Difference between revisions of "Transformation of AA to 5-HPETE"

From ISMOC
Jump to: navigation, search
(5-LOX Parameters)
 
(19 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]]
 +
 +
ALOX5 encodes the protein 5-LOX, which is responsible for the generation of 5-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 ==
 
 
[[File:R11_AA_-_HPETE5.jpg |center|500px]]
 
[[File:R11_AA_-_HPETE5.jpg |center|500px]]
  
 
==Chemical equation==
 
==Chemical equation==
  
<center><math> AA \rightleftharpoons PGH2 </math></center>
+
<center><math> PGH2 \rightleftharpoons 5-HPETE </math></center>
  
 
== Rate equation ==
 
== Rate equation ==
  
 +
[[File:R11.PNG|center|500px]]
  
== 5-LOX Parameters ==
+
== 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 21: Line 24:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 26: Line 30:
 
|<math> mM </math>
 
|<math> mM </math>
 
|Human  
 
|Human  
|Recombinant 5-Lipoxygenase
+
|Expression Vector:  Baculovirus, Sf9 insect cells
 +
Enzyme: Recombinant 5-Lipoxygenase
 +
pH: 5.6
 +
Temperature:37
 +
|256
 
|<ref name="Shirumalla2006”>[http://www.ncbi.nlm.nih.gov/pubmed/17039282 Shirumalla R. K. “RBx 7,796: A novel inhibitor of 5-lipoxygenase.” Inflamm Res. 2006 Dec ; 55 (12) : 517-27.]</ref>   
 
|<ref name="Shirumalla2006”>[http://www.ncbi.nlm.nih.gov/pubmed/17039282 Shirumalla R. K. “RBx 7,796: A novel inhibitor of 5-lipoxygenase.” Inflamm Res. 2006 Dec ; 55 (12) : 517-27.]</ref>   
 
|-
 
|-
Line 32: Line 40:
 
|<math> mM </math>
 
|<math> mM </math>
 
|Human  
 
|Human  
|PMN Leukocyte
+
|Expression Vector: Polymorphonuclear Leukocytes
 +
Enzyme: 5-Lipoxygenase
 +
pH:7.5
 +
Temperature: 22
 +
|512
 
|<ref name="Soberman1988"> [http://www.ncbi.nlm.nih.gov/pubmed/3070300 Soberman R. J. "5- and 15(omega-6)-lipoxygenases from human polymorphonuclear leukocytes.'' Methods Enzymol. 1988; 163:344-9.]</ref>
 
|<ref name="Soberman1988"> [http://www.ncbi.nlm.nih.gov/pubmed/3070300 Soberman R. J. "5- and 15(omega-6)-lipoxygenases from human polymorphonuclear leukocytes.'' Methods Enzymol. 1988; 163:344-9.]</ref>
 
|-
 
|-
Line 38: Line 50:
 
|<math> mM </math>
 
|<math> mM </math>
 
|Human  
 
|Human  
|Polymorphonuclear Leukocytes
+
|Expression Vector: Polymorphonuclear Leukocytes
 +
Enzyme: 5-Lipoxygenase
 +
pH:7.5
 +
Temperature: 22
 +
|512
 
|<ref name="Soberman1985”>[http://www.ncbi.nlm.nih.gov/pubmed/3920219 Soberman R. J. “Characterization and separation of the arachidonic acid 5-lipoxygenase and linoleic acid omega-6 lipoxygenase (arachidonic acid 15-lipoxygenase) of human polymorphonuclear leukocytes.” J Biol Chem. 1985 Apr 10;260(7):4508-15.]</ref>   
 
|<ref name="Soberman1985”>[http://www.ncbi.nlm.nih.gov/pubmed/3920219 Soberman R. J. “Characterization and separation of the arachidonic acid 5-lipoxygenase and linoleic acid omega-6 lipoxygenase (arachidonic acid 15-lipoxygenase) of human polymorphonuclear leukocytes.” J Biol Chem. 1985 Apr 10;260(7):4508-15.]</ref>   
 
|-
 
|-
 
|}
 
|}
  
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the 5-LOX Kms distribution
 +
! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 1.27E-02 || 2.74E+00 || -3.76E+00 || 7.73E-01
 +
|}
 +
 +
[[Image:33.jpg|none|thumb|500px|The estimated probability distribution for 5-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>===
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the 5-LOX Kmp distribution
 +
! Mode (mM) !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 1.25E-02 || -3.63E+00 || 8.68E-01
 +
|}
 +
 +
[[Image:34.jpg|none|thumb|500px|The estimated probability distribution for 5-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 50: Line 87:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 55: Line 93:
 
|per minute
 
|per minute
 
|Potato
 
|Potato
|Potato Tubers, pH 5.5,
+
|Expression Vector:Potato Tubers
 +
Enzyme: 5-Lipoxygenase
 +
pH:5.5
 +
Temperature: 23
 +
|16
 
|<ref name="Mulliez1987”>[http://www.sciencedirect.com/science/article/pii/0167483887902056 Mulliez E., “5-Lipoxygenase from potato tubers. Improved purification and physicochemical characteristics” Biochimica et Biophysica Acta, 1987;916(1):13-23.]</ref>   
 
|<ref name="Mulliez1987”>[http://www.sciencedirect.com/science/article/pii/0167483887902056 Mulliez E., “5-Lipoxygenase from potato tubers. Improved purification and physicochemical characteristics” Biochimica et Biophysica Acta, 1987;916(1):13-23.]</ref>   
 
|-
 
|-
  
 
|}
 
|}
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the 5-LOX kcat distribution
 +
! Mode (min-1) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 1.50E+03 || 1.05E+00 || 7.31E+00 || 4.99E-02
 +
|}
 +
 +
[[Image:35.jpg|none|thumb|500px|The estimated probability distribution for 5-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"
 +
|+  style="text-align: left;" | Literature values
 +
|-
 +
! Value
 +
! Units
 +
! Species
 +
! Notes
 +
! Weight
 +
! Reference
 +
|-
 +
|97.3
 +
|<math> ppm </math>
 +
|Human
 +
|Expression Vector: Lung
 +
Enzyme: 5-LOX
 +
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>
 +
|-
 +
|49.8
 +
|<math> ppm </math>
 +
|Human
 +
|Expression Vector: Esophagus
 +
Enzyme: 5-LOX
 +
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>
 +
|-
 +
|31.9
 +
|<math> ppm </math>
 +
|Human
 +
|Expression Vector: Oral Cavity
 +
Enzyme: 5-LOX
 +
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>
 +
|-
 +
|}
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the 5-LOX concentration distribution
 +
! Mode (ppm) !! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 4.96E+01 || 2.74E-04|| 1.60E+00 || 4.09E+00 || 4.28E-01
 +
|}
 +
 +
[[Image:158.jpg|none|thumb|500px|The estimated probability distribution for 5-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"
 +
|+  style="text-align: left;" | Literature values
 +
|-
 +
!  Gibbs Free Energy Change
 +
! Units
 +
! Species
 +
! Notes
 +
! Weight
 +
! Reference
 +
|-
 +
|(-15.9) - 18.01
 +
|kcal/mol
 +
|Soybean
 +
|Expression Vector: Soybean
 +
Enzyme: Lipoxygenase-1
 +
pH:Not stated
 +
Temperature: Not stated
 +
|8
 +
|<ref name="Tejero2004”>[http://pubs.acs.org/doi/pdf/10.1021/jp040114n Tejero I., “Hydrogen Abstraction by Soybean Lipoxygenase-1. Density Functional Theory Study on
 +
Active Site Models in Terms of Gibbs Free Energies” J. Phys. Chem. B, 2004, 108 (36), pp 13831–13838]</ref> 
 +
|-
 +
|(-69.979996)
 +
|kcal/mol
 +
|Not stated
 +
|Estimated
 +
Enzyme: 5-Lipoxygenase
 +
Substrate: Arachidonate
 +
Product: 5-HPETE
 +
pH: 7.3
 +
ionic strength: 0.25
 +
|64
 +
|<ref name="MetaCyc”>[http://metacyc.org/META/NEW-IMAGE?type=REACTION&object=ARACHIDONATE-5-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 5-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:36.jpg|none|thumb|500px|The estimated probability distribution for 5-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 08:17, 21 August 2019

Return to overview

ALOX5 encodes the protein 5-LOX, which is responsible for the generation of 5-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

R11 AA - HPETE5.jpg

Chemical equation

 PGH2 \rightleftharpoons 5-HPETE

Rate equation

R11.PNG

Parameters

Kms

Literature values
Value Units Species Notes Weight Reference
5.10E-03  mM Human Expression Vector: Baculovirus, Sf9 insect cells

Enzyme: Recombinant 5-Lipoxygenase pH: 5.6 Temperature:37

256 [1]
1.20E-02  mM Human Expression Vector: Polymorphonuclear Leukocytes

Enzyme: 5-Lipoxygenase pH:7.5 Temperature: 22

512 [2]
6.31E-02  mM Human Expression Vector: Polymorphonuclear Leukocytes

Enzyme: 5-Lipoxygenase pH:7.5 Temperature: 22

512 [3]
Description of the 5-LOX Kms distribution
Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
1.27E-02 2.74E+00 -3.76E+00 7.73E-01
The estimated probability distribution for 5-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

Description of the 5-LOX Kmp distribution
Mode (mM) Location parameter (µ) Scale parameter (σ)
1.25E-02 -3.63E+00 8.68E-01
The estimated probability distribution for 5-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
1500 + 75 per minute Potato Expression Vector:Potato Tubers

Enzyme: 5-Lipoxygenase pH:5.5 Temperature: 23

16 [4]
Description of the 5-LOX kcat distribution
Mode (min-1) Confidence Interval Location parameter (µ) Scale parameter (σ)
1.50E+03 1.05E+00 7.31E+00 4.99E-02
The estimated probability distribution for 5-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.

Literature values
Value Units Species Notes Weight Reference
97.3  ppm Human Expression Vector: Lung

Enzyme: 5-LOX pH: 7.5 Temperature: 37 °C

1024 [5]
49.8  ppm Human Expression Vector: Esophagus

Enzyme: 5-LOX pH: 7.5 Temperature: 37 °C

1024 [6]
31.9  ppm Human Expression Vector: Oral Cavity

Enzyme: 5-LOX pH: 7.5 Temperature: 37 °C

1024 [6]
Description of the 5-LOX concentration distribution
Mode (ppm) Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
4.96E+01 2.74E-04 1.60E+00 4.09E+00 4.28E-01
The estimated probability distribution for 5-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
(-15.9) - 18.01 kcal/mol Soybean Expression Vector: Soybean

Enzyme: Lipoxygenase-1 pH:Not stated Temperature: Not stated

8 [7]
(-69.979996) kcal/mol Not stated Estimated

Enzyme: 5-Lipoxygenase Substrate: Arachidonate Product: 5-HPETE pH: 7.3 ionic strength: 0.25

64 [8]
Description of the 5-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 5-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


Related Reactions