Difference between revisions of "Limonene Synthase"

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You can go back to main page of the kinetic model [http://www.systemsbiology.ls.manchester.ac.uk/wiki/index.php/Kinetic_Model_of_Monoterpenoid_Biosynthesis_Wiki '''here'''].
 
You can go back to main page of the kinetic model [http://www.systemsbiology.ls.manchester.ac.uk/wiki/index.php/Kinetic_Model_of_Monoterpenoid_Biosynthesis_Wiki '''here'''].
  
''' Model construction progress : '''
+
Limonene synthase (LIMS) is not native to ''E. coli'' and a heterologous LIMS gene from ''Mentha spicata'' was engineered into the cell <ref name="AlonsoGutierrez2013">[https://www.sciencedirect.com/science/article/pii/S109671761300058X Alonso-Gutierrez, J., et al.](2013). "Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production." Metabolic Engineering 19: 33-41.</ref>.  
 
 
{| class="wikitable"
 
|-
 
! style="border:2px solid black; padding: 5px; width: 150px;" |Enzyme
 
! style="border:2px solid black; padding: 5px; width: 200px;" | Pathway
 
! style="border:2px solid black; padding: 5px; width: 70px;" | Keq
 
! style="border:2px solid black; padding: 5px; width: 70px;" | Kcat
 
! style="border:2px solid black; padding: 5px; width: 70px;" | VmaxF
 
! style="border:2px solid black; padding: 5px; width: 70px;" | Km<sub>GPP</sub>
 
! style="border:2px solid black; padding: 5px; width: 70px;" | Km<sub>Sub2</sub>
 
! style="border:2px solid black; padding: 5px; width: 70px;" | [GPP]
 
! style="border:2px solid black; padding: 5px; width: 70px;" | [Sub2]
 
! style="border:2px solid black; padding: 5px; width: 70px;" | VmaxR
 
! style="border:2px solid black; padding: 5px; width: 70px;" | Km<sub>Lim</sub>
 
! style="border:2px solid black; padding: 5px; width: 70px;" | Km<sub>PP</sub>
 
! style="border:2px solid black; padding: 5px; width: 70px;" | [Limonene]
 
! style="border:2px solid black; padding: 5px; width: 70px;" | [PP]
 
|-
 
| style="border:2px solid black; padding: 5px; text-align:center;" | '''02_LimSynth'''
 
| style="border:2px solid black; padding: 5px; text-align:center;" | Limonene Biosynthesis
 
| style="border:2px solid black; padding: 5px;  background:#C70039; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; color:white;"| 1
 
| style="border:2px solid black; padding: 5px;  background:#C70039; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; color:white;"| 5
 
| style="border:2px solid black; padding: 5px;  background:#C70039; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; color:white;"| 3
 
| style="border:2px solid black; padding: 5px;  background:#C70039; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center;color:white;"| >6
 
| style="border:2px solid black; padding: 5px;  background:#d0e5f5; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; "| no Sub2
 
| style="border:2px solid black; padding: 5px;  background:#C70039; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; color:white;"| 4
 
| style="border:2px solid black; padding: 5px;  background:#d0e5f5; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; "| no Sub2
 
| style="border:2px solid black; padding: 5px;  background:#C70039; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; color:white;"| estimated
 
| style="border:2px solid black; padding: 5px;  background:#C70039; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; color:white;"| estimated
 
| style="border:2px solid black; padding: 5px;  background:#C70039; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; color:white;"| estimated
 
| style="border:2px solid black; padding: 5px;  background:#C70039; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; color:white;"| estimated
 
| style="border:2px solid black; padding: 5px;  background:#C70039; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center; color:white;"| estimated
 
|}
 
 
 
'''Legend''':
 
 
 
{|
 
|-
 
|Have not started ··
 
|1 -2 data found ··
 
|3-4 data found ··
 
|sufficient data found/estimated ··
 
|data distribution generated ··
 
|data sampled
 
|-
 
|style="border-bottom:1px solid #abd5f5; background:#d0e5f5; padding:0.2em 0.5em; font-size:110%; font-weight:bold; text-align:center;"|to do
 
|style="background-color: #8CF506;" |
 
|style="background-color: #F5F106;" |
 
|style="background-color: #FFC300;" |
 
|style="background-color: #FF5733;" |
 
|style="background-color: #C70039; font-size:110%; font-weight:bold; color:white; text-align:center;" | DONE!
 
|}
 
 
 
 
 
== What we know ==
 
 
 
=== Issues ===
 
 
 
=== Strategies ===
 
 
 
== Reaction catalysed ==
 
 
 
 
 
  
 
:<math>
 
:<math>
Line 72: Line 9:
 
</math>
 
</math>
  
== Metabolite Background Information ==
 
  
Long metabolite names are abbreviated in the model for clarity and standard identification purposes.
+
== Reaction rate ==
  
{| class="wikitable" style="text-align:center"
+
The reaction rate for LIMS is modelled using the reversible Michaelis-Menten equation <ref name="Sauro2011">Sauro, H. M. (2011). Appendix B: List of Common Rate Laws. Enzyme Kinetics for Systems Biology. United States of America, Future Skills Software: 279-290.</ref>, and is shown below:
|-
 
! Metabolite
 
! Abbreviation
 
! Chemical Formula
 
! Molar mass (g/mol)
 
! ChEBI
 
! ChEMBL
 
! PubChem
 
|-
 
| geranyl diphosphate
 
| GPP
 
| C<sub>10</sub>H<sub>20</sub>O<sub>7</sub>P<sub>2</sub>
 
| 314.209
 
| 17211
 
| 41432
 
| 445995
 
|-
 
| (-)-4S-limonene
 
| Limonene
 
| C<sub>10</sub>H<sub>16</sub>
 
| 136.24
 
| 15384
 
| 449062
 
| 22311 or 439250
 
|-
 
| diphosphate
 
| PP
 
| O<sub>7</sub>P<sub>2</sub>
 
| 173.94
 
|
 
|
 
| 644102
 
|-
 
| limonene synthase
 
| LimSynth
 
|
 
| 72.4 kDa <ref name="Turner1999"> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC59327/ Turner,G. et. al.]1999. "Limonene synthase, the enzyme responsible for monoterpene biosynthesis in peppermint, is localized to leucoplasts of oil gland secretory cells", Plant Physiology 120(3): 879-886</ref> ; 60kDa <ref name="Maruyama2002">[http://www.ncbi.nlm.nih.gov/pubmed/12033511 Maruyama, T. et. al. ]2002. "Molecular cloning, functional expression and characterization of ''d''-Limonene synthase from ''Agastache rugosa''" Biol. Pharm. Bull. 25(5): 661-665</ref>
 
|
 
|
 
|
 
|-
 
|}
 
 
 
== Equation Rate ==
 
 
 
The reversible Michaelis-Menten equation to model the dynamic changes of LimSynth is:
 
  
 
:<math>
 
:<math>
  
V_\mathrm{LimSynth} =  Vmax_\mathrm{forward} * \cfrac {\cfrac{[GPP]}{Km_\mathrm{GPP}} * \left ( 1 - \cfrac {[Limonene]*[PP]}{[GPP]*K_\mathrm{eq}} \right )}{1 + \cfrac {[GPP]}{Km_\mathrm{GPP}} + \cfrac {[Limonene]}{Km_\mathrm{Limonene}}  + \cfrac {[PP]}{Km_\mathrm{PP}}  + \cfrac {[Limonene]*[PP]}{Km_\mathrm{Limonene}*Km_\mathrm{PP}}}
+
V_\mathrm{LimSynth} =  Kcat_\mathrm{LIMS}*[LIMS] * \cfrac {\cfrac{[GPP]}{Km_\mathrm{GPP}} * \left ( 1 - \cfrac {[Limonene]*[PP]}{[GPP]*K_\mathrm{eq}} \right )}{1 + \cfrac {[GPP]}{Km_\mathrm{GPP}} + \cfrac {[Limonene]}{Km_\mathrm{Limonene}}  + \cfrac {[PP]}{Km_\mathrm{PP}}  + \cfrac {[Limonene]*[PP]}{Km_\mathrm{Limonene}*Km_\mathrm{PP}}}
  
 
</math>
 
</math>
Line 136: Line 26:
 
! scope="col" style="width: 50px; background: #ADD8E6;" | Units
 
! scope="col" style="width: 50px; background: #ADD8E6;" | Units
 
|-
 
|-
| V<sub>LimSynth</sub> || Reaction rate for Limonene Synthase ||  
+
| V<sub>LimSynth</sub> || Reaction rate for Limonene Synthase || μM/min
 
|-
 
|-
| V<sub>max<sub>forward</sub></sub> || Maximum reaction rate towards the production of limonene || ref
+
| K<sub>cat<sub>LIMS</sub></sub> || Turnover number for limonene synthase || min<sup>-1</sup>
 
|-
 
|-
| Km<sub>GPP</sub> || Michaelis-Menten constant for GPP || mM
+
| Km<sub>GPP</sub> || Michaelis-Menten constant for GPP || μM
 
|-
 
|-
| Km<sub>Limonene</sub> || Michaelis-Menten constant for Limonene || mM
+
| Km<sub>Limonene</sub> || Michaelis-Menten constant for Limonene ||μM
 
|-
 
|-
| Km<sub>PP</sub> || Michaelis-Menten constant for PP || mM
+
| Km<sub>PP</sub> || Michaelis-Menten constant for PP || μM
 
|-
 
|-
| K<sub>eq</sub> || Equilibrium constant ||  
+
| K<sub>eq</sub> || Equilibrium constant || dimensionless
 
|-
 
|-
| [GPP] || GPP concentration || mM
+
| [GPP] || GPP concentration || μM
 
|-
 
|-
| [Limonene] || Limonene concentration || mM
+
| [Limonene] || Limonene concentration || μM
 
|-
 
|-
| [PP]|| PP concentration || mM
+
| [PP]|| PP concentration || μM
 
|}
 
|}
  
== Strategies for estimating the kinetic parameter values ==
 
  
=== Calculating the Equilibrium Constant ===
+
== Parameterisation ==
 
+
The parameterisation of LIMS for this model was performed according to our DIPPER protocol <ref name="Tsig2018>[https://www.nature.com/articles/s41596-018-0056-z Tsigkinopoulou, A., et al.]  (2018). "Defining informative priors for ensemble modeling in systems biology." Nature protocols 13: 2643-2663.</ref>. Here, we list the thermodynamic and kinetic paramater values obtained from the literature, weights assigned and  the log-normal distribution parameter values calculated.
==== Standard Gibbs Free energy ====
+
===Thermodynamic parameter values===
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>.
+
Gibbs free energy values for LIMS are obtained 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> and Equilibrator [http://equilibrator.weizmann.ac.il/]. Table 2 summarizes the Δ<sub>r</sub>G° values found for LIMS and the calculated Keq. These Keq values are given an arbitrary equal weight of 1 as the Δ<sub>r</sub>G° values obtained were calculated from a group contribution method and do not have any measurement conditions that would allow us to assess the Keq values according to the weighting scheme set out in (insert link here).
 
 
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:
 
:<math>
 
 
 
K_\mathrm{eq} = exp \left ( \cfrac {-ΔG^{°'}}{RT} \right )
 
 
 
</math>
 
 
 
 
 
<math>
 
 
 
= exp \left (  \cfrac {-(- 117.36396 \text { kJmol}^{-1})}{ (8.31 \text{ JK}^{-1} \text { mol}^{-1} * 289 K} \right )
 
 
 
</math>
 
 
 
<math>
 
 
 
= exp \left (  \cfrac { + 117.36396 \text { kJmol}^{-1} }{ 2401.59 \text{ JK}^{-1}\text { mol}^{-1} }\right)
 
</math>
 
 
 
<math>
 
= exp \left ( \cfrac{ 117.364 * 10^3 \text { Jmol}^{-1}}{2401.59 \text{ JK}^{-1}\text { mol}^{-1}} \right)
 
</math>
 
 
 
<math>
 
 
 
=exp \left ( 48.8693 \right )
 
</math>
 
 
 
<math>
 
= 1.6736 * 10^{21}
 
</math>
 
 
 
 
 
where;
 
 
 
{|
 
|-
 
| style="width: 30pt;" | '''K<sub>eq</sub>'''
 
| style="width: 400pt;" | Equilibrium constant
 
  
 +
{| class="wikitable"
 +
! style="font-weight: bold;border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;"" | Δ<sub>r</sub>G°(kcal/mol)
 +
! style="font-weight: bold;" | Keq
 +
! style="font-weight: bold;" | Error (±)
 +
! style="font-weight: bold;" | Source
 +
! style="font-weight: bold;" | Weight
 
|-
 
|-
| '''-ΔG<sup>°</sup>''' || Gibbs free energy change. For Limonene Synthase it is -117.364 kJmol<sup>-1</sup>
+
| -28.050
 +
| 3.843E+20
 +
| N/A
 +
| MetaCyc
 +
| 1
 
|-
 
|-
| '''R''' || Gas constant with a value of 8.31 JK<sup>-1</sup>mol<sup>-1</sup>
+
| -42.161 ± 2.844
 +
| 8.711E+30
 +
| 5.876E+29
 +
| Equilibrator
 +
| 1
 
|-
 
|-
| '''T''' || Temperature which is always expressed in Kelvin
 
 
|}
 
|}
  
== Kinetic Parameter Values ==
+
=== Kinetic Parameter Values ===
  
Values for the kinetic parameter required to simulate this model can be obtained from published and unpublished literature.
+
{| class="wikitable"
 
+
|+ Table 2: Km for GPP values for LIMS
A more detailed descriptions of the values listed above can be found [[ Limonene Synthase: Detailed information on the kinetic values obtained from the literature | '''HERE''' ]], where I've linked and highlighted where these data came from.
+
| align="center" style="background:#f0f0f0;"|'''Parameter'''
 
+
| align="center" style="background:#f0f0f0;"|'''Value'''
=== Substrate, Product & Enzyme Concentration Values ===
+
| align="center" style="background:#f0f0f0;"|'''Error'''
{| class="wikitable sortable"  
+
| align="center" style="background:#f0f0f0;"|'''Weight'''
|-
+
| align="center" style="background:#f0f0f0;"|'''Error type'''
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Concentration
+
| align="center" style="background:#f0f0f0;"|'''Description'''
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Unit
+
| align="center" style="background:#f0f0f0;"|'''References'''
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Substrate / Product
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Directionality
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 150px;" | Organism
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 300px;" | Method notes
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 10px;" | References
 
|-
 
| 25
 
| µM
 
| GPP
 
| forward
 
| ''E. coli''
 
|
 
| <ref name="Williams1998"> Williams, D.C. et. al. 1998. [http://www.ncbi.nlm.nih.gov/pubmed/9724535 "Truncation of Limonene Synthase preprotein provides a fully active 'pseudomature' form of this monoterpene cyclase and reveals the function of the amino-terminal arginine pair ",Biochemistry, 37:12213-12220] </ref>
 
|-
 
| 10
 
| µM
 
| GPP
 
| forward
 
| ''Cannabis sativa L.''
 
|
 
| <ref name="Gunnewich2006"> Gunnewich, N., et al. 2006.[https://www.researchgate.net/publication/42089356 "Functional expression and characterization of trichome-specific (-)-limonene synthase and (+)-α-pinene synthase from ''Cannabis sativa''", Natural Product Communications, 0(0): pp1-10]  </ref>
 
|-
 
| 10
 
| µM
 
| GPP
 
| forward
 
| ''Mentha sp.''
 
|
 
| <ref name="Alonso1992">Alonso et. al. 1992. [http://www.ncbi.nlm.nih.gov/pubmed/1559995 "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]</ref>
 
 
|-
 
|-
| 2
+
| Km_gpp_LIMS||47.4||3.8||128||0||LIMS gene from Lavandula angustifolia was expressed in E. coli. The kinetics were measured in vitro at 30°C||<ref name="Landmann2007">[https://www.sciencedirect.com/science/article/pii/S0003986107003013 Landmann, C., et al.] (2007). "Cloning and characterization of three terpene synthases from lavender (''Lavandula angustifolia'')." Archives of Biochemistry and Biophysics 465: 417-429.</ref>
| µM
 
| GPP
 
| forward
 
| ''Citrus limon''
 
|
 
| <ref name="Lucker2002"> Lücker, J. et. al. 2002.[http://www.ncbi.nlm.nih.gov/pubmed/12084056 "Monoterpene biosynthesis in lemon (''Citrus limon''). cDNA isolation and functional analysis of four monoterpene synthases", Eur. J. Biochem. 269: pp3160-3171]  </ref>
 
 
|-
 
|-
| 150
+
| Km_gpp_LIMS||130||NaN||32||0||LIMS gene from Citrus sinensis (orange) was expressed in E. coli. The Km was measured in vitro at 20°C.||<ref name="Entova2013">[Entova, S.](2013). Kinetic characterization, crystallization, and photosynthetic expression of (+)-$R-limonene synthase from C. sinensis. Department of Biochemistry. Massachusetts, Brandeis University. Master's: 55.</ref>
| µg
 
| Limonene synthase
 
| -
 
| ''E. coli''
 
|
 
| <ref name="Williams1998"> </ref>
 
 
|-
 
|-
| 0.07
+
| Km_gpp_LIMS||6.8||NaN||32||0||LIMS gene from Cannabis sativa L. var. 'Skunk' plants was expressed in E. coli. The kinetics were measured at 40°C.||<ref name="Gunnewich2007"> [https://www.researchgate.net/publication/42089356_Functional_expression_and_characterization_of_trichome-specific_--limonene_synthase_and_-a-pinene_synthase_from_Cannabis_sativa Günnewich, N., Page, J.E., Köllner, T.G., Degenhardt, J., & Kutchan, T.M] 2007. "Functional expression and characterization of trichome-specific (-)-limonene synthase and (+)-α-pinene synthase from ''Cannabis sativa'' ". Nat. Prod. Comm. 2(3): 223-232.  </ref>
| µM
 
| Limonene synthase
 
| -
 
| ''Citrus sinensis''
 
| with 200µM GPP as substrate, at 20°C, pH7.5
 
| <ref name="Entova2013">Entova, S. 2013. [http://bir.brandeis.edu/handle/10192/25158 "Kinetic characterization, crystallization, and photosynthetic expression of (+)-4R-limonene synthase from ''C. sinensis''"], Masters Thesis, Brandeis Univeristy</ref>
 
 
|-
 
|-
| 0.26
+
| Km_gpp_LIMS||0.7||NaN||128||0||LIMS gene from Citrus limon (lemon) was expressed in E. col. Kinetics were measured in vitro at 30°C.||<ref name="Lucker2002">[https://febs.onlinelibrary.wiley.com/doi/full/10.1046/j.1432-1033.2002.02985.x Lücker, J., et al.] (2002). "Monoterpene biosynthesis in lemon (''Citrus limon'') cDNA isolation and functional analysis of four monoterpene synthases." Eur. J. Biochem. 269: 3160-3171.
| µM
+
</ref>
| Limonene synthase
 
| -
 
| ''Citrus sinensis''
 
| with 200µM GPP, at 37°C, pH7.5
 
| <ref name="Entova2013"></ref>
 
 
|-
 
|-
| 200
+
| Km_gpp_LIMS||1.25||NaN||16||0||LIMS isolated from Ricciocarpos natans. Kinetics measured at 32°C and pH7.0. ||<ref name="Adam1996">[https://www.sciencedirect.com/science/article/pii/S0003986196903525 Adam, K.-P., et al.] (1996). "Partial purification and characterization of a monoterpene cyclase, limonene synthase, from the liverwort ''Ricciocarpus natans''." Archives of Biochemistry and Biophysics 332(2): 352-356. </ref>
| µM
 
| GPP
 
| forward
 
| ''Citrus sinensis''
 
| used for Limonene synthase activity assay at 20°C and 37°C, pH 7.5
 
| <ref name="Entova2013"></ref>
 
|-
 
| 100
 
| µM
 
| GPP
 
| -
 
| ''Citrus limon''
 
|
 
| <ref name="Lucker2002"></ref>
 
|-
 
| 0.1
 
| µM
 
| GPP
 
| -
 
| ''Citrus limon''
 
|
 
| <ref name="Lucker2002"></ref>
 
 
|-
 
|-
 +
| Km_gpp_LIMS||1.8||NaN||32||0||LIMS isolated from Mentha x piperita (peppermint). Kinetics were measured at 30°C.||<ref name="Rajaonarivony1992">[https://www.sciencedirect.com/science/article/pii/0003986192905436 Rajaonarivony, J. I. M., et al.] (1992). "Characterization and mechanism of (4S)-limonene synthase, a monoterpene cyclase from the glandular trichomes of peppermint (Mentha X piperita)." Archives of Biochemistry and Biophysics 296(1): 49-57.</ref>
 
|}
 
|}
  
=== Km Values ===
+
{| class="wikitable"
{| class="wikitable sortable"  
+
|+ Table 3: Turnover number values for LIMS
|-
+
| align="center" style="background:#f0f0f0;"|'''Parameter'''
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Km (mM)
+
| align="center" style="background:#f0f0f0;"|'''Value'''
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Unit
+
| align="center" style="background:#f0f0f0;"|'''Error'''
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Substrate / Product
+
| align="center" style="background:#f0f0f0;"|'''Weight'''
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Directionality
+
| align="center" style="background:#f0f0f0;"|'''Error type'''
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 150px;" | Organism
+
| align="center" style="background:#f0f0f0;"|'''Description'''
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 300px;" | Method notes
+
| align="center" style="background:#f0f0f0;"|'''References'''
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 10px;" | References
 
|-
 
| 0.13
 
| mM
 
| GPP
 
| forward
 
| ''Citrus sinensis''
 
| Enzyme assay, pH 7.5, 20°C
 
| <ref name="Entova2013"> </ref>
 
|-
 
| 0.00125 
 
| mM
 
| GPP
 
| forward
 
| ''Ricciocarpos natans''
 
|
 
| <ref name="Adam1996"> Adam, K. et. al. 1996. "Partial purification and characterization of a monoterpene cyclase, limonene synthase, from the liverwort ''Ricciocarpos natans''. 332(2):pp 352-356.</ref>
 
|-
 
| 0.0018
 
| mM
 
| GPP
 
| forward
 
| Mentha piperita
 
|
 
| Ref
 
|-
 
| 0.01176 ± 0.00245
 
| mM
 
| GPP
 
| forward
 
| ''Cannabis sativa'' L.
 
|
 
| <ref name="Gunnewich2008"></ref>
 
|-
 
| 0.0031
 
| mM
 
| GPP
 
| forward
 
| Citrus limon
 
|
 
| ref
 
|-
 
| 0.016
 
| mM
 
| GPP
 
| forward
 
| ''Escherichia coli''
 
|
 
| <ref name="Williams1998"></ref>
 
|-
 
| 0.0067
 
| mM
 
| GPP
 
| forward
 
| ''Escherichia coli'' (wt)
 
|
 
| <ref name="Ogura1997"> Ogura, K. & Koyama, T. 1997, "Dynamic aspects of Natural Products Chemistry". pp 1-23.</ref>
 
|-
 
| 0.0068
 
| mM
 
| GPP
 
| forward
 
| ''Cannabis sativa L.''
 
| enzyme assay, pH7.5, 40°C
 
| <ref name="Gunnewich2006"></ref>
 
|-
 
| 0.0086
 
| mM
 
| GPP
 
| forward
 
| ''Escherichia coli'' (Q53).
 
|
 
| <ref name="Williams1998"></ref>
 
|-
 
| 0.006
 
| mM
 
| GPP
 
| forward
 
| ''Escherichia coli'' (E57).
 
|
 
| <ref name="Williams1998"></ref>
 
|-
 
| 0.0126
 
| mM
 
| GPP
 
| forward
 
| ''Escherichia coli'' (R58).
 
|
 
| <ref name="Williams1998"></ref>
 
|-
 
| 0.0299
 
| mM
 
| GPP
 
| forward
 
| ''Escherichia coli'' (R59).
 
|
 
| <ref name="Williams1998"></ref>
 
 
|-
 
|-
| 0.0324
+
| Kcat_LIMS||0.72||NaN||128||0||LIMS gene from Lavandula angustifolia was expressed in E. coli. The kinetics were measured in vitro at 30°C||<ref name="Landmann2007" />
| mM
 
| GPP
 
| forward
 
| ''Escherichia coli'' (R58P59)
 
|
 
| <ref name="Williams1998"></ref>
 
 
|-
 
|-
| 0.0275
+
| Kcat_LIMS||7.8||NaN||32||0||LIMS gene from Citrus sinensis (orange) was expressed in E. coli. The enzyme activities were measured in vitro at 20°C and 37°C.||<ref name="Entova2013" />
| mM
 
| GPP
 
| forward
 
| ''Escherichia coli'' (R58A59)
 
|
 
| <ref name="Williams1998"></ref>
 
 
|-
 
|-
| 0.0188
+
| Kcat_LIMS||2.4||NaN||32||0||LIMS gene from Citrus sinensis (orange) was expressed in E. coli. The enzyme activities were measured in vitro at 20°C and 37°C.||<ref name="Entova2013" />
| mM
 
| GPP
 
| forward
 
| ''Escherichia coli'' (S60)
 
|
 
| <ref name="Williams1998"></ref>
 
 
|-
 
|-
| 0.0007
+
| Kcat_LIMS||4.92||NaN||32||0||LIMS gene from Cannabis sativa L. var. 'Skunk' plants was expressed in E. coli. The kinetics were measured at 40°C.||<ref name="Gunnewich2007" />
| mM
 
| GPP
 
| forward
 
| ''Citrus limon''
 
|
 
| <ref name="Lucker2002"></ref>
 
|-
 
| 0.00625 ± 0.00041
 
| mM
 
| GPP
 
| forward
 
| ''Cannabis sativa'' L
 
|
 
| <ref name="Gunnewich2008"></ref>
 
 
|-
 
|-
 
|}
 
|}
  
=== Vmax values ===
+
=== BRENDA data ===
 +
To further enrich the kinetic parameter values for LIMS, parameter values from EC 4 to EC 4.2.3.* that can be obtained from BRENDA is downloaded. These BRENDA data is integrated with the rest of the kinetic parameter values using our ‘BRENDA Add-on’ protocol. In the BRENDA Add-On protocol, we’ve specified six different ‘EC cases’ that are arranged in order of rank. These EC cases are essentially six different datasets of parameter values downloaded from BRENDA that are filtered according to the specific enzyme class and organism of interest. For this case study example, six different ‘EC case’ datasets were downloaded from BRENDA each for Km and Kcat parameters (Tables below).
  
{| class="wikitable sortable"
+
{| class="wikitable"
 +
|+ Table 7: Input matrix for Km values from BRENDA for EC 4.2.3.16
 +
|+  align="bottom" style="caption-side: bottom; text-align: left;" |Parameter value and uncertainty is in µM. Each row represents EC case 2 – 6 respectively. EC case 1 is discarded as number of values obtained were <50. .
 +
|+  align="bottom" style="caption-side: bottom; text-align: left;" |*Uncertainty values in this table correspond to the standard deviation calculated from SEM reported in literature
 +
|+  align="bottom" style="caption-side: bottom; text-align: left;" |** Uncertainty type is multiplicative, therefore ‘1’ is defined.
 +
 
 +
! style="font-weight: bold;" | Parameter value
 +
! style="font-weight: bold;" | Uncertainty*
 +
! style="font-weight: bold;" | Weight
 +
! style="font-weight: bold;" | Uncertainty type**
 
|-
 
|-
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Vmax
+
| 6.80
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Unit
+
| 14.9566
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Directionality
+
| 11.9024
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 150px;" | Organism
+
| 1
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 300px;" | Organism
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 10px;" | References
 
 
|-
 
|-
| 0.08
+
| 49
| µmol/min/mg
+
| 69.0555
| forward
+
| 7.4390
| ''Cannabis sativa'' L.
+
| 1
|
 
| <ref name="Gunnewich2008"> Gunnewich, N. 2008. "Expression and characterization of terpene synthases from ''Cannabis sativa'' L. and ''Salvia sclarea'' L. Doctoral thesis.  </ref>
 
 
|-
 
|-
| 0.12 ± 0.01
+
| 121
| µmol/min/mg
+
| 36.1126
| forward
+
| 2.9756
| ''Cannabis sativa''
+
| 1
|
 
| <ref name="Gunnewich2008"> </ref>
 
 
|-
 
|-
| 0.4748
+
| 500
| µmol/min/mg
+
| 36.9586
| forward
+
| 1.4878
| ''Citrus limon''
+
| 1
|
 
| References
 
|-
 
| 0.53
 
| µM/min
 
| forward
 
| ''Citrus sinensis''
 
| 200µM GPP, 20°C, [E]: 0.07µM, pH7.5
 
| <ref name= "Entova2013"></ref>
 
|-
 
| 0.64
 
| µM/min
 
| forward
 
| ''Citrus sinensis''
 
| 200µM GPP, 37°C, [E]: 0.26µM, pH7.5
 
| <ref name= "Entova2013"></ref>
 
|-
 
| Vmax
 
| Unit
 
| Directionality
 
| Organism
 
|
 
| References
 
 
|-
 
|-
 +
| 300
 +
| 23.8770
 +
| 0.5951
 +
| 1
 
|}
 
|}
  
==== Kcat values ====
+
{| class="wikitable"
 
+
|+ Input matrix for K<sub>cat</sub> values from BRENDA for EC 4.2.3.16
{| class="wikitable sortable"
+
|+  align="bottom" style="caption-side: bottom; text-align: left;" |Parameter value and uncertainty is in µM. Each row represents EC case 2 – 6 respectively. EC case 1 is discarded as number of values obtained were <50. .
|-
+
|+  align="bottom" style="caption-side: bottom; text-align: left;" |*Uncertainty values in this table correspond to the standard deviation calculated from SEM reported in literature
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Kcat
+
|+  align="bottom" style="caption-side: bottom; text-align: left;" |** Uncertainty type is multiplicative, therefore ‘1’ is defined.
! style="border: 1px solid black; padding: 5px; background: #ffdead;" | Unit
+
! style="font-weight: bold;" | Parameter value
! style="border: 1px solid black; padding: 5px; background: #ffdead;" | Directionality
+
! style="font-weight: bold;" | Uncertainty*
! style="border: 1px solid black; padding: 5px; background: #ffdead;" | Organism
+
! style="font-weight: bold;" | Weight
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 300px;" | Method notes
+
! style="font-weight: bold;" | Uncertainty type**
! style="border: 1px solid black; padding: 5px; background: #ffdead;" | Reference
 
|-
 
| 0.13
 
| s<sup>-1</sup>
 
| forward
 
| ''Citrus sinensis''
 
| 200mM GPP, 20°C, [E]: 0.07 mM, pH7.5
 
| <ref name="Entova2013"></ref>
 
|-
 
| 0.04
 
| s<sup>-1</sup>
 
| forward
 
| ''Citrus sinensis''
 
| 200mM GPP, 37°C, [E]: 0.26mM, pH7.5
 
| <ref name="Entova2013"></ref>
 
|-
 
| 0.3
 
| s<sup>-1</sup>
 
| forward
 
| ''Mentha piperita'' & ''Mentha spicata''
 
| pH6.5, 40°C, enzyme assay
 
| <ref name="Alonso1992">Alonso et. al. 1992. [http://www.ncbi.nlm.nih.gov/pubmed/1559995 "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]</ref>
 
|-
 
| 0.09
 
| s<sup>-1</sup>
 
| forward
 
| ''Cannabis sativa '' L.
 
|
 
| <ref name="Gunnewich2008"></ref>
 
 
|-
 
|-
| 0.13
+
| 2.040
| s<sup>-1</sup>
+
| 38.2439
| forward
+
| 9.5610
| ''Cannabis sativa L.''
+
| 1
|  
 
| <ref name="Gunnewich2008"></ref>
 
 
|-
 
|-
| 0.02
+
| 17.400
| s<sup>-1</sup>
+
| 109.1960
| forward
+
| 5.9756
| ''E. coli''
+
| 1
|
 
| <ref name= "Williams1998"></ref>
 
 
|-
 
|-
| 0.082
+
| 200.698
| s<sup>-1</sup>
+
| 177.0428
| forward
+
| 2.3902
| ''Cannabis sativa L.''
+
| 1
|
 
| <ref name="Gunnewich2006"> Günnewich et. al. 2006. [https://www.researchgate.net/publication/42089356 "Functional expression and characterization of trichome-specific (-)-limonene synthase and (+)-α-pinene synthase from ''Cannabis sativa''", Natural Product Communications, 0(0):1-10]</ref>
 
 
|-
 
|-
| 0.000039
+
| 192.000
| s<sup>-1</sup>
+
| 44.6715
| forward
+
| 1.1951
| ''Citrus sinenesis''
+
| 1
| enzyme assay, with 40 μM GPP, 37°C
 
| <ref name="Olsen2011"> Olsen, S. N. 2011. [http://bir.brandeis.edu/handle/10192/24424?show=full] "Isolation, purification, and characterization of (+)-4R-limonene synthase: The first step in exploring enzyme stereospecificity in terpenoid biosynthesis" Masters Thesis, Brandeis University, </ref>
 
|-
 
| 0.0024
 
| s<sup>-1</sup>
 
| forward
 
| ''E. coli'' (wt)
 
|
 
| <ref name= "Ogura1997"></ref>
 
|-
 
| 0.0020
 
| s<sup>-1</sup>
 
| forward
 
| ''E. coli'' (preprotein)
 
|
 
| <ref name= "Williams1998"></ref>
 
|-
 
| 0.0036
 
| s<sup>-1</sup>
 
| forward
 
| ''E. coli'' (Q54)
 
|
 
| <ref name= "Ogura1997"></ref> <ref name="Williams1998"></ref>
 
|-
 
| 0.0034
 
| s<sup>-1</sup>
 
| forward
 
| ''E. coli'' (E57)
 
|
 
| <ref name= "Ogura1997"></ref> <ref name="Williams1998"></ref>
 
|-
 
| 0.0037
 
| s<sup>-1</sup>
 
| forward
 
| ''E. coli'' (R58)
 
|
 
| <ref name= "Ogura1997"></ref> <ref name="Williams1998"></ref>
 
|-
 
| <0.0004
 
| s<sup>-1</sup>
 
| forward
 
| ''E. coli'' (R59)
 
|
 
| <ref name= "Ogura1997"></ref> <ref name="Williams1998"></ref>
 
|-
 
| <0.0004
 
| s<sup>-1</sup>
 
| forward
 
| ''E. coli'' (R58P59)
 
|
 
| <ref name= "Ogura1997"></ref> <ref name="Williams1998"></ref>
 
|-
 
| <0.0004
 
| s<sup>-1</sup>
 
| forward
 
| ''E. coli'' (R58A59)
 
|
 
| <ref name= "Ogura1997"></ref> <ref name="Williams1998"></ref>
 
|-
 
| <0.0004
 
| s<sup>-1</sup>
 
| forward
 
| ''E. coli'' (S60)
 
|
 
| <ref name= "Ogura1997"></ref> <ref name="Williams1998"></ref>
 
 
|-
 
|-
 +
| 168.000
 +
| 62.4126
 +
| 0.4780
 +
| 1
 
|}
 
|}
  
=== Extracting Information from Limonene Production Rates ===
+
=== Log-normal distribution parameters ===
  
The production rates would reflect on the flux for this enzyme, and this would provide provide the insights on the Vmax of this enzyme.  
+
The Mode, Confidence Interval (CI) factor, mu and sigma for each parameter distribution is calculated using our scripts as detailed in the DIPPER protocol <ref name="Tsig2018>[https://www.nature.com/articles/s41596-018-0056-z Tsigkinopoulou, A., et al.]  (2018). "Defining informative priors for ensemble modeling in systems biology." Nature protocols 13: 2643-2663.</ref>.  
  
{| class="wikitable" style="width: 60%; height: 200px;"
+
{| class="wikitable"
 +
| align="center" style="background:#f0f0f0;"|'''Parameter'''
 +
| align="center" style="background:#f0f0f0;"|'''Brenda Add-on'''
 +
| align="center" style="background:#f0f0f0;"|'''Mode'''
 +
| align="center" style="background:#f0f0f0;"|'''CI Factor'''
 +
| align="center" style="background:#f0f0f0;"|'''Mu'''
 +
| align="center" style="background:#f0f0f0;"|'''Sigma'''
 +
|-
 +
| Km_gpp_LIMS||✘||6.8||7.6504||3.3719||1.2062
 
|-
 
|-
! style="border: 1px solid black; padding: 5px; background: #ffdead;"| Amount produced (mg/L)
+
| Kcat_LIMS||||0.8001||2.6307||0.3424||0.7519
! style="border: 1px solid black; padding: 5px; background: #ffdead;"| Time (H)
 
! style="border: 1px solid black; padding: 5px; background: #ffdead;"| Organism
 
! style="border: 1px solid black; padding: 5px; background: #ffdead;"| Description
 
! style="border: 1px solid black; padding: 5px; background: #ffdead;"| Reaction Flux (µM/s)
 
|- style="height: 100px;"
 
| 5  || 24 || style="width: 150px;" | Escherichia coli || style="width: 1200px;" |  Possible reason for the low limonene production might due to the insufficient supply of IPP and DMAPP <ref name="Carter2013">Carter, Ora A. et. al.2013. [http://www.sciencedirect.com/science/article/pii/S0031942203002048 "Monoterpene biosynthesis pathway construction in ''Escherichia coli''",Phytochemistry, 64:425–433, 2003.]</ref>. || 0.0255
 
|- style="height: 100px;"
 
| 335 || style="width: 50px;" | 48 || Escherichia coli || Engineered E.coli in which heterologous MVA pathway was installed <ref name= "AlonsoGutierez2013">Alonso-Gutierez et. al. 2013. [http://www.sciencedirect.com/science/article/pii/S109671761300058X "Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production", Metabolic Engineering, 19:33-41]</ref>. || 0.8537
 
|- style="height: 100px;"
 
| 35.8 || 48 || Escherichia coli || E.coli was engineered to express GPPS, LS, DXS, and IDI <ref name="Du2014"> Du et. al. 2014. [http://www.bioresourcesbioprocessing.com/content/1/1/10 "Enhanced limonene production by optimizing the expression of limonene biosynthesis and MEP pathway genes in E.coli", Bioprocessing and Bioprocessing, 1:10]</ref> . || 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 <ref name="Du2014"></ref>. || 0.0124
+
| Km_gpp_LIMS||✔||||||||
 
|-
 
|-
| 17.4 || 48 || Escherichia coli || Using a plasmid with DXS and IDI over expressed <ref name="Du2014"></ref>. || 0.0445
+
| Kcat_LIMS||✔||||||||
 
|-
 
|-
| 430 || 72 || Escherichia coli || <ref name= "AlonsoGutierez2013"> </ref> || 0.7306
 
 
|}
 
|}
  
=== Parameter estimation ===
+
=== Log-normal distribution parameter estimation ===
  
 
This section can be found [[ LimSynth: Parameter Estimation | ''' HERE ''']]
 
This section can be found [[ LimSynth: Parameter Estimation | ''' HERE ''']]

Latest revision as of 14:14, 29 November 2018

You can go back to main page of the kinetic model here.

Limonene synthase (LIMS) is not native to E. coli and a heterologous LIMS gene from Mentha spicata was engineered into the cell [1].



geranyl diphosphate \rightleftharpoons (−)-(4S)-limonene + diphosphate


Reaction rate

The reaction rate for LIMS is modelled using the reversible Michaelis-Menten equation [2], and is shown below:



V_\mathrm{LimSynth} =  Kcat_\mathrm{LIMS}*[LIMS] * \cfrac {\cfrac{[GPP]}{Km_\mathrm{GPP}} * \left ( 1 - \cfrac {[Limonene]*[PP]}{[GPP]*K_\mathrm{eq}} \right )}{1 + \cfrac {[GPP]}{Km_\mathrm{GPP}} + \cfrac {[Limonene]}{Km_\mathrm{Limonene}}  + \cfrac {[PP]}{Km_\mathrm{PP}}  + \cfrac {[Limonene]*[PP]}{Km_\mathrm{Limonene}*Km_\mathrm{PP}}}

where :

Parameter Description Units
VLimSynth Reaction rate for Limonene Synthase μM/min
KcatLIMS Turnover number for limonene synthase min-1
KmGPP Michaelis-Menten constant for GPP μM
KmLimonene Michaelis-Menten constant for Limonene μM
KmPP Michaelis-Menten constant for PP μM
Keq Equilibrium constant dimensionless
[GPP] GPP concentration μM
[Limonene] Limonene concentration μM
[PP] PP concentration μM


Parameterisation

The parameterisation of LIMS for this model was performed according to our DIPPER protocol [3]. Here, we list the thermodynamic and kinetic paramater values obtained from the literature, weights assigned and the log-normal distribution parameter values calculated.

Thermodynamic parameter values

Gibbs free energy values for LIMS are obtained from MetaCyc (EC 4.2.3.16) is -28.049988 kcal/mol [4] and Equilibrator [1]. Table 2 summarizes the ΔrG° values found for LIMS and the calculated Keq. These Keq values are given an arbitrary equal weight of 1 as the ΔrG° values obtained were calculated from a group contribution method and do not have any measurement conditions that would allow us to assess the Keq values according to the weighting scheme set out in (insert link here).

ΔrG°(kcal/mol) Keq Error (±) Source Weight
-28.050 3.843E+20 N/A MetaCyc 1
-42.161 ± 2.844 8.711E+30 5.876E+29 Equilibrator 1

Kinetic Parameter Values

Table 2: Km for GPP values for LIMS
Parameter Value Error Weight Error type Description References
Km_gpp_LIMS 47.4 3.8 128 0 LIMS gene from Lavandula angustifolia was expressed in E. coli. The kinetics were measured in vitro at 30°C [5]
Km_gpp_LIMS 130 NaN 32 0 LIMS gene from Citrus sinensis (orange) was expressed in E. coli. The Km was measured in vitro at 20°C. [6]
Km_gpp_LIMS 6.8 NaN 32 0 LIMS gene from Cannabis sativa L. var. 'Skunk' plants was expressed in E. coli. The kinetics were measured at 40°C. [7]
Km_gpp_LIMS 0.7 NaN 128 0 LIMS gene from Citrus limon (lemon) was expressed in E. col. Kinetics were measured in vitro at 30°C. [8]
Km_gpp_LIMS 1.25 NaN 16 0 LIMS isolated from Ricciocarpos natans. Kinetics measured at 32°C and pH7.0. [9]
Km_gpp_LIMS 1.8 NaN 32 0 LIMS isolated from Mentha x piperita (peppermint). Kinetics were measured at 30°C. [10]
Table 3: Turnover number values for LIMS
Parameter Value Error Weight Error type Description References
Kcat_LIMS 0.72 NaN 128 0 LIMS gene from Lavandula angustifolia was expressed in E. coli. The kinetics were measured in vitro at 30°C [5]
Kcat_LIMS 7.8 NaN 32 0 LIMS gene from Citrus sinensis (orange) was expressed in E. coli. The enzyme activities were measured in vitro at 20°C and 37°C. [6]
Kcat_LIMS 2.4 NaN 32 0 LIMS gene from Citrus sinensis (orange) was expressed in E. coli. The enzyme activities were measured in vitro at 20°C and 37°C. [6]
Kcat_LIMS 4.92 NaN 32 0 LIMS gene from Cannabis sativa L. var. 'Skunk' plants was expressed in E. coli. The kinetics were measured at 40°C. [7]

BRENDA data

To further enrich the kinetic parameter values for LIMS, parameter values from EC 4 to EC 4.2.3.* that can be obtained from BRENDA is downloaded. These BRENDA data is integrated with the rest of the kinetic parameter values using our ‘BRENDA Add-on’ protocol. In the BRENDA Add-On protocol, we’ve specified six different ‘EC cases’ that are arranged in order of rank. These EC cases are essentially six different datasets of parameter values downloaded from BRENDA that are filtered according to the specific enzyme class and organism of interest. For this case study example, six different ‘EC case’ datasets were downloaded from BRENDA each for Km and Kcat parameters (Tables below).

Table 7: Input matrix for Km values from BRENDA for EC 4.2.3.16 Parameter value and uncertainty is in µM. Each row represents EC case 2 – 6 respectively. EC case 1 is discarded as number of values obtained were <50. . *Uncertainty values in this table correspond to the standard deviation calculated from SEM reported in literature ** Uncertainty type is multiplicative, therefore ‘1’ is defined.
Parameter value Uncertainty* Weight Uncertainty type**
6.80 14.9566 11.9024 1
49 69.0555 7.4390 1
121 36.1126 2.9756 1
500 36.9586 1.4878 1
300 23.8770 0.5951 1
Input matrix for Kcat values from BRENDA for EC 4.2.3.16 Parameter value and uncertainty is in µM. Each row represents EC case 2 – 6 respectively. EC case 1 is discarded as number of values obtained were <50. . *Uncertainty values in this table correspond to the standard deviation calculated from SEM reported in literature ** Uncertainty type is multiplicative, therefore ‘1’ is defined.
Parameter value Uncertainty* Weight Uncertainty type**
2.040 38.2439 9.5610 1
17.400 109.1960 5.9756 1
200.698 177.0428 2.3902 1
192.000 44.6715 1.1951 1
168.000 62.4126 0.4780 1

Log-normal distribution parameters

The Mode, Confidence Interval (CI) factor, mu and sigma for each parameter distribution is calculated using our scripts as detailed in the DIPPER protocol [3].

Parameter Brenda Add-on Mode CI Factor Mu Sigma
Km_gpp_LIMS 6.8 7.6504 3.3719 1.2062
Kcat_LIMS 0.8001 2.6307 0.3424 0.7519
Km_gpp_LIMS
Kcat_LIMS

Log-normal distribution parameter estimation

This section can be found HERE

Simulations

Simulations performed can be found HERE.

References

  1. Alonso-Gutierrez, J., et al.(2013). "Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production." Metabolic Engineering 19: 33-41.
  2. Sauro, H. M. (2011). Appendix B: List of Common Rate Laws. Enzyme Kinetics for Systems Biology. United States of America, Future Skills Software: 279-290.
  3. 3.0 3.1 Tsigkinopoulou, A., et al. (2018). "Defining informative priors for ensemble modeling in systems biology." Nature protocols 13: 2643-2663.
  4. Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."
  5. 5.0 5.1 Landmann, C., et al. (2007). "Cloning and characterization of three terpene synthases from lavender (Lavandula angustifolia)." Archives of Biochemistry and Biophysics 465: 417-429.
  6. 6.0 6.1 6.2 [Entova, S.](2013). Kinetic characterization, crystallization, and photosynthetic expression of (+)-$R-limonene synthase from C. sinensis. Department of Biochemistry. Massachusetts, Brandeis University. Master's: 55.
  7. 7.0 7.1 Günnewich, N., Page, J.E., Köllner, T.G., Degenhardt, J., & Kutchan, T.M 2007. "Functional expression and characterization of trichome-specific (-)-limonene synthase and (+)-α-pinene synthase from Cannabis sativa ". Nat. Prod. Comm. 2(3): 223-232.
  8. Lücker, J., et al. (2002). "Monoterpene biosynthesis in lemon (Citrus limon) cDNA isolation and functional analysis of four monoterpene synthases." Eur. J. Biochem. 269: 3160-3171.
  9. Adam, K.-P., et al. (1996). "Partial purification and characterization of a monoterpene cyclase, limonene synthase, from the liverwort Ricciocarpus natans." Archives of Biochemistry and Biophysics 332(2): 352-356.
  10. Rajaonarivony, J. I. M., et al. (1992). "Characterization and mechanism of (4S)-limonene synthase, a monoterpene cyclase from the glandular trichomes of peppermint (Mentha X piperita)." Archives of Biochemistry and Biophysics 296(1): 49-57.