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Molecule Parameter List for R

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
R participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000020

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
PKA_200347Network
Shared_Object_PKA_2003 PKA AC 
Gs 
This model consists of receptor-ligand interaction, G-protein activation, Adenylyl cyclase mediated formation of cAMP and activation of PKA in the neuron. Demonstration programs using this model described in Bhalla US. (2004) Biophys J. 87(2):733-44 to generate a dose-response curve using stochastic calculations are available here.

R acting as a Molecule in  
PKA_2003 Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
RPKA_2003
Accession No. : 47
Gs
Pathway No. : 198
0.08331000No
A typical number of receptors per cell is about 50000.

R acting as a Substrate in a reaction in  
PKA_2003 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.
 NameAccession NamePathway NameKfKbKdtauReagents
1L-bind-RPKA_2003
Accession No. : 47
Gs
Pathway No. : 198
0.1
(uM^-1 s^-1)
0.1
(s^-1)
Kd(bf) = 1(uM)-Substrate
L
R

Product
L.R
  Ligand binding to receptor. From Gether et al JBC 270:28268-28275 (1995) the binding to the purified receptor is at about 1 uM, but the conformational change only happens at 30 uM. We'll take 1 uM for this, since it is already much weaker binding than to the R.Gs complex. The time-course from this paper appears remarkably slow, based on physiological data I estimate more like 10 sec.
2R-bind-GabcPKA_2003
Accession No. : 47
Gs
Pathway No. : 198
0.2
(uM^-1 s^-1)
0.1
(s^-1)
Kd(bf) = 0.5(uM)-Substrate
GDP.Gabc
R

Product
R.GDP.Gabc
  Receptor binding to Gs. Scale it to the same slow rates described by Fay et al for L.R to L.R.G. From detailed balance, Kd is 50.



Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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