. 2022 Oct 22;121(23):4600–4614. doi: 10.1016/j.bpj.2022.10.031

Table 2.

Reactions implemented in the coarse-grained model of CK assembly

			Reaction pair
Binding reactions

CortI_QA + IQGAP1_C	⇌	IQGAP1:CortI
CortI_QA + IQGAP2_C	⇌	IQGAP2:CortI	A1f, A1r
CortI_QB + IQGAP1_C	⇌	CortI:IQGAP1
CortI_L+ PIP2_H	⇌	CortI:PIP2
CortI_M + MyoII_C	⇌	CortI:MyoII
MyoII_QA + IQGAP1_M	⇌	IQGAP1:MyoII
MyoII_QA + IQGAP2_M	⇌	IQGAP2:MyoII	B1f, B1r
MyoII_QB + IQGAP1_M	⇌	IQGAP1:MyoII
MyoII_Dk + MyoII_Dk, $k = 1, \dots, 5$	⇌	(MyoII_dimer)_Dk	C1f, C1r
(MyoII_dimer)_Tk + (MyoII_dimer)Tm, $k + m = 6$	⇌	(MyoII_tetramer)_Tk,m
(MyoII_tetramer)_Tk + (MyoII_dimer)_Tm, $k + m = 6$	⇌	(MyoII_hexamer)_Tk,m

Transition reactions
A1f:	→ IQGAP2:CortI	(CortI_QA)_-state0 → (CortI_QA)_{-allosteric_reg}	A2f
B1f:	→ IQGAP2:MyoII	(MyoII_QA)_-state0 → (MyoII_QA)_{-allosteric_reg}	B2f
C1f:	→ (MyoII_dimer)_Dk	((MyoII_dimer)_Dk)_-state0 → ((MyoII_dimer)_Dk)_-_tetra	C2f
A1r:	← IQGAP2:CortI	(CortI_QA)_{-allosteric_reg} → (CortI_QA)_-state0	A2r
B1r:	← IQGAP2:MyoII	(MyoII_QA)_{-allosteric_reg} → (MyoII_QA)_-state0	B2r
C1r:	← (MyoII_dimer)_Dk	((MyoII_dimer)_Dk)_-tetra → ((MyoII_dimer)_Dk)_-_state0	C2r

Allosteric reactions

A2f:	(CortI_QA)_{-allosteric_reg}	(CortI_QB)_-state0 → (CortI_QB)_{-allosteric_reg}
B2f:	(MyoII_QA)_{-allosteric_reg}	(MyoII_QB)_-state0 → (MyoII_QB)_{-allosteric_reg}
C2f:	((MyoII_dimer)_Dk)_-tetra	((MyoII_dimer)_Tk_)-state0 → ((MyoII_dimer)_Tk)_-_tetra
A2r:	(CortI_QA)_-state0	(CortI_QB)_{-allosteric_reg} → (CortI_QB)_-state0
B2r:	(MyoII_QA)_-state0	(MyoII_QB)_{-allosteric_reg} → (MyoII_QB)_-state0
C2r:	((MyoII_dimer)_Dk)_-state0	((MyoII_dimer)_Tk)_-tetra → ((MyoII_dimer)_Tk)_-state0

Bimolecular binding reactions occur between specified pairs of domains (Table 1 and Fig. 1A). Myosin II dimerization occurs between five pairs of domains along the myosin II tail, while tetramerization occurs between five pairs of tetramerization domains also along the tail, given that the molecule has already formed a parallel dimer (Fig. 1B). The table lists only the bimolecular entities formed, but higher-order ensembles are formed when further domains bind. Transition reactions specify a binding-dependent change in the state of a particular domain. Allosteric reactions specify a change in the state of a particular domain, given that there has been a change in the state of the indicated allosteric site. The reaction pair column indicates the dependency of transition and allosteric reactions on given binding reactions. For example, binding of CortI_QA with IQGAP2_C leads to the transition reaction, A1f, which then leads to an allosteric transition, A2f, in the CortI_QB domain. The reverse unbinding reactions similarly cause a sequential change in states; e.g., A1r triggers A2r, which then leads to an allosteric reaction. Dependencies for transition and allosteric reactions are also listed on the left-hand side of the described reactions.