Team:NTU-Taida/Modeling/Parameters

Parameter

Description 

Value 

Reference

α_TetR

TetR max. production rate

0.8 μM/min

[5]

α_FadR

FadR max. production rate

100 μM/min

a.

α_GLP-1

GLP-1 max. production rate

1.23 μM/min

a.

α_LacI

LacI max. production rate

0.8 μM/min

[1]

k_s1

AHL_i production rate

0.01 1/min

[2]

ρ_R

LuxR-AHL dimerization rate

0.5 1/(μM³*min)

[1]

β_TetR

TetR repression coefficient

0.13 μM

a.

β_FA

FA repression coefficient

10 μM

[1]

β_FadR

FadR repression coefficient

0.13 μM

[1]

β_LacI

LacI repression coefficient

0.8 μM

[1]

β_R

LuxR-AHL repression coefficient

0.01 μM

[1]

γ_TetR

TetR degradation rate

0.0692 1/min

a.

γ_LacI

LacI degradation rate

0.0231 1/min

[1]

γ_GLP-1

GLP-1 degradation rate

0.0731/min

[1]

γ_LuxI

LuxI degradation rate

0.0167 1/min

[3]

k_s0

AHL_i degradation rate

1 1/min

[2]

k_se

AHL_e degradation rate

1 1/min

[2]

γ_R

LuxR-AHL degradation rate

0.0231 1/min

[1]

γ_RFP

RFP degradation rate

0.0041 1/min

[4]

n₁

FadR cooperativity coefficient

3

a.

n₂

FA cooperativity coefficient

2

a.

n₃

LuxR-AHL cooperativity coefficient

3

[1]

n₅

TetR cooperativity coefficient

2

[2]

n₆

LacI cooperativity coefficient

4

[1]

η

AHL Diffusion rate across the cell membrane

2

[2]

η_ext

Average diffusion rate for all cells

1

[2]

Parameter

Description 

Value 

Reference

[E]_t

Total active enzyme

50 uM

[8]

K_m

Reaction rate constant

47.9

[6][7]

D_FA

FA Diffusion Constant

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d

Thickness of the unstirred water layer

190 um

[9]

Kcat/ molecular weight

Catalytic Rate constant

1.8*10^-3

[6][7]

Parameter

Description 

Value 

Reference

cd

E. coli Cell Density

0.1

D_FA

FA Diffusion Constant

6.46* 10^-10m^2 /s

D_AHL

AHL Diffusion Constant

4.9e-6 cm2/s

[9]

γAHL,ext

AHL cell-external degradation

8.0225e-006/s

Derived from 1 day half-life at pH 7 <a href="https://2011.igem.org/Team:ETH_Zurich/Modeling/References#Ref7" title="Team:ETH Zurich/Modeling/References">[7]</a>

Source

[1]

Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005

[2]

Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing, PNAS vol. 101 no. 30, 2004

[3]

MIT igem 2010

[4]

Michael Halter, Alex Tona, Kiran Bhadriraju, Anne L. Plant, John T. Elliott, Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts, Cytometry Part A, Volume 71A Issue 10, 2007

[5]

Wilfried Weber, Markus Rimann, Manuela Spielmann, Bettina Keller, Marie Daoud-El Baba, Dominique Aubel, Cornelia C Weber & Martin Fussenegger, Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology, volume 22, number 11, 2004

[6]

Sulaiman Al-Zuhair, Masitah Hasan, K.B. Ramachandran, Kinetics of the enzymatic hydrolysis of palm oil by lipase, Process Biochemistry

Volume 38, Issue 8, 2003

[7]

Ho-Shing Wu, Ming-Ju Tsai, Kinetics of tributyrin hydrolysis by lipase, Enzyme and Microbial Technology, Volume 35, Issues 6–7, 2004

[8]

Bengt Borgstrom, Luminal Digestion of Fats, Handbook of Physiology, The Gastrointestinal System, Intestinal Absorption and Secretion, 1991

[9]

Sallee VL, Dietschy JM., Determinants of intestinal mucosal uptake of short- and medium-chain fatty acids and alcohols, Journal of Lipid Research, 1973