// DOQCS : http://doqcs.ncbs.res.in/ // Accession Name = CO_activation_of_GC // Accession Number = 28 // Transcriber = Sudhir Sivakumaran, NCBS // Developer = Sudhir Sivakumaran, NCBS // Species = Bovine // Tissue = Lungs // Cell Compartment = Cytosol // Notes = Carbon Monoxide is an activator of soluble Guanylyl Cyclase and has been implicated as a neuronal messenger [Ingi T. et al. Neuron (1996) 16(4):835-42].
CO binds to the heme group on sGC, similar to NO binding. Exogenous CO at similar conc. to endogenous levels were used to study the extent of activation of GC. Olfactory receptor neurons were used by Ingi et al., to investigate the relationship of CO to cGMP levels, as these cells have high levels of HO activity but no NOS activity.
Kharitonov VG. et al. Proc Natl Acad Sci U S A. (1995) 92(7):2568-71 and
Kharitonov VG. et al. Biochemistry (1999) 38(33):10699-706 report the presence of a six coordinate and a five coordinate intermediate of carboxy GC, induced by CO. Considering that activation of sGC by CO is similar in almost all tissues, some rates have been taken from original published works cited as references in Kharitonov et al., and Ingi et al., the primary datasources, this model is based on. //genesis // kkit Version 11 flat dumpfile // Saved on Thu Dec 8 12:03:13 2005 include kkit {argv 1} FASTDT = 1e-05 SIMDT = 0.001 CONTROLDT = 1 PLOTDT = 0.1 MAXTIME = 600 TRANSIENT_TIME = 30 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1.6667e-21 VERSION = 11.0 setfield /file/modpath value /home2/bhalla/scripts/modules kparms //genesis initdump -version 3 -ignoreorphans 1 simobjdump doqcsinfo filename accessname accesstype transcriber developer \ citation species tissue cellcompartment methodology sources \ model_implementation model_validation x y z simobjdump table input output alloced step_mode stepsize x y z simobjdump xtree path script namemode sizescale simobjdump xcoredraw xmin xmax ymin ymax simobjdump xtext editable simobjdump xgraph xmin xmax ymin ymax overlay simobjdump xplot pixflags script fg ysquish do_slope wy simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \ link savename file version md5sum mod_save_flag x y z simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \ z simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \ geomname xtree_fg_req xtree_textfg_req x y z simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \ keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \ trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z simobjdump xtab input output alloced step_mode stepsize notes editfunc \ xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \ xtree_textfg_req x y z simobjdump transport input output alloced step_mode stepsize dt delay clock \ kf xtree_fg_req xtree_textfg_req x y z simobjdump proto x y z simundump geometry /kinetics/geometry 0 1.6667e-21 3 sphere "" white black \ 109 20 0 simundump group /kinetics/sGC 0 yellow black x 0 1 "" sGC \ /home2/bhalla/scripts/modules/sGC_0.g 0 0 0 106 19 0 simundump kpool /kinetics/sGC/cGMP 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ blue yellow 97 19 0 simundump kpool /kinetics/sGC/GTP 0 0 1000 1000 1000 1000 0 0 1 4 \ /kinetics/geometry 58 yellow 103 19 0 simundump kpool /kinetics/sGC/sGC 0 0 3 3 3 3 0 0 1 0 /kinetics/geometry 27 \ yellow 108 16 0 simundump kreac /kinetics/sGC/CObindsGCa 0 0.12 28 "" white yellow 106 13 0 simundump kpool /kinetics/sGC/Heme 0 0 11.3 11.3 11.3 11.3 0 0 1 0 \ /kinetics/geometry 53 yellow 107 4 0 simundump kpool /kinetics/sGC/CO 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 62 \ yellow 107 10 0 simundump kpool /kinetics/sGC/Hemeoxyg2 0 0 2 2 2 2 0 0 1 0 \ /kinetics/geometry 20 yellow 102 7 0 simundump kenz /kinetics/sGC/Hemeoxyg2/HOXY 0 0 0 0 0 1 0.46789 1.4224 0.3556 \ 0 0 "" red 20 "" 104 7 0 simundump kpool /kinetics/sGC/GC6-CO 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 0 \ yellow 104 16 0 simundump kreac /kinetics/sGC/K 0 0.95 0 "" white yellow 102 13 0 simundump kreac /kinetics/sGC/k 0 1000 0 "" white yellow 98 13 0 simundump kpool /kinetics/sGC/GC5_CO 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 8 \ yellow 100 16 0 simundump kenz /kinetics/sGC/GC5_CO/activeGC 0 0 0 0 0 1 545.4 218.16 54.54 0 \ 1 "" red 8 "" 100 17 0 simundump kpool /kinetics/sGC/dissoCO 0 0 0.1142 0.1142 0.1142 0.1142 0 0 1 4 \ /kinetics/geometry 22 yellow 100 10 0 simundump kpool /kinetics/sGC/PDE 0 0 5 5 5 5 0 0 1 0 /kinetics/geometry 51 \ yellow 95 13 0 simundump kenz /kinetics/sGC/PDE/kenz 0 0 0 0 0 1 9.675 15.48 3.87 0 0 "" red \ 51 "" 95 14 0 simundump kpool /kinetics/sGC/5prime_GMP 0 0 0 0 0 0 0 0 1 0 \ /kinetics/geometry 34 yellow 93 19 0 simundump kpool /kinetics/sGC/Ery_HbO2 0 0 5 5 5 5 0 0 1 0 /kinetics/geometry \ 62 yellow 96 10 0 simundump kpool /kinetics/sGC/COHb 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 0 \ yellow 96 4 0 simundump kreac /kinetics/sGC/CObindsHbO2 0 0.17 0.0078 "" white yellow 98 7 \ 0 simundump doqcsinfo /kinetics/doqcsinfo 0 db28.g New_pathway pathway \ " Sudhir Sivakumaran, NCBS" " Sudhir Sivakumaran, NCBS" "citation here" \ bovine Lung Cytosol "Quantitative match to experiments, Qualitative" \ In-house "Exact GENESIS implementation" \ "Replicates original data , Approximates original data " 109 21 0 simundump xgraph /graphs/conc1 0 0 600 0 0.00034388 0 simundump xgraph /graphs/conc2 0 0 600 0 9.0568 0 simundump xplot /graphs/conc1/cGMP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /graphs/conc2/CO.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 62 0 0 1 simundump xgraph /moregraphs/conc3 0 0 600 0 6.1089e-05 0 simundump xgraph /moregraphs/conc4 0 0 600 0 0.064304 0 simundump xplot /moregraphs/conc3/GC5_CO.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 8 0 0 1 simundump xplot /moregraphs/conc4/GC6-CO.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 0 0 0 1 simundump xcoredraw /edit/draw 0 91 111 2 23 simundump xtree /edit/draw/tree 0 \ /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ "edit_elm.D ; drag_from_edit.w " auto 0.6 simundump xtext /file/notes 0 1 xtextload /file/notes \ "Carbon Monoxide is an activator of soluble Gunalyl Cyclase and has been implicated as " \ "a neuronal messenger.(Ingi et al., 1996, Neuron, 16:835-842). CO binds to the heme group" \ "on sGC, similar to NO binding. Exogenous CO at similar conc. to endogenous levels blocked" \ "the NO-mediated cGMP release.(Ingi et al., 1996)" \ "Olfactory receptor neurons have been used by Ingi et al., to investigate the relationship" \ "of CO to cGMP levels, as these cells have high levels of HO activity but no NOS activity." \ "Kharitonov et al., PNAS, 1995, 92:2568-2571, report the presence of a six and five co-ordinate" \ "intermediate of carboxy GC, induced by CO. They ofcourse used purified GC from bovine lung. But " \ "considering CO activity is almost similar in different tissues, one or two rates have been used" \ "from their reported data." addmsg /kinetics/sGC/GC5_CO/activeGC /kinetics/sGC/cGMP MM_PRD pA addmsg /kinetics/sGC/PDE/kenz /kinetics/sGC/cGMP REAC sA B addmsg /kinetics/sGC/GC5_CO/activeGC /kinetics/sGC/GTP REAC sA B addmsg /kinetics/sGC/CObindsGCa /kinetics/sGC/sGC REAC A B addmsg /kinetics/sGC/sGC /kinetics/sGC/CObindsGCa SUBSTRATE n addmsg /kinetics/sGC/CO /kinetics/sGC/CObindsGCa SUBSTRATE n addmsg /kinetics/sGC/GC6-CO /kinetics/sGC/CObindsGCa PRODUCT n addmsg /kinetics/sGC/Hemeoxyg2/HOXY /kinetics/sGC/Heme REAC sA B addmsg /kinetics/sGC/Hemeoxyg2/HOXY /kinetics/sGC/CO MM_PRD pA addmsg /kinetics/sGC/CObindsGCa /kinetics/sGC/CO REAC A B addmsg /kinetics/sGC/Hemeoxyg2/HOXY /kinetics/sGC/Hemeoxyg2 REAC eA B addmsg /kinetics/sGC/Hemeoxyg2 /kinetics/sGC/Hemeoxyg2/HOXY ENZYME n addmsg /kinetics/sGC/Heme /kinetics/sGC/Hemeoxyg2/HOXY SUBSTRATE n addmsg /kinetics/sGC/CObindsGCa /kinetics/sGC/GC6-CO REAC B A addmsg /kinetics/sGC/K /kinetics/sGC/GC6-CO REAC A B addmsg /kinetics/sGC/GC6-CO /kinetics/sGC/K SUBSTRATE n addmsg /kinetics/sGC/GC5_CO /kinetics/sGC/K PRODUCT n addmsg /kinetics/sGC/GC5_CO /kinetics/sGC/k SUBSTRATE n addmsg /kinetics/sGC/dissoCO /kinetics/sGC/k PRODUCT n addmsg /kinetics/sGC/K /kinetics/sGC/GC5_CO REAC B A addmsg /kinetics/sGC/k /kinetics/sGC/GC5_CO REAC A B addmsg /kinetics/sGC/GC5_CO /kinetics/sGC/GC5_CO/activeGC ENZYME n addmsg /kinetics/sGC/GTP /kinetics/sGC/GC5_CO/activeGC SUBSTRATE n addmsg /kinetics/sGC/k /kinetics/sGC/dissoCO REAC B A addmsg /kinetics/sGC/CObindsHbO2 /kinetics/sGC/dissoCO REAC A B addmsg /kinetics/sGC/PDE/kenz /kinetics/sGC/PDE REAC eA B addmsg /kinetics/sGC/PDE /kinetics/sGC/PDE/kenz ENZYME n addmsg /kinetics/sGC/cGMP /kinetics/sGC/PDE/kenz SUBSTRATE n addmsg /kinetics/sGC/PDE/kenz /kinetics/sGC/5prime_GMP MM_PRD pA addmsg /kinetics/sGC/CObindsHbO2 /kinetics/sGC/Ery_HbO2 REAC A B addmsg /kinetics/sGC/CObindsHbO2 /kinetics/sGC/COHb REAC B A addmsg /kinetics/sGC/dissoCO /kinetics/sGC/CObindsHbO2 SUBSTRATE n addmsg /kinetics/sGC/Ery_HbO2 /kinetics/sGC/CObindsHbO2 SUBSTRATE n addmsg /kinetics/sGC/COHb /kinetics/sGC/CObindsHbO2 PRODUCT n addmsg /kinetics/sGC/cGMP /graphs/conc1/cGMP.Co PLOT Co *cGMP.Co *blue addmsg /kinetics/sGC/CO /graphs/conc2/CO.Co PLOT Co *CO.Co *62 addmsg /kinetics/sGC/GC5_CO /moregraphs/conc3/GC5_CO.Co PLOT Co *GC5_CO.Co *8 addmsg /kinetics/sGC/GC6-CO /moregraphs/conc4/GC6-CO.Co PLOT Co *GC6-CO.Co *0 enddump // End of dump call /kinetics/sGC/notes LOAD \ "This model features the basis of CO activating sGC. Kharitonov et al.," \ "1995, PNAS, 92:2568-2571, report the presence of a six coordinate" \ "and an active five coord carboxy species, in the activation " \ "mechanism, though the five coord sp. is present in small amounts." \ "" call /kinetics/sGC/GTP/notes LOAD \ "Under in vivo conditions, GTP is present in excess, ~ 1mM." call /kinetics/sGC/sGC/notes LOAD \ "sGC is enriched in purkine cells ~3 uM (Conc from Shinya Kuroda, assumed on " \ "the basis of reported data in Ariano et al., 1982, PNAS,79: 297-300)" \ "soluble Guanylyl Cyclase localization is virtually identical to that of" \ "HO-2 in numerous brain regions.(Ingi et al., 1995, J Neurosci., 15:8214-8222)," \ "in contrast to discrepancies in the localization of NOS and sGC in the brain." call /kinetics/sGC/CObindsGCa/notes LOAD \ "This gives rise to the six co-ordinate carboxy GC." \ "Kharitonov et al., 1995, PNAS, 92:2568-2571 report CO association and" \ "dissociation rates at 1.2e5 /M/sec and 28 /sec respectively." \ "Kharitonov et al., 1999, Biochemistry, 38(33):10699-10706 report" \ "Ka at 7.86 +- 0.50 /mM." call /kinetics/sGC/Heme/notes LOAD \ "Total cellular heme determined spectrophotometrically to be 1.5 nmol/mg protein." \ "(Ingi et al., 1996, Neuron,16:835-842), a value resembling reported heme content" \ "in neuronal tissues. " \ "Ingi et al., also reports in J Neurosci. 1996,16(18):5621-5628, that Brain" \ "has significant levels of heme (1.3 nmol/mg protein)" \ "Conc calculated/used 21.3" call /kinetics/sGC/CO/notes LOAD \ "CO is an endogenous modulator of sGC. It is produced by the" \ "oxidative cleavage by HO to yield CO and Biliverdin. It also" \ "binds to the heme group on sGC as NO and it may be competetive" \ "to NO with regard to the binding to the heme prosthetic group." \ "Like NO, it binds to the Iron in the heme, and activate Guanylyl Cyclase." \ "(Brune et al., 1987, Mol. Pharmacol.32, 497-504), Kharitonov" \ "et al., 1995, PNAS, 92:2568-2571)" \ "Because of the gaseous nature of CO, and its high affinity for hemoprotein," \ "its very difficult to determine the exact intracellular concentration of CO." \ "Endogenous CO level was calculated to be 50-160 pmol/mg protein or" \ "10-30 uM, by Ingi et al., J Neursoci 1996, 16(18): 5621-5628, on the assumption" \ "that the amount of CO produced for 10-30 mins is an effective concentration in the" \ "cell, taking into account the diffusion of CO. " \ "Using exogenous CO at the endogenous levels of 10-30 uM, significant " \ "elevation of GC activity is observed, though CO does not seem to be a " \ "rapid stimulator, but works as a modulator, producing slower and " \ "long-term effects (Ingi et al., 1996, J Neurosci.,16(18):5621-5628)." \ "" call /kinetics/sGC/Hemeoxyg2/notes LOAD \ "Heme oxygenase 2 (HO-2)-Highly expressed in Brain (Sun et al.," \ "1990, J Biol. Chem., 265: 8212-8217), with discrete neuronal localization" \ "demonstrated throughout the brain with in situ hybridisation and " \ "immunohistochemical studies (Verma et al., 1993, Science, 259:" \ "381-384). Mol. Wt. of HO-2 is 36 kDa.(Migita et al., JBC,1998,273(2):945-949.)" \ "Three mammalian isoforms have been identified. HO-1, is inducible " \ "and highly concentrated in tissues and involved in catabolism of heme proteins." \ "HO-3, is an isoform with low catalytic activity, with uncertain physiological role." \ "(Montellano, PRO., 2000, Curr Opin in Chem Biol, 4:221-227)" call /kinetics/sGC/Hemeoxyg2/HOXY/notes LOAD \ "Ingi et al., J Neurosci., 1996, 16(18):5621-5628, report the production" \ "rates of heme precursors and metabolites. The rate reported for CO from heme" \ "is 2.9 pmol/mg protein over 6 hr. Their results indicate high HO activity in brain" \ "(along with significant levels of heme) at around 280pmol of bilirubin/mg/min." \ "Montellano PRO, Curr. Opin. in Chem. Biol, 2000,4:221-227 and refs cited in his paper" \ "were also studied initially." \ "Km for free heme is around 3.8 +/- 0.5 uM.(Bonkovsky et al.," \ "1990, 189(1):155-166)" call /kinetics/sGC/GC6-CO/notes LOAD \ "The six-coordinate form of sGC bound to CO. This mechanism has been " \ "proved with results by Kharitonov et al., PNAS, 1995, 92:2568-2571." \ "Most of the Carboxy derivative of GC is six-coordinate." call /kinetics/sGC/K/notes LOAD \ "The transition from six co-ordinate to the five co-ordinate" \ "carboxy GC." \ "CO dissociation rate for 6 coord sp for heme is 0.95 /sec." \ "(Kharitonov et al., 1995, PNAS, 92:2568-2571)" call /kinetics/sGC/k/notes LOAD \ "The dissociation of CO from the active five co-ordinate GC. " \ "rate from Kharitonov et al., PNAS, 1995, 92:2568-2571." \ "Further justification include the fact that Soret absorption" \ "spectrum of GC-NO suggesting almost complete sonversion to five" \ "co-ordinate species. So, assuming that the five co-ord species" \ "is more active than the basal form, irrespective of the Ligand," \ "the percentage of five co-ordinate intermediate induced by CO " \ "was calculated to be 3% to 1.5%.(Kharitonov et al., 1995, PNAS)" \ "using mean value, ~ 2 +- 1 %, and kobs = 28/sec, k = 1*10^3/sec." \ "(Kharitonov et al., PNAS, 1995, 92:2568-2571)" call /kinetics/sGC/GC5_CO/notes LOAD \ "The active five coordinate Carboxy GC. Kharitonov et al., PNAS, 1995, 92:2568-2571 " \ "report the presence of a five coord carboxy species during the activation of GC by CO," \ "similar to the presence of a five coord species in the nitroxyl GC, during NO activation" \ "of sGC." call /kinetics/sGC/GC5_CO/activeGC/notes LOAD \ "Friebe et al., 1996, EMBO Journal, 15(24): 6863-6868 and back" \ "refs cited in their paper. " \ "They have studied the potentiation by YC-1 of CO activated sGC." \ "In the absence of YC-1, they report 3 fold stimulation of GC by" \ "CO, with 218 +- 11 nmol/min/mg of cGMP." \ "Vmax / Km increased by 100 X." call /kinetics/sGC/dissoCO/notes LOAD \ "The erythrocyte-associated hemoglobin has a critical role" \ "of being the primary CO-scavenging system. Locally generated" \ "CO is eliminated by hemoglobin in circulating erythrocytes and" \ "is gradually released into the alveolar space of the lung, where" \ "molecular oxygen is alternately bound to the heme. Most of the CO" \ "(Carbon Monoxide) generated in the body is exhaled into the " \ "airway." \ "(Suematsu M, Gasteroenterology 2001;120:1227-1240 and" \ "personal correspondence)" call /kinetics/sGC/PDE/notes LOAD \ "Phosphodiesterase : Degrades cGMP to 5prime_GMP" \ "Conc from Kotera et al., Eur J Biochem., 1997; 249:434-442" \ "and Kuroda et al., J Neurosci, 2001, 21(15):5693-5702" call /kinetics/sGC/PDE/kenz/notes LOAD \ "Km / Vmax -- 2 uM / 3.87 sec^-1." \ "rates from Turko et al., 1998, Biochem J, 329:505-510" \ "and Kuroda et al., J Neurosci, 2001, 21(15):5693-5702" call /kinetics/sGC/Ery_HbO2/notes LOAD \ "Erythrocyte associated hemoglobin -- This supposedly is the " \ "primary CO-scavenging system. " \ "(Suematsu M, personal correspondence)" call /kinetics/sGC/COHb/notes LOAD \ "Carboxy Hemoglobin, from which CO subsequently is released " \ "into the alveolar space of the lung, where molecular oxygen " \ "is alternately bound to the heme. Most of the CO generated " \ "in the body is thus exhaled into the airway." \ "(Suematsu M, personal correspondence)" call /kinetics/sGC/CObindsHbO2/notes LOAD \ "CO binds to hemoglobin, predominantly the erythrocyte associated" \ "hemoglobin. The affinity of hemoglobin for CO is 200-250 times" \ "that of oxygen, while relative affinities of heme proteins" \ "(myoglobin), cytochrome oxidase and cytochrome P-450 for CO" \ "are much lower. " \ "CO binds reversibly to hemoglobin to form Carboxy hemoglobin," \ "(COHb) from which CO is exhaled through the lungs. Primary " \ "source for rates, Migita et al., JBC, 1998, 273(2): 945-949," \ "and refs cited in their paper." call /kinetics/doqcsinfo/notes LOAD \ "Carbon Monoxide is an activator of soluble Guanylyl Cyclase and has been implicated as a neuronal messenger [Ingi T. et al. Neuron (1996) 16(4):835-42].
CO binds to the heme group on sGC, similar to NO binding. Exogenous CO at similar conc. to endogenous levels were used to study the extent of activation of GC. Olfactory receptor neurons were used by Ingi et al., to investigate the relationship of CO to cGMP levels, as these cells have high levels of HO activity but no NOS activity.
Kharitonov VG. et al. Proc Natl Acad Sci U S A. (1995) 92(7):2568-71 and
Kharitonov VG. et al. Biochemistry (1999) 38(33):10699-706 report the presence of a six coordinate and a five coordinate intermediate of carboxy GC, induced by CO. Considering that activation of sGC by CO is similar in almost all tissues, some rates have been taken from original published works cited as references in Kharitonov et al., and Ingi et al., the primary datasources, this model is based on." complete_loading