NCBS Home page
Accession List
Pathway List
Search
Authorized Users
Help
News archives

Enter a Search String

Special character and space not allowed in the query term. Search string should be at least 2 characters long.
Search in: Search for Match By


 
Result: 1 - 5 of 5 rows are displayed

Reaction List for pathway CaM (Pathway Number 81) 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 CaM-TR2-bind-CaCaM

Pathway No. 81
72
(uM^-2 s^-1)
72
(s^-1)
Kd(af) = 1(uM)-  Substrate:
 CaM
 Ca
 Ca

 Products:
 CaM-TR2-Ca2
  We use the Martin et al 1985 Eur J Biochem 151(3):543-550 rates here, plus the Drabikowski and Brzeska 1982 JBC 257(19):11584-11590 binding consts. All are scaled by 3X to cell temperature. kf = 2e-10 kb = 72 Stemmer & Klee 1994 Biochem 33:6859-6866 have values of : K1=.9, K2=1.1. Assume 1.0uM for both
2 
  • CaM-TR2-Ca2-bind
    -Ca
  • CaM

    Pathway No. 81
    3.6
    (uM^-1 s^-1)
    10
    (s^-1)
    Kd(bf) = 2.7778(uM)-  Substrate:
     CaM-TR2-Ca2
     Ca

     Products:
     CaM-Ca3
      Stemmer and Klee 1994 Biochem 33:6859-6866 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
    3 CaM-Ca3-bind-CaCaM

    Pathway No. 81
    0.465
    (uM^-1 s^-1)
    10
    (s^-1)
    Kd(bf) = 21.5054(uM)-  Substrate:
     CaM-Ca3
     Ca

     Products:
     CaM-Ca4
      Use K3 = 21.5 uM here from Stemmer and Klee table 3. Stemmer and Klee 1994 Biochem 33:6859-6866 kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
    4 
  • neurogranin-bind
    -CaM
  • CaM

    Pathway No. 81
    0.3
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 3.3333(uM)-  Substrate:
     neurogranin
     CaM

     Products:
     neurogranin-CaM
      Surprisingly, no direct info on rates from neurogranin at this time. These rates are based on GAP-43 binding studies. As GAP-43 and neurogranin share near identity in the CaM/PKC binding regions, and also similarity in phosph and dephosph rates, I am borrowing GAP-43 kinetic info. See Alexander et al JBC 262:13 6108-6113 1987
    5 
  • dephosph-neurogr
    anin
  • CaM

    Pathway No. 81
    0.005
    (s^-1)
    0
    (s^-1)
    --  Substrate:
     neurogranin*

     Products:
     neurogranin
      This is put in to keep the basal levels of neurogranin* experimentally reasonable. From various papers, specially Ramakers et al JBC 270:23 1995 13892-13898, it looks like the basal level of phosph is between 20 and 40%. I estimate around 25 % The kf of 0.005 gives around this level at basal PKC activity levels of 0.1 uM active PKC.

     
    Result: 1 - 5 of 5 rows are displayed



    Database compilation and code copyright (C) 2005, Upinder S. Bhalla and NCBS/TIFR
    This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details.