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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
cAMP_pathway25Network
Shared_Object_cAMP_pathway PKA AC 
Gs 
This is a model of the canonical cAMP signaling pathway:
Ligand->Receptor->G-protein->Cyclase->cAMP->PKA.
It also includes phosphodiesterases to balance out cAMP formation.Bhalla US Methods Enzymol. 2002;345:3-23

R acting as a Molecule in  
cAMP_pathway Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
RcAMP_pathway
Accession No. : 25
Gs
Pathway No. : 137
0.08331000No
A typical number of receptors per cell is about 50000.

R acting as a Substrate in a reaction in  
cAMP_pathway 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-RcAMP_pathway
Accession No. : 25
Gs
Pathway No. : 137
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-GabccAMP_pathway
Accession No. : 25
Gs
Pathway No. : 137
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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