mode (ppm) Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
3.14E+02 1.74E-03 1.38E+00 5.85E+00 3.09E-01
The estimated probability distribution for PHGPx concentration. 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.

Keq

Literature values
Gibbs Free Energy Change Units Species Notes Weight Reference
(-26.941177) kcal/mol Not stated Estimated

Enzyme: PHGPx Substrate:a hydroperoxy-fatty-acyl-[lipid] Product: a hydroxy-fatty-acyl-[lipid] pH: 7.3 ionic strength: 0.25

64 [6]
Description of the PHGPx Keq distribution
Mode Confidence Interval Location parameter (µ) Scale parameter (σ)
5.90E+19 1.00E+01 4.63E+01 8.90E-01
The estimated probability distribution for PHGPx 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.

Related Reactions

  1. ↑ 1.0 1.1 Liu L. "Functional mimicry of the active site of glutathione peroxidase by glutathione imprinted selenium-containing protein. Biomacromolecules. 2008 Jan;9(1):363-8. doi: 10.1021/bm7008312. Epub 2007 Dec 29.
  2. ↑ 2.0 2.1 Zheng K. "A novel selenium-containing glutathione transferase zeta1-1, the activity of which surpasses the level of some native glutathione peroxidases. Int J Biochem Cell Biol. 2008;40(10):2090-7. doi: 10.1016/j.biocel.2008.02.006. Epub 2008 Feb 15.
  3. ↑ Hiratsuka A. "Subunit Ya-specific glutathione peroxidase activity toward cholesterol 7-hydroperoxides of glutathione S-transferases in cytosols from rat liver and skin. J Biol Chem. 1997 Feb 21;272(8):4763-9.
  4. ↑ 4.0 4.1 4.2 M. Wilhelm Mass-spectrometry-based draft of the human proteome Nature, 2014 509, 582–587
  5. ↑ M. Kim A draft map of the human proteome Nature, 2014 509, 575–581
  6. ↑ Caspi et al 2014, "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases," Nucleic Acids Research 42:D459-D471
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