Difference between revisions of "Transformation of K6PGF1a to exK6PGF1a by PGT"
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== Transport Parameters == | == Transport Parameters == | ||
− | + | ===K<sub>ms</sub>=== | |
{|class="wikitable sortable" | {|class="wikitable sortable" | ||
− | |+ style="text-align: left;" | | + | |+ style="text-align: left;" | Literature values |
|- | |- | ||
! Value | ! Value | ||
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! Species | ! Species | ||
! Notes | ! Notes | ||
+ | ! Weight | ||
! Reference | ! Reference | ||
|- | |- | ||
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pH: 7.5 | pH: 7.5 | ||
Temp: 37 °C | Temp: 37 °C | ||
+ | |2048 | ||
|<ref name="Kraft2010"> [https://www.ncbi.nlm.nih.gov/pubmed/20019365 M. Kraft ''The prostaglandin transporter OATP2A1 is expressed in human ocular tissues and transports the antiglaucoma prostanoid latanoprost.'' Invest Ophthalmol Vis Sci. 2010 May;51(5):2504-11. doi: 10.1167/iovs.09-4290. Epub 2009 Dec 17.]</ref> | |<ref name="Kraft2010"> [https://www.ncbi.nlm.nih.gov/pubmed/20019365 M. Kraft ''The prostaglandin transporter OATP2A1 is expressed in human ocular tissues and transports the antiglaucoma prostanoid latanoprost.'' Invest Ophthalmol Vis Sci. 2010 May;51(5):2504-11. doi: 10.1167/iovs.09-4290. Epub 2009 Dec 17.]</ref> | ||
|- | |- | ||
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pH: unknown | pH: unknown | ||
Temp: 37 °C | Temp: 37 °C | ||
+ | |512 | ||
|<ref name="Gose2016"> [https://www.ncbi.nlm.nih.gov/pubmed/26692285 Gose T. ''Prostaglandin transporter (OATP2A1/SLCO2A1) contributes to local disposition of eicosapentaenoic acid-derived PGE3.'' Prostaglandins Other Lipid Mediat. 2016 Jan;122:10-7. doi: 10.1016/j.prostaglandins.2015.12.003. Epub 2015 Dec 10.]</ref> | |<ref name="Gose2016"> [https://www.ncbi.nlm.nih.gov/pubmed/26692285 Gose T. ''Prostaglandin transporter (OATP2A1/SLCO2A1) contributes to local disposition of eicosapentaenoic acid-derived PGE3.'' Prostaglandins Other Lipid Mediat. 2016 Jan;122:10-7. doi: 10.1016/j.prostaglandins.2015.12.003. Epub 2015 Dec 10.]</ref> | ||
|- | |- | ||
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pH: unknown | pH: unknown | ||
Temp: 37 °C | Temp: 37 °C | ||
+ | |512 | ||
|<ref name="Gose2016"> [https://www.ncbi.nlm.nih.gov/pubmed/26692285 Gose T. ''Prostaglandin transporter (OATP2A1/SLCO2A1) contributes to local disposition of eicosapentaenoic acid-derived PGE3.'' Prostaglandins Other Lipid Mediat. 2016 Jan;122:10-7. doi: 10.1016/j.prostaglandins.2015.12.003. Epub 2015 Dec 10.]</ref> | |<ref name="Gose2016"> [https://www.ncbi.nlm.nih.gov/pubmed/26692285 Gose T. ''Prostaglandin transporter (OATP2A1/SLCO2A1) contributes to local disposition of eicosapentaenoic acid-derived PGE3.'' Prostaglandins Other Lipid Mediat. 2016 Jan;122:10-7. doi: 10.1016/j.prostaglandins.2015.12.003. Epub 2015 Dec 10.]</ref> | ||
|- | |- | ||
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pH: unknown | pH: unknown | ||
Temp: unknown | Temp: unknown | ||
+ | |192 | ||
|<ref name="Chi2010"> [http://www.sciencedirect.com/science/article/pii/S0006291X10005723 Chi Y. ''The prostaglandin transporter PGT transports PGH2'' Biochemical and Biophysical Research Communications, Volume 395, Issue 2, 30 April 2010, Pages 168–172]</ref> | |<ref name="Chi2010"> [http://www.sciencedirect.com/science/article/pii/S0006291X10005723 Chi Y. ''The prostaglandin transporter PGT transports PGH2'' Biochemical and Biophysical Research Communications, Volume 395, Issue 2, 30 April 2010, Pages 168–172]</ref> | ||
|- | |- | ||
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pH: 7 | pH: 7 | ||
Temperature: 27 | Temperature: 27 | ||
+ | |1024 | ||
|<ref name="Kanai1995"> [http://science.sciencemag.org/content/sci/268/5212/866.full.pdf Kanai N. ''Identification and Characterization of a | |<ref name="Kanai1995"> [http://science.sciencemag.org/content/sci/268/5212/866.full.pdf Kanai N. ''Identification and Characterization of a | ||
Prostaglandin Transporter'' Science 12 May 1995:Vol. 268, Issue 5212, pp. 866-869, DOI: 10.1126/science.7754369]</ref> | Prostaglandin Transporter'' Science 12 May 1995:Vol. 268, Issue 5212, pp. 866-869, DOI: 10.1126/science.7754369]</ref> | ||
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pH: 7 | pH: 7 | ||
Temperature: 27 | Temperature: 27 | ||
+ | |1024 | ||
|<ref name="Kanai1995"> [http://science.sciencemag.org/content/sci/268/5212/866.full.pdf Kanai N. ''Identification and Characterization of a | |<ref name="Kanai1995"> [http://science.sciencemag.org/content/sci/268/5212/866.full.pdf Kanai N. ''Identification and Characterization of a | ||
Prostaglandin Transporter'' Science 12 May 1995:Vol. 268, Issue 5212, pp. 866-869, DOI: 10.1126/science.7754369]</ref> | Prostaglandin Transporter'' Science 12 May 1995:Vol. 268, Issue 5212, pp. 866-869, DOI: 10.1126/science.7754369]</ref> | ||
Line 81: | Line 88: | ||
pH: 7 | pH: 7 | ||
Temperature: 27 | Temperature: 27 | ||
+ | |1024 | ||
|<ref name="Kanai1995"> [http://science.sciencemag.org/content/sci/268/5212/866.full.pdf Kanai N. ''Identification and Characterization of a | |<ref name="Kanai1995"> [http://science.sciencemag.org/content/sci/268/5212/866.full.pdf Kanai N. ''Identification and Characterization of a | ||
Prostaglandin Transporter'' Science 12 May 1995:Vol. 268, Issue 5212, pp. 866-869, DOI: 10.1126/science.7754369]</ref> | Prostaglandin Transporter'' Science 12 May 1995:Vol. 268, Issue 5212, pp. 866-869, DOI: 10.1126/science.7754369]</ref> | ||
Line 92: | Line 100: | ||
pH: 7 | pH: 7 | ||
Temperature: 27 | Temperature: 27 | ||
+ | |1024 | ||
|<ref name="SHIGEKAZU1996"> [http://molpharm.aspetjournals.org/content/molpharm/50/4/736.full.pdf Shigekazu I. ''Structural Determinants of Substrates for the Prostaglandin Transporter PGT'' Molecular Pharmacology October 1996, 50 (4) 736-742; DOI: https://doi.org/10.1124/mol.50.4.736]</ref> | |<ref name="SHIGEKAZU1996"> [http://molpharm.aspetjournals.org/content/molpharm/50/4/736.full.pdf Shigekazu I. ''Structural Determinants of Substrates for the Prostaglandin Transporter PGT'' Molecular Pharmacology October 1996, 50 (4) 736-742; DOI: https://doi.org/10.1124/mol.50.4.736]</ref> | ||
|- | |- | ||
− | | | + | |} |
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− | | | + | {| class="wikitable" |
− | + | |+ style="text-align: left;" | Description of the PGT Kms distribution | |
− | + | ! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ) | |
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+ | | 1.10E-03 || 9.42E+01 || -4.67E+00 || 1.45E+00 | ||
|} | |} | ||
+ | [[Image:141.jpg|none|thumb|500px|The estimated probability distribution for PGT 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>cat</sub>=== | ||
No data available on the turnover of PGT/ an organic molecule transporter therefore based upon estimates made by http://book.bionumbers.org/what-are-the-rates-of-membrane-transporters/ | No data available on the turnover of PGT/ an organic molecule transporter therefore based upon estimates made by http://book.bionumbers.org/what-are-the-rates-of-membrane-transporters/ | ||
{|class="wikitable sortable" | {|class="wikitable sortable" | ||
Line 145: | Line 123: | ||
! Transporter | ! Transporter | ||
! Notes | ! Notes | ||
+ | ! Weight | ||
! Reference | ! Reference | ||
|- | |- | ||
Line 152: | Line 131: | ||
|Organism: Bacteria Escherichia coli | |Organism: Bacteria Escherichia coli | ||
Back of the envelope calculation by BioNumbers: http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=102931 | Back of the envelope calculation by BioNumbers: http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=102931 | ||
+ | |8 | ||
|<ref name="Waygood1980"> [https://www.ncbi.nlm.nih.gov/pubmed/6992959?dopt=Abstract Waygood EB ''Enzyme I of the phosphoenolpyruvate: sugar phosphotransferase system of Escherichia coli. Purification to homogeneity and some properties.''Can J Biochem. 1980 Jan;58(1):40-8.]</ref> | |<ref name="Waygood1980"> [https://www.ncbi.nlm.nih.gov/pubmed/6992959?dopt=Abstract Waygood EB ''Enzyme I of the phosphoenolpyruvate: sugar phosphotransferase system of Escherichia coli. Purification to homogeneity and some properties.''Can J Biochem. 1980 Jan;58(1):40-8.]</ref> | ||
|- | |- | ||
Line 159: | Line 139: | ||
|Organism: Bacteria Escherichia coli | |Organism: Bacteria Escherichia coli | ||
Back of the envelop calculation on bionumbers http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=103159 | Back of the envelop calculation on bionumbers http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=103159 | ||
+ | |8 | ||
|<ref name="Naftalin2007"> [https://www.ncbi.nlm.nih.gov/pubmed/17325012?dopt=Abstract Naftalin R. J. ''ELactose permease H+-lactose symporter: mechanical switch or Brownian ratchet?''Biophys J. 2007 May 15;92(10):3474-91. Epub 2007 Feb 26.]</ref> | |<ref name="Naftalin2007"> [https://www.ncbi.nlm.nih.gov/pubmed/17325012?dopt=Abstract Naftalin R. J. ''ELactose permease H+-lactose symporter: mechanical switch or Brownian ratchet?''Biophys J. 2007 May 15;92(10):3474-91. Epub 2007 Feb 26.]</ref> | ||
|- | |- | ||
Line 166: | Line 147: | ||
|Organism: Budding yeast Saccharomyces cerevisiae | |Organism: Budding yeast Saccharomyces cerevisiae | ||
Back of the envelope calculation http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=101737 | Back of the envelope calculation http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=101737 | ||
+ | |8 | ||
|<ref name="Ye2001"> [https://www.ncbi.nlm.nih.gov/pubmed/11561293?dopt=Abstract Ye L. ''Expression and activity of the Hxt7 high-affinity hexose transporter of Saccharomyces cerevisiae''Yeast. 2001 Sep 30;18(13):1257-67.]</ref> | |<ref name="Ye2001"> [https://www.ncbi.nlm.nih.gov/pubmed/11561293?dopt=Abstract Ye L. ''Expression and activity of the Hxt7 high-affinity hexose transporter of Saccharomyces cerevisiae''Yeast. 2001 Sep 30;18(13):1257-67.]</ref> | ||
|- | |- | ||
|} | |} | ||
+ | |||
+ | {| class="wikitable" | ||
+ | |+ style="text-align: left;" | Description of the PGT kcat distribution | ||
+ | ! Mode (min-1) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ) | ||
+ | |- | ||
+ | | 1.33E+00 || 7.30E+00 || 9.20E-01 || 8.00E-01 | ||
+ | |} | ||
+ | |||
+ | [[Image:132.jpg|none|thumb|500px|The estimated probability distribution for PGT 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. ]] | ||
+ | |||
+ | === Transporter 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 177: | Line 172: | ||
! Species | ! Species | ||
! Notes | ! Notes | ||
+ | ! Weight | ||
! Reference | ! Reference | ||
|- | |- | ||
Line 186: | Line 182: | ||
pH: 7.5 | pH: 7.5 | ||
Temperature: 37 °C | Temperature: 37 °C | ||
+ | |2048 | ||
|<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 195: | Line 192: | ||
pH: 7.5 | pH: 7.5 | ||
Temperature: 37 °C | 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> | |<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 204: | Line 202: | ||
pH: 7.5 | pH: 7.5 | ||
Temperature: 37 °C | Temperature: 37 °C | ||
+ | |2048 | ||
|<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 PGT concentration distribution | ||
+ | ! Mode (ppm) !! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ) | ||
+ | |- | ||
+ | | 1.73E+01 ||9.57E-05|| 4.72E+00 || 3.90E+00 || 1.02E+00 | ||
+ | |} | ||
+ | |||
+ | |||
+ | [[Image:165.jpg|none|thumb|500px|The estimated probability distribution for PGT 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. ]] | ||
== References == | == References == | ||
<references/> | <references/> |
Latest revision as of 11:54, 30 May 2019
Contents
Rate equation
Transport Parameters
Kms
Value | Units | Species | Notes | Weight | Reference |
---|---|---|---|---|---|
0.0054 | mM | Human Eye | Vector: HEK-OATP2A1 or HEK-OATP2B1 and the respective vector controls
Substrate: Latanoprost, a prostaglandin F2a analogue pH: 7.5 Temp: 37 °C |
2048 | [1] |
0.000331 ± 0.000131 | mM | Transfected Human embryonic kidney cells (HEK293) | Substrate: PGE2
pH: unknown Temp: 37 °C |
512 | [2] |
0.007202 ± 0.000595 | mM | Transfected Human embryonic kidney cells (HEK293) | Substrate: PGE3
pH: unknown Temp: 37 °C |
512 | [2] |
0.000376 ± 3.4e-5 | mM | PGT-expressing Madin-Darby Canine Kidney Epithelial Cells (MDCK) cells | Substrate: PGH2
pH: unknown Temp: unknown |
192 | [3] |
9.40E-05 | mM | Human | Substrate: PGE2
Species: Human Vector: HeLa Cell Line pH: 7 Temperature: 27 |
1024 | [4] |
0.000423 | mM | Human | Substrate: TXB2
Species: Human Vector: HeLa Cell Line pH: 7 Temperature: 27 |
1024 | [4] |
0.007569 | mM | Human | Substrate: 6-Keto-PGF1a
Species: Human Vector: HeLa Cell Line pH: 7 Temperature: 27 |
1024 | [4] |
4.87E-05 | mM | Human | Substrate: PGE2
Species: Human Vector: HeLa Cell Line pH: 7 Temperature: 27 |
1024 | [5] |
Mode (mM) | Confidence Interval | Location parameter (µ) | Scale parameter (σ) |
---|---|---|---|
1.10E-03 | 9.42E+01 | -4.67E+00 | 1.45E+00 |
kcat
No data available on the turnover of PGT/ an organic molecule transporter therefore based upon estimates made by http://book.bionumbers.org/what-are-the-rates-of-membrane-transporters/
Value | Units | Transporter | Notes | Weight | Reference |
---|---|---|---|---|---|
3.5 | min-1 | Glucose transporter ptsI | Organism: Bacteria Escherichia coli
Back of the envelope calculation by BioNumbers: http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=102931 |
8 | [6] |
0.33 - 0.83 | min-1 | Rate of transport of H+/Lactose transporter | Organism: Bacteria Escherichia coli
Back of the envelop calculation on bionumbers http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=103159 |
8 | [7] |
3.28 | min-1 | Catalytic Rate of transporter HXT7 | Organism: Budding yeast Saccharomyces cerevisiae
Back of the envelope calculation http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=101737 |
8 | [8] |
Mode (min-1) | Confidence Interval | Location parameter (µ) | Scale parameter (σ) |
---|---|---|---|
1.33E+00 | 7.30E+00 | 9.20E-01 | 8.00E-01 |
Transporter concentration
To convert the enzyme concentration from ppm to mM, the following equation was used.
Value | Units | Species | Notes | Weight | Reference |
---|---|---|---|---|---|
125 | ppm | Human | Vector:Lung
Enzyme: SLCO2A1 pH: 7.5 Temperature: 37 °C |
2048 | [9] |
17.4 | ppm | Human | Expression Vector: Esophagus
Enzyme: SLCO2A1 pH: 7.5 Temperature: 37 °C |
2048 | [10] |
2.82 | ppm | Human | Vector:Gut
Enzyme: SLCO2A1 pH: 7.5 Temperature: 37 °C |
2048 | [9] |
Mode (ppm) | Mode (mM) | Confidence Interval | Location parameter (µ) | Scale parameter (σ) |
---|---|---|---|---|
1.73E+01 | 9.57E-05 | 4.72E+00 | 3.90E+00 | 1.02E+00 |
References
- ↑ M. Kraft The prostaglandin transporter OATP2A1 is expressed in human ocular tissues and transports the antiglaucoma prostanoid latanoprost. Invest Ophthalmol Vis Sci. 2010 May;51(5):2504-11. doi: 10.1167/iovs.09-4290. Epub 2009 Dec 17.
- ↑ 2.0 2.1 Gose T. Prostaglandin transporter (OATP2A1/SLCO2A1) contributes to local disposition of eicosapentaenoic acid-derived PGE3. Prostaglandins Other Lipid Mediat. 2016 Jan;122:10-7. doi: 10.1016/j.prostaglandins.2015.12.003. Epub 2015 Dec 10.
- ↑ Chi Y. The prostaglandin transporter PGT transports PGH2 Biochemical and Biophysical Research Communications, Volume 395, Issue 2, 30 April 2010, Pages 168–172
- ↑ 4.0 4.1 4.2 [http://science.sciencemag.org/content/sci/268/5212/866.full.pdf Kanai N. Identification and Characterization of a Prostaglandin Transporter Science 12 May 1995:Vol. 268, Issue 5212, pp. 866-869, DOI: 10.1126/science.7754369]
- ↑ Shigekazu I. Structural Determinants of Substrates for the Prostaglandin Transporter PGT Molecular Pharmacology October 1996, 50 (4) 736-742; DOI: https://doi.org/10.1124/mol.50.4.736
- ↑ Waygood EB Enzyme I of the phosphoenolpyruvate: sugar phosphotransferase system of Escherichia coli. Purification to homogeneity and some properties.Can J Biochem. 1980 Jan;58(1):40-8.
- ↑ Naftalin R. J. ELactose permease H+-lactose symporter: mechanical switch or Brownian ratchet?Biophys J. 2007 May 15;92(10):3474-91. Epub 2007 Feb 26.
- ↑ Ye L. Expression and activity of the Hxt7 high-affinity hexose transporter of Saccharomyces cerevisiaeYeast. 2001 Sep 30;18(13):1257-67.
- ↑ 9.0 9.1 M. Kim A draft map of the human proteome Nature, 2014 509, 575–581
- ↑ M. Wilhelm Mass-spectrometry-based draft of the human proteome Nature, 2014 509, 582–587