Molecules


Substrate
Attribute b˜1 indicates that an enzyme is bound to substrate and b˜0 indicates no enzyme is bound
Attributes Y1, Y2, and Y3 each refer to individual ITAMs.
Each ITAM can be unphosphorylated (Y˜U), phosphorylated on one tyrosine (Y˜P), or doubly phosphorylated (Y˜2P)

S(b~0~1,Y1~U~P~2P,Y2~U~P~2P,Y3~U~P~2P)

S b 0 1 Y1 U P 2P Y2 U P 2P Y3 U P 2P

Kinase

E(b)

E b

Phosphatase

F(b)

F b

ZAP-70

Z(b)

Z b

Species

S(b~0,Y1~U,Y2~U,Y3~U)

S b 0 Y1 U Y2 U Y3 U

E(b)

E b

F(b)

F b

Z(b)

Z b

Observables

Bound_ZAP Z(b!+)

Z b

Szero S(b~?,Y1~U!?,Y2~U!?,Y3~U!?)

S b ? Y1 ?U Y2 ?U Y3 ?U

Sone S(b~?,Y1~P!?,Y2~U!?,Y3~U!?)

S b ? Y1 ?P Y2 ?U Y3 ?U

Stwo S(b~?,Y1~2P!?,Y2~U!?,Y3~U!?)

S b ? Y1 ?2P Y2 ?U Y3 ?U

Sthree S(b~?,Y1~2P!?,Y2~P!?,Y3~U!?)

S b ? Y1 ?2P Y2 ?P Y3 ?U

Sfour S(b~?,Y1~2P!?,Y2~2P!?,Y3~U!?)

S b ? Y1 ?2P Y2 ?2P Y3 ?U

Sfive S(b~?,Y1~2P!?,Y2~2P!?,Y3~P!?)

S b ? Y1 ?2P Y2 ?2P Y3 ?P

Ssix S(b~?,Y1~2P!?,Y2~2P!?,Y3~2P!?)

S b ? Y1 ?2P Y2 ?2P Y3 ?2P

Reaction Rules


ITAM 1

E(b) + S(b~0,Y1~U,Y2~U,Y3~U) <-> E(b!1).S(b~1,Y1~U!1,Y2~U,Y3~U)

E ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 ⬇⬆U Y2 U Y3 U

E(b!1).S(b~1,Y1~U!1,Y2~U,Y3~U) -> E(b) + S(b~0,Y1~P,Y2~U,Y3~U)

E ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 ⬆U P take all branches, once each, in any order⬇ Y2 U Y3 U

F(b) + S(b~0,Y1~P,Y2~U,Y3~U) <-> F(b!1).S(b~1,Y1~P!1,Y2~U,Y3~U)

F ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 ⬇⬆P Y2 U Y3 U

F(b!1).S(b~1,Y1~P!1,Y2~U,Y3~U) -> F(b) + S(b~0,Y1~U,Y2~U,Y3~U)

F ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 U ⬆P take one or more branches, once each, in any order⬆ Y2 U Y3 U

E(b) + S(b~0,Y1~P,Y2~U,Y3~U) <-> E(b!1).S(b~1,Y1~P!1,Y2~U,Y3~U)

E ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 ⬇⬆P Y2 U Y3 U

E(b!1).S(b~1,Y1~P!1,Y2~U,Y3~U) -> E(b) + S(b~0,Y1~2P,Y2~U,Y3~U)

E ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 ⬆P 2P take all branches, once each, in any order⬇ Y2 U Y3 U

F(b) + S(b~0,Y1~2P,Y2~U,Y3~U) <-> F(b!1).S(b~1,Y1~2P!1,Y2~U,Y3~U)

F ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 ⬇⬆2P Y2 U Y3 U

F(b!1).S(b~1,Y1~2P!1,Y2~U,Y3~U) -> F(b) + S(b~0,Y1~P,Y2~U,Y3~U)

F ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 P ⬆2P take one or more branches, once each, in any order⬆ Y2 U Y3 U

ITAM 2

E(b) + S(b~0,Y2~U,Y1~2P,Y3~U) <-> E(b!1).S(b~1,Y2~U!1,Y1~2P,Y3~U)

E ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 2P Y2 ⬇⬆U Y3 U

E(b!1).S(b~1,Y2~U!1,Y1~2P,Y3~U) -> E(b) + S(b~0,Y2~P,Y1~2P,Y3~U)

E ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 2P Y2 ⬆U P take all branches, once each, in any order⬇ Y3 U

F(b) + S(b~0,Y2~P,Y1~2P,Y3~U) <-> F(b!1).S(b~1,Y2~P!1,Y1~2P,Y3~U)

F ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 2P Y2 ⬇⬆P Y3 U

F(b!1).S(b~1,Y2~P!1,Y1~2P,Y3~U) -> F(b) + S(b~0,Y2~U,Y1~2P,Y3~U)

F ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 2P Y2 U ⬆P take one or more branches, once each, in any order⬆ Y3 U

E(b) + S(b~0,Y2~P,Y1~2P,Y3~U) <-> E(b!1).S(b~1,Y2~P!1,Y1~2P,Y3~U)

E ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 2P Y2 ⬇⬆P Y3 U

E(b!1).S(b~1,Y2~P!1,Y1~2P,Y3~U) -> E(b) + S(b~0,Y2~2P,Y1~2P,Y3~U)

E ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 2P Y2 ⬆P 2P take all branches, once each, in any order⬇ Y3 U

F(b) + S(b~0,Y2~2P,Y1~2P,Y3~U) <-> F(b!1).S(b~1,Y2~2P!1,Y1~2P,Y3~U)

F ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 2P Y2 ⬇⬆2P Y3 U

F(b!1).S(b~1,Y2~2P!1,Y1~2P,Y3~U) -> F(b) + S(b~0,Y2~P,Y1~2P,Y3~U)

F ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 2P Y2 P ⬆2P take one or more branches, once each, in any order⬆ Y3 U

ITAM 3

E(b) + S(b~0,Y3~U,Y2~2P,Y1~2P) <-> E(b!1).S(b~1,Y3~U!1,Y2~2P,Y1~2P)

E ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 2P Y2 2P Y3 ⬇⬆U

E(b!1).S(b~1,Y3~U!1,Y2~2P,Y1~2P) -> E(b) + S(b~0,Y3~P,Y2~2P,Y1~2P)

E ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 2P Y2 2P Y3 ⬆U P take all branches, once each, in any order⬇

F(b) + S(b~0,Y3~P,Y2~2P,Y1~2P) <-> F(b!1).S(b~1,Y3~P!1,Y2~2P,Y1~2P)

F ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 2P Y2 2P Y3 ⬇⬆P

F(b!1).S(b~1,Y3~P!1,Y2~2P,Y1~2P) -> F(b) + S(b~0,Y3~U,Y2~2P,Y1~2P)

F ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 2P Y2 2P Y3 U ⬆P take one or more branches, once each, in any order⬆

E(b) + S(b~0,Y3~P,Y2~2P,Y1~2P) <-> E(b!1).S(b~1,Y3~P!1,Y2~2P,Y1~2P)

E ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 2P Y2 2P Y3 ⬇⬆P

E(b!1).S(b~1,Y3~P!1,Y2~2P,Y1~2P) -> E(b) + S(b~0,Y3~2P,Y2~2P,Y1~2P)

E ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 2P Y2 2P Y3 ⬆P 2P take all branches, once each, in any order⬇

F(b) + S(b~0,Y3~2P,Y2~2P,Y1~2P) <-> F(b!1).S(b~1,Y3~2P!1,Y2~2P,Y1~2P)

F ⬇⬆b ⬇⬆ S b 0 1 take all branches, once each, in any order⬇⬆ Y1 2P Y2 2P Y3 ⬇⬆2P

F(b!1).S(b~1,Y3~2P!1,Y2~2P,Y1~2P) -> F(b) + S(b~0,Y3~P,Y2~2P,Y1~2P)

F ⬆b ⬆ S b 0 1 take one or more branches, once each, in any order⬆ Y1 2P Y2 2P Y3 P ⬆2P take one or more branches, once each, in any order⬆

ZAP70 binding

Z(b) + S(Y1~2P) <-> Z(b!1).S(Y1~2P!1)

Z ⬇⬆b ⬇⬆ S b 0 ?1 Y1 ⬇⬆2P Y2 U P ?2P Y3 U P ?2P

Z(b) + S(Y2~2P) <-> Z(b!1).S(Y2~2P!1)

Z ⬇⬆b ⬇⬆ S b 0 ?1 Y1 U P ?2P Y2 ⬇⬆2P Y3 U P ?2P

Z(b) + S(Y3~2P) <-> Z(b!1).S(Y3~2P!1)

Z ⬇⬆b ⬇⬆ S b 0 ?1 Y1 U P ?2P Y2 U P ?2P Y3 ⬇⬆2P