Difference between revisions of "Team:Peshawar/Model"

$$\mathbf{[CO]+[CooA] \longleftrightarrow [(CooA)2CO]}$$ $$\mathbf{[(CooA)2CO] \longleftrightarrow [(CooA)2CO.Pr]}$$ $k_{on1} = \textrm{formation rate constant}$
$\gamma_1 = \textrm{degradation rate constant}$
$P_{exp} = \textrm{probability of promoter to be activated}$ $$P_{exp} = \frac{\textrm{number of situations in which the promoter will be activated}}{\textrm{total number of situations}} = \frac{w}{z}$$ $$ w=\textrm{[(CooA)2CO.Pr]}=\frac{\textrm{[(CooA)2CO]}}{K_p}$$ $$\frac{d(mRNA)}{dt}=k_{on1}.P_{exp}-\gamma_1.[mRNA]$$ $$\textrm{Change in the concentration of the chromprotein} = \textrm{formation rate} - \textrm{degration rate}$$ $$ z=w+1=\frac{\textrm{[(CooA)2CO]}}{K_p}+1$$ $$\textrm{Total number of situations} = \textrm{Number of situations in which the promoter will be activated} - \textrm{Number of situations in which the promoter will not be acitvated}$$ $$P_{exp} = \frac{w}{z} = \frac{\frac{\textrm{[(CooA)2CO]}}{K_p}}{\frac{\textrm{[(CooA)2CO]}}{K_p}+1}$$ $$P_{exp} = \frac{\frac{\textrm{[CooA]}.\frac{\frac{\textrm{CO}}{K_I}}{1+\frac{\textrm{CO}}{K_I}}}{K_p}} {1+\frac{\textrm{[CooA]}.\frac{\frac{\textrm{CO}}{K_I}}{1+\frac{\textrm{CO}}{K_I}}}{K_p}} $$ $$[mRNA]=\frac{k_{on1}.P_{exp}}{\gamma_1}(1-e^{-\gamma_1t})$$ $$\frac{d\textrm{[CP]}}{dt} = k_{on2}.\textrm{[mRNA]}-\gamma_2\textrm{[CP]}$$ $$\textrm{[CP]} = k_{on2}.\frac{k_{on1}.P_{exp}}{\gamma_1.\gamma_2}(1-e^{-\gamma_2t}) + k_{on2}.\frac{k_{on1}.P_{exp}}{\gamma_1(\gamma_1-\gamma_2)}(e^{-\gamma_2t}-e^{-\gamma_1t})$$ $$\frac{d\textrm{[mCP]}}{dt} = k_{transcription}\textrm{[PYeaR]} - \gamma_m \textrm{[mCP]} $$ $$\frac{d\textrm{[CP]}}{dt}=k_{translation}\textrm{[mCP]}-\gamma_p\textrm{[CP]}$$ $$\frac{[\textrm{NO}^*]}{[\textrm{NO}_T]} = \frac{1}{1+\left(\frac{NsrR}{K_{NO}} \right)^n}$$ $$\textrm{[PYeaR]}activity = \frac{\beta}{1+ \left( \frac{\textrm{NO}^*}{K_{d(\textrm{NsrR})}} \right)}$$ $$\frac{d[\textrm{mCP}]}{dt} = \frac{k_{transcription}[\textrm{PYeaR}]}{1 + \left(\frac{[\textrm{NsrR}]}{\left(1+\left[\frac{[\textrm{NO}]}{K_{NO}}\right]^n \right)}\right) k_{d(\textrm{NsrR})} } - \gamma_m [\textrm{mCP}]$$ $$K=\frac{k_{transcription}[\textrm{PYeaR}]}{1 + \left(\frac{[\textrm{NsrR}]}{\left(1+\left[\frac{[\textrm{NO}]}{K_{NO}}\right]^n \right)}\right) k_{d(\textrm{NsrR})} }$$ $$\frac{d[\textrm{mCP}]}{dt} = K - \gamma_m [\textrm{mCP}]$$ $$[\textrm{mCP}]=\frac{K}{\gamma_m} - \frac{K}{\gamma_m}e^{-\gamma_mt}$$ $$[\textrm{CP}]=\frac{K k_{translation}}{\gamma_p \gamma_m} + \frac{K k_{translation}}{{\gamma_m}^2-\gamma_p \gamma_m} e^{-\gamma_mt} - \left(\frac{K k_{translation}}{\gamma_p \gamma_m} + \frac{K k_{translation}}{{\gamma_m}^2-\gamma_p \gamma_m} \right)e^{-\gamma_pt} $$

Parameter	Description	Value
$[\textrm{PYeaR}]$	Concentration of PYeaR	1 copy/cell
$k_{transcription}$	Rate of chromoprotein mRNA synthesis	0.167$\textrm{min}^{-1}$
$k_{translation}$	Rate of chromoprotein synthesis	$0.0011\textrm{min}^{-1}$
$\gamma_m$	mRNA degradation rate	$0.19\textrm{min}^{-1}$
$\gamma_p$	Chromoprotein degradation rate	$0.18\textrm{min}^{-1}$
$K_{\textrm{NO}}$	Dissociation constant of NO	$0.12\textrm{min}^{-1}$
$K_{\textrm{d(NsrR)}}$	Dissociation constant of NsrR	0.035 mM
n	Cooperativity of NO binding to NsrR	2

Header Cell 1	Header Cell 2	Header Cell 3
Row 1 Cell 1	Row 1 Cell 2	ConfirmReject
Row 2 Cell 1	Row 2 Cell 2	ConfirmReject
Row 3 Cell 1	Row 3 Cell 2	ConfirmReject
Row 4 Cell 1	Row 4 Cell 2	ConfirmReject