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Molecule Parameter List for CaNAB

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
CaNAB participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000010

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.

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

    Accession No. : 59
  • PP2B
    Pathway No. : 238
    10.09No
    We assume that the A and B subunits of PP2B are always bound under physiol conditions. Up to 1% of brain protein = 25 uM. I need to work out how it is distributed between cytosolic and particulate fractions. Tallant and Cheung '83 Biochem 22 3630-3635 have conc in many species, average for mammalian brain is around 1 uM.

    CaNAB 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
    Ca-bind-CaNAB
  • AMPAR_traff_
    model0

    Accession No. : 59
  • PP2B
    Pathway No. : 238
    10008
    (uM^-2 s^-1)
    1
    (s^-1)
    Kd(af) = 0.01(uM)-Substrate
    Ca
    Ca
    CaNAB

    Product
    CaNAB-Ca2
    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 



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