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Molecule Parameter List for Ca

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
Ca participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000061

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
mRNA synthesis94Network
kinetics,  compartment_1,  compartment_2 
The model consists of three major pathways: Calcium-calmodulin dependent protein kinase IV (CaMKIV), Mitogen-activated protein kinase (MAPK) and Protein Phosphatase 1 (PP1). Each of these converged on CREB activation. We also modeled further interactions with Transducer of regulated CREB activity 1 (TORC1) and the protein kinase A (PKA) pathway.

Ca acting as a Molecule in  mRNA synthesis Network
NameAccession NamePathway NameInitial Conc.
(uM)		Volume
(fL)		Buffered
CamRNA synthesis
Accession No. : 94		kinetics
Pathway No. : 1112		0.081000Yes

Ca acting as a Substrate in a reaction in  mRNA synthesis 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_dash_Ca3_
    dash_bind_dash_
    Ca
    		• mRNA synthesis
    Accession No. : 94    		kinetics
    Pathway No. : 1112    		0.465
    (uM^-1 s^-1)    		10
    (s^-1)    		Kd(bf) = 21.5051(uM)-Substrate
    Ca
    CaM_dash_Ca3

    Product
    CaM_dash_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
    2
  • CaM_dash_bind_
    dash_Ca
    		• mRNA synthesis
    Accession No. : 94    		kinetics
    Pathway No. : 1112    		8.4846
    (uM^-1 s^-1)    		8.4853
    (s^-1)    		Kd(bf) = 1.0001(uM)-Substrate
    Ca
    CaM

    Product
    CaM_dash_Ca
      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 !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853
    3
  • CaM_dash_Ca2_
    dash_bind_dash_
    Ca
    		• mRNA synthesis
    Accession No. : 94    		kinetics
    Pathway No. : 1112    		3.6001
    (uM^-1 s^-1)    		10
    (s^-1)    		Kd(bf) = 2.7777(uM)-Substrate
    Ca
    CaM_dash_Ca2

    Product
    CaM_dash_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
    4
  • CaM_dash_Ca_
    dash_bind_dash_
    Ca
    		• mRNA synthesis
    Accession No. : 94    		kinetics
    Pathway No. : 1112    		8.4846
    (uM^-1 s^-1)    		8.4853
    (s^-1)    		Kd(bf) = 1.0001(uM)-Substrate
    Ca
    CaM_dash_Ca

    Product
    CaM_dash_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 !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853
    5
  • Ca_dash_bind_
    dash_CaNAB_
    dash_Ca2
    		• mRNA synthesis
    Accession No. : 94    		kinetics
    Pathway No. : 1112    		3599.928
    (uM^-2 s^-1)    		1
    (s^-1)    		Kd(af) = 0.0167(uM)-Substrate
    Ca
    Ca
    CaNAB_dash_Ca2

    Product
    CaNAB_dash_Ca4
      This process is probably much more complicated and involves CaM. However, as I can't find detailed info I am bundling this into a single step. Based on Steemer and Klee pg 6863, the Kact is 0.5 uM. kf/kb = 1/(0.5 * 6e5)^2 = 1.11e-11
    6
  • Ca_dash_bind_
    dash_CaNAB
    		• mRNA synthesis
    Accession No. : 94    		kinetics
    Pathway No. : 1112    		10008360
    (uM^-2 s^-1)    		1
    (s^-1)    		Kd(af) = 0.0003(uM)-Substrate
    Ca
    Ca
    CaNAB

    Product
    CaNAB_dash_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 

    Ca acting as a Product in a reaction in      mRNA synthesis 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_stochmRNA synthesis
    Accession No. : 94    		kinetics
    Pathway No. : 1112    		100
    (s^-1)    		100
    (s^-1)    		Keq = 1(uM)0.005secSubstrate
    Ca_input

    Product
    Ca


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