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Molecule Parameter List for cAMP | 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 | AMPAR_traff_
model0 | 59 | Network |
Shared_Object_AMPAR_traff_model0, CaMKII, CaM,
PP1, PP2B, PP1_PSD,
PKA, AC, AMPAR,
AMPAR_memb | | This is model 0 from Hayer and Bhalla, PLoS Comput Biol 2005. It has a bistable model of AMPAR traffick, plus a
non-bistable model of CaMKII. This differs from the reference model (model 1) in that model0 lacks degradation and turno
ver reactions for AMPAR. |
cAMP acting as a Molecule in AMPAR_traff_model0 Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | cAMP | AMPAR_traff_
model0
Accession No. : 59 | AC
Pathway No. : 241 | 0 | 0.09 | No | | The conc of this has been a problem. Schaecter and Benowitz use 50 uM, but Shinomura et al have < 5. So I have altered the cAMP-dependent rates in the PKA model to reflect this. |
cAMP acting as a Substrate for an Enzyme in AMPAR_traff_model0 Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | cAMP-PDE /
PDE | AMPAR_traff_
model0
Accession No. : 59 | AC
Pathway No. : 241 | 19.8411 | 10 | 4 | explicit E-S complex | Substrate
cAMP
Product
AMP
| | | Best rates are from Conti et al Biochem 34 7979-7987 1995. Though these are for the Sertoli cell form, it looks like they carry nicely into alternatively spliced brain form. See Sette et al JBC 269:28 18271-18274 Km ~2 uM, Vmax est ~ 10 umol/min/mg for pure form. Brain protein is 93 kD but this was 67. So k3 ~10, k2 ~40, k1 ~4.2e-6 | | 2 | cAMP-PDE* /
PDE* | AMPAR_traff_
model0
Accession No. : 59 | AC
Pathway No. : 241 | 19.8413 | 20 | 4 | explicit E-S complex | Substrate
cAMP
Product
AMP
| | | This form has about twice the activity of the unphosphorylated form. See Sette et al JBC 269:28 18271-18274 1994. We'll ignore cGMP effects for now. | | 3 | PDE1 /
PDE1 | AMPAR_traff_
model0
Accession No. : 59 | AC
Pathway No. : 241 | 39.6999 | 1.667 | 4.0012 | explicit E-S complex | Substrate
cAMP
Product
AMP
| | | Rate is 1/6 of the CaM stim form. We'll just reduce all lf k1, k2, k3 so that the Vmax goes down 1/6. | | 4 | CaM.PDE1 /
CaM.PDE1 | AMPAR_traff_
model0
Accession No. : 59 | AC
Pathway No. : 241 | 39.6831 | 10 | 4 | explicit E-S complex | Substrate
cAMP
Product
AMP
| | | Max activity ~10umol/min/mg in presence of lots of CaM. Affinity is low, 40 uM. k3 = 10, k2 = 40, k1 = (50/40) / 6e5. |
cAMP acting as a Product of an Enzyme in AMPAR_traff_model0 Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | AC1-CaM /
kenz | AMPAR_traff_
model0
Accession No. : 59 | AC
Pathway No. : 241 | 299.998 | 4.5 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
ATP
Product
cAMP
| | | 17 Feb 2005 Halved Vmax as the amount of enzyme has been doubled to get an integer value in the spine. 18 Feb 2005. Updated Km from BRENDA: EC No 4.6.1.1 Rat Km: 0.95 mM Turnover 12/sec. Human Km: 0.3 mM 12 umol/min/mg for mammalia, turnover is 12/sec See PMID 8663304 by Dessauer and Gilman JBC 271 1996 Unfortunately turnover range is from 34 down to 0.1 in different studies, according to BRENDA. | | 2 | AC2* /
kenz | AMPAR_traff_
model0
Accession No. : 59 | AC
Pathway No. : 241 | 300.002 | 2 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
ATP
Product
cAMP
| | | Reduced Km to match expt data for basal activation of AC2 by PKC. Now k1 = 2.9e-6, k2 = 72, k3 = 18 18 Feb: Raised Km to 300 based on BRENDA data. Unlikely to make much difference, given the vast amount of ATP. |
cAMP acting as a Substrate in a reaction in AMPAR_traff_model0 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 | cAMP-bind-site-B
1 | AMPAR_traff_
model0
Accession No. : 59 | PKA
Pathway No. : 240 | 54
(uM^-1 s^-1) | 33
(s^-1) | Kd(bf) = 0.6111(uM) | - | Substrate
R2C2
cAMP
Product
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. | | 2 | cAMP-bind-site-B
2 | AMPAR_traff_
model0
Accession No. : 59 | PKA
Pathway No. : 240 | 54
(uM^-1 s^-1) | 33
(s^-1) | Kd(bf) = 0.6111(uM) | - | Substrate
R2C2-cAMP
cAMP
Product
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 | | 3 | cAMP-bind-site-A
1 | AMPAR_traff_
model0
Accession No. : 59 | PKA
Pathway No. : 240 | 75.0006
(uM^-1 s^-1) | 110
(s^-1) | Kd(bf) = 1.4667(uM) | - | Substrate
R2C2-cAMP2
cAMP
Product
R2C2-cAMP3
| | 4 | cAMP-bind-site-A
2 | AMPAR_traff_
model0
Accession No. : 59 | PKA
Pathway No. : 240 | 75.0006
(uM^-1 s^-1) | 32.5
(s^-1) | Kd(bf) = 0.4333(uM) | - | Substrate
R2C2-cAMP3
cAMP
Product
R2C2-cAMP4
| | 5 | cAMP_diffusion | AMPAR_traff_
model0
Accession No. : 59 | AC
Pathway No. : 241 | 300
(s^-1) | 5.4
(s^-1) | Not applicable** | - | Substrate
cAMP
Product
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. |
** This is a trasport reation between compartments of different volumes. Therefore Kd is not applicable. Please Note Kf, Kb units are in number of molecules instead of concentration
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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