Difference between revisions of "Team:ETH Zurich/Modeling/AHL Module"
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\begin{align*} | \begin{align*} | ||
\varnothing&\mathop{\xrightarrow{\hspace{4em}}}^{a_{\mathrm{LuxR}}} \text{LuxR}\\ | \varnothing&\mathop{\xrightarrow{\hspace{4em}}}^{a_{\mathrm{LuxR}}} \text{LuxR}\\ | ||
− | \text{AHL} + \text{LuxR} &\mathop{\ | + | \text{AHL} + \text{LuxR} &\mathop{\mathop{\xrightarrow{\hspace{4em}}}^{\xleftarrow{\hspace{4em}}}}_{k_{\mathrm{-LuxRAHL}}}^{k_{\mathrm{LuxRAHL}}} \text{LuxRAHL}\\ |
&\mathop{\xrightarrow{\hspace{4em}}}^{\displaystyle\mathop{\downarrow}^{\text{LuxRAHL}}} \text{LuxI}\\ | &\mathop{\xrightarrow{\hspace{4em}}}^{\displaystyle\mathop{\downarrow}^{\text{LuxRAHL}}} \text{LuxI}\\ | ||
\text{LuxI}&\mathop{\xrightarrow{\hspace{4em}}}^{a_{\mathrm{AHL}}}\text{AHL}+\text{LuxI}\\ | \text{LuxI}&\mathop{\xrightarrow{\hspace{4em}}}^{a_{\mathrm{AHL}}}\text{AHL}+\text{LuxI}\\ |
Revision as of 09:05, 17 August 2015
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AHL Module
Introduction
Chemical species
Name | Description |
---|---|
AHL | Signaling protein, Acyl homoserine lactone (30C6-HSL) |
LuxR | Regulator protein, that can bind to AHL to form a complex |
LuxRAHL | Complex of LuxR and AHL, activates transcription of LuxI |
LuxI | Autoinducer synthase |
Aiia | AHL-lactonase, N-Acyl Homoserine Lactone Lactonase |
Reactions
\begin{align*} \varnothing&\mathop{\xrightarrow{\hspace{4em}}}^{a_{\mathrm{LuxR}}} \text{LuxR}\\ \text{AHL} + \text{LuxR} &\mathop{\mathop{\xrightarrow{\hspace{4em}}}^{\xleftarrow{\hspace{4em}}}}_{k_{\mathrm{-LuxRAHL}}}^{k_{\mathrm{LuxRAHL}}} \text{LuxRAHL}\\ &\mathop{\xrightarrow{\hspace{4em}}}^{\displaystyle\mathop{\downarrow}^{\text{LuxRAHL}}} \text{LuxI}\\ \text{LuxI}&\mathop{\xrightarrow{\hspace{4em}}}^{a_{\mathrm{AHL}}}\text{AHL}+\text{LuxI}\\ \text{LuxR}&\mathop{\xrightarrow{\hspace{4em}}}^{d_{\mathrm{LuxR}}}\varnothing\\ \text{AHL}&\mathop{\xrightarrow{\hspace{4em}}}^{d_{\mathrm{AHL}}}\varnothing\\ \text{LuxRAHL}&\mathop{\xrightarrow{\hspace{4em}}}^{d_{\mathrm{LuxRAHL}}}\varnothing\\ \text{LuxI}&\mathop{\xrightarrow{\hspace{4em}}}^{d_{\mathrm{LuxI}}}\varnothing\\ \text{Aiia}+\text{AHL}&\mathop{\xrightarrow{\hspace{4em}}}^{K_{\mathrm{M}},v_{\mathrm{Aiia}}}\text{Aiia}\\ \end{align*}Equations
The equations are based on mass action kinetics and basic rate laws such as Hill equation.
Assumptions
- As LuxR is constitutively produced in this model, we considered that LuxR was constant. We used then the conservation of mass to derive the equations
- On the other hand, the binding and unbinding of LuxR to AHL is fast compared to the synthesis of LuxI. We used the quasi steady state approximation (QSSA)