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Molecule Parameter List for CaM-PSD

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
CaM-PSD participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000120

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • AMPAR_traff_
    model1
    		• 60Network
    Shared_Object_AMPAR_traff_model1,  CaMKII,  CaM,  
    PP1,  PP2B,  PP1_PSD,  
    PKA,  AC,  AMPAR,  
    AMPAR_memb 
    This is the basic model of AMPAR trafficking bistability. It is based on Hayer and Bhalla, PLoS Comput. Biol. 2005. It includes the degradation and turnover of AMPARs. The CaMKII portion of the model is not bistable.

    CaM-PSD acting as a Molecule in      AMPAR_traff_model1 Network
    NameAccession NamePathway NameInitial Conc.
    (uM)    		Volume
    (fL)    		Buffered
    CaM-PSD
  • AMPAR_traff_
    model1
    Accession No. : 60
    		• CaM
    Pathway No. : 246    		26.33330.01No
    There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al) Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying it is comparable to CaMK levels.

    CaM-PSD acting as a Product of an Enzyme in      AMPAR_traff_model1 Network
    Enzyme Molecule /
    Enzyme Activity    		Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    PKC-active  /

  • PKC-phosph-ng-Ca
    M_
    PSD
  • AMPAR_traff_
    model1
    Accession No. : 60
  • Shared_Object_
    AMPAR_traff_
    model1
    Pathway No. : 244
    		• 28.59560.354explicit E-S complexSubstrate

  • neurogranin-CaM_
    PSD

    Product
    CaM-PSD
  • neurogranin*_
    PSD
    • Rates are 60% those of PKC-phosph-neurogranin. See Huang et al ABB 305:2 570-580 1993

    CaM-PSD acting as a Substrate in a reaction in      AMPAR_traff_model1 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
    1
  • CaM-TR2-bind-Ca-
    PSD
  • AMPAR_traff_
    model1
    Accession No. : 60
    		• CaM
    Pathway No. : 246    		72
    (uM^-2 s^-1)    		72
    (s^-1)    		Kd(af) = 1(uM)-Substrate
    Ca-PSD
    Ca-PSD
    CaM-PSD

    Product
    CaM-TR2-Ca2-PSD
      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 !)....
    2

  • neurogranin-bind
    -CaM_
    PSD
  • AMPAR_traff_
    model1
    Accession No. : 60
    		• CaM
    Pathway No. : 246    		0.3
    (uM^-1 s^-1)    		1
    (s^-1)    		Kd(bf) = 3.3333(uM)-Substrate
    CaM-PSD
    neurogranin_PSD

    Product

  • neurogranin-CaM_
    PSD
    •   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


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