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name: Bhalla2004_CaMKII_2003
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type: Reaction
kinetic law: 221264
product: 221252
product: 221239
reactant: 221227
fast: false
reversible: false

221264
type: KineticLaw
local parameters: 053422
notes: k3*CaM_po_Ca_pc_n_minus_CaNAB_slash_dephosph_neurogranin_slash_dephosph_neurogranin_cplx

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units: 218846
value: 6.7E-13

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size: 1.0E-12
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initial concentration: 0.015
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953581
type: Reaction
kinetic law: 220240
product: 220228
reactant: 220216
reactant: 220203
notes: #s from Bramson et al CRC crit rev Biochem 15:2 93-124. They have a huge list of peptide substrates and I have chosen high-ish rates. These consts give too much PKA activity, so lower Vmax 1/3. Now, k1 = 3e-5, k2 = 36, k3 = 9 (still pretty fast). Also lower Km 1/3 so k1 = 1e-5 Cohen et al FEBS Lett 76:182-86 1977 say rate =30% PKA act on phosphokinase beta.
fast: false
reversible: true

220240
type: KineticLaw
local parameters: 053373
local parameters: 053372
notes: k1*PP1_slash_I1*PKA_minus_active-k2*PKA_minus_active_slash_PKA_minus_phosph_minus_I1_slash_PKA_minus_phosph_minus_I1_cplx

053373
type: LocalParameter
units: 218846
value: 3.6E-11

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type: LocalParameter
units: 218882
value: 6.0E-12

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species: 952222

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
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in compartment: 952162

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type: SpeciesReference
stoichiometry: 1.0
species: 953082

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type: SpeciesReference
stoichiometry: 1.0
species: 952782

952782
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.8
initial amount: NaN
in compartment: 952162

953422
type: Reaction
kinetic law: 219744
product: 219732
product: 219720
reactant: 219708
notes: Let us assume that the equil in this case is very far over to the right. This is probably safe.
fast: false
reversible: true

219744
type: KineticLaw
local parameters: 053337
local parameters: 053336
notes: kf*PP1_slash_PP1_minus_I1-kb*PP1_minus_active*PP1_slash_I1

053337
type: LocalParameter
units: 218882
value: 0.0

053336
type: LocalParameter
units: 218846
value: 1.0E-12

219732
type: SpeciesReference
stoichiometry: 1.0
species: 952782

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type: SpeciesReference
stoichiometry: 1.0
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stoichiometry: 1.0
species: 952842

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type: Species
constant: false
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953662
type: Reaction
kinetic law: 220635
product: 220623
reactant: 220611
reactant: 220599
fast: false
reversible: true

220635
type: KineticLaw
local parameters: 053391
local parameters: 053389
notes: k1*CaMKII_slash_CaMKII_minus_CaM*CaMKII_slash_tot_autonomous_CaMKII-k2*CaMKII_slash_tot_autonomous_CaMKII_slash_auton_286_slash_auton_286_cplx

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type: LocalParameter
units: 218846
value: 2.0E-12

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type: LocalParameter
units: 218882
value: 1.4286E-14

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type: SpeciesReference
stoichiometry: 1.0
species: 952462

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
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type: Species
constant: false
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has only substance units: false
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species: 952302

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

953721
type: Reaction
kinetic law: 220877
product: 220865
product: 220853
reactant: 220841
fast: false
reversible: false

220877
type: KineticLaw
local parameters: 053402
notes: k3*PP1_minus_active_slash_Deph_minus_thr305_slash_Deph_minus_thr305_cplx

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type: LocalParameter
units: 218846
value: 3.5E-13

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species: 952482

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stoichiometry: 1.0
species: 952362

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type: Species
constant: false
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species: 952522

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constant: true
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has only substance units: false
initial concentration: 0.09
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type: Species
constant: false
boundary condition: true
has only substance units: false
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initial amount: NaN
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953821
type: Reaction
kinetic law: 221362
product: 221350
product: 221338
reactant: 221325
fast: false
reversible: false

221362
type: KineticLaw
local parameters: 053427
notes: k3*CaM_po_Ca_pc_n_minus_CaNAB_slash_dephosph_inhib1_slash_dephosph_inhib1_cplx

053427
type: LocalParameter
units: 218846
value: 3.4E-13

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stoichiometry: 1.0
species: 953162

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stoichiometry: 1.0
species: 952782

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species: 952742

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

953782
type: Reaction
kinetic law: 221215
product: 221203
reactant: 221191
reactant: 221179
notes: From Seki et al ABB 316(2):673-679
fast: false
reversible: true

221215
type: KineticLaw
local parameters: 053421
local parameters: 053419
notes: k1*CaM_slash_neurogranin_star_*CaM_po_Ca_pc_n_minus_CaNAB-k2*CaM_po_Ca_pc_n_minus_CaNAB_slash_dephosph_neurogranin_slash_dephosph_neurogranin_cplx

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type: LocalParameter
units: 218846
value: 2.67E-12

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type: LocalParameter
units: 218882
value: 3.336E-13

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species: 952722

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constant: false
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953762
type: Reaction
kinetic law: 221119
product: 221107
reactant: 221095
reactant: 221083
fast: false
reversible: true

221119
type: KineticLaw
local parameters: 053416
local parameters: 053414
notes: k1*CaMKII_slash_CaMKII_minus_thr286*PP1_minus_active-k2*PP1_minus_active_slash_Deph_thr286b_slash_Deph_thr286b_cplx

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type: LocalParameter
units: 218846
value: 1.4E-12

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type: LocalParameter
units: 218882
value: 3.432E-13

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stoichiometry: 1.0
species: 952582

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type: Species
constant: false
boundary condition: false
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initial concentration: 0.0
initial amount: NaN
in compartment: 952162

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stoichiometry: 1.0
species: 952482

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stoichiometry: 1.0
species: 952362

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kind: LITRE

953442
type: Reaction
kinetic law: 219792
product: 219780
reactant: 219768
reactant: 219756
notes: This process is probably much more complicated and involves CaM. However, as I can\'t find detailed info I am bundling this into a single step. Based on Steemer and Klee pg 6863, the Kact is 0.5 uM. kf/kb = 1/(0.5 * 6e5)^2 = 1.11e-11
fast: false
reversible: true

219792
type: KineticLaw
local parameters: 053340
local parameters: 053338
notes: kf*Ca^2*PP2B_slash_CaNAB_minus_Ca2-kb*CaNAB_minus_Ca4

053340
type: LocalParameter
units: 218846
value: 1.0E-12

053338
type: LocalParameter
units: 218932
value: 3.6E-12

219780
type: SpeciesReference
stoichiometry: 1.0
species: 952922

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

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type: SpeciesReference
stoichiometry: 1.0
species: 952982

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type: Species
constant: false
boundary condition: false
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initial concentration: 0.0
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in compartment: 952162

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species: 953102

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type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.08
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kind: LITRE

953262
type: Reaction
kinetic law: 219382
product: 219370
reactant: 219358
reactant: 219346
notes: Affinity is up 1000X. Time to release is about 20 sec, so the kb is OK at 0.1 This makes Kf around 1.6666e-3
fast: false
reversible: true

219382
type: KineticLaw
local parameters: 053320
local parameters: 053319
notes: kf*CaMKII_slash_CaMKII_minus_thr286*CaM_minus_Ca4-kb*CaMKII_slash_CaMKII_minus_thr286_star__minus_CaM

053320
type: LocalParameter
units: 218846
value: 1.0E-13

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type: LocalParameter
units: 218882
value: 1.0002E-9

219370
type: SpeciesReference
stoichiometry: 1.0
species: 952322

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

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type: SpeciesReference
stoichiometry: 1.0
species: 952262

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

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stoichiometry: 1.0
species: 952362

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kind: SECOND

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kind: MOLE

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type: SBMLUnit
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kind: LITRE

952422
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

953501
type: Reaction
kinetic law: 219938
product: 219926
reactant: 219914
reactant: 219901
fast: false
reversible: true

219938
type: KineticLaw
local parameters: 053346
local parameters: 053345
notes: kf*CaM_minus_Ca3*CaNAB_minus_Ca4-kb*PP2B_slash_CaMCa3_minus_CaNAB

053346
type: LocalParameter
units: 218846
value: 1.0E-12

053345
type: LocalParameter
units: 218882
value: 2.238E-12

219926
type: SpeciesReference
stoichiometry: 1.0
species: 953002

953002
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

219914
type: SpeciesReference
stoichiometry: 1.0
species: 952922

219901
type: SpeciesReference
stoichiometry: 1.0
species: 952682

952682
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

952542
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

953402
type: Reaction
kinetic law: 219696
product: 219683
reactant: 219671
reactant: 219659
notes: K inhib = 1nM from Cohen Ann Rev Bioch 1989, 4 nM from Foukes et al Assume 2 nM. kf /kb = 8.333e-4
fast: false
reversible: true

219696
type: KineticLaw
local parameters: 053335
local parameters: 053334
notes: kf*PP1_slash_I1_star_*PP1_minus_active-kb*PP1_slash_PP1_minus_I1_star_

053335
type: LocalParameter
units: 218846
value: 1.0E-13

053334
type: LocalParameter
units: 218882
value: 4.9998E-10

219683
type: SpeciesReference
stoichiometry: 1.0
species: 952822

952822
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

219671
type: SpeciesReference
stoichiometry: 1.0
species: 952482

219659
type: SpeciesReference
stoichiometry: 1.0
species: 952802

952802
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: 952162

953742
type: Reaction
kinetic law: 221023
product: 221011
reactant: 220999
reactant: 220986
fast: false
reversible: true

221023
type: KineticLaw
local parameters: 053411
local parameters: 053409
notes: k1*CaMKII_slash_CaMKII_star__star__star_*PP1_minus_active-k2*PP1_minus_active_slash_Deph_minus_thr286c_slash_Deph_minus_thr286c_cplx

053411
type: LocalParameter
units: 218846
value: 1.4E-12

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type: LocalParameter
units: 218882
value: 3.432E-13

221011
type: SpeciesReference
stoichiometry: 1.0
species: 952562

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

220999
type: SpeciesReference
stoichiometry: 1.0
species: 952482

220986
type: SpeciesReference
stoichiometry: 1.0
species: 952342

953562
type: Reaction
kinetic law: 220191
product: 220179
product: 220167
product: 220155
reactant: 220143
fast: false
reversible: false

220191
type: KineticLaw
local parameters: 053371
notes: k3*PKC_minus_active_slash_PKC_minus_phosph_minus_ng_minus_CaM_slash_PKC_minus_phosph_minus_ng_minus_CaM_cplx

053371
type: LocalParameter
units: 218846
value: 3.5E-13

220179
type: SpeciesReference
stoichiometry: 1.0
species: 953062

220167
type: SpeciesReference
stoichiometry: 1.0
species: 952642

220155
type: SpeciesReference
stoichiometry: 1.0
species: 952602

952602
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 20.0
initial amount: NaN
in compartment: 952162

220143
type: SpeciesReference
stoichiometry: 1.0
species: 952202

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

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kind: LITRE

953861
type: Reaction
kinetic law: 221506
product: 221494
reactant: 221482
reactant: 221470
notes: PP2A does most of the dephosph of I1 at basal Ca levels. See the review by Cohen in Ann Rev Biochem 1989. For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6
fast: false
reversible: true

221506
type: KineticLaw
local parameters: 053436
local parameters: 053434
notes: k1*PP1_slash_I1_star_*PP2A-k2*PP2A_slash_PP2A_minus_dephosph_minus_I1_slash_PP2A_minus_dephosph_minus_I1_cplx

053436
type: LocalParameter
units: 218846
value: 2.5E-11

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type: LocalParameter
units: 218882
value: 3.96E-12

221494
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stoichiometry: 1.0
species: 952882

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constant: false
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initial concentration: 0.0
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in compartment: 952162

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species: 952862

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type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.12
initial amount: NaN
in compartment: 952162

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species: 952802

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constant: false
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has only substance units: false
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kind: MOLE

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kind: LITRE

953242
type: Reaction
kinetic law: 219334
product: 219321
reactant: 219309
reactant: 219297
notes: This is tricky. There is some cooperativity here arising from interactions between the subunits of the CAMKII holoenzyme. However, the stoichiometry is 1. Kb/Kf = 6e4 #/cell. Rate is fast (see Hanson et al Neuron 12 943-956 1994) so lets say kb = 10. This gives kf = 1.6667e-4 H&S AnnRev Biochem 92 give tau for dissoc as 0.2 sec at low Ca, 0.4 at high. Low Ca = 100 nM = physiol.
fast: false
reversible: true

219334
type: KineticLaw
local parameters: 053318
local parameters: 053317
notes: kf*CaM_minus_Ca4*CaMKII_slash_CaMKII-kb*CaMKII_slash_CaMKII_minus_CaM

053318
type: LocalParameter
units: 218846
value: 5.0E-12

053317
type: LocalParameter
units: 218882
value: 4.99998E-11

219321
type: SpeciesReference
stoichiometry: 1.0
species: 952302

219309
type: SpeciesReference
stoichiometry: 1.0
species: 952282

952282
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 70.0
initial amount: NaN
in compartment: 952162

219297
type: SpeciesReference
stoichiometry: 1.0
species: 952262

953022
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

953482
type: Reaction
kinetic law: 219889
product: 219877
reactant: 219865
reactant: 219853
notes: Disabled. See notes for PP2B7.g
fast: false
reversible: true

219889
type: KineticLaw
local parameters: 053344
local parameters: 053343
notes: kf*CaNAB_minus_Ca4*CaM_minus_TR2_minus_Ca2-kb*PP2B_slash_CaMCa2_minus_CANAB

053344
type: LocalParameter
units: 218846
value: 1.0E-12

053343
type: LocalParameter
units: 218882
value: 2.4E-13

219877
type: SpeciesReference
stoichiometry: 1.0
species: 953022

219865
type: SpeciesReference
stoichiometry: 1.0
species: 952702

952702
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

219853
type: SpeciesReference
stoichiometry: 1.0
species: 952922

953521
type: Reaction
kinetic law: 220035
product: 220023
reactant: 220011
reactant: 219999
notes: Rates from Huang et al ABB 305:2 570-580 1993
fast: false
reversible: true

220035
type: KineticLaw
local parameters: 053367
local parameters: 053366
notes: k1*CaM_slash_neurogranin*PKC_minus_active-k2*PKC_minus_active_slash_PKC_minus_phosph_minus_neurogranin_slash_PKC_minus_phosph_minus_neurogranin_cplx

053367
type: LocalParameter
units: 218846
value: 2.34E-12

053366
type: LocalParameter
units: 218882
value: 1.02E-13

220023
type: SpeciesReference
stoichiometry: 1.0
species: 952182

220011
type: SpeciesReference
stoichiometry: 1.0
species: 953062

219999
type: SpeciesReference
stoichiometry: 1.0
species: 952662

952942
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

953841
type: Reaction
kinetic law: 221410
product: 221398
reactant: 221386
reactant: 221374
fast: false
reversible: true

221410
type: KineticLaw
local parameters: 053431
local parameters: 053429
notes: k1*PP1_slash_PP1_minus_I1_star_*CaM_po_Ca_pc_n_minus_CaNAB-k2*CaM_po_Ca_pc_n_minus_CaNAB_slash_dephosph_minus_PP1_minus_I_star__slash_dephosph_minus_PP1_minus_I_star__cplx

053431
type: LocalParameter
units: 218846
value: 1.36E-12

053429
type: LocalParameter
units: 218882
value: 3.42E-13

221398
type: SpeciesReference
stoichiometry: 1.0
species: 952762

952762
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

221386
type: SpeciesReference
stoichiometry: 1.0
species: 953162

221374
type: SpeciesReference
stoichiometry: 1.0
species: 952822

953582
type: Reaction
kinetic law: 220290
product: 220277
product: 220264
reactant: 220252
fast: false
reversible: false

220290
type: KineticLaw
local parameters: 053374
notes: k3*PKA_minus_active_slash_PKA_minus_phosph_minus_I1_slash_PKA_minus_phosph_minus_I1_cplx

053374
type: LocalParameter
units: 218846
value: 9.0E-12

220277
type: SpeciesReference
stoichiometry: 1.0
species: 953082

220264
type: SpeciesReference
stoichiometry: 1.0
species: 952802

220252
type: SpeciesReference
stoichiometry: 1.0
species: 952222

953382
type: Reaction
kinetic law: 219647
product: 219635
reactant: 219623
notes: This is put in to keep the basal levels of neurogranin* experimentally reasonable. From various papers, specially Ramakers et al JBC 270:23 1995 13892-13898, it looks like the basal level of phosph is between 20 and 40%. I est around 25 % The kf of 0.005 gives around this level at basal PKC activity levels of 0.1 uM active PKC.
fast: false
reversible: true

219647
type: KineticLaw
local parameters: 053333
local parameters: 053332
notes: kf*CaM_slash_neurogranin_star_-kb*CaM_slash_neurogranin

053333
type: LocalParameter
units: 218846
value: 0.0

053332
type: LocalParameter
units: 218846
value: 5.0E-15

219635
type: SpeciesReference
stoichiometry: 1.0
species: 952662

219623
type: SpeciesReference
stoichiometry: 1.0
species: 952642

218834
type: SBMLUnit
exponent: 9.0
scale: -6
multipler: 1.0
kind: MOLE

218822
type: SBMLUnit
exponent: -9.0
scale: 0
multipler: 1.0
kind: LITRE

953921
type: Reaction
kinetic law: 221652
product: 221640
product: 221627
reactant: 221615
fast: false
reversible: false

221652
type: KineticLaw
local parameters: 053442
notes: k3*PP2A_slash_PP2A_minus_dephosph_minus_PP1_minus_I_star__slash_PP2A_minus_dephosph_minus_PP1_minus_I_star__cplx

053442
type: LocalParameter
units: 218846
value: 6.0E-12

221640
type: SpeciesReference
stoichiometry: 1.0
species: 952862

221627
type: SpeciesReference
stoichiometry: 1.0
species: 952842

221615
type: SpeciesReference
stoichiometry: 1.0
species: 952902

953702
type: Reaction
kinetic law: 220829
product: 220817
reactant: 220805
reactant: 220792
fast: false
reversible: true

220829
type: KineticLaw
local parameters: 053401
local parameters: 053399
notes: k1*CaMKII_slash_CaMKII_star__star__star_*PP1_minus_active-k2*PP1_minus_active_slash_Deph_minus_thr305_slash_Deph_minus_thr305_cplx

053401
type: LocalParameter
units: 218846
value: 1.4E-12

053399
type: LocalParameter
units: 218882
value: 3.432E-13

220817
type: SpeciesReference
stoichiometry: 1.0
species: 952522

220805
type: SpeciesReference
stoichiometry: 1.0
species: 952482

220792
type: SpeciesReference
stoichiometry: 1.0
species: 952342

953641
type: Reaction
kinetic law: 220539
product: 220527
reactant: 220514
reactant: 220502
notes: See Hanson and Schulman again, for afterburst rates of phosph.
fast: false
reversible: true

220539
type: KineticLaw
local parameters: 053386
local parameters: 053384
notes: k1*CaMKII_slash_CaMKII_minus_thr286*CaMKII_slash_tot_autonomous_CaMKII-k2*CaMKII_slash_tot_autonomous_CaMKII_slash_auton_305_slash_auton_305_cplx

053386
type: LocalParameter
units: 218846
value: 2.4E-11

053384
type: LocalParameter
units: 218882
value: 1.71426E-13

220527
type: SpeciesReference
stoichiometry: 1.0
species: 952442

952442
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

220514
type: SpeciesReference
stoichiometry: 1.0
species: 953142

220502
type: SpeciesReference
stoichiometry: 1.0
species: 952362

953042
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

218688
type: SBMLUnit
exponent: 5.0
scale: -6
multipler: 1.0
kind: MOLE

218676
type: SBMLUnit
exponent: -5.0
scale: 0
multipler: 1.0
kind: LITRE

953642
type: Reaction
kinetic law: 220587
product: 220575
product: 220563
reactant: 220551
fast: false
reversible: false

220587
type: KineticLaw
local parameters: 053387
notes: k3*CaMKII_slash_tot_autonomous_CaMKII_slash_auton_305_slash_auton_305_cplx

053387
type: LocalParameter
units: 218846
value: 6.0E-12

220575
type: SpeciesReference
stoichiometry: 1.0
species: 953142

220563
type: SpeciesReference
stoichiometry: 1.0
species: 952342

220551
type: SpeciesReference
stoichiometry: 1.0
species: 952442

953621
type: Reaction
kinetic law: 220440
product: 220427
reactant: 220414
reactant: 220401
fast: false
reversible: true

220440
type: KineticLaw
local parameters: 053381
local parameters: 053379
notes: k1*CaMKII_slash_CaMKII_minus_CaM*CaMKII_slash_tot_CaM_CaMKII-k2*CaMKII_slash_tot_CaM_CaMKII_slash_CaM_act_286_slash_CaM_act_286_cplx

053381
type: LocalParameter
units: 218846
value: 2.0E-12

053379
type: LocalParameter
units: 218882
value: 2.20068E-14

220427
type: SpeciesReference
stoichiometry: 1.0
species: 952422

220414
type: SpeciesReference
stoichiometry: 1.0
species: 953122

220401
type: SpeciesReference
stoichiometry: 1.0
species: 952302

953941
type: Reaction
kinetic law: 221700
product: 221688
reactant: 221676
reactant: 221664
notes: The rates here are so slow I do not know if we should even bother with this enz reacn. These numbers are from Liu and Storm. Other refs suggest that the Km stays the same but the Vmax goes to 10% of the CaM stim levels. Prev: k1=2.2e-9, k2 = 0.0052, k3 = 0.0013 New : k1=5.7e-8, k2=.136, k3=.034
fast: false
reversible: true

221700
type: KineticLaw
local parameters: 053446
local parameters: 053444
notes: k1*PP1_slash_I1_star_*CaNAB_minus_Ca4-k2*CaNAB_minus_Ca4_slash_dephosph_inhib1_noCaM_slash_dephosph_inhib1_noCaM_cplx

053446
type: LocalParameter
units: 218846
value: 1.36E-13

053444
type: LocalParameter
units: 218882
value: 3.42E-14

221688
type: SpeciesReference
stoichiometry: 1.0
species: 952942

221676
type: SpeciesReference
stoichiometry: 1.0
species: 952922

221664
type: SpeciesReference
stoichiometry: 1.0
species: 952802

953681
type: Reaction
kinetic law: 220683
product: 220671
product: 220659
reactant: 220647
fast: false
reversible: false

220683
type: KineticLaw
local parameters: 053392
notes: k3*CaMKII_slash_tot_autonomous_CaMKII_slash_auton_286_slash_auton_286_cplx

053392
type: LocalParameter
units: 218846
value: 5.0E-13

220671
type: SpeciesReference
stoichiometry: 1.0
species: 953142

220659
type: SpeciesReference
stoichiometry: 1.0
species: 952322

220647
type: SpeciesReference
stoichiometry: 1.0
species: 952462

953722
type: Reaction
kinetic law: 220925
product: 220913
reactant: 220901
reactant: 220889
notes: See Cohen et al
fast: false
reversible: true

220925
type: KineticLaw
local parameters: 053406
local parameters: 053404
notes: k1*CaMKII_slash_CaMK_minus_thr306*PP1_minus_active-k2*PP1_minus_active_slash_Deph_minus_thr306_slash_Deph_minus_thr306_cplx

053406
type: LocalParameter
units: 218846
value: 1.4E-12

053404
type: LocalParameter
units: 218882
value: 3.432E-13

220913
type: SpeciesReference
stoichiometry: 1.0
species: 952542

220901
type: SpeciesReference
stoichiometry: 1.0
species: 952482

220889
type: SpeciesReference
stoichiometry: 1.0
species: 952382

952382
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

219285
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

218798
type: SBMLUnit
exponent: 8.0
scale: -6
multipler: 1.0
kind: MOLE

218786
type: SBMLUnit
exponent: -8.0
scale: 0
multipler: 1.0
kind: LITRE

953682
type: Reaction
kinetic law: 220732
product: 220719
reactant: 220707
reactant: 220695
notes: The rates are from Stralfors et al Eur J Biochem 149 295-303 giving Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14. Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so k1 becomes 5.72e-6 Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10 to 5.72e-7, 1.4, 0.35
fast: false
reversible: true

220732
type: KineticLaw
local parameters: 053396
local parameters: 053394
notes: k1*CaMKII_slash_CaMKII_minus_thr286_star__minus_CaM*PP1_minus_active-k2*PP1_minus_active_slash_Deph_minus_thr286_slash_Deph_minus_thr286_cplx

053396
type: LocalParameter
units: 218846
value: 1.4E-12

053394
type: LocalParameter
units: 218882
value: 3.432E-13

220719
type: SpeciesReference
stoichiometry: 1.0
species: 952502

952502
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

220707
type: SpeciesReference
stoichiometry: 1.0
species: 952482

220695
type: SpeciesReference
stoichiometry: 1.0
species: 952322

953502
type: Reaction
kinetic law: 219987
product: 219975
reactant: 219963
reactant: 219950
fast: false
reversible: true

219987
type: KineticLaw
local parameters: 053364
local parameters: 053347
notes: kf*CaM_minus_Ca4*CaNAB_minus_Ca4-kb*PP2B_slash_CaMCa4_minus_CaNAB

053364
type: LocalParameter
units: 218846
value: 1.0E-12

053347
type: LocalParameter
units: 218882
value: 6.0E-10

219975
type: SpeciesReference
stoichiometry: 1.0
species: 953042

219963
type: SpeciesReference
stoichiometry: 1.0
species: 952922

219950
type: SpeciesReference
stoichiometry: 1.0
species: 952262

219163
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

219151
type: SBMLUnit
exponent: -6.0
scale: -6
multipler: 1.0
kind: MOLE

219138
type: SBMLUnit
exponent: 7.0
scale: 0
multipler: 1.0
kind: LITRE

953802
type: Reaction
kinetic law: 221313
product: 221301
reactant: 221289
reactant: 221276
fast: false
reversible: true

221313
type: KineticLaw
local parameters: 053426
local parameters: 053424
notes: k1*PP1_slash_I1_star_*CaM_po_Ca_pc_n_minus_CaNAB-k2*CaM_po_Ca_pc_n_minus_CaNAB_slash_dephosph_inhib1_slash_dephosph_inhib1_cplx

053426
type: LocalParameter
units: 218846
value: 1.36E-12

053424
type: LocalParameter
units: 218882
value: 3.42E-13

221301
type: SpeciesReference
stoichiometry: 1.0
species: 952742

221289
type: SpeciesReference
stoichiometry: 1.0
species: 953162

221276
type: SpeciesReference
stoichiometry: 1.0
species: 952802

953522
type: Reaction
kinetic law: 220083
product: 220071
product: 220059
reactant: 220047
fast: false
reversible: false

220083
type: KineticLaw
local parameters: 053368
notes: k3*PKC_minus_active_slash_PKC_minus_phosph_minus_neurogranin_slash_PKC_minus_phosph_minus_neurogranin_cplx

053368
type: LocalParameter
units: 218846
value: 5.8E-13

220071
type: SpeciesReference
stoichiometry: 1.0
species: 953062

220059
type: SpeciesReference
stoichiometry: 1.0
species: 952642

220047
type: SpeciesReference
stoichiometry: 1.0
species: 952182

219260
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

219248
type: SBMLUnit
exponent: -8.0
scale: -6
multipler: 1.0
kind: MOLE

219236
type: SBMLUnit
exponent: 9.0
scale: 0
multipler: 1.0
kind: LITRE

952402
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

953462
type: Reaction
kinetic law: 219841
product: 219829
reactant: 219817
reactant: 219805
notes: going on the experience with CaM, we put the fast (high affinity) sites first. We only know (Stemmer and Klee) that the affinity is < 70 nM. Assuming 10 nM at first, we get kf = 2.78e-8, kb = 1. Try 20 nM. kf = 7e-9, kb = 1
fast: false
reversible: true

219841
type: KineticLaw
local parameters: 053342
local parameters: 053341
notes: kf*PP2B_slash_CaNAB*Ca^2-kb*PP2B_slash_CaNAB_minus_Ca2

053342
type: LocalParameter
units: 218846
value: 1.0E-12

053341
type: LocalParameter
units: 218932
value: 1.0008E-8

219829
type: SpeciesReference
stoichiometry: 1.0
species: 952982

219817
type: SpeciesReference
stoichiometry: 2.0
species: 953102

219805
type: SpeciesReference
stoichiometry: 1.0
species: 952962

953602
type: Reaction
kinetic law: 220388
product: 220375
product: 220362
reactant: 220350
fast: false
reversible: false

220388
type: KineticLaw
local parameters: 053377
notes: k3*CaMKII_slash_tot_CaM_CaMKII_slash_CaM_act_305_slash_CaM_act_305_cplx

053377
type: LocalParameter
units: 218846
value: 6.0E-12

220375
type: SpeciesReference
stoichiometry: 1.0
species: 953122

220362
type: SpeciesReference
stoichiometry: 1.0
species: 952342

220350
type: SpeciesReference
stoichiometry: 1.0
species: 952402

953601
type: Reaction
kinetic law: 220338
product: 220326
reactant: 220314
reactant: 220302
notes: Rates from autocamtide phosphorylation, from Hanson and Schulman JBC 267:24 17216-17224 1992. Jan 1 1998: Speed up 12x to match fig 5.
fast: false
reversible: true

220338
type: KineticLaw
local parameters: 053376
local parameters: 053375
notes: k1*CaMKII_slash_CaMKII_minus_thr286*CaMKII_slash_tot_CaM_CaMKII-k2*CaMKII_slash_tot_CaM_CaMKII_slash_CaM_act_305_slash_CaM_act_305_cplx

053376
type: LocalParameter
units: 218846
value: 2.4E-11

053375
type: LocalParameter
units: 218882
value: 2.64084E-13

220326
type: SpeciesReference
stoichiometry: 1.0
species: 952402

220314
type: SpeciesReference
stoichiometry: 1.0
species: 953122

220302
type: SpeciesReference
stoichiometry: 1.0
species: 952362

953302
type: Reaction
kinetic law: 219467
product: 219455
reactant: 219442
reactant: 219430
notes: Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !)....
fast: false
reversible: true

219467
type: KineticLaw
local parameters: 053324
local parameters: 053323
notes: kf*CaM_slash_CaM*Ca^2-kb*CaM_minus_TR2_minus_Ca2

053324
type: LocalParameter
units: 218846
value: 7.2E-11

053323
type: LocalParameter
units: 218932
value: 7.2E-11

219455
type: SpeciesReference
stoichiometry: 1.0
species: 952702

219442
type: SpeciesReference
stoichiometry: 2.0
species: 953102

219430
type: SpeciesReference
stoichiometry: 1.0
species: 952602

952145
type: Compartment
constant: true
size: 1.0E-18
spatial dimensions: 3.0

953842
type: Reaction
kinetic law: 221458
product: 221446
product: 221434
reactant: 221422
fast: false
reversible: false

221458
type: KineticLaw
local parameters: 053432
notes: k3*CaM_po_Ca_pc_n_minus_CaNAB_slash_dephosph_minus_PP1_minus_I_star__slash_dephosph_minus_PP1_minus_I_star__cplx

053432
type: LocalParameter
units: 218846
value: 3.4E-13

221446
type: SpeciesReference
stoichiometry: 1.0
species: 953162

221434
type: SpeciesReference
stoichiometry: 1.0
species: 952842

221422
type: SpeciesReference
stoichiometry: 1.0
species: 952762

953542
type: Reaction
kinetic law: 220131
product: 220119
reactant: 220107
reactant: 220095
notes: Rates are 60% those of PKC-phosph-neurogranin. See Huang et al ABB 305:2 570-580 1993
fast: false
reversible: true

220131
type: KineticLaw
local parameters: 053370
local parameters: 053369
notes: k1*CaM_slash_neurogranin_minus_CaM*PKC_minus_active-k2*PKC_minus_active_slash_PKC_minus_phosph_minus_ng_minus_CaM_slash_PKC_minus_phosph_minus_ng_minus_CaM_cplx

053370
type: LocalParameter
units: 218846
value: 1.4E-12

053369
type: LocalParameter
units: 218882
value: 6.12E-14

220119
type: SpeciesReference
stoichiometry: 1.0
species: 952202

220107
type: SpeciesReference
stoichiometry: 1.0
species: 953062

220095
type: SpeciesReference
stoichiometry: 1.0
species: 952622

952622
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 952162

219113
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

219101
type: SBMLUnit
exponent: -5.0
scale: -6
multipler: 1.0
kind: MOLE

219089
type: SBMLUnit
exponent: 6.0
scale: 0
multipler: 1.0
kind: LITRE

953881
type: Reaction
kinetic law: 221555
product: 221543
product: 221530
reactant: 221518
fast: false
reversible: false

221555
type: KineticLaw
local parameters: 053437
notes: k3*PP2A_slash_PP2A_minus_dephosph_minus_I1_slash_PP2A_minus_dephosph_minus_I1_cplx

053437
type: LocalParameter
units: 218846
value: 6.0E-12

221543
type: SpeciesReference
stoichiometry: 1.0
species: 952862

221530
type: SpeciesReference
stoichiometry: 1.0
species: 952782

221518
type: SpeciesReference
stoichiometry: 1.0
species: 952882

953961
type: Reaction
kinetic law: 221749
product: 221737
product: 221725
reactant: 221712
fast: false
reversible: false

221749
type: KineticLaw
local parameters: 053447
notes: k3*CaNAB_minus_Ca4_slash_dephosph_inhib1_noCaM_slash_dephosph_inhib1_noCaM_cplx

053447
type: LocalParameter
units: 218846
value: 3.4E-14

221737
type: SpeciesReference
stoichiometry: 1.0
species: 952922

221725
type: SpeciesReference
stoichiometry: 1.0
species: 952782

221712
type: SpeciesReference
stoichiometry: 1.0
species: 952942

953781
type: Reaction
kinetic law: 221167
product: 221155
product: 221143
reactant: 221131
fast: false
reversible: false

221167
type: KineticLaw
local parameters: 053417
notes: k3*PP1_minus_active_slash_Deph_thr286b_slash_Deph_thr286b_cplx

053417
type: LocalParameter
units: 218846
value: 3.5E-13

221155
type: SpeciesReference
stoichiometry: 1.0
species: 952482

221143
type: SpeciesReference
stoichiometry: 1.0
species: 952282

221131
type: SpeciesReference
stoichiometry: 1.0
species: 952582

953761
type: Reaction
kinetic law: 221071
product: 221059
product: 221047
reactant: 221035
fast: false
reversible: false

221071
type: KineticLaw
local parameters: 053412
notes: k3*PP1_minus_active_slash_Deph_minus_thr286c_slash_Deph_minus_thr286c_cplx

053412
type: LocalParameter
units: 218846
value: 3.5E-13

221059
type: SpeciesReference
stoichiometry: 1.0
species: 952482

221047
type: SpeciesReference
stoichiometry: 1.0
species: 952382

221035
type: SpeciesReference
stoichiometry: 1.0
species: 952562

953622
type: Reaction
kinetic law: 220490
product: 220478
product: 220466
reactant: 220453
fast: false
reversible: false

220490
type: KineticLaw
local parameters: 053382
notes: k3*CaMKII_slash_tot_CaM_CaMKII_slash_CaM_act_286_slash_CaM_act_286_cplx

053382
type: LocalParameter
units: 218846
value: 5.0E-13

220478
type: SpeciesReference
stoichiometry: 1.0
species: 953122

220466
type: SpeciesReference
stoichiometry: 1.0
species: 952322

220453
type: SpeciesReference
stoichiometry: 1.0
species: 952422

953342
type: Reaction
kinetic law: 219563
product: 219551
reactant: 219539
reactant: 219527
notes: Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
fast: false
reversible: true

219563
type: KineticLaw
local parameters: 053329
local parameters: 053328
notes: kf*CaM_minus_Ca3*Ca-kb*CaM_minus_Ca4

053329
type: LocalParameter
units: 218846
value: 1.0E-11

053328
type: LocalParameter
units: 218882
value: 4.65E-13

219551
type: SpeciesReference
stoichiometry: 1.0
species: 952262

219539
type: SpeciesReference
stoichiometry: 1.0
species: 953102

219527
type: SpeciesReference
stoichiometry: 1.0
species: 952682

953322
type: Reaction
kinetic law: 219515
product: 219503
reactant: 219491
reactant: 219479
notes: K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10
fast: false
reversible: true

219515
type: KineticLaw
local parameters: 053327
local parameters: 053325
notes: kf*CaM_minus_TR2_minus_Ca2*Ca-kb*CaM_minus_Ca3

053327
type: LocalParameter
units: 218846
value: 1.0E-11

053325
type: LocalParameter
units: 218882
value: 3.6E-12

219503
type: SpeciesReference
stoichiometry: 1.0
species: 952682

219491
type: SpeciesReference
stoichiometry: 1.0
species: 953102

219479
type: SpeciesReference
stoichiometry: 1.0
species: 952702

953901
type: Reaction
kinetic law: 221603
product: 221591
reactant: 221579
reactant: 221567
notes: k1 changed from 3.3e-6 to 6.6e-6
fast: false
reversible: true

221603
type: KineticLaw
local parameters: 053441
local parameters: 053439
notes: k1*PP1_slash_PP1_minus_I1_star_*PP2A-k2*PP2A_slash_PP2A_minus_dephosph_minus_PP1_minus_I_star__slash_PP2A_minus_dephosph_minus_PP1_minus_I_star__cplx

053441
type: LocalParameter
units: 218846
value: 2.5E-11

053439
type: LocalParameter
units: 218882
value: 3.96E-12

221591
type: SpeciesReference
stoichiometry: 1.0
species: 952902

221579
type: SpeciesReference
stoichiometry: 1.0
species: 952862

221567
type: SpeciesReference
stoichiometry: 1.0
species: 952822

953741
type: Reaction
kinetic law: 220974
product: 220962
product: 220949
reactant: 220937
fast: false
reversible: false

220974
type: KineticLaw
local parameters: 053407
notes: k3*PP1_minus_active_slash_Deph_minus_thr306_slash_Deph_minus_thr306_cplx

053407
type: LocalParameter
units: 218846
value: 3.5E-13

220962
type: SpeciesReference
stoichiometry: 1.0
species: 952482

220949
type: SpeciesReference
stoichiometry: 1.0
species: 952282

220937
type: SpeciesReference
stoichiometry: 1.0
species: 952542

953282
type: Reaction
kinetic law: 219418
product: 219406
reactant: 219394
notes: This reaction represents one of the big unknowns in CaMK-II biochemistry: what maintains the basal level of phosphorylation on thr 286 ? See Hanson and Schulman Ann Rev Biochem 1992 61:559-601, specially pg 580, for review. I have not been able to find any compelling mechanism in the literature, but fortunately the level of basal activity is well documented.
fast: false
reversible: true

219418
type: KineticLaw
local parameters: 053322
local parameters: 053321
notes: kf*CaMKII_slash_CaMKII-kb*CaMKII_slash_CaMKII_minus_thr286

053322
type: LocalParameter
units: 218846
value: 0.0

053321
type: LocalParameter
units: 218846
value: 3.0E-15

219406
type: SpeciesReference
stoichiometry: 1.0
species: 952362

219394
type: SpeciesReference
stoichiometry: 1.0
species: 952282

953362
type: Reaction
kinetic law: 219611
product: 219599
reactant: 219587
reactant: 219575
notes: Surprisingly, no direct info on rates from neurogranin at this time. These rates are based on GAP-43 binding studies. As GAP-43 and neurogranin share near identity in the CaM/PKC binding regions, and also similarity in phosph and dephosph rates, I am borrowing GAP-43 kinetic info. See Alexander et al JBC 262:13 6108-6113 1987
fast: false
reversible: true

219611
type: KineticLaw
local parameters: 053331
local parameters: 053330
notes: kf*CaM_slash_neurogranin*CaM_slash_CaM-kb*CaM_slash_neurogranin_minus_CaM

053331
type: LocalParameter
units: 218846
value: 1.0E-12

053330
type: LocalParameter
units: 218882
value: 3.0E-13

219599
type: SpeciesReference
stoichiometry: 1.0
species: 952622

219587
type: SpeciesReference
stoichiometry: 1.0
species: 952602

219575
type: SpeciesReference
stoichiometry: 1.0
species: 952662

953701
type: Reaction
kinetic law: 220780
product: 220768
product: 220756
reactant: 220744
fast: false
reversible: false

220780
type: KineticLaw
local parameters: 053397
notes: k3*PP1_minus_active_slash_Deph_minus_thr286_slash_Deph_minus_thr286_cplx

053397
type: LocalParameter
units: 218846
value: 3.5E-13

220768
type: SpeciesReference
stoichiometry: 1.0
species: 952482

220756
type: SpeciesReference
stoichiometry: 1.0
species: 952302

220744
type: SpeciesReference
stoichiometry: 1.0
species: 952502