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Molecule Parameter List for CaM-TR2-Ca2

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-TR2-Ca2 participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000021

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Ajay_Bhalla_
    2004_PKM_Tuning
    		• 76Network
    PKC,  Shared_Object_Ajay_Bhalla_2004_PKM_tuning,  PLA2,  
    PLCbeta,  Gq,  MAPK,  
    Ras,  EGFR,  Sos,  
    PLC_g,  CaMKII,  CaM,  
    PP1,  PP2B,  PKA,  
    AC,  PKM 
    This model is taken from the Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the reference feedforward model from Figure 8a.

    CaM-TR2-Ca2 acting as a Molecule in      Ajay_Bhalla_2004_PKM_Tuning Network
    NameAccession NamePathway NameInitial Conc.
    (uM)    		Volume
    (fL)    		Buffered
    CaM-TR2-Ca2
  • Ajay_Bhalla_
    2004_PKM_Tuning
    Accession No. : 76
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_tuning
    Pathway No. : 312
    		• 01.5No
    This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not.

    CaM-TR2-Ca2 acting as a Substrate in a reaction in      Ajay_Bhalla_2004_PKM_Tuning 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-Ca2-bind
    -Ca
  • Ajay_Bhalla_
    2004_PKM_Tuning
    Accession No. : 76
    		• CaM
    Pathway No. : 323    		3.6
    (uM^-1 s^-1)    		10
    (s^-1)    		Kd(bf) = 2.7778(uM)-Substrate
    Ca
    CaM-TR2-Ca2

    Product
    CaM-Ca3
      K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10
    2
  • CaM-Ca2-bind-CaN
    AB
  • Ajay_Bhalla_
    2004_PKM_Tuning
    Accession No. : 76
    		• PP2B
    Pathway No. : 325    		0.24
    (uM^-1 s^-1)    		1
    (s^-1)    		Kd(bf) = 4.1666(uM)-Substrate
    CaM-TR2-Ca2
    CaNAB-Ca4

    Product
    CaMCa2-CANAB
      Disabled. See notes for PP2B7.g

    CaM-TR2-Ca2 acting as a Product in a reaction in      Ajay_Bhalla_2004_PKM_Tuning 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
    CaM-TR2-bind-Ca
  • Ajay_Bhalla_
    2004_PKM_Tuning
    Accession No. : 76
    		• CaM
    Pathway No. : 323    		72.0001
    (uM^-2 s^-1)    		72
    (s^-1)    		Kd(af) = 1(uM)-Substrate
    Ca
    Ca
    CaM

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


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