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. 2023 Aug 17;12:e80152. doi: 10.7554/eLife.80152

Table 12. Parameters for the coarse-grained model published in Pepke et al., 2010 and adapted by Chang et al., 2019 and this work.

Pepke et al., 2010 rate adaptation for the coarse-grained model a⁢d⁢a⁢p⁢t⁢(a,b,c,d,C⁢a)=a⋅bc+d⋅C⁢a. Refer to Figure 18 for definition of variables.

REACTIONS Value Reference
Coarse-grained model, CaM-Ca reactions
CaM0+2 Ca⇒ CaM2C CaM2N+2 Ca⇒ CaM4 kf2⁢C=a⁢d⁢a⁢p⁢t⁢(ko⁢n1⁢C,ko⁢n2⁢C,ko⁢f⁢f1⁢C,ko⁢n2⁢C,C⁢a) Pepke et al., 2010
CaM0+2 Ca⇒ CaM2N CaM2C+2 Ca⇒ CaM4 kf2⁢N=a⁢d⁢a⁢p⁢t⁢(ko⁢n1⁢N,ko⁢n2⁢N,ko⁢f⁢f1⁢N,ko⁢n2⁢N,C⁢a) Pepke et al., 2010
CaM2C⇒ CaM0+2 Ca CaM4⇒ CaM2N+2 Ca kb2⁢C=a⁢d⁢a⁢p⁢t⁢(ko⁢f⁢f1⁢C,ko⁢f⁢f2⁢C,ko⁢f⁢f1⁢C,ko⁢n2⁢C,C⁢a) Pepke et al., 2010
CaM2N⇒ CaM0+2 Ca CaM4⇒ CaM2C+2 Ca kb2⁢N=a⁢d⁢a⁢p⁢t⁢(ko⁢f⁢f1⁢N,ko⁢f⁢f2⁢N,ko⁢f⁢f1⁢N,ko⁢n2⁢N,C⁢a) Pepke et al., 2010
kon1C=5 μM−1s−1 1.2 to 9.6 μM-1s-1 (Pepke et al., 2010)
kon2C=10 μM−1s−1 5 to 35 μM-1s-1 (Pepke et al., 2010)
kon1N=100 μM−1s−1 25 to 260 μM-1s-1 (Pepke et al., 2010)
kon2N=200 μM−1s−1 50 to 300 μM-1s-1 (Pepke et al., 2010)
koff1C=50 s−1 10 to 70 s-1 (Pepke et al., 2010)
koff2C=10 s−1 8.5 to 10 s-1 (Pepke et al., 2010)
koff1N=2000 s−1 1 . 103 to 4 . 103 s-1 (Pepke et al., 2010)

koff2N=500 s−1 		0.5 . 103 to > 1.103 s-1 (Pepke et al., 2010)
Coarse-grained model, KCaM-Ca reactions
KCaM0+2 Ca⇒ KCaM2C KCaM2N+2 Ca⇒ KCaM4 kfK2C=adapt(konK1C,konK2C,koffK1C,konK2C,Ca) Pepke et al., 2010
KCaM0+2 Ca⇒ KCaM2N KCaM2C+2 Ca⇒ KCaM4 kfK⁢2⁢N=a⁢d⁢a⁢p⁢t⁢(ko⁢nK⁢1⁢N,ko⁢nK⁢2⁢N,ko⁢f⁢fK⁢1⁢N,ko⁢nK⁢2⁢N,C⁢a) Pepke et al., 2010
KCaM2C⇒ KCaM0+2 Ca KCaM4⇒ KCaM2N+2 Ca kbK⁢2⁢C=a⁢d⁢a⁢p⁢t⁢(ko⁢f⁢fK⁢1⁢C,ko⁢f⁢fK⁢2⁢C,ko⁢f⁢fK⁢1⁢C,ko⁢nK⁢2⁢C,C⁢a) Pepke et al., 2010
KCaM2N⇒ KCaM0+2 Ca KCaM4⇒ KCaM2C+2 Ca kbK⁢2⁢N=a⁢d⁢a⁢p⁢t⁢(ko⁢f⁢fK⁢1⁢N,ko⁢f⁢fK⁢2⁢N,ko⁢f⁢fK⁢1⁢N,ko⁢nK⁢2⁢N,C⁢a) Pepke et al., 2010
ko⁢nK⁢1⁢C=44⁢μ⁢M-1⁢s-1 Pepke et al., 2010
ko⁢nK⁢2⁢C=44⁢μ⁢M-1⁢s-1 Pepke et al., 2010
ko⁢nK⁢1⁢N=76⁢μ⁢M-1⁢s-1 Pepke et al., 2010
ko⁢nK⁢2⁢N=76⁢μ⁢M-1⁢s-1 Pepke et al., 2010
koffK1C=33 s−1 Pepke et al., 2010
koffK2C=0.8 s−1 0.49 to 4.9 s-1 (Pepke et al., 2010)
ko⁢f⁢fK⁢1⁢N=300⁢s-1 Pepke et al., 2010
koffK2N=20 s−1 6 to 60 s-1 (Pepke et al., 2010)
Coarse-grained model, CaM-mKCaM reactions
CaM0+mKCaM⇒ mKCaM0 kfC⁢a⁢M⁢0=0.0038⁢μ⁢M-1⁢s-1 Pepke et al., 2010
CaM2C+mKCaM⇒ mKCaM2C kfC⁢a⁢M⁢2⁢C=0.92⁢μ⁢M-1⁢s-1 Pepke et al., 2010
CaM2N+mKCaM⇒ mKCaM2N kfC⁢a⁢M⁢2⁢N=0.12⁢μ⁢M-1⁢s-1 Pepke et al., 2010
CaM4+mKCaM
⇒ mKCaM4		 kfCaM4=30 μM−1s−1 14 to 60 μM-1s-1 (Pepke et al., 2010)
mKCaM0⇒ CaM0+mKCaM kbC⁢a⁢M⁢0=5.5⁢s-1 Pepke et al., 2010
mKCaM2C⇒ CaM2C+mKCaM kbC⁢a⁢M⁢2⁢C=6.8⁢s-1 Pepke et al., 2010
mKCaM2N⇒ CaM2N+mKCaM kbC⁢a⁢M⁢2⁢N=1.7⁢s-1 Pepke et al., 2010
mKCaM4
⇒ CaM0+mKCaM		 kbCaM4=1.5 s−1 1.1 to 2.3 s-1 (Pepke et al., 2010)
Coarse-grained model, self-phosphorylation reactions
KCaM0⇒ PCaM0 KCaM2N⇒ PCaM2N KCaM2C⇒ PCaM2C KCaM4⇒ PCaM4 k1=12.6⁢s-1 Chang et al., 2019
Fraction of activated CaMKII F=C⁢a⁢M⁢K⁢I⁢I/m⁢K⁢C⁢a⁢Mc⁢o⁢n see Equation 19 (Chang et al., 2019)
PCaM0⇒ P+CaM0 PCaM2N⇒ P+CaM2N PCaM2C⇒ P+CaM2C PCaM4⇒ P+CaM4 k2=0.33⁢s-1 0.33⁢s-1 ; adapted from Chang et al., 2019
P⇒mKCaM k3=4⋅0.17⁢s-1 0.17⁢s-1 adapted from Chang et al., 2019
P⇒P2 k4=4⋅0.041⁢s-1 0.041⁢s-1 adapted from Chang et al., 2019
P2⇒P k5=8⋅0.017⁢s-1 0.017⁢s-1 adapted from Chang et al., 2019
Calcineurin model, CaM-CaM4 reactions
CaM4+mCaN⇒mCaNCaM4 kfC⁢a⁢N=10.75⁢μ⁢M-1⁢s-1 46⁢μ⁢M-1⁢s-1⁢ (Quintana et al., 2005)
mCaNCaM4⇒CaM4+mCaN kbC⁢a⁢N=0.02⁢s-1⁢ fit (Fujii et al., 2013) see Figure 20