Difference between revisions of "Kinetic Model of Monoterpenoid Biosynthesis Wiki"
Aliah.hawari (talk | contribs) (→Description of the model) |
Aliah.hawari (talk | contribs) (→Description of the model) |
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rect 537 959 639 1001 [[Limonene-3-hydroxylase (L3H)]] | rect 537 959 639 1001 [[Limonene-3-hydroxylase (L3H)]] | ||
rect 180 962 279 998 [[Limonene-6-Hydroxylase (L6H)]] | rect 180 962 279 998 [[Limonene-6-Hydroxylase (L6H)]] | ||
+ | rect 537 714 639 751 [[IPDH|isopiperitenol dehydrogenase]] | ||
+ | rect 799 709 901 751 [[Isopiperitenol Reductase (IPR)]] | ||
+ | rect 950 814 1054 855 [[Isopulegone Isomerase (IPGI)]] | ||
+ | rect 731 1013 833 1054 [[Pulegone Reductase (PGR)]] | ||
+ | rect 658 1244 760 1282 [[MNMR]] | ||
+ | rect 792 1239 894 1278 [[MMR]] | ||
+ | rect 1010 1013 1112 1057 [[Menthofuran synthase (MFS)]] | ||
+ | rect 5 1066 104 1108 [[CDH]] | ||
+ | rect 0 1280 104 1316 [[OYE]] | ||
+ | rect 141 1377 243 1414 [[CHMO]] | ||
+ | rect 364 508 464 544 [[IDI]] | ||
+ | rect 112 391 214 430 [[Diphosphomelvalonate decarboxylase (DMD)]] | ||
+ | rect 364 396 464 435 [[Hydroxymethylbutenyl diphosphate reductase (HMBPPR)]] | ||
+ | rect 362 578 464 619 [[Geranyl diphosphate synthase (GPPS)]] | ||
desc bottom-right | desc bottom-right |
Revision as of 15:14, 16 March 2016
This wiki page describes the construction and simulation of a kinetic model of Monoterpenoid Biosynthesis.
Contents
Monoterpenoid Biosynthesis
Description of the model
To find out how each enzyme in the network is modelled, click on the rectangles in the figure on the left. Alternatively, you can click the enzyme names from the list below.
IPP and DMAPP Biosynthesis
Diphosphomelvalonate decarboxylase (DMD)
Hydroxymethylbutenyl diphosphate reductase (HMBPPR)
Limonene Biosynthesis
Geranyl diphosphate synthase (GPPS)
Peppermint Biosynthesis
Isopiperitenol Dehydrogenase (IPDH)
Isopiperitenol Reductase (IPR)
Mint Biosynthesis
Spearmint Biosynthesis
Methanofuran Biosynthesis
Reversible Michaelis-Menten equation
All reactions in this model are described using reversible Michaelis-Menten equation.
Kinetic Parameters
Strategies for Estimating Kinetic Parameter Values
Using Equilibrium Constant (Keq) in the reversible Michaelis-Menten equation
Using the equilibrium constant in the reversible Michaelis-Menten reaction reduces the need to obtain or estimate Vmaxreverse parameter value, which is often not available in literature.
Using the Haldane relationship, the equilibrium constant (Keq) can be written as:
- Failed to parse (Cannot store math image on filesystem.): {\color{Red}K_\mathrm{eq}} = \frac{Vmax_\mathrm{forward} * Km_\mathrm{product} }{Vmax_\mathrm{reverse} * Km_\mathrm{substrate}}
The reversible Michaelis-Menten rate equation can then be rewritten to contain the equilibrium constant (Keq) instead of using the ratio of the Vmax values.
- Failed to parse (Cannot store math image on filesystem.): v_\mathrm{reaction} = Vmax_\mathrm{forward} * \cfrac {\cfrac{[S]}{Km_\mathrm{substrate}} * \left ( 1 - \cfrac {[P]}{[S]* \color{red}K_\mathrm{eq}} \right )} {1 + \cfrac {[S]}{Km_\mathrm{substrate}} + \cfrac {[P]}{Km_\mathrm{product}}}
where [S] and [P] corresponds to the concentration of the substrate and product respectively.
Calculating the Equilibrium Constant (Keq)
The equilibrium constant can be calculated from the ratio of the forward and reverse reaction rates as described in the above section, given that the values for these rates are known. Unfortunately, the information for these values are often difficult to find, especially for reverse reaction rates (Vmaxreverse).
As an alternative, the equlibrium constant, Keq, can also be calculated from the Gibbs free energy of a reaction, ΔGr, using the Van't Hoff isotherm equation:
and by dividing both sides of the equation with RT, and later take the exponents of both sides, the Keq can be calculated by this equation:
where;
Keq | Equilibrium constant |
-ΔG° | Gibbs free energy change |
R | Gas constant with a value of 8.31 JK-1mol-1 |
T | Temperature which is always expressed in kelvin |
List of kinetic parameter values
Lists of values retrieved from published and unpublished sources for the kinetics of all the enzymes included in this study can be found here.
Data gathering progress:
Enzyme | Pathway | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
---|---|---|---|---|---|---|---|---|---|---|---|---|
01_GPPS | Limonene Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
01_L3H | Peppermint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] | ||
01_L6H | Spearmint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] | ||
01_MFS | Methanofuran Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
01_PGR | Mint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
02_CDH | Spearmint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
02_IPDH | Peppermint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
02_LimSynth | Limonene Biosynthesis | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] | |||
02_MNMR (menthone) | Mint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
02a_IPDH | Spearmint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
03_IPR | Peppermint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
03_MMR (menthone) | Mint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
03_OYE | Spearmint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
04_CHMO | Spearmint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
04_IPGI | Peppermint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
04_MNMR (isomenthone) | Mint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
enzyme | Pathway | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
04_MNMR (isomenthone) | Mint Biosynthesis | Keq | VmaxF | KmSub1 | KmSub2 | [Sub1] | [Sub2] | VmaxR | KmProd1 | KmProd2 | [Prod1] | [Prod2] |
Abbreviations
List of abbreviations used in this study can be found here
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