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Molecule Parameter List for CaM-Ca4

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-Ca4 participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000052

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.

    CaM-Ca4 acting as a Molecule in  
    AMPAR_traff_model0 Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    CaM-Ca4
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaM
    Pathway No. : 236
    00.09No

    CaM-Ca4 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
    1CaMKII-bind-CaM
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaMKII
    Pathway No. : 235
    49.9997
    (uM^-1 s^-1)
    5
    (s^-1)
    Kd(bf) = 0.1(uM)-Substrate
    CaM-Ca4
    CaMKII

    Product
    CaMKII-CaM
      This is tricky. There is some cooperativity here arising from interactions between the subunits of the CAMKII holoenzyme. However, the stoichiometry is 1. Kb/Kf = 6e4 #/cell. Rate is fast (see Hanson et al Neuron 12 943-956 1994) so lets say kb = 10. This gives kf = 1.6667e-4 H&S AnnRev Biochem 92 give tau for dissoc as 0.2 sec at low Ca, 0.4 at high. Low Ca = 100 nM = physiol.
    2
  • CaMK-thr286-bind
    -CaM
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaMKII
    Pathway No. : 235
    1000.19
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 0.0001(uM)-Substrate
    CaM-Ca4
    CaMKII-thr286

    Product
  • CaMKII-thr286*-C
    aM

  •   Affinity is up 1000X. Time to release is about 20 sec, so the kb is OK at 0.1 This makes Kf around 1.6666e-3
    3
  • CaMCa4-bind-CaNA
    B
  • AMPAR_traff_
    model0

    Accession No. : 59
  • PP2B
    Pathway No. : 238
    599.994
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.0017(uM)-Substrate
    CaM-Ca4
    CaNAB-Ca4

    Product
    CaM_Ca_n-CaNAB
    4CaM-bind-AC1
  • AMPAR_traff_
    model0

    Accession No. : 59
  • AC
    Pathway No. : 241
    49.9997
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.02(uM)-Substrate
    AC1
    CaM-Ca4

    Product
    AC1-CaM
      Half-max at 20 nM CaM (Tang et al JBC 266:13 8595-8603 1991 kb/kf = 20 nM = 12000 #/cell so kf = kb/12000 = kb * 8.333e-5
    5CaM_bind_PDE1
  • AMPAR_traff_
    model0

    Accession No. : 59
  • AC
    Pathway No. : 241
    719.982
    (uM^-1 s^-1)
    5
    (s^-1)
    Kd(bf) = 0.0069(uM)-Substrate
    CaM-Ca4
    PDE1

    Product
    CaM.PDE1
      For olf epi PDE1, affinity is 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec. Then kf = 5 / (0.007 * 6e5) = 1.2e-3

    CaM-Ca4 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
    1CaM-Ca3-bind-Ca
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaM
    Pathway No. : 236
    0.465
    (uM^-1 s^-1)
    10
    (s^-1)
    Kd(bf) = 21.5054(uM)-Substrate
    Ca
    CaM-Ca3

    Product
    CaM-Ca4
      Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
    2equilib
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaM
    Pathway No. : 236
    540
    (s^-1)
    60
    (s^-1)
    Not applicable**-Substrate
    CaM-Ca4-PSD

    Product
    CaM-Ca4
      Diffusional equilibrium between PSD- and cytosolic compartment. According to D. Bary in Cell Movements 2nd ed 2001 D for proteins is 5e-7 cm^2/s giving 10 ms for a translocation of 1 um.
    ** 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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