// DOQCS : http://doqcs.ncbs.res.in/ // Accession Name = SERCA // Accession Number = 37 // Transcriber = Pradeep Kumar S, NCBS // Developer = J. Mahaney, J. Autry and L. Jones // Species = Canine // Tissue = Cardiac; expressed in Baculovirus infected Sf21(Spodoptera frugiperda) insect cells. // Cell Compartment = Microsomes // Notes = All the constants are from:
Mahaney JE. et al. Biophys J. (2000) 78(3) 1306-23.
New Insights on cardiac Ca-ATPase (expressed in Sf21 cells) regulation by Phosphlamban. //genesis // kkit Version 11 flat dumpfile // Saved on Thu Dec 8 15:49:14 2005 include kkit {argv 1} FASTDT = 0.0001 SIMDT = 0.001 CONTROLDT = 5 PLOTDT = 0.1 MAXTIME = 60 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 0 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 8 \ 10 0 simundump kpool /kinetics/E1 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 37 black \ -6 2 0 simundump kpool /kinetics/E2 0 0 0.1509 0.1509 0.1509 0.1509 0 0 1 0 \ /kinetics/geometry white black -4 -3 0 simundump kpool /kinetics/Ca 0 0 0.268 0.268 0.268 0.268 0 0 1 4 \ /kinetics/geometry 54 black -2 9 0 simundump kpool /kinetics/MgATP 0 0 1 1 1 1 0 0 1 0 /kinetics/geometry white \ black 5 9 0 simundump kpool /kinetics/ADP 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 38 black \ 3 -3 0 simundump kreac /kinetics/reac6 0 35 0 "" white black 4 -1 0 simundump kpool /kinetics/pi 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 48 black \ 0 -3 0 simundump kreac /kinetics/reac7 0 0.3 0.7 "" white black 1 -1 0 simundump kreac /kinetics/reac8 0 0.4 0 "" white black -2 -1 0 simundump kpool /kinetics/CaE1 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 39 \ black -2 4 0 simundump kreac /kinetics/reac2 0 50 120 "" white black -6 5 0 simundump kreac /kinetics/reac1 0 0.35 0.35 "" white black -6 -1 0 simundump kreac /kinetics/reac3 0 0.4 0.4 "" white black -1 6 0 simundump kreac /kinetics/reac4 0 80 3.2 "" white black 3 6 0 simundump kreac /kinetics/reac5 0 4 0 "" white black 6 6 0 simundump kpool /kinetics/EP 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry blue \ black 3 2 0 simundump kpool /kinetics/EPi 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 38 black \ -1 2 0 simundump kpool /kinetics/CaE1_prime 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ 41 black 1 4 0 simundump kpool /kinetics/Ca2E1_prime 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ 40 black 4 4 0 simundump kpool /kinetics/CaE1_prime_ATP 0 0 0 0 0 0 0 0 1 0 \ /kinetics/geometry 39 black 6 2 0 simundump doqcsinfo /kinetics/doqcsinfo 0 db37.g SERCA pathway \ "Pradeep Kumar S, NCBS" " J. Mahaney, J. Autry and L. Jones" \ "citation here" " Canine" \ " Cardiac; expressed in Baculovirus infected Sf21(Spodoptera frugiperda) insect cells." \ Microsomes "Quantitative match to experiments, Qualitative" In-house \ "Exact GENESIS implementation" "Approximates original data " 8 11 0 simundump xgraph /graphs/conc1 0 45.967 49.785 0.12629 0.56983 0 simundump xgraph /graphs/conc2 0 0 60 0 0.1 0 simundump xplot /graphs/conc1/pi.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 48 0 0 1 simundump xplot /graphs/conc2/EP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xgraph /moregraphs/conc3 0 0 60 0 1 0 simundump xgraph /moregraphs/conc4 0 0 60 0 1 0 simundump xcoredraw /edit/draw 0 -8 13 -5 12 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 \ "studies of the cardiac Ca-ATPase Expressed in Sf21 Cells: New Insights" \ "modeled according to scheme-3 and the constants are picked up from the" \ "table-6 of the above source." addmsg /kinetics/reac2 /kinetics/E1 REAC A B addmsg /kinetics/reac1 /kinetics/E1 REAC B A addmsg /kinetics/reac1 /kinetics/E2 REAC A B addmsg /kinetics/reac8 /kinetics/E2 REAC B A addmsg /kinetics/reac2 /kinetics/Ca REAC A B addmsg /kinetics/reac4 /kinetics/Ca REAC A B addmsg /kinetics/reac5 /kinetics/MgATP REAC A B addmsg /kinetics/reac6 /kinetics/ADP REAC B A addmsg /kinetics/CaE1_prime_ATP /kinetics/reac6 SUBSTRATE n addmsg /kinetics/EP /kinetics/reac6 PRODUCT n addmsg /kinetics/ADP /kinetics/reac6 PRODUCT n addmsg /kinetics/reac8 /kinetics/pi REAC B A addmsg /kinetics/EP /kinetics/reac7 SUBSTRATE n addmsg /kinetics/EPi /kinetics/reac7 PRODUCT n addmsg /kinetics/pi /kinetics/reac8 PRODUCT n addmsg /kinetics/EPi /kinetics/reac8 SUBSTRATE n addmsg /kinetics/E2 /kinetics/reac8 PRODUCT n addmsg /kinetics/reac2 /kinetics/CaE1 REAC B A addmsg /kinetics/reac3 /kinetics/CaE1 REAC A B addmsg /kinetics/E1 /kinetics/reac2 SUBSTRATE n addmsg /kinetics/CaE1 /kinetics/reac2 PRODUCT n addmsg /kinetics/Ca /kinetics/reac2 SUBSTRATE n addmsg /kinetics/E2 /kinetics/reac1 SUBSTRATE n addmsg /kinetics/E1 /kinetics/reac1 PRODUCT n addmsg /kinetics/CaE1 /kinetics/reac3 SUBSTRATE n addmsg /kinetics/CaE1_prime /kinetics/reac3 PRODUCT n addmsg /kinetics/CaE1_prime /kinetics/reac4 SUBSTRATE n addmsg /kinetics/Ca2E1_prime /kinetics/reac4 PRODUCT n addmsg /kinetics/Ca /kinetics/reac4 SUBSTRATE n addmsg /kinetics/CaE1_prime_ATP /kinetics/reac5 PRODUCT n addmsg /kinetics/Ca2E1_prime /kinetics/reac5 SUBSTRATE n addmsg /kinetics/MgATP /kinetics/reac5 SUBSTRATE n addmsg /kinetics/reac6 /kinetics/EP REAC B A addmsg /kinetics/reac7 /kinetics/EP REAC A B addmsg /kinetics/reac7 /kinetics/EPi REAC B A addmsg /kinetics/reac8 /kinetics/EPi REAC A B addmsg /kinetics/reac3 /kinetics/CaE1_prime REAC B A addmsg /kinetics/reac4 /kinetics/CaE1_prime REAC A B addmsg /kinetics/reac4 /kinetics/Ca2E1_prime REAC B A addmsg /kinetics/reac5 /kinetics/Ca2E1_prime REAC A B addmsg /kinetics/reac5 /kinetics/CaE1_prime_ATP REAC B A addmsg /kinetics/reac6 /kinetics/CaE1_prime_ATP REAC A B addmsg /kinetics/pi /graphs/conc1/pi.Co PLOT Co *pi.Co *48 addmsg /kinetics/EP /graphs/conc2/EP.Co PLOT Co *EP.Co *blue enddump // End of dump call /kinetics/E1/notes LOAD \ "Intermediate from of Ca-ATPase (SERCA2a) which is ready" \ "to bind to first Ca." call /kinetics/E2/notes LOAD \ "Concentration was calculatd from the literature source " \ "Mahaney et al. Biophysical Journal 78(3) 1306-1323" \ "" \ "In case of EP formation and Pi liberation E2 is set to " \ "calculated concentration (0.1509uM), in case EP decompostion E2 is set" \ "to 0uM." \ "" \ "Calculations of initial SERCA2a concentration:" \ "" \ "Data:" \ " 8.3% of the total protein is SERCA2a." \ " 0.2mg SF21 microsome was taken." \ " molecular wt of SERCA2a is 110,000 Da." \ " Thus E2 conc in moles is " \ " (8.3 * 0.2 * 1e-6 )/11 = 0.1509uM. " \ "" call /kinetics/Ca/notes LOAD \ "" \ "For simulation of EP formation and Pi liberation time couse at" \ "various [ca2+] the concentrations were obtained from the literature" \ "source Mahaney et al. Biophysical Journal 78(3) 1306-1323" \ "********************************************************************" \ "In case of EP decomposition after phosphorylation" \ " with 1uM ATP for 30s at 0 deg centigrade. At 30s 5mM EGTA " \ "(final conc) was added to the reaction mixture to remove all" \ "traces of ionized Ca2+ form the reaction mixture and thus to " \ "reduced the ionized [Ca2+]." \ "Actual concentration of left over calcium was calculated using" \ "EGTA - Free Calcium concentration calculator - a web based" \ "program by entering the experimental constants furnished in" \ "the literature source Mahaney et al Biophysical Journal 78(3)" \ "1306-1323." \ "Calculator program can be found at:- " \ "http://www.stanford.edu/~cpatton/webmaxclitel15.htm" \ "************************************************************" \ "" \ "" \ "" \ "" \ "" call /kinetics/MgATP/notes LOAD \ "Conc of ATP was taken from the literature source Mahaney et al." \ "" call /kinetics/ADP/notes LOAD \ "ADP obtained as a result of phosporylation of SERCA2a with ATP." call /kinetics/reac6/notes LOAD \ "kf and kb were directly taken from the table-6 literature source" \ "Mahaney et al. Biophysical Journal 78(3) 1306-1323." call /kinetics/pi/notes LOAD \ "Phosphate liberated due to EP decompostion and is propostion " \ "to EP steady state level." call /kinetics/reac7/notes LOAD \ "kf and kb were taken from the literature source Mahaney et al." \ "Biophysical Journal 78(3) 1206-1323. " \ "Some minor adjustments for steps 7 and 8 were required to prduce" \ "a precise simulation of the EP formation and Pi liberation time course" \ "" call /kinetics/reac8/notes LOAD \ "kf and kb were taken from the literature source Mahaney et al." \ "Biophysical Journal 78(3) 1306-1323." \ "some minor adjustments for step7 and step8 were required to produce" \ "a precise simulation of the EP formation and Pi liberation time" \ "course as claimed by the author of above literature." call /kinetics/CaE1/notes LOAD \ "1 Ca bond state of SERCA2a " call /kinetics/reac2/notes LOAD \ "Kinetic constants for this step had substantial effects on the" \ "steady state EP level. For " \ "" \ "SERCA2a alone the kf was 200uM" \ "SERCA2a + Wild type Phospholamban kf was reduced to 100uM " \ "SERCA2a + L37A Phospholamban kf was reduced to 50um as specified" \ "by the author (Mahaney et al Biophysical Journal 78(3) 1320 )." \ "kb in all the cases were maintained at 120." call /kinetics/reac1/notes LOAD \ "kf and kb are the picked up from the table-6 of Mahaney et al" \ "Biophysical Journal 78(3) 1306-1323." call /kinetics/reac3/notes LOAD \ "kf and kb were taken form table-6 leterature source (Mahaney et al" \ "Biophysical journal 78(3) 1306-1323. " call /kinetics/reac4/notes LOAD \ "kf and kb were taken for the table - 6 literature source" \ "Mahaney et al Biophysical Journal 78(3) 1306-1323." call /kinetics/reac5/notes LOAD \ "kf and kb were taken from Mahaney et al Biophysical Journal" \ "78(3) 1306-1323." call /kinetics/EP/notes LOAD \ "Phosphoenzyne: formation and decomposition of which is" \ "monitured on a time course under 3 condition." \ "1. SERCA2a alone" \ "2. SERCA2a + Wild type phospholamban" \ "3. SERCA2a + L37A phospholamban" call /kinetics/EPi/notes LOAD \ "Phosphoenzyme decompostion intermeditate state." call /kinetics/CaE1_prime/notes LOAD \ "Intermediate form which is result of conformational changes" \ "in the enzymes which makes it to bind to 2nd Ca in the next" \ "step" call /kinetics/Ca2E1_prime/notes LOAD \ "2 Ca bond state of the Enzyme SERCA2a." call /kinetics/CaE1_prime_ATP/notes LOAD \ "Phosporylated form of the Ca-SERCA2a." call /kinetics/doqcsinfo/notes LOAD \ "All the constants are from:
Mahaney JE. et al. Biophys J. (2000) 78(3) 1306-23.
New Insights on cardiac Ca-ATPase (expressed in Sf21 cells) regulation by Phosphlamban." complete_loading