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

From ISMOC
Jump to: navigation, search
 
(6 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
[[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]]
  
−
LOX enzymes oxidise AA to generate hydroxy fatty acids. In the skin, the 12-LOX isoform of LOX is more active than others. This isoform is highly expressed in the resident cells of both compartments, epidermal keratinocytes and dermal fibroblasts (Dowd, Kobza Black et al. 1985). The 12- LOX enzyme catalyses the addition of O2 at the C-12 position of AA, producing 12-HPETE.
+
The 12- LOX enzyme catalyses the addition of O2 at the C-12 position of AA, producing 12-HPETE. The formation of the unstable hydroperoxy fatty acids (HPETE) begins with the abstraction of a hydrogen radical at the allylic position between two double bonds. The structure undergoes a rearrangement reaction which results in the formation of a conjugated diene system. The insertion of molecular oxygen and a hydrogen leads to the formation of the final structure, a hydroperoxy fatty acid.  
  
 
== Reaction ==
 
== Reaction ==
Line 9: Line 9:
 
==Chemical equation==
 
==Chemical equation==
  
−
<center><math> AA \rightleftharpoons PGH2 </math></center>
+
<center><math> AA \rightleftharpoons 12-HPETE </math></center>
  
 
== Rate equation ==
 
== Rate equation ==
Line 15: Line 15:
 
[[File:R19.PNG|center|500px]]
 
[[File:R19.PNG|center|500px]]
  
−
== 12-LOX Parameters ==
+
== Enzyme Parameters ==
−
 
+
=== K<sub>ms</sub>===
 
{|class="wikitable sortable"  
 
{|class="wikitable sortable"  
−
|+  style="text-align: left;" | Michaelis-Menten Constants
+
|+  style="text-align: left;" | Literature values
 
|-
 
|-
 
! Value
 
! Value
Line 24: Line 24:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 33: Line 34:
 
pH: 7.4
 
pH: 7.4
 
Temperature: 37°C.
 
Temperature: 37°C.
 +
|2048
 
|<ref name="Lagarde1984"> [http://www.ncbi.nlm.nih.gov/pubmed/6433902 Lagarde M. "Subcellular localization and some properties of lipoxygenase activity in human blood platelets.'' Biochem J. 1984 Sep 1;222(2):495-500.]</ref>   
 
|<ref name="Lagarde1984"> [http://www.ncbi.nlm.nih.gov/pubmed/6433902 Lagarde M. "Subcellular localization and some properties of lipoxygenase activity in human blood platelets.'' Biochem J. 1984 Sep 1;222(2):495-500.]</ref>   
 
|-
 
|-
Line 42: Line 44:
 
pH: 7
 
pH: 7
 
Temperature: 24
 
Temperature: 24
 +
|512
 
|<ref name="Hada1991"> [http://www.ncbi.nlm.nih.gov/pubmed/1851637 Hada T. "Catalytic properties of human platelet 12-lipoxygenase as compared with the enzymes of other origins.'' Biochim Biophys Acta. 1991 Apr 24;1083(1):89-93.]</ref>   
 
|<ref name="Hada1991"> [http://www.ncbi.nlm.nih.gov/pubmed/1851637 Hada T. "Catalytic properties of human platelet 12-lipoxygenase as compared with the enzymes of other origins.'' Biochim Biophys Acta. 1991 Apr 24;1083(1):89-93.]</ref>   
 
|-
 
|-
Line 51: Line 54:
 
pH: 8
 
pH: 8
 
Temperature: 37
 
Temperature: 37
 +
|256
 
|<ref name="Chen1993"> [http://www.ncbi.nlm.nih.gov/pubmed/8319693 Chen X. S. "Purification and characterization of recombinant histidine-tagged human platelet 12-lipoxygenase expressed in a baculovirus/insect cell system.'' Eur J Biochem. 1993 Jun 15;214(3):845-52.]</ref>   
 
|<ref name="Chen1993"> [http://www.ncbi.nlm.nih.gov/pubmed/8319693 Chen X. S. "Purification and characterization of recombinant histidine-tagged human platelet 12-lipoxygenase expressed in a baculovirus/insect cell system.'' Eur J Biochem. 1993 Jun 15;214(3):845-52.]</ref>   
 
|-
 
|-
Line 60: Line 64:
 
pH: 7.4
 
pH: 7.4
 
Temperature: 37
 
Temperature: 37
 +
|2048
 
|<ref name="Romano1993"> [http://www.ncbi.nlm.nih.gov/pubmed/8250832 Romano M. "Lipoxin synthase activity of human platelet 12-lipoxygenase.'' Biochem J. 1993 Nov 15;296 ( Pt 1):127-33.]</ref>   
 
|<ref name="Romano1993"> [http://www.ncbi.nlm.nih.gov/pubmed/8250832 Romano M. "Lipoxin synthase activity of human platelet 12-lipoxygenase.'' Biochem J. 1993 Nov 15;296 ( Pt 1):127-33.]</ref>   
 
|-
 
|-
 
|}
 
|}
  
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the 12-LOX Kms distribution
 +
! Mode (mM) !! Confidence Interval !! Location parameter (σ) !! Scale parameter (σ)
 +
|-
 +
| 7.60E-03 || 4.34E+00 || -4.48E+00 || 6.30E-01
 +
|}
 +
 +
[[Image:61.jpg|none|thumb|500px|The estimated probability distribution for 12-LOX 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 12-LOX Kmp distribution
 +
! Mode (mM) !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 7.30E-03 || -4.52E+00 || 6.28E-01
 +
|}
 +
 +
[[Image:62.jpg|none|thumb|500px|The estimated probability distribution for 12-LOX 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"  
 
{|class="wikitable sortable"  
−
|+  style="text-align: left;" | Enzyme Turnover Numbers
+
|+  style="text-align: left;" | Literature values
 
|-
 
|-
 
! Value
 
! Value
Line 71: Line 97:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 80: Line 107:
 
pH: 7.5
 
pH: 7.5
 
Temperature: 25
 
Temperature: 25
 +
|256
 
|<ref name="Wecksler2009"> [www.ncbi.nlm.nih.gov/pubmed/19469483 Wecksler A. "Mechanistic Investigations of Human Reticulocyte 15- and Platelet 12-Lipoxygenases with Arachidonic Acid'' Biochemistry, 2009, 48 (26), pp 6259–6267]</ref>
 
|<ref name="Wecksler2009"> [www.ncbi.nlm.nih.gov/pubmed/19469483 Wecksler A. "Mechanistic Investigations of Human Reticulocyte 15- and Platelet 12-Lipoxygenases with Arachidonic Acid'' Biochemistry, 2009, 48 (26), pp 6259–6267]</ref>
 
|-
 
|-
Line 89: Line 117:
 
pH: 7.4
 
pH: 7.4
 
Temperature: 37
 
Temperature: 37
 +
|1024
 
|<ref name="Richards1997"> [http://pubs.acs.org/doi/abs/10.1021/bi963051a Richards K. "Leukocyte 12-Lipoxygenase:  Expression, Purification, and Investigation of the Role of Methionine Residues in Turnover-Dependent Inactivation and 5,8,11,14-Eicosatetraynoic Acid Inhibition'' Biochemistry, 1997, 36 (22), pp 6692–6699]</ref>
 
|<ref name="Richards1997"> [http://pubs.acs.org/doi/abs/10.1021/bi963051a Richards K. "Leukocyte 12-Lipoxygenase:  Expression, Purification, and Investigation of the Role of Methionine Residues in Turnover-Dependent Inactivation and 5,8,11,14-Eicosatetraynoic Acid Inhibition'' Biochemistry, 1997, 36 (22), pp 6692–6699]</ref>
 
|-
 
|-
 
|}
 
|}
  
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the 12-LOX kcat distribution
 +
! Mode (min-1) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 4.87E+02 || 1.20E+00 || 6.22E+00 || 1.80E-01
 +
|}
 +
 +
[[Image:63.jpg|none|thumb|500px|The estimated probability distribution for 12-LOX 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 [[Common equations#Enzyme concentration (mM)|equation]] was used.
  
 
{|class="wikitable sortable"  
 
{|class="wikitable sortable"  
Line 101: Line 142:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 110: Line 152:
 
pH: 7.5
 
pH: 7.5
 
Temperature: 37 °C
 
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>
 
|<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>
 
|-
 
|-
Line 119: Line 162:
 
pH: 7.5
 
pH: 7.5
 
Temperature: 37 °C
 
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>
 
|<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>
 
|-
 
|-
Line 128: Line 172:
 
pH: 7.5
 
pH: 7.5
 
Temperature: 37 °C
 
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>
 
|<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>
 
|-
 
|-
Line 137: Line 182:
 
pH: 7.5
 
pH: 7.5
 
Temperature: 37 °C
 
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>
 
|<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 12-LOX concentration distribution
 +
! Mode (ppm) !! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 4.98E-01 ||2.76E-06 || 7.23E+00 || 7.12E-01 || 1.19E+00
 +
|}
 +
 +
[[Image:156.jpg|none|thumb|500px|The estimated probability distribution for 12-LOX 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"  
 
{|class="wikitable sortable"  
−
|+  style="text-align: left;" | Gibbs Free Energy Change
+
|+  style="text-align: left;" | Literature values
 
|-
 
|-
−
! Value
+
! Gibbs Free Energy Change
 
! Units
 
! Units
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 159: Line 216:
 
pH: 7.3  
 
pH: 7.3  
 
ionic strength: 0.25
 
ionic strength: 0.25
 +
|64
 
|<ref name="MetaCyc”>[http://metacyc.org/META/NEW-IMAGE?type=REACTION&object=ARACHIDONATE-12-LIPOXYGENASE-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>
 
|<ref name="MetaCyc”>[http://metacyc.org/META/NEW-IMAGE?type=REACTION&object=ARACHIDONATE-12-LIPOXYGENASE-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 12-LOX Keq distribution
 +
! Mode !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 2.27E+51 || 1.00E+01 || 1.19E+02 || 8.90E-01
 +
|}
 +
 +
[[Image:64.jpg|none|thumb|500px|The estimated probability distribution for 12-LOX 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.  ]]
  
 
== References ==
 
== References ==

Latest revision as of 09:18, 21 August 2019

Return to overview

The 12- LOX enzyme catalyses the addition of O2 at the C-12 position of AA, producing 12-HPETE. The formation of the unstable hydroperoxy fatty acids (HPETE) begins with the abstraction of a hydrogen radical at the allylic position between two double bonds. The structure undergoes a rearrangement reaction which results in the formation of a conjugated diene system. The insertion of molecular oxygen and a hydrogen leads to the formation of the final structure, a hydroperoxy fatty acid.

Reaction

R179AA - HPETE12.jpg

Chemical equation

AA \rightleftharpoons 12-HPETE

Rate equation

R19.PNG

Enzyme Parameters

Kms

Literature values
Value Units Species Notes Weight Reference
7.20E-03 mM Human Expression Vector: Platelet

Enzyme: 12-Lipoxygenase pH: 7.4 Temperature: 37°C.

2048 [1]
8.00E-02 mM Human Expression Vector: Platelet

Enzyme: 12-Lipoxygenase pH: 7 Temperature: 24

512 [2]
1.00E-02 mM Human Platlet Expression Vector: Baculovirus

Enzyme: 12-Lipoxygenase pH: 8 Temperature: 37

256 [3]
7.90E-03 ± 8.00E-04 mM Human Expression Vector: Platelets

Enzyme:12-Lipoxygenase pH: 7.4 Temperature: 37

2048 [4]
Description of the 12-LOX Kms distribution
Mode (mM) Confidence Interval Location parameter (σ) Scale parameter (σ)
7.60E-03 4.34E+00 -4.48E+00 6.30E-01
The estimated probability distribution for 12-LOX 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 12-LOX Kmp distribution
Mode (mM) Location parameter (µ) Scale parameter (σ)
7.30E-03 -4.52E+00 6.28E-01
The estimated probability distribution for 12-LOX 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
336 ± 12 per minute Human Expression Vector: Human reticulocyte

Enzyme: 15-lipoxygenase-1 pH: 7.5 Temperature: 25

256 [5]
504 per minute Wild Boar Expression Vector: E. coli.

Enzyme: 12-Lipoxygenase pH: 7.4 Temperature: 37

1024 [6]
Description of the 12-LOX kcat distribution
Mode (min-1) Confidence Interval Location parameter (µ) Scale parameter (σ)
4.87E+02 1.20E+00 6.22E+00 1.80E-01
The estimated probability distribution for 12-LOX 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.

12-LOX Abundance
Value Units Species Notes Weight Reference
19.8 ppm Human Expression Vector: Spleen

Enzyme: 12-LOX pH: 7.5 Temperature: 37 °C

1024 [7]
1.60 ppm Human Expression Vector: Liver

Enzyme: 12-LOX pH: 7.5 Temperature: 37 °C

1024 [8]
0.28 ppm Human Expression Vector: Gut

Enzyme: 12-LOX pH: 7.5 Temperature: 37 °C

1024 [8]
0.11 ppm Human Expression Vector: Pancreas

Enzyme: 12-LOX pH: 7.5 Temperature: 37 °C

1024 [8]
Description of the 12-LOX concentration distribution
Mode (ppm) Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
4.98E-01 2.76E-06 7.23E+00 7.12E-01 1.19E+00
The estimated probability distribution for 12-LOX 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
(-69.979996) kcal/mol Not stated Estimated

Enzyme: 12-LOX Substrate: Arachidonate Product: 12-HPETE pH: 7.3 ionic strength: 0.25

64 [9]
Description of the 12-LOX Keq distribution
Mode Confidence Interval Location parameter (µ) Scale parameter (σ)
2.27E+51 1.00E+01 1.19E+02 8.90E-01
The estimated probability distribution for 12-LOX 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.

References

  1. ↑ Lagarde M. "Subcellular localization and some properties of lipoxygenase activity in human blood platelets. Biochem J. 1984 Sep 1;222(2):495-500.
  2. ↑ Hada T. "Catalytic properties of human platelet 12-lipoxygenase as compared with the enzymes of other origins. Biochim Biophys Acta. 1991 Apr 24;1083(1):89-93.
  3. ↑ Chen X. S. "Purification and characterization of recombinant histidine-tagged human platelet 12-lipoxygenase expressed in a baculovirus/insect cell system. Eur J Biochem. 1993 Jun 15;214(3):845-52.
  4. ↑ Romano M. "Lipoxin synthase activity of human platelet 12-lipoxygenase. Biochem J. 1993 Nov 15;296 ( Pt 1):127-33.
  5. ↑ [www.ncbi.nlm.nih.gov/pubmed/19469483 Wecksler A. "Mechanistic Investigations of Human Reticulocyte 15- and Platelet 12-Lipoxygenases with Arachidonic Acid Biochemistry, 2009, 48 (26), pp 6259–6267]
  6. ↑ Richards K. "Leukocyte 12-Lipoxygenase:  Expression, Purification, and Investigation of the Role of Methionine Residues in Turnover-Dependent Inactivation and 5,8,11,14-Eicosatetraynoic Acid Inhibition Biochemistry, 1997, 36 (22), pp 6692–6699
  7. ↑ M. Wilhelm Mass-spectrometry-based draft of the human proteome Nature, 2014 509, 582–587
  8. ↑ 8.0 8.1 8.2 M. Kim A draft map of the human proteome Nature, 2014 509, 575–581
  9. ↑ 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

Related Reactions

Retrieved from ‘http://www.systemsbiology.ls.manchester.ac.uk/wiki/index.php?title=Transformation_of_AA_to_12-HPETE&oldid=7481’