// 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