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Molecule Parameter List for neurogranin_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
neurogranin_PSD participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1001111

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • AMPAR_traff_
    model0
  • 59Network
    Shared_Object_AMPAR_traff_model0 CaMKII CaM 
    PP1 PP2B PP1_PSD 
    PKA AC AMPAR 
    AMPAR_memb 
    This is model 0 from Hayer and Bhalla, PLoS Comput Biol 2005. It has a bistable model of AMPAR traffick, plus a non-bistable model of CaMKII. This differs from the reference model (model 1) in that model0 lacks degradation and turno ver reactions for AMPAR.

    neurogranin_PSD acting as a Molecule in  
    AMPAR_traff_model0 Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    neurogranin_PSD
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaM
    Pathway No. : 236
    100.01No
    Also known as RC3 and p17 and BICKS. Conc in brain >> 2 uM from Martzen and Slemmon J neurosci 64 92-100 1995 but others say less without any #s. Conc in dend spines is much higher than overall, so it could be anywhere from 2 uM to 50. We will estimate 10 uM as a starting point. Gerendasy et al JBC 269:35 22420-22426 1994 have a skeleton model (no numbers) indicating CaM-Ca(n) binding.

    neurogranin_PSD acting as a Substrate for an Enzyme in  
    AMPAR_traff_model0 Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    PKC-active  /

  • PKC-phosph-neuro
    granin_
    PSD
  • AMPAR_traff_
    model0

    Accession No. : 59
  • Shared_Object_
    AMPAR_traff_
    model0

    Pathway No. : 234
  • 28.62730.584.03448explicit E-S complexSubstrate
    neurogranin_PSD

    Product
  • neurogranin*_
    PSD

  • Rates from Huang et al ABB 305:2 570-580 1993

    neurogranin_PSD acting as a Product of an Enzyme in  
    AMPAR_traff_model0 Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    CaM_Ca_n-CaNAB  /
  • dephosph_
    neurogranin_PSD
  • AMPAR_traff_
    model0

    Accession No. : 59
  • PP2B
    Pathway No. : 238
    10.0120.673.98507explicit E-S complexSubstrate
  • neurogranin*_
    PSD


    Product
    neurogranin_PSD
  • From Seki et al ABB 316(2):673-679

    neurogranin_PSD acting as a Substrate in a reaction in  
    AMPAR_traff_model0 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

  • neurogranin-bind
    -CaM_
    PSD
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaM
    Pathway No. : 236
    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

    neurogranin_PSD acting as a Product in a reaction in  
    AMPAR_traff_model0 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

  • dephosph-neurogr
    anin_
    PSD
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaM
    Pathway No. : 236
    0.005
    (s^-1)
    0
    (s^-1)
    --Substrate
  • neurogranin*_
    PSD


    Product
    neurogranin_PSD
  • 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.



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