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Reaction List for Accession AMPAR_CaMKII_strong_coupling (Accession Number 64)

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-CaNABPP2B

Pathway No. 276		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, we get kf = 2.78e-8, kb = 1. Try 20 nM. kf = 7e-9, kb = 1 
2 
  • CaMK-thr286-bind
    -CaM
    		• CaMKII

    Pathway No. 272    		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
    3 
  • CaMKII-thr286-bi
    nd-CaM-PSD
  • Shared_Object_
    AMPAR_CaMKII_
    strong_coupling
    Pathway No. 271
    		• 1000.02
    (uM^-1 s^-1)    		0.1
    (s^-1)    		Kd(bf) = 0.0001(uM)-  Substrate:
  •  CaMKII-thr286-PS
    D
     CaM-Ca4-PSD

     Products:
  •  CaMKII-thr286-Ca
    M-PSD
    •   Same values as for the main compartment Can the main compartment pool of Ca/CaM be used?
    4 CaM_bind_PDE1AC

    Pathway No. 278    		719.982
    (uM^-1 s^-1)    		5
    (s^-1)    		Kd(bf) = 0.0069(uM)-  Substrate:
     PDE1
     CaM-Ca4

     Products:
     CaM.PDE1
      For olf epi PDE1, affinity is 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec. Then kf = 5 / (0.007 * 6e5) = 1.2e-3
    5 
  • CaMCa4-bind-CaNA
    B
    		• PP2B

    Pathway No. 276    		599.994
    (uM^-1 s^-1)    		1
    (s^-1)    		Kd(bf) = 0.0017(uM)-  Substrate:
     CaM-Ca4
     CaNAB-Ca4

     Products:
     CaM_Ca_n-CaNAB
    6 equilib
  • Shared_Object_
    AMPAR_CaMKII_
    strong_coupling
    Pathway No. 271
    		• 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.
    7 Inact-PP1PP1

    Pathway No. 274    		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
    8 Inact-PP1
  • Shared_Object_
    AMPAR_CaMKII_
    strong_coupling
    Pathway No. 271
    		• 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
    9 cAMP_diffusionAC

    Pathway No. 278    		300
    (s^-1)    		5.4
    (s^-1)    		Not applicable**-  Substrate:
     cAMP

     Products:
     cAMP_in_dend
      Represents diffusion, from a volume of 9e-20 to 5e-18. Assuming neck dimensions of 0.1 x 0.1 microns, this works out to a diffusion const of about 270 um^2/sec, which is pretty conservative. It is what cAMP does in frog cilia.
    10 Ca_stoch_cyt
  • Shared_Object_
    AMPAR_CaMKII_
    strong_coupling
    Pathway No. 271
    		• 100
    (s^-1)    		100
    (s^-1)    		Keq = 1(uM)0.005sec  Substrate:
     Ca_control_cyt

     Products:
     Ca
    11 Ca_stoch_PSD
  • Shared_Object_
    AMPAR_CaMKII_
    strong_coupling
    Pathway No. 271
    		• 100
    (s^-1)    		100
    (s^-1)    		Keq = 1(uM)0.005sec  Substrate:
     Ca_control_PSD

     Products:
     Ca-PSD
    12 
  • cAMP-bind-site-A
    1
    		• PKA

    Pathway No. 277    		75.0006
    (uM^-1 s^-1)    		110
    (s^-1)    		Kd(bf) = 1.4667(uM)-  Substrate:
     R2C2-cAMP2
     cAMP

     Products:
     R2C2-cAMP3
    13 
  • cAMP-bind-site-A
    2
    		• PKA

    Pathway No. 277    		75.0006
    (uM^-1 s^-1)    		32.5
    (s^-1)    		Kd(bf) = 0.4333(uM)-  Substrate:
     cAMP
     R2C2-cAMP3

     Products:
     R2C2-cAMP4
    14 
  • CaM-TR2-bind-Ca-
    PSD
    		• CaM

    Pathway No. 273    		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 !)....
    15 CaM-TR2-bind-CaCaM

    Pathway No. 273    		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 !)....
    16 Release-C1PKA

    Pathway No. 277    		60
    (s^-1)    		17.9998
    (uM^-1 s^-1)    		Kd(cb) = 0.3(uM)-  Substrate:
     R2C2-cAMP4

     Products:
     PKA-active
     R2C-cAMP4
      This has to be fast, as the activation of PKA by cAMP is also fast. kf was 10
    17 Release-C2PKA

    Pathway No. 277    		60
    (s^-1)    		17.9998
    (uM^-1 s^-1)    		Kd(cb) = 0.3(uM)-  Substrate:
     R2C-cAMP4

     Products:
     PKA-active
     R2-cAMP4
    18 inhib-PKAPKA

    Pathway No. 277    		59.9994
    (uM^-1 s^-1)    		1
    (s^-1)    		Kd(bf) = 0.0167(uM)-  Substrate:
     PKA-active
     PKA-inhibitor

     Products:
     inhibited-PKA
      This has to be set to zero for matching the expts in vitro. In vivo we need to consider the inhibition though. kf = 1e-5 kb = 1
    19 
  • cAMP-bind-site-B
    1
    		• PKA

    Pathway No. 277    		54
    (uM^-1 s^-1)    		33
    (s^-1)    		Kd(bf) = 0.6111(uM)-  Substrate:
     R2C2
     cAMP

     Products:
     R2C2-cAMP
      Hasler et al FASEB J 6:2734-2741 1992 say Kd =1e-7M for type II, 5.6e-8 M for type I. Take mean which comes to 2e-13 #/cell Smith et al PNAS USA 78:3 1591-1595 1981 have better data. First kf/kb=2.1e7/M = 3.5e-5 (#/cell). Ogreid and Doskeland Febs Lett 129:2 287-292 1981 have figs suggesting time course of complete assoc is < 1 min.
    20 
  • cAMP-bind-site-B
    2
    		• PKA

    Pathway No. 277    		54
    (uM^-1 s^-1)    		33
    (s^-1)    		Kd(bf) = 0.6111(uM)-  Substrate:
     R2C2-cAMP
     cAMP

     Products:
     R2C2-cAMP2
      For now let us set this to the same Km (1e-7M) as site B. This gives kf/kb = .7e-7M * 1e6 / (6e5^2) : 1/(6e5^2) = 2e-13:2.77e-12 Smith et al have better values. They say that this is cooperative, so the consts are now kf/kb =8.3e-4
     
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