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Accession Type:
Network
CaMKII_model3
Shared_Object_
CaMKII_model3
 Molecule
 Enzyme
 Reaction
CaMKII
CaM
PP1
PP2B
PP1_PSD
AC
PKA

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Molecule List for pathway Shared_Object_CaMKII_model3 (Pathway Number 263)

 Name Initial Conc. (uM) Volume (fL) Buffered
1286P-PSD00.01No
   
2actCaMKII-PSD20.01No
   
3act_CaMKII_cyt20.09No
   
4basal_CaMKII_cyt20.09Yes
   
5basal_CaMKII_PSD20.01No
   
6basal_CaMKII_PSD_control20.01Yes
   
7Ca0.080.09No
   
8Ca-PSD0.080.01No
   
9CaM-Ca300.09No
   
10CaM-Ca3-PSD0.00250.01No
   
11CaM-Ca400.09No
   
12CaM-Ca4-PSD00.01No
   
13CaM-TR2-Ca200.09No
    This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not.
14CaM-TR2-Ca2-PSD00.01No
    This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not.
15CaMKII***-PSD00.01No
   
16CaMKII-CaM-PSD00.01No
   
17CaMKII-PSD00.01No
   
18CaMKII-thr286-CaM-PSD00.01No
   
19CaMKII-thr286-PSD00.01No
   
20CaMKII-thr305-PSD00.01No
   
21cAMP00.09No
    The conc of this has been a problem. Schaecter and Benowitz use 50 uM, but Shinomura et al have < 5. So I have altered the cAMP-dependent rates in the PKA model to reflect this.
22CaM_Ca_n-CaNAB00.09No
   
23CaNAB-Ca400.09No
   
24Ca_control_cyt0.080.09Yes
   
25Ca_control_PSD0.080.01Yes
   
26NMDAR1200.01No
    The stochiometry is a bit off here. Each NMDAR actually binds to a holoenzyme, about 12 CaMKII subunits. But our CaMKII calculations are in terms of individual subunits. So as a hack, we put in much more NMDAR than is actually there.
27PKA-active00.09No
   
28PKC-active0.10.09No
   
29PKC-control0.10.09Yes
   
30PP1-active1.80.09No
    Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM
31PP1-active_PSD40.01No
    Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM
32PP2A0.11110.09No
   
33tot-auto-PSD20.01No
   
34tot-CaM-CaMKII-PSD00.01No
   
35tot_CaMKII_cyt220.09No
   
36tot_CaMKII_PSD20.01No
   

Summed Molecule List

  Target Inputs
1 286P-PSD
  • CaMKII-thr286-Ca
    M-PSD

  • CaMKII-thr286-PS
    D

  • 2 actCaMKII-PSD
  • CaMKII-thr286-Ca
    M-PSD

    CaMKII-CaM-PSD
    tot-auto-PSD
  • 3 act_CaMKII_cyttot_CaM_CaMKII
  • tot_autonomous_
    CaMKII

  • 4 tot-auto-PSD
  • CaMKII-thr286-PS
    D

    CaMKII***-PSD
  • basal_CaMKII_
    PSD

  • 5 tot-CaM-CaMKII-PSD
  • CaMKII-thr286-Ca
    M-PSD

    CaMKII-CaM-PSD
  • 6 tot_CaMKII_cytCaMKII-CaM
  • CaMKII-thr286*-C
    aM

    CaMKII-thr286
    CaMKII***
    CaMK-thr305
    CaMKII
  • basal_CaMKII_
    cyt

  • 7 tot_CaMKII_PSDactCaMKII-PSD
    CaMKII-PSD
  • CaMKII-thr305-PS
    D



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