Difference between revisions of "Enolase"
(→Parameters with uncertainty) |
|||
(15 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
+ | [[Category:Uncertainty]] | ||
'''Enolase''', also known as phosphopyruvate hydratase, catalysis the conversion of [http://en.wikipedia.org/wiki/2-phosphoglycerate 2-phosphoglycerate] (2-PG) to [http://en.wikipedia.org/wiki/Phosphoenolpyruvate phosphoenolpyruvate] (PEP). This is the penultimate step of glycolysis. | '''Enolase''', also known as phosphopyruvate hydratase, catalysis the conversion of [http://en.wikipedia.org/wiki/2-phosphoglycerate 2-phosphoglycerate] (2-PG) to [http://en.wikipedia.org/wiki/Phosphoenolpyruvate phosphoenolpyruvate] (PEP). This is the penultimate step of glycolysis. | ||
Line 7: | Line 8: | ||
Mono-substrate reversible Michaelis-Menten equation is used. <ref name="Hernandez2011"> Marín-Hernández A, Gallardo-Pérez JC, Rodríguez-Enríquez S et al (2011) Modeling cancer glycolysis. Biochim Biophys Acta 1807:755–767 ([http://dx.doi.org/10.1016/j.bbabio.2010.11.006 doi]) </ref> | Mono-substrate reversible Michaelis-Menten equation is used. <ref name="Hernandez2011"> Marín-Hernández A, Gallardo-Pérez JC, Rodríguez-Enríquez S et al (2011) Modeling cancer glycolysis. Biochim Biophys Acta 1807:755–767 ([http://dx.doi.org/10.1016/j.bbabio.2010.11.006 doi]) </ref> | ||
<center><math> \frac{V_{mf}\frac{[2PG]}{K_{2PG}}-V_{mr}\frac{[PEP]}{K_{PEP}}}{1 + \frac{[2PG]}{K_{2PG}} + \frac{[PEP]}{K_{PEP}}} </math></center> | <center><math> \frac{V_{mf}\frac{[2PG]}{K_{2PG}}-V_{mr}\frac{[PEP]}{K_{PEP}}}{1 + \frac{[2PG]}{K_{2PG}} + \frac{[PEP]}{K_{PEP}}} </math></center> | ||
+ | |||
+ | Modified rate law to take Thermodynamic constraint into consideration | ||
+ | |||
+ | <center><math> \frac{V_{mf}\frac{[2PG]}{K_{2PG}} \left( 1 -\frac{[PEP]}{K_{eq} [2PG]} \right)}{1 + \frac{[2PG]}{K_{2PG}} + \frac{[PEP]}{K_{PEP}}} </math></center> | ||
==Parameter values== | ==Parameter values== | ||
Line 17: | Line 22: | ||
|- | |- | ||
|<math>V_{mf}</math> | |<math>V_{mf}</math> | ||
− | |0. | + | |0.34 <ref name="Hernandez_2006"> Marín-Hernández A , Rodríguez-Enríquez S, Vital-González P A, ''et al.'' (2006). ''Determining and understanding the control of glycolysis in fast-growth tumor cells. Flux control by an over-expressed but strongly product-inhibited hexokinase''. FEBS J., 273 , pp. 1975–1988([http://dx.doi.org/doi:10.1111/j.1742-4658.2006.05214.x doi]) </ref> |
− | |<math> mM min^{-1} </math> | + | |<math> \text{mM min}^{-1} </math> |
|rowspan="4"|HeLa cell line | |rowspan="4"|HeLa cell line | ||
|rowspan="4"| | |rowspan="4"| | ||
|- | |- | ||
|<math>V_{mr}</math> | |<math>V_{mr}</math> | ||
− | |0. | + | |0.38<ref name="Hernandez2011"></ref> |
− | |<math> mM min^{-1} </math> | + | |<math> \text{mM min}^{-1} </math> |
|- | |- | ||
|<math>Km_{2PG}</math> | |<math>Km_{2PG}</math> | ||
Line 35: | Line 40: | ||
|} | |} | ||
− | == | + | ==Parameters with uncertainty== |
+ | * Three values for <math>Km_{2PG}</math> is collected. The values are 0.20 <ref name="Pietkiewicz_2009">Pietkiewicz, J., Gamian, A., Staniszewska, M., & Danielewicz, R. (2009), ''Inhibition of human muscle-specific enolase by methylglyoxal and irreversible formation of advanced glycation end products'', Journal of Enzyme Inhibition and Medicinal Chemistry, 24, 356–364</ref>, 0.199 <ref name="Pietkiewicz_2009"></ref>, 0.038 <ref name="Hernandez2011"></ref>. The mean and std. dev. is <math>0.145 \pm 0.07</math> | ||
+ | |||
+ | * Similarly for <math>Km_{PEP}</math> three reported values are 0.58, 0.702, 0.06. The uncertainty is then <math>0.44 \pm 0.276</math>. | ||
+ | |||
+ | * In Pietkiewicz et. al. (2009) <ref name="Pietkiewicz_2009"></ref> <math>V_{mr}</math> is reported as 1.4 <math>mmol/min^{-1}</math> and Marín-Hernández et. al. (2011) <ref name="Hernandez2011"></ref> reported it to be 0.4. The mean and the std. dev. calculated from these two values are <math>0.9 \pm 0.5</math>. | ||
+ | |||
+ | {|class="wikitable" | ||
+ | ! Parameter | ||
+ | ! Value | ||
+ | ! Units | ||
+ | ! Organism | ||
+ | ! Remarks | ||
+ | |- | ||
+ | |<math>V_{mf}</math> | ||
+ | |<math>0.36 \pm 0.15 (5)</math> <ref name="Hernandez_2006"> Marín-Hernández A , Rodríguez-Enríquez S, Vital-González P A, ''et al.'' (2006). ''Determining and understanding the control of glycolysis in fast-growth tumor cells. Flux control by an over-expressed but strongly product-inhibited hexokinase''. FEBS J., 273 , pp. 1975–1988([http://dx.doi.org/doi:10.1111/j.1742-4658.2006.05214.x doi]) </ref> <br><math>23.4 \pm 9.75</math> | ||
+ | |<math>U\cdot(\text{mg protein})^{-1}</math><br><math> \text{mM min}^{-1} </math> | ||
+ | |HeLa cell line | ||
+ | |rowspan="4"| | ||
+ | |- | ||
+ | |<math>V_{mr}</math> | ||
+ | |<math>0.9 \pm 0.5</math> | ||
+ | |<math> \text{mM min}^{-1} </math> | ||
+ | |- | ||
+ | |<math>Km_{2PG}</math> | ||
+ | |<math>0.145 \pm 0.07</math> | ||
+ | |mM | ||
+ | |Human muscle | ||
+ | |- | ||
+ | |<math>Km_{PEP}</math> | ||
+ | |<math>0.44 \pm 0.276</math> | ||
+ | |mM | ||
+ | |Human muscle | ||
+ | |} | ||
+ | |||
+ | === Equilibrium constant === | ||
+ | {|class="wikitable" | ||
+ | ! Equilibrium constant | ||
+ | ! Conditions | ||
+ | ! Source | ||
+ | |- | ||
+ | | 3.6 | ||
+ | | pH=7, T=25°C | ||
+ | | Voet et al.<ref name="voet">Voet, D., Voet., J.G. and Pratt, C. W. (1999) Fundamentals of biochemistry, Wiley</ref> from Newshole et al. (1973) <ref name="newshole73">Newshole, E.A. and Stuart, C. (1973) Regulation in Metabolism, Wiley</ref>p 97:<br/> | ||
+ | <math>\Delta G' = -3.2\ kJ.mol^{-1}</math>, <math>Keq = exp(-\frac{\Delta G'}{RT}) = exp(\frac{3200}{8.31*298.15}) \approx 3.6</math> | ||
+ | |- | ||
+ | | 6.7 | ||
+ | | T=25°C | ||
+ | | Bergmeyer ''Methods of enzymatic analysis'' page 449<ref name="bermeyer74">Bergmeyer H.U. (1974) ''Methods of enzymatic analysis'', Publisher: Verlag Chemie (vol 1)</ref> | ||
+ | |- | ||
+ | | 2.03 | ||
+ | | pH=7, T=297.15 K | ||
+ | | From Meyerhof et al. (1947)<ref name="meyerhof49">Meyerhof O. and Oesper P. (1947) J. Biol. Chem. 170(1):1-22 [[http://www.jbc.org/content/170/1.toc J. Biol. Chem.]]</ref>: | ||
+ | <math>\Delta G' = -1.757\ kJ.mol^{-1}</math>, <math>Keq = exp(-\frac{\Delta G'}{RT}) = exp(\frac{1757}{8.31*298.15}) \approx 2.03</math> | ||
+ | |- | ||
+ | | 4.29 | ||
+ | | pH=7, T=298.15 K, c(MgSO4,mol dm-3) =0.001 | ||
+ | | From Wold et al. (1957) (NIST database<ref name="nist">Goldberg R.N., Tewari Y.B. and Bhat T.N. (2004) Bioinformatics 20(16):2874-2877 [[http://www.ncbi.nlm.nih.gov/pubmed?term=15145806 pmid: 15145806]]</ref> [[http://xpdb.nist.gov/enzyme_thermodynamics/enzyme_data1.pl?T1=57WOL/BAL_1173 57WOL/BAL_1173]]) | ||
+ | |- | ||
+ | | 3.92 | ||
+ | | pH=7, T=298.15 K, c(MgSO4,mol dm-3) =0.01 | ||
+ | | From Wold et al. (1957) (NIST database<ref name="nist"></ref> [[http://xpdb.nist.gov/enzyme_thermodynamics/enzyme_data1.pl?T1=57WOL/BAL_1173 57WOL/BAL_1173]]) | ||
+ | |} | ||
+ | |||
+ | *Taking average from these values give <math>4.1 \pm 1.68</math> | ||
==References== | ==References== | ||
<references/> | <references/> |
Latest revision as of 11:07, 16 October 2014
Enolase, also known as phosphopyruvate hydratase, catalysis the conversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP). This is the penultimate step of glycolysis.
Contents
Chemical equation
Rate equation
Mono-substrate reversible Michaelis-Menten equation is used. [1]
Modified rate law to take Thermodynamic constraint into consideration
Parameter values
Parameter | Value | Units | Organism | Remarks |
---|---|---|---|---|
0.34 [2] | HeLa cell line | |||
0.38[1] | ||||
0.038[1] | mM | |||
0.06[1] | mM |
Parameters with uncertainty
- Three values for is collected. The values are 0.20 [3], 0.199 [3], 0.038 [1]. The mean and std. dev. is
- Similarly for three reported values are 0.58, 0.702, 0.06. The uncertainty is then .
- In Pietkiewicz et. al. (2009) [3] is reported as 1.4 and Marín-Hernández et. al. (2011) [1] reported it to be 0.4. The mean and the std. dev. calculated from these two values are .
Parameter | Value | Units | Organism | Remarks |
---|---|---|---|---|
[2] |
HeLa cell line | |||
mM | Human muscle | |||
mM | Human muscle |
Equilibrium constant
Equilibrium constant | Conditions | Source |
---|---|---|
3.6 | pH=7, T=25°C | Voet et al.[4] from Newshole et al. (1973) [5]p 97: , |
6.7 | T=25°C | Bergmeyer Methods of enzymatic analysis page 449[6] |
2.03 | pH=7, T=297.15 K | From Meyerhof et al. (1947)[7]:
, |
4.29 | pH=7, T=298.15 K, c(MgSO4,mol dm-3) =0.001 | From Wold et al. (1957) (NIST database[8] [57WOL/BAL_1173]) |
3.92 | pH=7, T=298.15 K, c(MgSO4,mol dm-3) =0.01 | From Wold et al. (1957) (NIST database[8] [57WOL/BAL_1173]) |
- Taking average from these values give
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 Marín-Hernández A, Gallardo-Pérez JC, Rodríguez-Enríquez S et al (2011) Modeling cancer glycolysis. Biochim Biophys Acta 1807:755–767 (doi)
- ↑ 2.0 2.1 Marín-Hernández A , Rodríguez-Enríquez S, Vital-González P A, et al. (2006). Determining and understanding the control of glycolysis in fast-growth tumor cells. Flux control by an over-expressed but strongly product-inhibited hexokinase. FEBS J., 273 , pp. 1975–1988(doi)
- ↑ 3.0 3.1 3.2 Pietkiewicz, J., Gamian, A., Staniszewska, M., & Danielewicz, R. (2009), Inhibition of human muscle-specific enolase by methylglyoxal and irreversible formation of advanced glycation end products, Journal of Enzyme Inhibition and Medicinal Chemistry, 24, 356–364
- ↑ Voet, D., Voet., J.G. and Pratt, C. W. (1999) Fundamentals of biochemistry, Wiley
- ↑ Newshole, E.A. and Stuart, C. (1973) Regulation in Metabolism, Wiley
- ↑ Bergmeyer H.U. (1974) Methods of enzymatic analysis, Publisher: Verlag Chemie (vol 1)
- ↑ Meyerhof O. and Oesper P. (1947) J. Biol. Chem. 170(1):1-22 [J. Biol. Chem.]
- ↑ 8.0 8.1 Goldberg R.N., Tewari Y.B. and Bhat T.N. (2004) Bioinformatics 20(16):2874-2877 [pmid: 15145806]