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 - 20 of 57 rows are displayed Previous of 3  Next

Reaction List for Accession AMPAR_CaMKII_weak_coupling (Accession Number 65)

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 equilib
  • Shared_Object_
    AMPAR_CaMKII_
    weak_coupling
    Pathway No. 281
    		• 540
    (s^-1)    		60
    (s^-1)    		Not applicable**-  Substrate:
     CaM-Ca4-PSD

     Products:
     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.
    2 Inact-PP1
  • Shared_Object_
    AMPAR_CaMKII_
    weak_coupling
    Pathway No. 281
    		• 499.98
    (uM^-1 s^-1)    		0.1
    (s^-1)    		Kd(bf) = 0.0002(uM)-  Substrate:
     I1*
     PP1-active_PSD

     Products:
     PP1-I1*
      K inhib = 1nM from Cohen Ann Rev Bioch 1989, 4 nM from Foukes et al Assume 2 nM. kf /kb = 8.333e-4
    3 CaM-Ca3-bind-Ca
  • Shared_Object_
    AMPAR_CaMKII_
    weak_coupling
    Pathway No. 281
    		• 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. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
    4 endo_const
  • Shared_Object_
    AMPAR_CaMKII_
    weak_coupling
    Pathway No. 281
    		• 0.0004
    (s^-1)    		0.0014
    (s^-1)    		Not applicable**-  Substrate:
     GluR23_M

     Products:
     GluR23_I
    5 PKC-stoch-input
  • Shared_Object_
    AMPAR_CaMKII_
    weak_coupling
    Pathway No. 281
    		• 2.5
    (s^-1)    		2.5
    (s^-1)    		Keq = 1(uM)0.2sec  Substrate:
     PKC-control

     Products:
     PKC-active
    6 Ca_stoch_cyt
  • Shared_Object_
    AMPAR_CaMKII_
    weak_coupling
    Pathway No. 281
    		• 100
    (s^-1)    		100
    (s^-1)    		Keq = 1(uM)0.005sec  Substrate:
     Ca_control_cyt

     Products:
     Ca
    7 Ca_stoch_PSD
  • Shared_Object_
    AMPAR_CaMKII_
    weak_coupling
    Pathway No. 281
    		• 100
    (s^-1)    		100
    (s^-1)    		Keq = 1(uM)0.005sec  Substrate:
     Ca_control_PSD

     Products:
     Ca-PSD
    8 turnover
  • Shared_Object_
    AMPAR_CaMKII_
    weak_coupling
    Pathway No. 281
    		• 0.018
    (s^-1)    		1
    (s^-1)    		Not applicable**-  Substrate:
     AMPAR_bulk

     Products:
     A_B
      Represents both synthesis and degradation of the receptor. The rate is set to be rather fast for now. The forward rate also includes scaling terms because the AMPAR_bulk is in the dendritic volume of 5e-18. This means that we need to lower Kf to account for the difference in volumes. Effectively Kf is 1/sec, but the scaled version becomes 9e-20/5e-18 = 0.018
    9 CaMKII-bind-CaMCaMKII

    Pathway No. 282    		49.9997
    (uM^-1 s^-1)    		5
    (s^-1)    		Kd(bf) = 0.1(uM)-  Substrate:
     CaM-Ca4
     CaMKII

     Products:
     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.
    10 
  • CaMK-thr286-bind
    -CaM
    		• CaMKII

    Pathway No. 282    		1000.19
    (uM^-1 s^-1)    		0.1
    (s^-1)    		Kd(bf) = 0.0001(uM)-  Substrate:
     CaMKII-thr286
     CaM-Ca4

     Products:
  •  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
    11 CaM-TR2-bind-CaCaM

    Pathway No. 283    		71.999
    (uM^-2 s^-1)    		72
    (s^-1)    		Kd(af) = 1(uM)-  Substrate:
     CaM
     Ca
     Ca

     Products:
     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 !)....
    12 
  • CaM-TR2-Ca2-bind
    -Ca
    		• CaM

    Pathway No. 283    		3.6
    (uM^-1 s^-1)    		10
    (s^-1)    		Kd(bf) = 2.7778(uM)-  Substrate:
     CaM-TR2-Ca2
     Ca

     Products:
     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
    13 
  • neurogranin-bind
    -CaM
    		• CaM

    Pathway No. 283    		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
    14 
  • dephosph-neurogr
    anin
    		• CaM

    Pathway No. 283    		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 est around 25 % The kf of 0.005 gives around this level at basal PKC activity levels of 0.1 uM active PKC.
    15 
  • CaM-TR2-bind-Ca-
    PSD
    		• CaM

    Pathway No. 283    		72
    (uM^-2 s^-1)    		72
    (s^-1)    		Kd(af) = 1(uM)-  Substrate:
     CaM-PSD
     Ca-PSD
     Ca-PSD

     Products:
     CaM-TR2-Ca2-PSD
      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 !)....
    16 
  • CaM-TR2-Ca2-bind
    -Ca-PSD
    		• CaM

    Pathway No. 283    		3.6
    (uM^-1 s^-1)    		10
    (s^-1)    		Kd(bf) = 2.7778(uM)-  Substrate:
     CaM-TR2-Ca2-PSD
     Ca-PSD

     Products:
     CaM-Ca3-PSD
      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
    17 
  • CaM-Ca3-bind-Ca-
    PSD
    		• CaM

    Pathway No. 283    		0.465
    (uM^-1 s^-1)    		10
    (s^-1)    		Kd(bf) = 21.5048(uM)-  Substrate:
     CaM-Ca3-PSD
     Ca-PSD

     Products:
     CaM-Ca4-PSD
      Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
    18 

  • neurogranin-bind
    -CaM_
    PSD
    		• CaM

    Pathway No. 283    		0.3
    (uM^-1 s^-1)    		1
    (s^-1)    		Kd(bf) = 3.3333(uM)-  Substrate:
     neurogranin_PSD
     CaM-PSD

     Products:
  •  
    neurogranin-CaM_
    PSD
    •   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
    19 

  • dephosph-neurogr
    anin_
    PSD
    		• CaM

    Pathway No. 283    		0.005
    (s^-1)    		0
    (s^-1)    		--  Substrate:
  •  neurogranin*_
    PSD

     Products:
     neurogranin_PSD
    •   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 est around 25 % The kf of 0.005 gives around this level at basal PKC activity levels of 0.1 uM active PKC.
    20 Inact-PP1PP1

    Pathway No. 284    		499.981
    (uM^-1 s^-1)    		0.1
    (s^-1)    		Kd(bf) = 0.0002(uM)-  Substrate:
     I1*
     PP1-active

     Products:
     PP1-I1*
      K inhib = 1nM from Cohen Ann Rev Bioch 1989, 4 nM from Foukes et al Assume 2 nM. kf /kb = 8.333e-4
     
    Result: 1 - 20 of 57 rows are displayed Previous of 3  Next


    Database compilation and code copyright (C) 2022, 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.