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Molecule Parameter List for NMDAR

The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by color.
Statistics
NMDAR participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000022

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
CaMKII_model363Network
Shared_Object_CaMKII_model3 CaMKII CaM 
PP1 PP2B PP1_PSD 
AC PKA 
This is the complete model of CaMKII bistability, model 3. It exhibits bistability in CaMKII activation due to autophosphorylation at the PSD and local saturation of PP1. This version of model 3 includes PKA regulatory input. This has little effect on the deterministic calculations, but the PKA pathway introduces a lot of noise which causes a difference in stochastic runs.

NMDAR acting as a Molecule in  
CaMKII_model3 Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
NMDARCaMKII_model3
Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 1200.01No
    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.

    NMDAR acting as a Substrate in a reaction in  
    CaMKII_model3 Network
    Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.
     NameAccession NamePathway NameKfKbKdtauReagents
    1transloc_1CaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 0
    (#^-1 s^-1)
    0
    (s^-1)
    Not applicable**-Substrate
    CaMKII-CaM
    NMDAR

    Product
    CaMKII-CaM-PSD
      Rates to match curve in fig2 from Shen and Meyer, Science 284:162-166(1999), calculated for 6:1 alpha:beta CaMKII heterodimers
    2transloc_2CaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 0
    (#^-1 s^-1)
    0
    (s^-1)
    Not applicable**-Substrate
  • CaMKII-thr286*-C
    aM

    NMDAR

    Product
  • CaMKII-thr286-Ca
    M-PSD

  •   Same as for transloc_1
    ** This is a trasport reation between compartments of different volumes. Therefore Kd is not applicable. Please Note Kf, Kb units are in number of molecules instead of concentration

    NMDAR acting as a Product in a reaction in  
    CaMKII_model3 Network
    Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.
     NameAccession NamePathway NameKfKbKdtauReagents
    1back_1CaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 0.3
    (s^-1)
    0
    (#^-1 s^-1)
    Not applicable**-Substrate
    CaMKII-PSD

    Product
    CaMKII
    NMDAR
      Rates set by the translocation experiments of Shen and Meyer, Science 1999.
    2back_2CaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 0.3
    (s^-1)
    0
    (#^-1 s^-1)
    Not applicable**-Substrate
  • CaMKII-thr305-PS
    D


    Product
    CaMK-thr305
    NMDAR
  •   Same as for back_1
    ** This is a trasport reation between compartments of different volumes. Therefore Kd is not applicable. Please Note Kf, Kb units are in number of molecules instead of concentration



    Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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