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Result: 1 - 5 of 5 rows are displayed

Reaction List for pathway PP2B (Pathway Number 83) in Accession Synaptic_Network (Accession Number 16)

Entries are grouped according to Pathway Number and they are alternately color coded using  and  color.
Further ordering can be done to the table header.  indicates that ordering is done according to ascending or descending order.
Keq is calculated only for first order reactions.
Kd is calculated only for second order reactions. [nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules]
  Reaction
Name
Pathway Name / 
Pathway No.
KfKbKdtauReagents
1 
  • Ca-bind-CaNAB-Ca
    2
  • PP2B

    Pathway No. 83
    3.6
    (uM^-2 s^-1)
    1
    (s^-1)
    Kd(af) = 0.527(uM)-  Substrate:
     Ca
     Ca
     CaNAB-Ca2

     Products:
     CaNAB-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 1994 Biochem 33:6859-6866, this specific parm on pg 6863, the Kact is 0.5 uM. Assume binding is fast, 1 sec.
    2 Ca-bind-CaNABPP2B

    Pathway No. 83
    10008
    (uM^-2 s^-1)
    1
    (s^-1)
    Kd(af) = 0.01(uM)-  Substrate:
     CaNAB
     Ca
     Ca

     Products:
     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. This doesn't really matter much because it will always be bound at physiological Ca.
    3 
  • CaM-Ca2-bind-CaN
    AB
  • PP2B

    Pathway No. 83
    0.24
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 4.1667(uM)-  Substrate:
     CaNAB-Ca4
     CaM-TR2-Ca2

     Products:
     CaMCa2-CANAB
      Based on Stemmer and Klee 1994 Biochem 33:6859-6866 This model is actually a simplification of the detail they report. In this model the Ca-binding affinity of CaM is not changed by binding to CaN. Rates here come from a detailed-balance argument. The reference rate is for CaMCa4 binding to CaNAB. This rate should be 1/2500 of that.
    4 
  • CaMCa3-bind-CaNA
    B
  • PP2B

    Pathway No. 83
    2.238
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.4468(uM)-  Substrate:
     CaM-Ca3
     CaNAB-Ca4

     Products:
     CaMCa3-CaNAB
      Rates derived from the CaMCa4 binding to CaNAB-Ca4 step. Due to detailed balance calculations taking the Ca affinity for CaM into account, this reaction should be 250 times slower. Close.
    5 
  • CaMCa4-bind-CaNA
    B
  • PP2B

    Pathway No. 83
    600
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.0017(uM)-  Substrate:
     CaM-Ca4
     CaNAB-Ca4

     Products:
     CaMCa4-CaNAB
      This step is the starting point for calculating all the CaM-binding steps to CaNAB-Ca4. The calculation goes like this: From Stemmer and Klee 1994 Biochem 33 6859-6866 we have rates for Ca binding to CaM.Ca4.CaN. From detailed balance (Kd must be 1 around a loop) we can set ratios of Kds for CaMCa3 binding to CaN, and CaM-Ca2 binding to CaN. Thus those rates can come once we know the Kd for the current reaction of CaMCa4 binding to CaN. We'll ignore the Ca binding steps to CaM.Ca4.CaN since the reactions around the remaining part of the loop will settle pretty fast to the same levels. Finally, we estimate the kf=0.001 here from a series of simulations matching the curves in Stemmer and Klee.

     
    Result: 1 - 5 of 5 rows are displayed



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