Imported:YPM/Non-specific dephosphorylation

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Category:Reactions - Yeast Pheromone Response Model Back to main model page


General Notes

In order to simulate the effect of non-specific phosphatases in the cell, we will add first order reactions for the dephosphorylation of phosphorylated proteins in the model. For proteins like Kss1 and Fus3, the rate of non-specific dephosphorylation is likely to be insignificant, but for proteins like Ste11 and Ste7, where no phosphatases have been identified, these reactions will be important for keeping the amount of phosphorylated protein in check in the absence of pheromone.

We will assume that all phosphorylated proteins are dephosphorylated by non-specific phosphatases at the same rate, kcat_nonspecific_dephosph.

In order to simplify the reactions, we will assume that the non-specific phosphatases can act on proteins regardless of what other proteins they are bound to.

Dig1 dephosphorylation

<modelRxnFull><modelRxnRule> 

Dig1(PO4_site~PO4) -> Dig1(PO4_site~none)

</modelRxnRule>

Dig2 dephosphorylation

<modelRxnFull><modelRxnRule> 

Dig2(PO4_site~PO4) -> Dig2(PO4_site~none)

</modelRxnRule>

Far1 dephosphorylation

<modelRxnFull><modelRxnRule> 

Far1(S87~PO4) -> Far1(S87~none)

</modelRxnRule> <modelRxnRule> 

Far1(T306~PO4) -> Far1(T306~none)

</modelRxnRule>

Fus3 dephosphorylation

<modelRxnFull><modelRxnRule> 

Fus3(T180~PO4) -> Fus3(T180~none)

</modelRxnRule><modelRxnRule> 

Fus3(Y182~PO4) -> Fus3(Y182~none)

</modelRxnRule>

Kss1 dephosphorylation

<modelRxnFull><modelRxnRule> 

Kss1(T183~PO4) -> Kss1(T183~none)

</modelRxnRule><modelRxnRule> 

Kss1(Y185~PO4) -> Kss1(Y185~none)

</modelRxnRule>

Sst2 dephosphorylation

<modelRxnFull><modelRxnRule> 

Sst2(S539~PO4) -> Sst2(S539~none)

</modelRxnRule>

Ste2 dephosphorylation

<modelRxnFull><modelRxnRule> 

Ste2(S338_S339~PO4) -> Ste2(S338_S339~none)

</modelRxnRule>

Ste7 dephosphorylation

<modelRxnFull><modelRxnRule> 

Ste7(S359_T363~pSpT) -> Ste7(S359_T363~pS)

</modelRxnRule><modelRxnRule> 

Ste7(S359_T363~pS) -> Ste7(S359_T363~none)

</modelRxnRule>

Ste11 dephosphorylation

<modelRxnFull><modelRxnRule> 

Ste11(S302_S306_T307~pSpSpT) -> Ste11(S302_S306_T307~pSpS)

</modelRxnRule><modelRxnRule> 

Ste11(S302_S306_T307~pSpS) -> Ste11(S302_S306_T307~pS)

</modelRxnRule><modelRxnRule> 

Ste11(S302_S306_T307~pS) -> Ste11(S302_S306_T307~none)

</modelRxnRule>

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