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BIOMD0000000198 - Stone1996_NOsGC

 

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Reference Publication
Publication ID: 8573563
Stone JR, Marletta MA.
Spectral and kinetic studies on the activation of soluble guanylate cyclase by nitric oxide.
Biochemistry 1996 Jan; 35(4): 1093-1099
Department of Biological Chemistry, School of Medicine, College of Pharmacy, University of Michigan, Ann Arbor 48109-1065, USA.  [more]
Model
Original Model: DOQCS logo
Submitter: Sharat Vayttaden
Submission ID: MODEL4779732381
Submission Date: 24 Oct 2008 14:11:14 UTC
Last Modification Date: 11 Apr 2016 16:07:22 UTC
Creation Date: 21 Oct 2008 15:19:25 UTC
Encoders:  Lukas Endler
   Vijayalakshmi Chelliah
   James R Stone
   Michael A Marletta
set #1
bqbiol:occursIn Taxonomy Bos taurus
bqbiol:isVersionOf Gene Ontology regulation of guanylate cyclase activity
Gene Ontology nitric oxide mediated signal transduction
Notes
This features the two step binding of NO to soluble Guanylyl Cyclase as proposed by Stone JR, Marletta MA. Biochemistry (1996) 35(4):1093-9 . There is a fast step binding scheme and a slow step binding scheme. The difference lies in the binding of a NO to a non-heme site on sGC, which may not necessarily be the same site of binding during the initial binding. The rates have been directly used models.

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To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 8573563 Submission Date: 24 Oct 2008 14:11:14 UTC Last Modification Date: 11 Apr 2016 16:07:22 UTC Creation Date: 21 Oct 2008 15:19:25 UTC
Mathematical expressions
Reactions
r1fast r2fast r3fast r1slow
r2slow r3slow r4slow  
Rules
Assignment Rule (variable: NO_sGC_5coord_tot) Assignment Rule (variable: sGC_inact_tot) Assignment Rule (variable: extinction)  
Physical entities
Compartments Species
cytosol NO sGCfast NO_sGCfast
NO_sGCfast_6coord NO_sGCfast_5coord sGCslow
NO_sGCslow NO_sGCslow_6coord NO_sGCslow_6coord_NO_int
NO_sGCslow_5coord NO_sGC_5coord_tot sGC_inact_tot
Global parameters
k1 k2 k3 k4
k5 k6 k7 k8
k9 k10 k11 k12
ext_5coord ext_5coord_NO ext_6coord_NO extinction
Reactions (7)
 
 r1fast [NO] + [sGCfast] ↔ [NO_sGCfast];  
 
 r2fast [NO_sGCfast] → [NO_sGCfast_6coord];  
 
 r3fast [NO_sGCfast_6coord] ↔ [NO_sGCfast_5coord];  
 
 r1slow [NO] + [sGCslow] ↔ [NO_sGCslow];  
 
 r2slow [NO_sGCslow] → [NO_sGCslow_6coord];  
 
 r3slow [NO] + [NO_sGCslow_6coord] ↔ [NO_sGCslow_6coord_NO_int];  
 
 r4slow [NO_sGCslow_6coord_NO_int] ↔ [NO_sGCslow_5coord];  
 
Rules (3)
 
 Assignment Rule (name: NO_sGC_5coord_tot) NO_sGC_5coord_tot = NO_sGCfast_5coord+NO_sGCslow_5coord
 
 Assignment Rule (name: sGC_inact_tot) sGC_inact_tot = sGCfast+NO_sGCfast+NO_sGCfast_6coord+sGCslow+NO_sGCslow+NO_sGCslow_6coord+NO_sGCslow_6coord_NO_int
 
 Assignment Rule (name: ext) extinction = e5c*(sGCfast+NO_sGCfast+sGCslow+NO_sGCslow)+e5c_NO*(NO_sGCfast_5coord+NO_sGCslow_5coord)+e6c_NO*(NO_sGCfast_6coord+NO_sGCslow_6coord+NO_sGCslow_6coord_NO_int)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 NO
Compartment: cytosol
Initial concentration: 0.5
 
 sGCfast
Compartment: cytosol
Initial concentration: 0.112
 
 NO_sGCfast
Compartment: cytosol
Initial concentration: 0.0
 
 NO_sGCfast_6coord
Compartment: cytosol
Initial concentration: 0.0
 
 NO_sGCfast_5coord
Compartment: cytosol
Initial concentration: 0.0
 
 sGCslow
Compartment: cytosol
Initial concentration: 0.288
 
 NO_sGCslow
Compartment: cytosol
Initial concentration: 0.0
 
 NO_sGCslow_6coord
Compartment: cytosol
Initial concentration: 0.0
 
 NO_sGCslow_6coord_NO_int
Compartment: cytosol
Initial concentration: 0.0
 
 NO_sGCslow_5coord
Compartment: cytosol
Initial concentration: 0.0
 
  NO_sGC_5coord_tot
Compartment: cytosol
Initial concentration: 0.0
 
  sGC_inact_tot
Compartment: cytosol
Initial concentration: 0.0
 
Global Parameters (16)
 
   k1
Value: 700.0   (Units: peruMpersec)
Constant
 
   k2
Value: 800.0   (Units: persec)
Constant
 
   k3
Value: 850.0   (Units: persec)
Constant
 
   k4
Value: 20.0   (Units: persec)
Constant
 
   k5
Value: 0.2   (Units: persec)
Constant
 
   k6
Value: 700.0   (Units: peruMpersec)
Constant
 
   k7
Value: 800.0   (Units: persec)
Constant
 
   k8
Value: 850.0   (Units: persec)
Constant
 
   k9
Value: 5.0   (Units: peruMpersec)
Constant
 
   k10
Value: 25.0   (Units: persec)
Constant
 
   k11
Value: 1.6   (Units: persec)
Constant
 
   k12
Value: 0.02   (Units: persec)
Constant
 
 ext_5coord
Value: 0.11   (Units: peruMpercm)
Constant
 
 ext_5coord_NO
Value: 0.025   (Units: peruMpercm)
Constant
 
 ext_6coord_NO
Value: 0.064   (Units: peruMpercm)
Constant
 
  extinction
Value: NaN   (Units: percm)
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000198

Curator's comment: (updated: 24 Oct 2008 15:10:40 BST)

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