Difference between revisions of "Simulating DBR Biotransformation"

Revision as of 13:56, 15 August 2016

Figure 1: Overview of simulating DBR biotransformation from Toogood, et. al, 2015.

SUMMARY This DBR simulation is of the biotransformation experiment as described in Toogood, et. al. (2015) ^[1]. The experiment observed a percentage yield of 40% and 33% of menthone and isomenthone respectively after 24 hours. An overview of the simulation including the concentration of enzyme, substrate and cofactor is shown in Figure 1. Ensemble modelling of this reaction was carried out for 200 samples where the kinetic parameters were sampled randomly from 7 probability distributions. To describe the production variability of menthone to isomenthone, a variability factor (X1 and X2) were included in the reaction equation. These variabililty factors were calculated from the average product ratio sampled from a probability distribution.

Average Product Ratio

Figure 2: Probability distribution of average product ratio values

Yield ratio of menthone:isomenthone were reported in Toogood, et. al.(2015) ^[1] (40:33), Solodar (1976) ^[2] (70:30) and Ringer, et. al. (2003) ^[3] (55:45).

Figure 3: Kernel density plot of average product ratio sampled

References

↑ ^1.0 ^1.1 Toogood, H.S. et. al.2015.Enzymatic menthol production: One-pot approach using engineered Escherichia coli , ACS Synthetic Biology, 4:1112-1123.
↑ Solodar,J. 1976. Stereoselective reduction of menthone and isomenthone by dissolving alkali metals and by hydrogen with group 8 metals on carbon, J. Org. Chem. 41(21):3461-3464
↑ Ringer, K.L. et. al.. 2003.Monoterpene double-bond reductases of the (-)-menthol biosynthetic pathway:isolation and characterization of cDNAs encoding (-)-isopiperitenone reductase and (+)-pulegone reductase of peppermint, Arc. Biochem. Biophysics, 418:80-92

[Toogood2015-1] 1.0 ^1.1 Toogood, H.S. et. al.2015.Enzymatic menthol production: One-pot approach using engineered Escherichia coli , ACS Synthetic Biology, 4:1112-1123.

[Solodar1976-2] Solodar,J. 1976. Stereoselective reduction of menthone and isomenthone by dissolving alkali metals and by hydrogen with group 8 metals on carbon, J. Org. Chem. 41(21):3461-3464

[Ringer2003-3] Ringer, K.L. et. al.. 2003.Monoterpene double-bond reductases of the (-)-menthol biosynthetic pathway:isolation and characterization of cDNAs encoding (-)-isopiperitenone reductase and (+)-pulegone reductase of peppermint, Arc. Biochem. Biophysics, 418:80-92

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-The DBR model was used to simulate the production of menthone and isomenthone through the biotransformation experiment performed by Toogood, H.S. ''et. al.'', 2015 <ref name="Toogood2015"> Toogood, H.S. ''et. al.''2015.[http://www.ncbi.nlm.nih.gov/pubmed/26017480 "Enzymatic menthol production: One-pot approach using engineered ''Escherichia coli''], ACS Synthetic Biology, '''4''':1112-1123.</ref>.
+[[File: DBR_biotrans_toogood_simulation.png | left| thumb| '''Figure 1''': Overview of simulating DBR biotransformation from Toogood, ''et. al'', 2015.|700px]]
+'''SUMMARY'''
+This DBR simulation is of the biotransformation experiment as described in Toogood, ''et. al.'' (2015) <ref name="Toogood2015"> Toogood, H.S. ''et. al.''2015.[http://www.ncbi.nlm.nih.gov/pubmed/26017480 '''Enzymatic menthol production: One-pot approach using engineered ''Escherichia coli'' '''], ACS Synthetic Biology, '''4''':1112-1123.</ref>. The experiment observed a percentage yield of 40% and 33% of menthone and isomenthone respectively after 24 hours. An overview of the simulation including the concentration of enzyme, substrate and cofactor is shown in Figure 1. Ensemble modelling of this reaction was carried out for 200 samples where the kinetic parameters were sampled randomly from 7 probability distributions. To describe the production variability of menthone to isomenthone, a variability factor (X1 and X2) were included in the reaction equation. These variabililty factors were calculated from the average product ratio sampled from a probability distribution.
+==Average Product Ratio==
+[[File: 09_DBR_biotrans_01.png |left| thumb| '''Figure 2''': Probability distribution of average product ratio values| 500px]]
+Yield ratio of menthone:isomenthone were reported in Toogood, ''et. al.''(2015) <ref name="Toogood2015"></ref> (40:33), Solodar (1976) <ref name="Solodar1976"> [http://pubs.acs.org/doi/pdf/10.1021/jo00883a031 Solodar,J. 1976. '''Stereoselective reduction of menthone and isomenthone by dissolving alkali metals and by hydrogen with group 8 metals on carbon'''], J. Org. Chem. '''41'''(21):3461-3464</ref> (70:30) and Ringer, ''et. al.'' (2003) <ref name="Ringer2003">[http://www.ncbi.nlm.nih.gov/pubmed/13679086 Ringer, K.L. ''et. al.''. 2003.'''Monoterpene double-bond reductases of the (-)-menthol biosynthetic pathway:isolation and characterization of cDNAs encoding (-)-isopiperitenone reductase and (+)-pulegone reductase of peppermint], Arc. Biochem. Biophysics, '''418''':80-92</ref> (55:45).
+[[File: 10_DBR_biotrans_02.png |left| thumb| '''Figure 3''': Kernel density plot of average product ratio sampled| 500px]]
-[[File: DBR_biotrans_toogood_simulation.png | 700px]]
-[[File: 09_DBR_biotrans_01.png]]
-[[File: 10_DBR_biotrans_02.png]]
 ==References ==
 <references/>

Difference between revisions of "Simulating DBR Biotransformation"

Revision as of 13:56, 15 August 2016

Average Product Ratio

References

Navigation menu

Personal tools

Namespaces

Variants

Views

More

Search

Navigation

Tools