|
Enter a Search String | | Special character and space not allowed in the query term.
Search string should be at least 2 characters long. |
Molecule Parameter List for CaNAB-Ca4 | 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 |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | Synaptic_
Network | 16 | Network |
Shared_Object_Synaptic_Network, PKC, PLA2,
PLCbeta, Gq, MAPK,
Ras, EGFR, Sos,
PLC_g, CaMKII, CaM,
PP1, PP2B, PKA,
AC, CaRegulation | This model is an annotated version of the synaptic signaling network.
The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated.
Bhalla US Biophys J. 2002 Aug;83(2):740-52
Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62 |
CaNAB-Ca4 acting as a Molecule in Synaptic_Network Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | CaNAB-Ca4 | Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 0 | 1000 | No | | Four calciums bound to CaN. This has an activity in absence of CaM. Perrino et al 1992 JBC 267(22):15965-15969 |
CaNAB-Ca4 acting as an Enzyme in Synaptic_Network Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | CaNAB-Ca4 /
dephosph_
inhib1_noCaM
| Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 4.97076 | 0.034 | 4 | explicit E-S complex | Substrate
I1*
Product
I1
| | The rates here are so slow I do not know if we should even bother with this enzyme reaction. These numbers are from Liu and Storm JBC 1989 264(22):12800-12804 They say that the CaM-free form of CaN operates at about the same Km of 5 uM, but at a much lower Vmax of 1 nmol/min/mg. Other estimates of activity without CaM suggest 10% activity, which is what I use here. |
CaNAB-Ca4 acting as a Substrate in a reaction in Synaptic_Network 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. |
| | Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | 1 | CaM-Ca2-bind-CaN
AB | Synaptic_
Network
Accession No. : 16 | PP2B
Pathway No. : 83 | 0.24
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 4.1667(uM) | - | Substrate
CaM-TR2-Ca2
CaNAB-Ca4
Product
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. | | 2 | CaMCa3-bind-CaNA
B | Synaptic_
Network
Accession No. : 16 | PP2B
Pathway No. : 83 | 2.238
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.4468(uM) | - | Substrate
CaM-Ca3
CaNAB-Ca4
Product
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. | | 3 | CaMCa4-bind-CaNA
B | Synaptic_
Network
Accession No. : 16 | PP2B
Pathway No. : 83 | 600
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0017(uM) | - | Substrate
CaM-Ca4
CaNAB-Ca4
Product
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. |
CaNAB-Ca4 acting as a Product in a reaction in Synaptic_Network 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. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | Ca-bind-CaNAB-Ca
2 | Synaptic_
Network
Accession No. : 16 | PP2B
Pathway No. : 83 | 3.6
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.527(uM) | - | Substrate
Ca
Ca
CaNAB-Ca2
Product
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. |
| 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. |
|
