Difference between revisions of "Limonene Synthase"
Aliah.hawari (talk | contribs) (→More detailed information of the values obtained from the literature is listed here .) |
Aliah.hawari (talk | contribs) (→Strategies for estimating the kinetic parameter values) |
||
Line 94: | Line 94: | ||
=== Calculating the Equilibrium Constant === | === Calculating the Equilibrium Constant === | ||
+ | |||
+ | ==== Standard Gibbs Free energy ==== | ||
+ | Standard Gibbs Free energy for Limonene Synthase from MetaCyc [http://biocyc.org/META/new-image?object=4.2.3.16-RXN (EC 4.2.3.16)] is -28.049988 kcal/mol <ref name="Latendresse2013"> Latendresse M. (2013). [http://www.biocyc.org/PGDBConceptsGuide.shtml#gibbs. "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."] </ref>. | ||
+ | |||
+ | SI derived unit for Gibbs free energy is Joules per mol (J mol<sup>-1</sup>). 1 kJ·mol<sup>−1</sup> is equal to 0.239 kcal·mol<sup>−1</sup>. | ||
+ | |||
+ | Therefore, the Gibbs free energy for Limonene synthase in kJ mol<sup>-1</sup> is: | ||
+ | |||
+ | :<math> | ||
+ | |||
+ | \cfrac {1}{0.239 kcal.mol^-1} * -28.049988 kcal.mol^-1 | ||
+ | |||
+ | </math> | ||
+ | |||
+ | :<math> | ||
+ | |||
+ | = -117.36396 kJmol^-1 | ||
+ | |||
+ | </math> | ||
+ | |||
+ | ==== The Equilibrium Constant ==== | ||
The equilibrium constant can be calculated using the Van't Hoff Isotherm equation: | The equilibrium constant can be calculated using the Van't Hoff Isotherm equation: | ||
Line 143: | Line 164: | ||
|} | |} | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
=== Published Kinetic Parameter Values === | === Published Kinetic Parameter Values === |
Revision as of 12:58, 17 March 2016
You can go back to main page of the kinetic model here.
Contents
- 1 What we know
- 2 Reaction catalysed
- 3 Metabolite Background Information
- 4 Equation Rate
- 5 Strategies for estimating the kinetic parameter values
- 6 Simulations
- 7 References
What we know
Issues
Strategies
Reaction catalysed
Metabolite Background Information
Long metabolite names are abbreviated in the model for clarity and standard identification purposes.
Metabolite | Abbreviation | Chemical Formula | Molar mass (g/mol) | ChEBI | ChEMBL | PubChem |
---|---|---|---|---|---|---|
geranyl diphosphate | GPP | C10H20O7P2 | 314.209 | 17211 | 41432 | 445995 |
(-)-4S-limonene | Limonene | C10H16 | 136.24 | 15384 | 449062 | 22311 or 439250 |
diphosphate | PP | O7P2 | 173.94 | 644102 |
Equation Rate
Parameter | Description | Reference |
---|---|---|
VLimSynth | Reaction rate for Limonene Synthase | ref |
Vmaxforward | Maximum reaction rate towards the production of limonene | ref |
KmGPP | Michaelis-Menten constant for GPP | ref |
KmLimonene | Michaelis-Menten constant for Limonene | ref |
KmPP | Michaelis-Menten constant for PP | ref |
Keq | Equilibrium constant | ref |
[GPP] | GPP concentration | ref |
[Limonene] | Limonene concentration | ref |
[PP] | PP concentration | ref |
Strategies for estimating the kinetic parameter values
Calculating the Equilibrium Constant
Standard Gibbs Free energy
Standard Gibbs Free energy for Limonene Synthase from MetaCyc (EC 4.2.3.16) is -28.049988 kcal/mol [1].
SI derived unit for Gibbs free energy is Joules per mol (J mol-1). 1 kJ·mol−1 is equal to 0.239 kcal·mol−1.
Therefore, the Gibbs free energy for Limonene synthase in kJ mol-1 is:
- Failed to parse (Cannot store math image on filesystem.): \cfrac {1}{0.239 kcal.mol^-1} * -28.049988 kcal.mol^-1
- Failed to parse (Cannot store math image on filesystem.): = -117.36396 kJmol^-1
The Equilibrium Constant
The equilibrium constant can be calculated using the Van't Hoff Isotherm equation:
Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac {-(- 117.36396 \text { kJmol}^{-1})}{ (8.31 \text{ JK}^{-1} \text { mol}^{-1} * 289 K} \right )
Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac { + 117.36396 \text { kJmol}^{-1} }{ 2401.59 \text{ JK}^{-1}\text { mol}^{-1} }\right)
Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac{ 117.364 * 10^3 \text { Jmol}^{-1}}{2401.59 \text{ JK}^{-1}\text { mol}^{-1}} \right)
Failed to parse (Cannot store math image on filesystem.): =exp \left ( 48.8693 \right )
Failed to parse (Cannot store math image on filesystem.): = 1.6736 * 10^{21}
where;
Keq | Equilibrium constant |
-ΔG° | Gibbs free energy change. For Limonene Synthase it is -117.364 kJmol-1 |
R | Gas constant with a value of 8.31 JK-1mol-1 |
T | Temperature which is always expressed in kelvin |
Published Kinetic Parameter Values
Km Values
Km (mM) | Unit | Substrate / Product | Directionality | Organism | References |
---|---|---|---|---|---|
0.00125 | mM | GPP | forward | Ricciocarpos natans | Ref |
0.0018 | mM | GPP | forward | Mentha piperita | Ref |
0.00625 | mM | GPP | forward | Cannabis sativa L. | Ref |
0.00496 | mM | GPP | forward | Cannabis sativa L. | Ref |
0.0031 | mM | GPP | forward | Citrus limon | ref |
0.016 | mM | GPP | forward | Escherichia coli | Ref |
0.0068 | mM | GPP | forward | Cannabis sativa L. | Ref |
0.0067 | mM | GPP | forward | Cannabis sativa L. | Ref |
Vmax values
Vmax | Unit | Directionality | Organism | References |
---|---|---|---|---|
0.08 | µmol/min/mg | forward | Cannabis sativa L. | References |
0.13 | µmol/min/mg | forward | Cannabis sativa L. | References |
0.4748 | µmol/min/mg | forward | Citrus limon | References |
Vmax | Unit | Directionality | Organism | References |
Vmax | Unit | Directionality | Organism | References |
Vmax | Unit | Directionality | Organism | References |
Kcat values
Kcat | Unit | Organism | Reference |
---|---|---|---|
0.3 | s-1 | Mentha piperita & Mentha spicata | Alonso 1992 [2] |
0.08 | s-1 | Cannabis sativa L. | Reference |
0.14 | s-1 | Cannabis sativa L. | Reference |
0.02 | s-1 | E. coli | Reference |
0.082 | s-1 | Cannabis sativa L. | Reference |
0.081 | s-1 | Cannabis sativa L. | Reference |
Kcat | Unit | Organism | Reference |
Kcat | Unit | Organism | Reference |
Kcat | Unit | Organism | Reference |
Extracting Information from Limonene Production Rates
Production rates would reflect the flux for this reaction in the forward direction.
Amount produced (mg/L) | Time (H) | Organism | Description | Reaction Flux (µM/s) |
---|---|---|---|---|
5 | 24 | Escherichia coli | Possible reason for the low limonene production might due to the insufficient supply of IPP and DMAPP [3]. | 0.0255 |
335 | 48 | Escherichia coli | Engineered E.coli in which heterologous MVA pathway was installed [4]. | 0.8537 |
35.8 | 48 | Escherichia coli | E.coli was engineered to express GPPS, LS, DXS, and IDI [5] . | 0.0912 |
4.87 | 48 | Escherichia coli | This was the initial titer. The study established a limonene biosynthesis pathway in E.coli using four different polycistronic operons based on 3 vectors with varied expression strength [5]. | 0.0124 |
17.4 | 48 | Escherichia coli | Using a plasmid with DXS and IDI over expressed [5]. | 0.0445 |
430 | 72 | Escherichia coli | [4] | 0.7306 |
Detailed description of kinetic values obtained from literature
A more detailed descriptions of the values listed above can be found here .
Simulations
these are mock simulation results
References
- ↑ Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."
- ↑ Alonso et. al. 1992. "Purification of 4S-Limonene Synthase, a Monoterpene Cyclase from the Glandular Trichomes of Peppermint (Mentha x piperita) and Spearmint (Mentha spicata)", The Journal of Biological Chemistry, 267(11):7582-7587
- ↑ Carter, Ora A. et. al.2013. "Monoterpene biosynthesis pathway construction in Escherichia coli",Phytochemistry, 64:425–433, 2003.
- ↑ 4.0 4.1 Alonso-Gutierez et. al. 2013. "Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production", Metabolic Engineering, 19:33-41 Cite error: Invalid
<ref>
tag; name "AlonsoGutierez2013" defined multiple times with different content - ↑ 5.0 5.1 5.2 Du et. al. 2014. "Enhanced limonene production by optimizing the expression of limonene biosynthesis and MEP pathway genes in E.coli", Bioprocessing and Bioprocessing, 1:10