// DOQCS : http://doqcs.ncbs.res.in/ // Accession Name = luciferase // Accession Number = 36 // Transcriber = Upinder S. Bhalla, NCBS // Developer = L. Yu. Brovko, O.A. Gandelman, T.E. Polenova, N.N. Ugarova // Species = E. Coli // Tissue = - // Cell Compartment = Cytosol // Notes = This model is based on L. Yu. Brovko et al 1994, Biochemistry (Moscow) 59(2):195-201, 1994. The model replicates reaction scheme 3, and uses rates from table 2, but there are discrepancies in simulated results both with their simulations (fig 4) and with their experimental data. The overall time-course and luciferase dependence of luminiscence (Figs 1, 2, 3a) are reasonable semi-quantitative matches. //genesis // kkit Version 11 flat dumpfile // Saved on Thu Dec 8 15:43:14 2005 include kkit {argv 1} FASTDT = 1e-05 SIMDT = 0.0001 CONTROLDT = 1 PLOTDT = 0.1 MAXTIME = 100 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1e-06 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 9.9998e-07 3 sphere "" white black 11 \ 4 0 simundump kpool /kinetics/E 0 0 1e-05 1e-05 5.9999e+09 5.9999e+09 0 0 \ 5.9999e+14 0 /kinetics/geometry blue black -6 -1 0 simundump kpool /kinetics/E.S1.S2 0 0 0 0 0 0 0 0 5.9999e+14 0 \ /kinetics/geometry 26 black 2 -1 0 simundump kpool /kinetics/E.S1_in 0 0 0 0 0 0 0 0 5.9999e+14 0 \ /kinetics/geometry blue black -2 4 0 simundump kpool /kinetics/E.S1 0 0 0 0 0 0 0 0 5.9999e+14 0 \ /kinetics/geometry blue black -2 1 0 simundump kpool /kinetics/E.S2 0 0 0 0 0 0 0 0 5.9999e+14 0 \ /kinetics/geometry 47 black -2 -3 0 simundump kpool /kinetics/E_in 0 0 0 0 0 0 0 0 5.9999e+14 0 \ /kinetics/geometry blue black -6 -7 0 simundump kreac /kinetics/k5 0 2.6e-05 0 "" white black -4 2 0 simundump kreac /kinetics/k1 0 3.3334e-17 6 "" white black -4 0 0 simundump kreac /kinetics/k1_prime 0 1.6667e-15 10 "" white black 1 2 0 simundump kreac /kinetics/k1_prime_2 0 1.6667e-15 10 "" white black -4 -2 0 simundump kreac /kinetics/k5_2 0 2.6e-05 0 "" white black -6 -5 0 simundump kreac /kinetics/k5_3 0 2.6e-05 0 "" white black -2 -5 0 simundump kreac /kinetics/k5_4 0 2.6e-05 0 "" white black 2 -5 0 simundump kreac /kinetics/k2 0 30 0 "" white black 4 -1 0 simundump kpool /kinetics/E.P1 0 0 0 0 0 0 0 0 5.9999e+14 0 \ /kinetics/geometry 1 black 6 -1 0 simundump kpool /kinetics/AMP 0 0 0 0 0 0 0 0 5.9999e+14 0 /kinetics/geometry \ blue black 4 -3 0 simundump kpool /kinetics/E.P 0 0 0 0 0 0 0 0 5.9999e+14 0 /kinetics/geometry \ 58 black 10 -1 0 simundump kreac /kinetics/k3 0 10 0 "" white black 8 -1 0 simundump kpool /kinetics/photon 0 0 0 0 0 0 0 0 5.9999e+14 0 \ /kinetics/geometry blue black 8 -3 0 simundump kreac /kinetics/k6 0 0.0003 0 "" white black 10 -5 0 simundump kpool /kinetics/E.P_in 0 0 0 0 0 0 0 0 5.9999e+14 0 \ /kinetics/geometry blue black 10 -7 0 simundump kpool /kinetics/E.S2_in 0 0 0 0 0 0 0 0 5.9999e+14 0 \ /kinetics/geometry blue black -2 -7 0 simundump kpool /kinetics/E.S1.S2_in 0 0 0 0 0 0 0 0 5.9999e+14 0 \ /kinetics/geometry blue black 2 -7 0 simundump kreac /kinetics/k4 0 0.1 1.6667e-15 "" white black 8 1 0 simundump kpool /kinetics/P 0 0 0 0 0 0 0 0 5.9999e+14 0 /kinetics/geometry \ blue black 12 -1 0 simundump kpool /kinetics/S1 0 0 1000 1000 5.9999e+17 5.9999e+17 0 0 \ 5.9999e+14 0 /kinetics/geometry blue black -6 0 0 simundump kpool /kinetics/S2 0 0 100 100 5.9999e+16 5.9999e+16 0 0 5.9999e+14 \ 0 /kinetics/geometry blue black -1 -1 0 simundump kreac /kinetics/k1_2 0 3.3334e-17 6 "" white black 0 -2 0 simundump doqcsinfo /kinetics/doqcsinfo 0 db36.g luciferase pathway \ "Upinder S. Bhalla, NCBS" \ " L. Yu. Brovko, O.A. Gandelman, T.E. Polenova, N.N. Ugarova" \ "citation here" "E. Coli" - Cytosol Qualitative \ "L. Yu. Brovko et al 1994, Biochemistry (Moscow) 59(2):195-201, 1994 ( peer-reviewed publication )" \ "Approximate implementation" "Approximates original data " 11 5 0 simundump xgraph /graphs/conc1 0 0 100 0 1.0776e+08 0 simundump xgraph /graphs/conc2 0 0 100 0 4.8924e-07 0 simundump xplot /graphs/conc2/E.S1.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /graphs/conc2/E.P1.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 1 0 0 1 simundump xplot /graphs/conc2/E.P.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 58 0 0 1 simundump xgraph /moregraphs/conc3 0 -1 100 0 9.7826e-06 0 simundump xgraph /moregraphs/conc4 0 0 100 0 5e-08 0 simundump xplot /moregraphs/conc3/E.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /moregraphs/conc3/E.S1.S2.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 26 0 0 1 simundump xplot /moregraphs/conc4/E.S2.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 47 0 0 1 simundump xcoredraw /edit/draw 0 -8 14 -9 7 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 \ "This model is based on L. Yu Brovko et al 1994," \ "Biochemistry (Moscow) 59(2):1994." \ "The model is according to their reaction scheme and rates, but" \ "there are discrepancies both with the simulated (fig 4) and" \ "with the experimental data in their paper. The overall time-course" \ "and luciferase dependence of luminescence (figs 1, 2, 3a) are" \ "reasonable semi-quantitative matches." addmsg /kinetics/k1 /kinetics/E REAC A B addmsg /kinetics/k1_prime_2 /kinetics/E REAC A B addmsg /kinetics/k5_2 /kinetics/E REAC A B addmsg /kinetics/k4 /kinetics/E REAC B A addmsg /kinetics/k1_prime /kinetics/E.S1.S2 REAC B A addmsg /kinetics/k5_4 /kinetics/E.S1.S2 REAC A B addmsg /kinetics/k2 /kinetics/E.S1.S2 REAC A B addmsg /kinetics/k1_2 /kinetics/E.S1.S2 REAC B A addmsg /kinetics/k5 /kinetics/E.S1_in REAC B A addmsg /kinetics/k5 /kinetics/E.S1 REAC A B addmsg /kinetics/k1 /kinetics/E.S1 REAC B A addmsg /kinetics/k1_prime /kinetics/E.S1 REAC A B addmsg /kinetics/k1_prime_2 /kinetics/E.S2 REAC B A addmsg /kinetics/k5_3 /kinetics/E.S2 REAC A B addmsg /kinetics/k1_2 /kinetics/E.S2 REAC A B addmsg /kinetics/k5_2 /kinetics/E_in REAC B A addmsg /kinetics/E.S1 /kinetics/k5 SUBSTRATE n addmsg /kinetics/E.S1_in /kinetics/k5 PRODUCT n addmsg /kinetics/E /kinetics/k1 SUBSTRATE n addmsg /kinetics/E.S1 /kinetics/k1 PRODUCT n addmsg /kinetics/S1 /kinetics/k1 SUBSTRATE n addmsg /kinetics/E.S1 /kinetics/k1_prime SUBSTRATE n addmsg /kinetics/E.S1.S2 /kinetics/k1_prime PRODUCT n addmsg /kinetics/S2 /kinetics/k1_prime SUBSTRATE n addmsg /kinetics/E /kinetics/k1_prime_2 SUBSTRATE n addmsg /kinetics/E.S2 /kinetics/k1_prime_2 PRODUCT n addmsg /kinetics/S2 /kinetics/k1_prime_2 SUBSTRATE n addmsg /kinetics/E /kinetics/k5_2 SUBSTRATE n addmsg /kinetics/E_in /kinetics/k5_2 PRODUCT n addmsg /kinetics/E.S2 /kinetics/k5_3 SUBSTRATE n addmsg /kinetics/E.S2_in /kinetics/k5_3 PRODUCT n addmsg /kinetics/E.S1.S2 /kinetics/k5_4 SUBSTRATE n addmsg /kinetics/E.S1.S2_in /kinetics/k5_4 PRODUCT n addmsg /kinetics/E.S1.S2 /kinetics/k2 SUBSTRATE n addmsg /kinetics/E.P1 /kinetics/k2 PRODUCT n addmsg /kinetics/AMP /kinetics/k2 PRODUCT n addmsg /kinetics/k2 /kinetics/E.P1 REAC B A addmsg /kinetics/k3 /kinetics/E.P1 REAC A B addmsg /kinetics/k2 /kinetics/AMP REAC B A addmsg /kinetics/k3 /kinetics/E.P REAC B A addmsg /kinetics/k6 /kinetics/E.P REAC A B addmsg /kinetics/k4 /kinetics/E.P REAC A B addmsg /kinetics/E.P1 /kinetics/k3 SUBSTRATE n addmsg /kinetics/E.P /kinetics/k3 PRODUCT n addmsg /kinetics/photon /kinetics/k3 PRODUCT n addmsg /kinetics/k3 /kinetics/photon REAC B A addmsg /kinetics/E.P /kinetics/k6 SUBSTRATE n addmsg /kinetics/E.P_in /kinetics/k6 PRODUCT n addmsg /kinetics/k6 /kinetics/E.P_in REAC B A addmsg /kinetics/k5_3 /kinetics/E.S2_in REAC B A addmsg /kinetics/k5_4 /kinetics/E.S1.S2_in REAC B A addmsg /kinetics/E.P /kinetics/k4 SUBSTRATE n addmsg /kinetics/P /kinetics/k4 PRODUCT n addmsg /kinetics/E /kinetics/k4 PRODUCT n addmsg /kinetics/k4 /kinetics/P REAC B A addmsg /kinetics/k1 /kinetics/S1 REAC A B addmsg /kinetics/k1_2 /kinetics/S1 REAC A B addmsg /kinetics/k1_prime /kinetics/S2 REAC A B addmsg /kinetics/k1_prime_2 /kinetics/S2 REAC A B addmsg /kinetics/E.S2 /kinetics/k1_2 SUBSTRATE n addmsg /kinetics/E.S1.S2 /kinetics/k1_2 PRODUCT n addmsg /kinetics/S1 /kinetics/k1_2 SUBSTRATE n addmsg /kinetics/E.S1 /graphs/conc2/E.S1.Co PLOT Co *E.S1.Co *blue addmsg /kinetics/E.P1 /graphs/conc2/E.P1.Co PLOT Co *E.P1.Co *1 addmsg /kinetics/E.P /graphs/conc2/E.P.Co PLOT Co *E.P.Co *58 addmsg /kinetics/E /moregraphs/conc3/E.Co PLOT Co *E.Co *blue addmsg /kinetics/E.S1.S2 /moregraphs/conc3/E.S1.S2.Co PLOT Co *E.S1.S2.Co *26 addmsg /kinetics/E.S2 /moregraphs/conc4/E.S2.Co PLOT Co *E.S2.Co *47 enddump // End of dump call /kinetics/E.S1/notes LOAD \ "S1 is ATP. E.S1 is luciferase.ATP" call /kinetics/E.S2/notes LOAD \ "S2 is Luciferin." call /kinetics/photon/notes LOAD \ "The photon pool is equivalent to the cumulative photon count." \ "The time derivative of this pool count (in number of photons, not" \ "in terms of concentration) will give the rate of production" \ "of photons." call /kinetics/S1/notes LOAD \ "S1 is ATP" \ "" call /kinetics/S2/notes LOAD \ "S2 = LH2" call /kinetics/doqcsinfo/notes LOAD \ "This model is based on L. Yu. Brovko et al 1994, Biochemistry (Moscow) 59(2):195-201, 1994. The model replicates reaction scheme 3, and uses rates from table 2, but there are discrepancies in simulated results both with their simulations (fig 4) and with their experimental data. The overall time-course and luciferase dependence of luminiscence (Figs 1, 2, 3a) are reasonable semi-quantitative matches." complete_loading