500.0 gsl 0.001 1.0 /kinetics[0]/MAPK[0]/MAPK_p_p[0]; /kinetics[0]/PKA[0]/PKA_active[0]; /kinetics[0]/CaMKII[0]/tot_CaM_CaMKII[0]; /kinetics[0]/PKC[0]/PKC_active[0]; /kinetics[0]/MAPK[0]/Raf_p_GTP_Ras[0]; /kinetics[0]/MAPK[0]/craf_1_p[0]; /kinetics[0]/Ca[0]/Ca[0]; /kinetics[0]/CaM[0]/CaM_Ca4[0]; /kinetics[0]/PLCbeta[0]/DAG[0]; /kinetics[0]/PLCbeta[0]/IP3[0]; /kinetics[0]/PLA2[0]/Arachidonic_Acid[0]; /kinetics[0]/Ras[0]/GTP_Ras[0]; /kinetics[0]/TrKB[0]/basal_TrKB_p[0]; /compartment_1[0]/CaStores[0]; /kinetics[0]/CaM[0]/CaM(Ca)n_CaNAB[0]; /kinetics[0]/CaM[0]/CaNAB_Ca4[0]; /kinetics[0]/PP1[0]/PP1_active[0]; /kinetics[0]/CaMKII[0]/actCaMKII[0]; /kinetics[0]/CaMKII[0]/CaMKII_thr286_CaM[0]; /kinetics[0]/CaMKII[0]/CaMKII_thr286[0]; /kinetics[0]/CaMKII[0]/CaMKII_p_p_p[0]; /kinetics[0]/CaMKII[0]/CaMKII_thr306[0]; /kinetics[0]/PP1[0]/I1[0] CubeMesh False CubeMesh False 3.8 0.0 red 0 0.0 0.0 18.8 0.0 cyan 0 0.0 0.0 33.0 0.0 orange 0 0.0 0.0 47.8 0.0 pink 0 0.0 0.0 61.9 0.0 yellow 0 0.0 0.0 77.0 0.0 pink 0 0.0 0.0 91.8 0.0 cyan 0 0.0 0.0 105.9 0.0 23 0 0.0 0.0 CoInit was .0624 121.0 0.0 23 0 0.0 0.0 11.0 -143.29858058 23 0 0.0 0.0 Marquez et al J. Immun 149,2560(92) est 1e6/cell for chromaffin cells We will use 1 uM as our initial concen 25.8 -143.29858058 24 0 0.0 0.0 69.8 -143.29858058 red 0 0.0 0.0 Calculated cytosolic was 20 nm from Wijkander and Sundler However, Leslie and Channon use about 400 nM. Need to confirm, but this is the value I use here. Another recalc of W_andS gives 1uM 149.9 0.0 yellow 1 0.0 0.0 164.8 0.0 yellow 1 0.0 0.0 179.7 0.0 cyan 1 0.0 0.0 193.8 0.0 cyan 1 0.0 0.0 208.9 0.0 pink 1 0.0 0.0 arachodonylphosphatidylcholine is the favoured substrate from Wijkander and Sundler, JBC 202 pp 873-880, 1991. Their assay used 30 uM substrate, which is what the kinetics in this model are based on. For the later model we should locate a more realistic value for APC. 222.9 0.0 yellow 1 0.0 0.0 Phosphorylated form of PLA2. Still need to hook it up using kinases. PKA: Wightman et al JBC 257 pp6650 1982 PKC: Many refs, eg Gronich et al JBC 263 pp 16645, 1988 but see Lin etal MAPK: Lin et al, Cell 72 pp 269, 1993. Show 3x with MAPK but not PKC alone Do not know if there is a Ca requirement for active phosphorylated state. 237.9 0.0 orange 1 0.0 0.0 252.9 0.0 orange 1 0.0 0.0 157.7 -143.29858058 darkgreen 1 0.0 0.0 Total PLC = 0.8 uM see Ryu et al JBC 262 (26) pp 12511 1987 296.9 0.0 cyan 2 0.0 0.0 310.9 0.0 green 2 0.0 0.0 325.9 0.0 cyan 2 0.0 0.0 This should really be labelled PLC-G*GTP-Ca. This is the activated form of the enzyme. Mahama and Linderman assume that the IP3 precursors are not rate-limiting, but I will include those for completeness as they may be needed later. 340.9 0.0 cyan 2 0.0 0.0 354.9 0.0 cyan 2 0.0 0.0 Phosphatidylcholine is the main (around 55%) metabolic product of DAG, follwed by PE (around 25%). Ref is Welsh and Cabot, JCB35:231-245(1987) 369.9 0.0 green 2 0.0 0.0 325.9 -143.29858058 green 2 0.0 0.0 Peak IP3 is perhaps 15 uM, basal _lessthan_= 0.2 uM. 340.9 -143.29858058 pink 2 0.0 0.0 384.9 0.0 green 2 0.0 0.0 I am implementing this as acting only on the Rec-Gq complex, based on a more complete model PLC_Gq48.g which showed that the binding to the rec alone contributed only a small amount. 442.9 0.0 seagreen 3 0.0 0.0 457.9 0.0 seagreen 3 0.0 0.0 589.9 0.0 orange 4 0.0 0.0 Couldn't find any ref to the actual conc of craf-1 but I should try Strom et al Oncogene 5 pp 345 In line with the other kinases in the cascade, I estimate the conc to be 0.2 uM. To init we use 0.15, which is close to equil 604.0 0.0 pink 4 0.0 0.0 618.8 0.0 pink 4 0.0 0.0 Conc is from Seger et al JBC 267:20 pp14373 (1992) mwt is 45/46 Kd We assume that phosphorylation on both ser and thr is needed for activiation. See Kyriakis et al Nature 358 417 1992 Init conc of total is 0.18 633.0 0.0 pink 4 0.0 0.0 conc is from Sanghera et al JBC 265 pp 52 (1990) A second calculation gives 3.1 uM, from same paper. They est MAPK is 1e-4x total protein, and protein is 15% of cell wt, so MAPK is 1.5e-5g/ml = 0.36uM. which is closer to our first estimate. Lets use this. 648.0 0.0 pink 4 0.0 0.0 Negative feedback by MAPK* by hyperphosphorylating craf-1* gives rise to this pool. Ueki et al JBC 269(22):15756-15761, 1994 663.0 0.0 hotpink 4 0.0 0.0 Haystead et al FEBS Lett. 306(1) pp 17-22 show that phosphorylation is strictly sequential, first tyr185 then thr183. 677.0 0.0 orange 4 0.0 0.0 MAPKK phosphorylates MAPK on both the tyr and thr residues, first tyr then thr. Refs: Seger et al JBC267:20 pp 14373 1992 The MAPKK itself is phosphorylated on ser as well as thr residues. Let us assume that the ser goes first, and that the sequential phosphorylation is needed. See Kyriakis et al Nature 358 417-421 1992 692.0 0.0 pink 4 0.0 0.0 Intermediately phophorylated, assumed inactive, form of MAPKK 707.0 0.0 pink 4 0.0 0.0 596.8 -143.29858058 red 4 0.0 0.0 611.0 -143.29858058 27 4 0.0 0.0 Guanine nucleotide exchange factor. This activates raf by exchanging bound GDP with GTP. I have left the GDP/GTP out of this reaction, it would be trivial to put them in. See Boguski _and McCormick. Possible candidate molecules: RasGRF, smgGDS, Vav (in dispute). rasGRF: Kcat= 1.2/min Km = 680 nM smgGDS: Kcat: 0.37 /min, Km = 220 nM. vav: Turnover up over baseline by 10X, 736.0 0.0 hotpink 5 0.0 0.0 Assume that SoS is present only at 50 nM. Revised to 100 nM to get equil to experimentally known levels. 751.0 0.0 hotpink 5 0.0 0.0 phosphorylated and thereby activated form of GEF. See, e.g. Orita et al JBC 268:34 25542-25546 1993, Gulbins et al. It is not clear whether there is major specificity for tyr or ser/thr. 764.9 0.0 hotpink 5 0.0 0.0 Only a very small fraction (7% unstim, 15% stim) of ras is GTP-bound. Gibbs et al JBC 265(33) 20437 780.0 0.0 orange 5 0.0 0.0 GDP bound form. See Rosen et al Neuron 12 1207-1221 June 1994. the activation loop is based on Boguski and McCormick Nature 366 643-654 93 Assume Ras is present at about the same level as craf-1, 0.2 uM. Hallberg et al JBC 269:6 3913-3916 1994 estimate upto 5-10% of cellular Raf is assoc with Ras. Given that only 5-10% of Ras is GTP-bound, we need similar amounts of Ras as Raf. 795.0 0.0 pink 5 0.0 0.0 808.9 0.0 red 5 0.0 0.0 GTPase-activating proteins. See Boguski and McCormick. Turn off Ras by helping to hydrolyze bound GTP. This one is probably NF1, ie., Neurofibromin as it is inhibited by AA and lipids, and expressed in neural cells. p120-GAP is also a possible candidate, but is less regulated. Both may exist at similar levels. See Eccleston et al JBC 268(36) pp27012-19 Level=.002 824.0 0.0 red 5 0.0 0.0 Phosphorylation-inactivated form of GEF. See Hordijk et al JBC 269:5 3534-3538 1994 and Buregering et al EMBO J 12:11 4211-4220 1993 837.9 0.0 hotpink 5 0.0 0.0 See Farnsworth et al Nature 376 524-527 1995 852.9 0.0 pink 5 0.0 0.0 Berkers et al JBC 266 say 22K hi aff recs. Sherrill and Kyte Biochemistry 35 use range 4-200 nM. These match, lets use them. 881.9 0.0 red 6 0.0 0.0 This is terribly simplified: there are many interesting intermediate stages, including dimerization and assoc with adapter molecules like Shc, that contribute to the activation of the EGFR. 896.9 0.0 red 6 0.0 0.0 912.0 0.0 red 6 0.0 0.0 925.9 0.0 red 6 0.0 0.0 4.5 -337.244064816 brown 7 0.0 0.0 There are 2 isoforms: 52 KDa and 46 KDa (See Okada et al JBC 270:35 pp 20737 1995). They are acted up on by the EGFR in very similar ways, and apparently both bind Grb2 similarly, so we'll bundle them together here. Sasaoka et al JBC 269:51 pp 32621 1994 show immunoprecs where it looks like there is at least as much Shc as Grb2. So we'll tentatively say there is 1 uM of Shc. 19.4 -337.244064816 orange 7 0.0 0.0 33.5 -337.244064816 orange 7 0.0 0.0 48.5 -337.244064816 orange 7 0.0 0.0 There is probably a lot of it in the cell: it is also known as Ash (abundant src homology protein I think). Also Waters et al JBC 271:30 18224 1996 say that only a small fraction of cellular Grb is precipitated out when SoS is precipitated. As most of the Sos seems to be associated with Grb2, it would seem like there is a lot of the latter. Say 1 uM. I haven't been able to find a decent.... 62.5 -337.244064816 orange 7 0.0 0.0 77.5 -337.244064816 orange 7 0.0 0.0 92.5 -337.244064816 red 7 0.0 0.0 I have tried using low (0.02 uM) initial concs, but these give a very flat response to EGF stim although the overall activation of Ras is not too bad. I am reverting to 0.1 because we expect a sharp initial response, followed by a decline. Sep 17 1997: The transient activation curve looks better with [Sos] = 0.05. Apr 26 1998: Some error there, it is better where it was at 0.1 106.5 -337.244064816 red 7 0.0 0.0 121.5 -337.244064816 42 7 0.0 0.0 148.2 -337.344554704 3 black 0.0 0.0 Amount from Homma et al JBC 263:14 6592-6598 1988 149.9 -191.131767366 pink 8 0.0 0.0 164.8 -191.131767366 pink 8 0.0 0.0 179.7 -191.131767366 pink 8 0.0 0.0 193.8 -191.131767366 pink 8 0.0 0.0 208.9 -191.131767366 33 8 0.0 0.0 Huge conc of CaMKII. In PSD it is 20-40% of protein, so we assume it is around 2.5% of protein in spine as a whole. This level is so high it is unlikely to matter much if we are off a bit. This comes to about 70 uM. 296.9 -191.131767366 palegreen 9 0.0 0.0 310.9 -191.131767366 palegreen 9 0.0 0.0 From Hanson and Schulman, the thr286 is responsible for autonomous activation of CaMKII. 325.9 -191.131767366 palegreen 9 0.0 0.0 From Hanson and Schulman, the CaMKII does a lot of autophosphorylation just after the CaM is released. This prevents further CaM binding and renders the enzyme quite independent of Ca. 340.9 -191.131767366 cyan 9 0.0 0.0 I am not sure if we need to endow this one with a lot of enzs. It is likely to be a short-lived intermediate, since it will be phosphorylated further as soon as the CAM falls off. 354.9 -191.131767366 red 9 0.0 0.0 This forms due to basal autophosphorylation, but I think it has to be considered as a pathway even if some CaM is floating around. In either case it will tend to block further binding of CaM, and will not display any enzyme activity. See Hanson and Schulman JBC 267:24 pp17216-17224 1992 369.9 -191.131767366 palegreen 9 0.0 0.0 317.1 -227.810576561 green 9 0.0 0.0 341.5 -186.207762844 29 33 0.0 0.0 320.4 -176.761713353 23 33 0.0 0.0 311.9 -197.965079764 blue 33 0.0 0.0 345.9 -183.796005527 30 33 1e-12 0.0 323.4 -182.891596533 12 5 0.0 0.0 442.9 -191.131767366 blue 10 0.0 0.0 There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al) Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying it is comparable to CaMK levels. 457.9 -191.131767366 pink 10 0.0 0.0 472.0 -191.131767366 red 10 0.0 0.0 The phosph form does not bind CaM (Huang et al ABB 305:2 570-580 1993) 486.9 -191.131767366 red 10 0.0 0.0 Also known as RC3 and p17 and BICKS. Conc in brain _greaterthan__greaterthan_ 2 uM from Martzen and Slemmon J neurosci 64 92-100 1995 but others say less without any #s. Conc in dend spines is much higher than overall, so it could be anywhere from 2 uM to 50. We will estimate 10 uM as a starting point. Gerendasy et al JBC 269:35 22420-22426 1994 have a skeleton model (no numbers) indicating CaM-Ca(n) binding .... 501.9 -191.131767366 red 10 0.0 0.0 516.0 -191.131767366 hotpink 10 0.0 0.0 645.6 -210.124356237 darkblue 10 0.0 0.0 560.0 -191.131767366 tan 10 0.0 0.0 This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not. 449.8 -334.530837834 pink 10 0.0 0.0 This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not. 464.9 -334.530837834 pink 10 0.0 0.0 Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM 589.9 -191.131767366 cyan 11 0.0 0.0 I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183). We treat it as non-compet, so it just turns the enz off without interacting with the binding site. Cohen et al ann rev bioch refer to results where conc is 1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM, we need _greaterthan_= 1.8 uM. 604.0 -191.131767366 orange 11 0.0 0.0 Dephosph is mainly by PP2B 618.8 -191.131767366 orange 11 0.0 0.0 633.0 -191.131767366 brown 11 0.0 0.0 648.0 -191.131767366 brown 11 0.0 0.0 We assume that the A and B subunits of PP2B are always bound under physiol conditions. Up to 1% of brain protein = 25 uM. I need to work out how it is distributed between cytosolic and particulate fractions. Tallant and Cheung '83 Biochem 22 3630-3635 have conc in many species, average for mammalian brain is around 1 uM. 736.0 -191.131767366 tan 12 0.0 0.0 751.0 -191.131767366 tan 12 0.0 0.0 764.9 -191.131767366 blue 12 0.0 0.0 780.0 -191.131767366 blue 12 0.0 0.0 795.0 -191.131767366 blue 12 0.0 0.0 881.9 -191.131767366 yellow 13 0.0 0.0 This is the R2C2 complex, consisting of 2 catalytic (C) subunits, and the R-dimer. See Taylor et al Ann Rev Biochem 1990 59:971-1005 for a review. The Doskeland and Ogreid review is better for numbers. Amount of PKA is about .5 uM. 896.9 -191.131767366 0 13 0.0 0.0 CoInit was .0624 912.0 -191.131767366 23 13 0.0 0.0 925.9 -191.131767366 23 13 0.0 0.0 940.9 -191.131767366 3 13 0.0 0.0 955.0 -191.131767366 23 13 0.0 0.0 969.9 -191.131767366 50 13 0.0 0.0 Starts at 0.15 for the test of fig 6 in Smith et al, but we aren't using that paper any more. 984.9 -191.131767366 52 13 0.0 0.0 About 25% of PKA C subunit is dissociated in resting cells without having any noticable activity. Doskeland and Ogreid Int J biochem 13 pp1-19 suggest that this is because there is a corresponding amount of inhibitor protein. 1000.0 -191.131767366 cyan 13 0.0 0.0 890.0 -334.530837834 cyan 13 0.0 0.0 The conc of this has been a problem. Schaecter and Benowitz use 50 uM, but Shinomura et al have _lessthan_ 5. So I have altered the cAMP-dependent rates in the PKA model to reflect this. 3.8 -382.263534732 green 14 0.0 0.0 ATP is present in all cells between 2 and 10 mM. See Lehninger. 18.8 -382.263534732 red 14 0.0 0.0 This version of cyclase is Calmodulin activated. Gs stims it but betagamma inhibits. 33.0 -382.263534732 orange 14 0.0 0.0 Starting conc at 20 nM. 47.8 -382.263534732 orange 14 0.0 0.0 This version is activated by Gs and by a betagamma and phosphorylation. 61.9 -382.263534732 yellow 14 0.0 0.0 77.0 -382.263534732 yellow 14 0.0 0.0 Starting at 0.015 uM. 91.8 -382.263534732 yellow 14 0.0 0.0 105.9 -382.263534732 orange 14 0.0 0.0 121.0 -382.263534732 green 14 0.0 0.0 The levels of the PDE are not known at this time. However, enough kinetic info and info about steady-state levels of cAMP etc are around to make it possible to estimate this. 11.0 -524.657706318 green 14 0.0 0.0 This form has about 2X activity as plain PDE. See Sette et al JBC 269:28 18271-18274 1994. 25.8 -524.657706318 green 14 0.0 0.0 CaM-Dependent PDE. Amount calculated from total rate in brain vs. specific rate. 39.9 -524.657706318 green 14 0.0 0.0 Activity up 6x following Ca-CaM binding. 55.0 -524.657706318 green 14 0.0 0.0 69.8 -524.657706318 pink 14 0.0 0.0 Varying the amount of (steady state) glu between .01 uM and up, the final amount of G*GTP complex does not change much. This means that the system should be reasonably robust wr to the amount of glu in the synaptic cleft. It would be nice to know how fast it is removed. 149.9 -382.263534732 green 15 0.0 0.0 From M_andL, Total # of receptors/cell = 1900 Vol of cell = 1e-15 (10 um cube). Navogadro = 6.023e23 so conversion from n to conc in uM is n/vol*nA * 1e3 = 1.66e-6 However, for typical synaptic channels the density is likely to be very high at the synapse. Use an estimate of 0.1 uM for now. this gives a total of about 60K receptors/cell, which is in line with Fay et at. 164.8 -382.263534732 green 15 0.0 0.0 This acts like an enzyme to activate the g proteins Assume cell has vol 1e-15 m^3 (10 uM cube), conversion factor to conc in uM is 6e5 179.7 -382.263534732 green 15 0.0 0.0 Fraction of Rec-Gq is 44% of rec, from Fay et al. Since this is not the same receptor, this value is a bit doubtful. Still, we adjust the rate consts in Rec-bind-Gq to match. 193.8 -382.263534732 green 15 0.0 0.0 208.9 -382.263534732 orange 15 0.0 0.0 These exist in a nebulous sense in this model, basically only to balance the conservation equations. The details of their reassociation with G-GDP are not modeled Resting level =0.0094, stim level =.0236 from all42.g ish. 296.9 -382.263534732 yellow 16 0.0 0.0 Activated G protein. Berstein et al indicate that about 20-40% of the total Gq alpha should bind GTP at steady stim. This sim gives more like 65%. 310.9 -382.263534732 red 16 0.0 0.0 325.9 -382.263534732 yellow 16 0.0 0.0 From M_andL, total Gprot = 1e5molecules/cell At equil, 92340 are here, 400 are in G*GTP, and another 600 are assoc with the PLC and 6475 are as G*GDP. This is OK. From Pang and Sternweis JBC 265:30 18707-12 1990 we get conc est 1.6 uM to 0.8 uM. A number of other factors are involved too. 340.9 -382.263534732 yellow 16 0.0 0.0 354.9 -382.263534732 red 16 0.0 0.0 MKP-1 dephosphoryates and inactivates MAPK in vivo: Sun et al Cell 75 487-493 1993. Levels of MKP-1 are regulated, and rise in 1 hour. Kinetics from Charles et al PNAS 90:5292-5296 1993. They refer to Charles et al Oncogene 7 187-190 who show that half-life of MKP1/3CH134 is 40 min. 80% deph of MAPK in 20 min Sep 17 1997: CoInit now 0.4x to 0.0032. See parm searches from jun96 on. 442.9 -382.263534732 hotpink 17 0.0 0.0 Refs: Pato et al Biochem J 293:35-41(93); Takai_andMieskes Biochem J 275:233-239 k1=1.46e-4, k2=1000,k3=250. these use kcat values for calponin. Also, units of kcat may be in min! revert to Vmax base: k3=6, k2=25,k1=3.3e-6 or 6,6,1e-6 CoInit assumed 0.1 uM. See NOTES for MAPK_Ras50.g. CoInit now 0.08 Sep 17 1997: Raise CoInt 1.4x to 0.224, see parm searches from jun 96 on. 457.9 -382.263534732 hotpink 17 0.0 0.0 472.0 -382.263534732 red 17 0.0 0.0 This pool represents intracellular calcium. Resting levels are around 80 nM, but this is subject to all sorts of influxes and pumps. 590.34 -443.019721141 61 darkgreen 0.0 0.0 represents the channels that leak Ca into the cytoplasm. Effects of membrane potential are not considered. The amount and total flux are constrained by the need to balance Ca flux and keep basal Ca around 80 nM. 590.14 -382.625298329 pink darkgreen 0.0 0.0 equivalent to the enzyme-substrate complex. 2 Ca are bound to the transporter. ATP is ignored. 590.9 -382.454465519 pink darkgreen 0.0 0.0 The calcium transporter levels are constrained by the resting levels of Ca in the cell. The rate of Ca sequestration depends on the amount of this pool. 590.64 -382.524808441 pink darkgreen 0.0 0.0 The number of the IP3Rs in the cell is present only implicitly in the model, and is lumped in with the total permeability of the IP3R pool. The latter is constrained by the height of the Ca transient. 591.3 -386.785579701 green darkgreen 0.0 0.0 This is the ligand-bound form of the IP3R. 590.9 -386.685089813 green darkgreen 0.0 0.0 The calcium electrogenic pump: Mc Burney and Neering, TINS 10(4), 1987, 164-169. We treat the pump as a simple Michaelis-Menten enzyme. Levels are constrained tightly by the need to keep resting Ca levels at 80 nM. 590.44 -383.12774777 pink darkgreen 0.0 0.0 Extracell Ca conc = 4 mM Extracell vol assumed 100 X cell vol. It is anyway kept buffered for the purposes of the model, so the concentration won't change. 590.4 -383.278482603 red darkgreen 0.0 0.0 This represents the pool of Ca leak channels. The conc gradient is so large that this pool needs only a small number of molecules. For an equilibrium at 0.1 uM we need flow of 36e3/sec. With a permeability of 0.01 and a conc gradient of 4mM-_greaterthan_0.1 uM (4e4) we get flux = N * perm * grad =_greaterthan_ N = 36e3 / (1e-2 * 4e3) = 900 if flux = 20e3, N =500, which is what we use. This works out to a concentration of 0.83 nM. 590.08 -383.318678558 hotpink darkgreen 0.0 0.0 This mechanism has taken a while to be more tightly confirmed as probably being the TRP channel. In this model the channel is implemented to match experimental observations about capacitative Ca entry. Levels are set by two constraints: the resting Ca levels, and the height of the response to IP3. 589.7 -383.147845748 hotpink darkgreen 0.0 0.0 represents the portion of the capacitative-Ca entry channel which is blocked when there is lots of Ca sequestered in the stores 589.69 -382.625298329 pink darkgreen 0.0 0.0 590.14 -382.022359 61 black 0.0 0.0 This isn't explicitly present in the M_andL model, but is obviously needed. I assume its conc is fixed at 1uM for now, which is a bit high. PLA2 is stim 7x by PIP2 @ 0.5 uM (Leslie and Channon BBA 1045:261(1990) Leslie and Channon say PIP2 is present at 0.1 - 0.2mol% range in membs, which comes to 50 nM. Ref is Majerus et al Cell 37 pp 701-703 1984 Lets use a lower level of 30 nM, same ref.... 736.0 -382.263534732 green 19 0.0 0.0 780.0 -382.263534732 43 19 0.0 0.0 795.0 -382.263534732 37 19 0.0 0.0 808.9 -382.263534732 brown 19 0.0 0.0 824.0 -382.263534732 cyan 19 0.0 0.0 837.9 -382.263534732 10 19 0.0 0.0 852.9 -382.263534732 44 19 0.0 0.0 742.9 -524.657706318 50 19 0.0 0.0 758.0 -524.657706318 37 19 0.0 0.0 795.0 -524.657706318 31 19 0.0 0.0 881.9 -382.263534732 53 20 0.0 0.0 896.9 -382.263534732 9 20 0.0 0.0 912.0 -382.263534732 39 20 0.0 0.0 925.9 -382.263534732 60 20 0.0 0.0 aaa 940.9 -382.263534732 25 20 0.0 0.0 955.0 -382.263534732 4 20 0.0 0.0 0.0 -572.490893104 yellow 21 0.0 0.0 13.9 -572.490893104 3 21 0.0 0.0 28.9 -572.490893104 38 21 0.0 0.0 42.9 -572.490893104 45 21 0.0 0.0 57.9 -572.490893104 red 21 0.0 0.0 106.8 -572.490893104 0 black 0.0 0.0 158.855383481 -567.042583884 28 22 0.0 0.0 173.755383481 -567.042583884 39 22 0.0 0.0 188.655383481 -567.042583884 25 22 0.0 0.0 202.755383481 -567.042583884 44 22 0.0 0.0 311.123385612 -571.689575605 46 23 0.0 0.0 325.123385612 -571.689575605 Pink 23 0.0 0.0 340.123385612 -571.689575605 48 23 0.0 0.0 355.123385612 -571.689575605 6 23 0.0 0.0 369.123385612 -571.689575605 45 23 0.0 0.0 442.9 -572.490893104 47 24 0.0 0.0 457.9 -572.490893104 59 24 0.0 0.0 472.0 -572.490893104 52 24 0.0 0.0 486.9 -572.490893104 56 24 0.0 0.0 501.9 -572.490893104 39 24 0.0 0.0 516.0 -572.490893104 60 24 0.0 0.0 Q.R= Quaternary complex.Ribosome 589.9 -572.490893104 blue 25 0.0 0.0 604.0 -572.490893104 pink 25 0.0 0.0 Q= Quaternary complex 618.8 -572.490893104 28 25 0.0 0.0 40S_complex consist of Quaternary complex, mRNA complex, 40S Ribosomes. 633.0 -572.490893104 hotpink 25 0.0 0.0 736.0 -572.490893104 cyan 26 0.0 0.0 751.0 -572.490893104 brown 26 0.0 0.0 764.9 -572.490893104 23 26 0.0 0.0 780.0 -572.490893104 red 26 0.0 0.0 795.0 -572.490893104 45 26 0.0 0.0 808.9 -572.490893104 1 26 0.0 0.0 824.0 -572.490893104 47 26 0.0 0.0 837.9 -572.490893104 2 26 0.0 0.0 881.9 -572.490893104 44 27 0.0 0.0 3.8 -763.723150358 32 28 0.0 0.0 18.8 -763.723150358 58 28 0.0 0.0 33.0 -763.723150358 45 28 0.0 0.0 47.8 -763.723150358 57 28 0.0 0.0 129.435847461 -757.621320357 42 29 0.0 0.0 138.535847461 -757.721810245 cyan 29 0.0 0.0 147.035847461 -757.822300133 pink 29 0.0 0.0 155.535847461 -757.520830468 21 29 0.0 0.0 164.238161469 -757.520830468 6 29 0.0 0.0 173.937390133 -757.714805795 60 29 0.0 0.0 185.141246814 -757.714805795 59 29 0.0 0.0 194.740475478 -757.910532234 31 black 0.0 0.0 296.9 -763.723150358 27 30 0.0 0.0 310.9 -763.723150358 50 30 0.0 0.0 325.9 -763.723150358 46 30 0.0 0.0 340.9 -763.723150358 52 30 0.0 0.0 354.9 -763.723150358 blue 30 0.0 0.0 It will contribute to mTOR independent translation. 369.9 -763.723150358 53 30 0.0 0.0 Inactivated form of S6K 442.9 -763.723150358 3 31 0.0 0.0 Activated form of S6 457.9 -763.723150358 7 31 0.0 0.0 472.0 -763.723150358 44 31 0.0 0.0 589.9 -763.723150358 40 32 0.0 0.0 604.0 -763.723150358 51 32 0.0 0.0 736.0 -763.723150358 45 33 0.0 0.0 751.0 -763.723150358 61 33 0.0 0.0 764.9 -763.723150358 46 33 0.0 0.0 780.0 -763.723150358 52 33 0.0 0.0 795.0 -763.723150358 59 33 0.0 0.0 Bychkov et al., 2011. 150ng/mg *0.5mg/ml /65000g/mol = 1.155385nM (which is too low, therefore increasing the concentration arbitrarily by 1000 fold) 881.9 -763.723150358 42 34 0.0 0.0 896.9 -763.723150358 24 34 0.0 0.0 Bychkov et al., 2011. 30ng/mg *0.5mg/ml /40000g/mol = 0.375nM (which is too low, therefore increasing the concentration arbitrarily by 1000 fold) 912.0 -763.723150358 19 34 0.0 0.0 925.9 -763.723150358 0 34 0.0 0.0 940.9 -763.723150358 53 34 0.0 0.0 955.0 -763.723150358 61 34 0.0 0.0 969.9 -763.723150358 39 34 0.0 0.0 984.9 -763.723150358 50 34 0.0 0.0 $\mathrm{PKC\_DAG\_AA\_p\_1686\_0\_}+\mathrm{PKC\_Ca\_memb\_p\_1690\_0\_}+\mathrm{PKC\_Ca\_AA\_p\_1688\_0\_}+\mathrm{PKC\_DAG\_memb\_p\_1692\_0\_}+\mathrm{PKC\_basal\_p\_1694\_0\_}+\mathrm{PKC\_AA\_p\_1696\_0\_}$ $\mathrm{CaMKII\_CaM\_2045\_0\_}+\mathrm{CaMKII\_thr286\_CaM\_2047\_0\_}$ $\mathrm{CaMKII\_thr286\_2051\_0\_}+\mathrm{CaMKII\_p\_p\_p\_2049\_0\_}+\mathrm{basal\_CaMKII\_2079\_0\_}$ $\mathrm{actCaMKII\_2083\_0\_}+\mathrm{CaMKII\_2043\_0\_}+\mathrm{CaMKII\_thr305\_2081\_0\_}$ $\mathrm{CaMKII\_thr286\_CaM\_2047\_0\_}+\mathrm{CaMKII\_CaM\_2045\_0\_}+\mathrm{tot\_auto\_2066\_0\_}$ $\mathrm{CaMCa4\_CaNAB\_2180\_0\_}+\mathrm{CaMCa3\_CaNAB\_2176\_0\_}+\mathrm{CaMCa2\_CaNAB\_2178\_0\_}$ Need est of rate of assoc of Ca and PKC. Assume it is fast The original parameter-searched kf of 439.4 has been scaled by 1/6e8 to account for change of units to n. Kf now 8.16e-7, kb=.6085 Raised kf to 1e-6 to match Ca curve, kb to .5 11.0 -18.8920989825 white 0 kinetics_1676_0_ * PKC_act_by_Ca_1726_0__Kf * PKC_cytosolic_1704_0_*Ca_2413_0_-kinetics_1676_0_ * PKC_act_by_Ca_1726_0__Kb * PKC_Ca_1684_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_act\_by\_Ca\_1726\_0\_\_Kf}\mathrm{PKC\_cytosolic\_1704\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_act\_by\_Ca\_1726\_0\_\_Kb}\mathrm{PKC\_Ca\_1684\_0\_}$ Need est of rate. Assume it is fast Obtained from param search kf raised 10 X : see Shinomura et al PNAS 88 5149-5153 1991. kf changed from 3.865e-7 to 2.0e-7 in line with closer analysis of Shinomura data. 26 June 1996: Corrected DAG data: reduce kf 15x from 2e-7 to 1.333e-8 25.8 -18.8920989825 white 0 kinetics_1676_0_ * PKC_act_by_DAG_1728_0__Kf * PKC_Ca_1684_0_*DAG_1815_0_-kinetics_1676_0_ * PKC_act_by_DAG_1728_0__Kb * PKC_Ca_DAG_1698_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_act\_by\_DAG\_1728\_0\_\_Kf}\mathrm{PKC\_Ca\_1684\_0\_}\mathrm{DAG\_1815\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_act\_by\_DAG\_1728\_0\_\_Kb}\mathrm{PKC\_Ca\_DAG\_1698\_0\_}$ 39.9 -18.8920989825 white 0 kinetics_1676_0_ * PKC_Ca_to_memb_1730_0__Kf * PKC_Ca_1684_0_-kinetics_1676_0_ * PKC_Ca_to_memb_1730_0__Kb * PKC_Ca_memb_p_1690_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_Ca\_to\_memb\_1730\_0\_\_Kf}\mathrm{PKC\_Ca\_1684\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_Ca\_to\_memb\_1730\_0\_\_Kb}\mathrm{PKC\_Ca\_memb\_p\_1690\_0\_}$ Raise kb from .087 to 0.1 to match data from Shinomura et al. Lower kf from 1.155 to 1.0 to match data from Shinomura et al. 55.0 -18.8920989825 white 0 kinetics_1676_0_ * PKC_DAG_to_memb_1732_0__Kf * PKC_Ca_DAG_1698_0_-kinetics_1676_0_ * PKC_DAG_to_memb_1732_0__Kb * PKC_DAG_memb_p_1692_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_DAG\_to\_memb\_1732\_0\_\_Kf}\mathrm{PKC\_Ca\_DAG\_1698\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_DAG\_to\_memb\_1732\_0\_\_Kb}\mathrm{PKC\_DAG\_memb\_p\_1692\_0\_}$ Schaechter and Benowitz We have to increase Kf for conc scaling Changed kf to 2e-9 on Sept 19, 94. This gives better match. 69.8 -18.8920989825 white 0 kinetics_1676_0_ * PKC_act_by_Ca_AA_1734_0__Kf * Arachidonic_Acid_1779_0_*PKC_Ca_1684_0_-kinetics_1676_0_ * PKC_act_by_Ca_AA_1734_0__Kb * PKC_Ca_AA_p_1688_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_act\_by\_Ca\_AA\_1734\_0\_\_Kf}\mathrm{Arachidonic\_Acid\_1779\_0\_}\mathrm{PKC\_Ca\_1684\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_act\_by\_Ca\_AA\_1734\_0\_\_Kb}\mathrm{PKC\_Ca\_AA\_p\_1688\_0\_}$ Assume slowish too. Schaechter and Benowitz 83.9 -18.8920989825 white 0 kinetics_1676_0_ * PKC_act_by_DAG_AA_1736_0__Kf * PKC_DAG_AA_1702_0_-kinetics_1676_0_ * PKC_act_by_DAG_AA_1736_0__Kb * PKC_DAG_AA_p_1686_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_act\_by\_DAG\_AA\_1736\_0\_\_Kf}\mathrm{PKC\_DAG\_AA\_1702\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_act\_by\_DAG\_AA\_1736\_0\_\_Kb}\mathrm{PKC\_DAG\_AA\_p\_1686\_0\_}$ Initial basal levels were set by kf = 1, kb = 20. In model, though, the basal levels of PKC activity are higher. 99.0 -18.8920989825 white 0 kinetics_1676_0_ * PKC_basal_act_1738_0__Kf * PKC_cytosolic_1704_0_-kinetics_1676_0_ * PKC_basal_act_1738_0__Kb * PKC_basal_p_1694_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_basal\_act\_1738\_0\_\_Kf}\mathrm{PKC\_cytosolic\_1704\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_basal\_act\_1738\_0\_\_Kb}\mathrm{PKC\_basal\_p\_1694\_0\_}$ Raise kf from 1.667e-10 to 2e-10 to get better match to data. 113.8 -18.8920989825 white 0 kinetics_1676_0_ * PKC_act_by_AA_1740_0__Kf * PKC_cytosolic_1704_0_*Arachidonic_Acid_1779_0_-kinetics_1676_0_ * PKC_act_by_AA_1740_0__Kb * PKC_AA_p_1696_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_act\_by\_AA\_1740\_0\_\_Kf}\mathrm{PKC\_cytosolic\_1704\_0\_}\mathrm{Arachidonic\_Acid\_1779\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_act\_by\_AA\_1740\_0\_\_Kb}\mathrm{PKC\_AA\_p\_1696\_0\_}$ kf raised 10 X based on Shinomura et al PNAS 88 5149-5153 1991 closer analysis of Shinomura et al: kf now 1e-8 (was 1.66e-8). Further tweak. To get sufficient AA synergy, increase kf to 1.5e-8 26 June 1996: Corrected DAG levels: reduce kf by 15x from 1.5e-8 to 1e-9 127.9 -18.8920989825 white 0 kinetics_1676_0_ * PKC_n_DAG_1742_0__Kf * PKC_cytosolic_1704_0_*DAG_1815_0_-kinetics_1676_0_ * PKC_n_DAG_1742_0__Kb * PKC_DAG_1700_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_n\_DAG\_1742\_0\_\_Kf}\mathrm{PKC\_cytosolic\_1704\_0\_}\mathrm{DAG\_1815\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_n\_DAG\_1742\_0\_\_Kb}\mathrm{PKC\_DAG\_1700\_0\_}$ Reduced kf to 0.66X to match Shinomura et al data. Initial: kf = 3.3333e-9 New: 2e-9 Newer: 2e-8 kb was 0.2 now 2. 18.8 -124.406481598 white 0 kinetics_1676_0_ * PKC_n_DAG_AA_1744_0__Kf * Arachidonic_Acid_1779_0_*PKC_DAG_1700_0_-kinetics_1676_0_ * PKC_n_DAG_AA_1744_0__Kb * PKC_DAG_AA_1702_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_n\_DAG\_AA\_1744\_0\_\_Kf}\mathrm{Arachidonic\_Acid\_1779\_0\_}\mathrm{PKC\_DAG\_1700\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PKC\_n\_DAG\_AA\_1744\_0\_\_Kb}\mathrm{PKC\_DAG\_AA\_1702\_0\_}$ Leslie and Channon BBA 1045 (1990) 261-270 fig6 pp267. 157.7 -18.8920989825 white 1 kinetics_1676_0_ * PLA2_Ca_act_1781_0__Kf * PLA2_cytosolic_1748_0_*Ca_2413_0_-kinetics_1676_0_ * PLA2_Ca_act_1781_0__Kb * PLA2_Ca_p_1750_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PLA2\_Ca\_act\_1781\_0\_\_Kf}\mathrm{PLA2\_cytosolic\_1748\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PLA2\_Ca\_act\_1781\_0\_\_Kb}\mathrm{PLA2\_Ca\_p\_1750\_0\_}$ 171.9 -18.8920989825 white 1 kinetics_1676_0_ * PIP2_PLA2_act_1783_0__Kf * temp_PIP2_2458_0_*PLA2_cytosolic_1748_0_-kinetics_1676_0_ * PIP2_PLA2_act_1783_0__Kb * PIP2_PLA2_p_1755_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PIP2\_PLA2\_act\_1783\_0\_\_Kf}\mathrm{temp\_PIP2\_2458\_0\_}\mathrm{PLA2\_cytosolic\_1748\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PIP2\_PLA2\_act\_1783\_0\_\_Kb}\mathrm{PIP2\_PLA2\_p\_1755\_0\_}$ 186.9 -18.8920989825 white 1 kinetics_1676_0_ * PIP2_Ca_PLA2_act_1785_0__Kf * temp_PIP2_2458_0_*PLA2_Ca_p_1750_0_-kinetics_1676_0_ * PIP2_Ca_PLA2_act_1785_0__Kb * PIP2_Ca_PLA2_p_1760_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PIP2\_Ca\_PLA2\_act\_1785\_0\_\_Kf}\mathrm{temp\_PIP2\_2458\_0\_}\mathrm{PLA2\_Ca\_p\_1750\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PIP2\_Ca\_PLA2\_act\_1785\_0\_\_Kb}\mathrm{PIP2\_Ca\_PLA2\_p\_1760\_0\_}$ 27 June 1996 Scaled kf down by 0.015 from 3.33e-7 to 5e-9 to fit with revised DAG estimates and use of mole-fraction to calculate eff on PLA2. 202.0 -18.8920989825 white 1 kinetics_1676_0_ * DAG_Ca_PLA2_act_1787_0__Kf * PLA2_Ca_p_1750_0_*DAG_1815_0_-kinetics_1676_0_ * DAG_Ca_PLA2_act_1787_0__Kb * DAG_Ca_PLA2_p_1765_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{DAG\_Ca\_PLA2\_act\_1787\_0\_\_Kf}\mathrm{PLA2\_Ca\_p\_1750\_0\_}\mathrm{DAG\_1815\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{DAG\_Ca\_PLA2\_act\_1787\_0\_\_Kb}\mathrm{DAG\_Ca\_PLA2\_p\_1765\_0\_}$ I need to check if the AA degradation pathway really leads back to APC. Anyway, it is a convenient buffered pool to dump it back into. For the purposes of the full model we use a rate of degradation of 0.2/sec Raised decay to 0.4 : see PLA35.g notes for Feb17 215.9 -18.8920989825 white 1 kinetics_1676_0_ * Degrade_AA_1789_0__Kf * Arachidonic_Acid_1779_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Degrade\_AA\_1789\_0\_\_Kf}\mathrm{Arachidonic\_Acid\_1779\_0\_}$ To start off, same kinetics as the PLA2-Ca-act direct pathway. Oops ! Missed out the Ca input to this pathway first time round. Let's raise the forward rate about 3x to 5e-6. This will let us reduce the rather high rates we have used for the kenz on PLA2*-Ca. In fact, it may be that the rates are not that different, just that this pathway for getting the PLA2 to the memb is more efficien.... 230.9 -18.8920989825 white 1 kinetics_1676_0_ * PLA2_p_Ca_act_1791_0__Kf * PLA2_p_1777_0_*Ca_2413_0_-kinetics_1676_0_ * PLA2_p_Ca_act_1791_0__Kb * PLA2_p_Ca_1772_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PLA2\_p\_Ca\_act\_1791\_0\_\_Kf}\mathrm{PLA2\_p\_1777\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PLA2\_p\_Ca\_act\_1791\_0\_\_Kb}\mathrm{PLA2\_p\_Ca\_1772\_0\_}$ 244.9 -18.8920989825 white 1 kinetics_1676_0_ * dephosphorylate_PLA2_p_1793_0__Kf * PLA2_p_1777_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{dephosphorylate\_PLA2\_p\_1793\_0\_\_Kf}\mathrm{PLA2\_p\_1777\_0\_}$ Affinity for Ca = 1uM without AlF, 0.1 with: from Smrcka et al science 251 pp 804-807 1991 so [Ca].kf = kb so kb/kf = 1 * 6e5 = 1/1.66e-6 11 June 1996: Raised affinity to 5e-6 to maintain balance. See notes. 303.9 -18.8920989825 white 2 kinetics_1676_0_ * Act_PLC_Ca_1821_0__Kf * PLC_1797_0_*Ca_2413_0_-kinetics_1676_0_ * Act_PLC_Ca_1821_0__Kb * PLC_Ca_1801_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Act\_PLC\_Ca\_1821\_0\_\_Kf}\mathrm{PLC\_1797\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Act\_PLC\_Ca\_1821\_0\_\_Kb}\mathrm{PLC\_Ca\_1801\_0\_}$ The enzyme is IP3 5-phosphomonesterase. about 45K. Actual products are Ins(1,4)P2, and cIns(1:2,4,5)P3. review in Majerus et al Science 234 1519-1526, 1986. Meyer and Stryer 1988 PNAS 85:5051-5055 est decay of IP3 at 1-3/sec 318.9 -18.8920989825 white 2 kinetics_1676_0_ * Degrade_IP3_1823_0__Kf * IP3_1817_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Degrade\_IP3\_1823\_0\_\_Kf}\mathrm{IP3\_1817\_0\_}$ These rates are the same as for degrading IP3, but I am sure that they could be improved. Lets double kf to 0.2, since the amount of DAG in the cell should be _lessthan_= 1uM. Need to double it again, for the same reason. kf now 0.5 27 June 1996 kf is now 0.02 to get 50 sec time course 30 Aug 1997: Raised kf to 0.11 to accomodate PLC_gamma 27 Mar 1998: kf now 0.15 for PLC_gamma 332.9 -18.8920989825 white 2 kinetics_1676_0_ * Degrade_DAG_1825_0__Kf * DAG_1815_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Degrade\_DAG\_1825\_0\_\_Kf}\mathrm{DAG\_1815\_0\_}$ Affinity for Gq is _greaterthan_ 20 nM (Smrcka et al Science251 804-807 1991) so [Gq].kf = kb so 40nM * 6e5 = kb/kf = 24e3 so kf = 4.2e-5, kb =1 347.9 -18.8920989825 white 2 kinetics_1676_0_ * Act_PLC_by_Gq_1827_0__Kf * PLC_Ca_1801_0_*G_pGTP_2329_0_-kinetics_1676_0_ * Act_PLC_by_Gq_1827_0__Kb * PLC_Ca_Gq_1806_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Act\_PLC\_by\_Gq\_1827\_0\_\_Kf}\mathrm{PLC\_Ca\_1801\_0\_}\mathrm{G\_pGTP\_2329\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Act\_PLC\_by\_Gq\_1827\_0\_\_Kb}\mathrm{PLC\_Ca\_Gq\_1806\_0\_}$ This process is assumed to be directly caused by the inactivation of the G*GTP to G*GDP. Hence, kf = .013 /sec = 0.8/min, same as the rate for Inact-G. kb = 0 since this is irreversible. We may be interested in studying the role of PLC as a GAP. If so, the kf would be faster here than in Inact-G 362.9 -18.8920989825 white 2 kinetics_1676_0_ * Inact_PLC_Gq_1829_0__Kf * PLC_Ca_Gq_1806_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Inact\_PLC\_Gq\_1829\_0\_\_Kf}\mathrm{PLC\_Ca\_Gq\_1806\_0\_}$ this binding does not produce active PLC. This step was needed to implement the described (Smrcka et al) increase in affinity for Ca by PLC once Gq was bound. The kinetics are the same as the binding step for Ca-PLC to Gq. June 1996: Changed the kf to 4.2e-5 to 4.2e-6 to preserve balance around the reactions. 376.9 -18.8920989825 white 2 kinetics_1676_0_ * PLC_bind_Gq_1831_0__Kf * G_pGTP_2329_0_*PLC_1797_0_-kinetics_1676_0_ * PLC_bind_Gq_1831_0__Kb * PLC_Gq_1811_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PLC\_bind\_Gq\_1831\_0\_\_Kf}\mathrm{G\_pGTP\_2329\_0\_}\mathrm{PLC\_1797\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PLC\_bind\_Gq\_1831\_0\_\_Kb}\mathrm{PLC\_Gq\_1811\_0\_}$ this step has a high affinity for Ca, from Smrcka et al. 0.1uM so kf /kb = 1/6e4 = 1.666e-5:1. See the Act-PLC-by-Gq reac. 11 Jun 1996: Raised kf to 5e-5 based on match to conc-eff curves from Smrcka et al. 391.9 -18.8920989825 white 2 kinetics_1676_0_ * PLC_Gq_bind_Ca_1833_0__Kf * PLC_Gq_1811_0_*Ca_2413_0_-kinetics_1676_0_ * PLC_Gq_bind_Ca_1833_0__Kb * PLC_Ca_Gq_1806_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PLC\_Gq\_bind\_Ca\_1833\_0\_\_Kf}\mathrm{PLC\_Gq\_1811\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PLC\_Gq\_bind\_Ca\_1833\_0\_\_Kb}\mathrm{PLC\_Ca\_Gq\_1806\_0\_}$ The rate consts give a total binding affinity of only 449.8 -18.8920989825 white 3 kinetics_1676_0_ * Antag_bind_Rec_Gq_1841_0__Kf * mGluRAntag_1837_0_*Rec_Gq_2311_0_-kinetics_1676_0_ * Antag_bind_Rec_Gq_1841_0__Kb * Blocked_Rec_Gq_1839_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Antag\_bind\_Rec\_Gq\_1841\_0\_\_Kf}\mathrm{mGluRAntag\_1837\_0\_}\mathrm{Rec\_Gq\_2311\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Antag\_bind\_Rec\_Gq\_1841\_0\_\_Kb}\mathrm{Blocked\_Rec\_Gq\_1839\_0\_}$ 596.8 -18.8920989825 white 4 kinetics_1676_0_ * mGluR_barr2_Raf_scaffolding_1903_0__Kf * craf_1_1865_0_*Internal_mGluR_p_dot_barr2_2814_0_-kinetics_1676_0_ * mGluR_barr2_Raf_scaffolding_1903_0__Kb * craf_1_p_1867_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{mGluR\_barr2\_Raf\_scaffolding\_1903\_0\_\_Kf}\mathrm{craf\_1\_1865\_0\_}\mathrm{Internal\_mGluR\_p\_dot\_barr2\_2814\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{mGluR\_barr2\_Raf\_scaffolding\_1903\_0\_\_Kb}\mathrm{craf\_1\_p\_1867\_0\_}$ Assume the binding is fast and limited only by the amount of Ras* available. So kf=kb/[craf-1] If kb is 1/sec, then kf = 1/0.2 uM = 1/(0.2 * 6e5) = 8.3e-6 Later: Raise it by 10 X to 4e-5 From Hallberg et al JBC 269:6 3913-3916 1994, 3% of cellular Raf is complexed with Ras. So we raise kb 4x to 4 This step needed to memb-anchor and activate Raf: Leevers et al Nature 369 411-414 (I don't.... 742.9 -18.8920989825 white 5 kinetics_1676_0_ * Ras_act_craf_1940_0__Kf * GTP_Ras_1922_0_*craf_1_p_1867_0_-kinetics_1676_0_ * Ras_act_craf_1940_0__Kb * Raf_p_GTP_Ras_1893_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Ras\_act\_craf\_1940\_0\_\_Kf}\mathrm{GTP\_Ras\_1922\_0\_}\mathrm{craf\_1\_p\_1867\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Ras\_act\_craf\_1940\_0\_\_Kb}\mathrm{Raf\_p\_GTP\_Ras\_1893\_0\_}$ SoS/GEF is present at 50 nM ie 3e4/cell. BetaGamma maxes out at 9e4. Assume we have 1/3 of the GEF active when the BetaGamma is 1.5e4. so 1e4 * kb = 2e4 * 1.5e4 * kf, so kf/kb = 3e-5. The rate of this equil should be reasonably fast, say 1/sec 758.0 -18.8920989825 white 5 kinetics_1676_0_ * bg_act_GEF_1942_0__Kf * inact_GEF_1912_0_*BetaGamma_2327_0_-kinetics_1676_0_ * bg_act_GEF_1942_0__Kb * GEF_Gprot_bg_1907_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{bg\_act\_GEF\_1942\_0\_\_Kf}\mathrm{inact\_GEF\_1912\_0\_}\mathrm{BetaGamma\_2327\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{bg\_act\_GEF\_1942\_0\_\_Kb}\mathrm{GEF\_Gprot\_bg\_1907\_0\_}$ 771.9 -18.8920989825 white 5 kinetics_1676_0_ * dephosph_GEF_1944_0__Kf * GEF_p_1917_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{dephosph\_GEF\_1944\_0\_\_Kf}\mathrm{GEF\_p\_1917\_0\_}$ This is extremely slow (1e-4), but it is significant as so little GAP actually gets complexed with it that the total GTP turnover rises only by 2-3 X (see Gibbs et al, JBC 265(33) 20437-20422) and Eccleston et al JBC 268(36) 27012-27019 kf = 1e-4 786.9 -18.8920989825 white 5 kinetics_1676_0_ * Ras_intrinsic_GTPase_1946_0__Kf * GTP_Ras_1922_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Ras\_intrinsic\_GTPase\_1946\_0\_\_Kf}\mathrm{GTP\_Ras\_1922\_0\_}$ Assume a reasonably good rate for dephosphorylating it, 1/sec 802.0 -18.8920989825 white 5 kinetics_1676_0_ * dephosph_GAP_1948_0__Kf * GAP_p_1926_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{dephosph\_GAP\_1948\_0\_\_Kf}\mathrm{GAP\_p\_1926\_0\_}$ We have no numbers for this. It is probably between the two extremes represented by the CaMKII phosph states, and I have used guesses based on this. kf=1e-4 kb=1 The reaction is based on Farnsworth et al Nature 376 524-527 1995 815.9 -18.8920989825 white 5 kinetics_1676_0_ * CaM_bind_GEF_1950_0__Kf * inact_GEF_1912_0_*CaM_Ca4_2091_0_-kinetics_1676_0_ * CaM_bind_GEF_1950_0__Kb * CaM_GEF_1935_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_bind\_GEF\_1950\_0\_\_Kf}\mathrm{inact\_GEF\_1912\_0\_}\mathrm{CaM\_Ca4\_2091\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_bind\_GEF\_1950\_0\_\_Kb}\mathrm{CaM\_GEF\_1935\_0\_}$ 830.9 -18.8920989825 white 5 kinetics_1676_0_ * dephosph_inact_GEF_p_1952_0__Kf * inact_GEF_p_1933_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{dephosph\_inact\_GEF\_p\_1952\_0\_\_Kf}\mathrm{inact\_GEF\_p\_1933\_0\_}$ Affinity of EGFR for EGF is complex: depends on [EGFR]. We'll assume fixed [EGFR] and use exptal affinity ~20 nM (see Sherrill and Kyte Biochem 1996 35 5705-5718, Berkers et al JBC 266:2 922-927 1991, Sorokin et al JBC 269:13 9752-9759 1994). Tau =~2 min (Davis et al JBC 263:11 5373-5379 1988) or Berkers Kass = 6.2e5/M/sec, Kdiss=3.5e-4/sec. Sherrill and Kyte have Hill Coeff=1.7 890.0 -18.8920989825 white 6 kinetics_1676_0_ * act_EGFR_1970_0__Kf * EGFR_1956_0_*EGF_1966_0_-kinetics_1676_0_ * act_EGFR_1970_0__Kb * L_dot_EGFR_1958_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{act\_EGFR\_1970\_0\_\_Kf}\mathrm{EGFR\_1956\_0\_}\mathrm{EGF\_1966\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{act\_EGFR\_1970\_0\_\_Kb}\mathrm{L\_dot\_EGFR\_1958\_0\_}$ See Helin and Beguinot JBC 266:13 1991 pg 8363-8368. In Fig 3 they have internalization tau about 10 min, equil at about 20% EGF available. So kf = 4x kb, and 1/(kf + kb) = 600 sec so kb = 1/3K = 3.3e-4, and kf = 1.33e-3. This doesn't take into account the unbound receptor, so we need to push the kf up a bit, to 0.002 903.9 -18.8920989825 white 6 kinetics_1676_0_ * Internalize_1972_0__Kf * L_dot_EGFR_1958_0_-kinetics_1676_0_ * Internalize_1972_0__Kb * Internal_L_dot_EGFR_1968_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Internalize\_1972\_0\_\_Kf}\mathrm{L\_dot\_EGFR\_1958\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Internalize\_1972\_0\_\_Kb}\mathrm{Internal\_L\_dot\_EGFR\_1968\_0\_}$ Time course of decline of phosph is 20 min. Part of this is the turnoff time of the EGFR itself. Lets assume a tau of 10 min for this dephosph. It may be wildly off. 11.5 -356.136163799 white 7 kinetics_1676_0_ * SHC_p_dephospho_2002_0__Kf * SHC_p_1983_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{SHC\_p\_dephospho\_2002\_0\_\_Kf}\mathrm{SHC\_p\_1983\_0\_}$ Sasaoka et al JBC 269:51 pp 32621 1994, table on pg 32623 indicates that this pathway accounts for about 50% of the GEF activation. (88% - 39%). Error is large, about 20%. Fig 1 is most useful in constraining rates. Chook et al JBC 271:48 pp 30472, 1996 say that the Kd is 0.2 uM for Shc binding to EGFR. The Kd for Grb direct binding is 0.7, so we'll ignore it. 26.5 -356.136163799 white 7 kinetics_1676_0_ * SHC_bind_Sos_dot_Grb2_2004_0__Kf * Sos_dot_Grb2_1989_0_*SHC_p_1983_0_-kinetics_1676_0_ * SHC_bind_Sos_dot_Grb2_2004_0__Kb * SHC_p_dot_Sos_dot_Grb2_1976_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{SHC\_bind\_Sos\_dot\_Grb2\_2004\_0\_\_Kf}\mathrm{Sos\_dot\_Grb2\_1989\_0\_}\mathrm{SHC\_p\_1983\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{SHC\_bind\_Sos\_dot\_Grb2\_2004\_0\_\_Kb}\mathrm{SHC\_p\_dot\_Sos\_dot\_Grb2\_1976\_0\_}$ Same rates as Grb2_bind_Sos: Porfiri and McCormick JBC 271:10 pp 5871 1996 show that the binding is not affected by the phosph. 40.5 -356.136163799 white 7 kinetics_1676_0_ * Grb2_bind_Sos_p_2006_0__Kf * Grb2_1987_0_*Sos_p_1991_0_-kinetics_1676_0_ * Grb2_bind_Sos_p_2006_0__Kb * Sos_p_dot_Grb2_1985_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Grb2\_bind\_Sos\_p\_2006\_0\_\_Kf}\mathrm{Grb2\_1987\_0\_}\mathrm{Sos\_p\_1991\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Grb2\_bind\_Sos\_p\_2006\_0\_\_Kb}\mathrm{Sos\_p\_dot\_Grb2\_1985\_0\_}$ The only clue I have to these rates is from the time courses of the EGF activation, which is around 1 to 5 min. The dephosph would be expected to be of the same order, perhaps a bit longer. Lets use 0.002 which is about 8 min. Sep 17: The transient activation curve matches better with kf = 0.001 55.5 -356.136163799 white 7 kinetics_1676_0_ * dephosph_Sos_2008_0__Kf * Sos_p_1991_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{dephosph\_Sos\_2008\_0\_\_Kf}\mathrm{Sos\_p\_1991\_0\_}$ As there are 2 SH3 domains, this reaction could be 2nd order. I have a Kd of 22 uM from peptide binding (Lemmon et al JBC 269:50 pg 31653). However, Chook et al JBC 271:48 pg30472 say it is 0.4uM with purified proteins, so we believe them. They say it is 1:1 binding. 70.5 -356.136163799 white 7 kinetics_1676_0_ * Grb2_bind_Sos_2010_0__Kf * Sos_1993_0_*Grb2_1987_0_-kinetics_1676_0_ * Grb2_bind_Sos_2010_0__Kb * Sos_dot_Grb2_1989_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Grb2\_bind\_Sos\_2010\_0\_\_Kf}\mathrm{Sos\_1993\_0\_}\mathrm{Grb2\_1987\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Grb2\_bind\_Sos\_2010\_0\_\_Kb}\mathrm{Sos\_dot\_Grb2\_1989\_0\_}$ 84.5 -356.136163799 white 7 kinetics_1676_0_ * Grb2_bind_SHC_2012_0__Kf * Grb2_1987_0_*SHC_p_1983_0_-kinetics_1676_0_ * Grb2_bind_SHC_2012_0__Kb * SHC_p_Grb2_clx_1995_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Grb2\_bind\_SHC\_2012\_0\_\_Kf}\mathrm{Grb2\_1987\_0\_}\mathrm{SHC\_p\_1983\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Grb2\_bind\_SHC\_2012\_0\_\_Kb}\mathrm{SHC\_p\_Grb2\_clx\_1995\_0\_}$ Nice curves from Homma et al JBC 263:14 6592-6598 1988 Fig 5c. The activity falls above 10 uM, but that is too high to reach physiologically anyway, so we'll ignore the higher pts and match the lower ones only. Half-max at 1 uM. But Wahl et al JBC 267:15 10447-10456 1992 have half-max at 56 nM which is what I'll use. 157.7 -210.023866348 white 8 kinetics_1676_0_ * Ca_act_PLC_g_2033_0__Kf * PLC_g_2016_0_*Ca_2413_0_-kinetics_1676_0_ * Ca_act_PLC_g_2033_0__Kb * Ca_dot_PLC_g_2020_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Ca\_act\_PLC\_g\_2033\_0\_\_Kf}\mathrm{PLC\_g\_2016\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Ca\_act\_PLC\_g\_2033\_0\_\_Kb}\mathrm{Ca\_dot\_PLC\_g\_2020\_0\_}$ Again, we refer to Homma et al and Wahl et al, for preference using Wahl. Half-Max of the phosph form is at 316 nM. Use kb of 10 as this is likely to be pretty fast. Did some curve comparisons, and instead of 316 nM giving a kf of 5.27e-5, we will use 8e-5 for kf. 16 Sep 97. As we are now phosphorylating the Ca-bound form, equils have shifted. kf should now be 2e-5 to match the curves. 171.9 -210.023866348 white 8 kinetics_1676_0_ * Ca_act_PLC_g_p_2035_0__Kf * PLC_g_p_2018_0_*Ca_2413_0_-kinetics_1676_0_ * Ca_act_PLC_g_p_2035_0__Kb * Ca_dot_PLC_g_p_2024_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Ca\_act\_PLC\_g\_p\_2035\_0\_\_Kf}\mathrm{PLC\_g\_p\_2018\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Ca\_act\_PLC\_g\_p\_2035\_0\_\_Kb}\mathrm{Ca\_dot\_PLC\_g\_p\_2024\_0\_}$ 186.9 -210.023866348 white 8 kinetics_1676_0_ * dephosph_PLC_g_2037_0__Kf * Ca_dot_PLC_g_p_2024_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{dephosph\_PLC\_g\_2037\_0\_\_Kf}\mathrm{Ca\_dot\_PLC\_g\_p\_2024\_0\_}$ 202.0 -210.023866348 white 8 kinetics_1676_0_ * PLC_g_p_dephospho_2039_0__Kf * PLC_g_p_2018_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PLC\_g\_p\_dephospho\_2039\_0\_\_Kf}\mathrm{PLC\_g\_p\_2018\_0\_}$ This is tricky. There is some cooperativity here arising from interactions between the subunits of the CAMKII holoenzyme. However, the stoichiometry is 1. Kb/Kf = 6e4 #/cell. Rate is fast (see Hanson et al Neuron 12 943-956 1994) so lets say kb = 10. This gives kf = 1.6667e-4 H_andS AnnRev Biochem 92 give tau for dissoc as 0.2 sec at low Ca, 0.4 at high. Low Ca = 100 nM = physiol. 303.9 -210.023866348 white 9 kinetics_1676_0_ * CaMKII_bind_CaM_2085_0__Kf * CaM_Ca4_2091_0_*CaMKII_2043_0_-kinetics_1676_0_ * CaMKII_bind_CaM_2085_0__Kb * CaMKII_CaM_2045_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaMKII\_bind\_CaM\_2085\_0\_\_Kf}\mathrm{CaM\_Ca4\_2091\_0\_}\mathrm{CaMKII\_2043\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaMKII\_bind\_CaM\_2085\_0\_\_Kb}\mathrm{CaMKII\_CaM\_2045\_0\_}$ Affinity is up 1000X. Time to release is about 20 sec, so the kb is OK at 0.1 This makes Kf around 1.6666e-3 318.9 -210.023866348 white 9 kinetics_1676_0_ * CaMKII_thr286_bind_CaM_2087_0__Kf * CaM_Ca4_2091_0_*CaMKII_thr286_2051_0_-kinetics_1676_0_ * CaMKII_thr286_bind_CaM_2087_0__Kb * CaMKII_thr286_CaM_2047_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaMKII\_thr286\_bind\_CaM\_2087\_0\_\_Kf}\mathrm{CaM\_Ca4\_2091\_0\_}\mathrm{CaMKII\_thr286\_2051\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaMKII\_thr286\_bind\_CaM\_2087\_0\_\_Kb}\mathrm{CaMKII\_thr286\_CaM\_2047\_0\_}$ Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10 479.9 -210.023866348 white 10 kinetics_1676_0_ * CaM_Ca3_bind_Ca_2123_0__Kf * CaM_Ca3_2101_0_*Ca_2413_0_-kinetics_1676_0_ * CaM_Ca3_bind_Ca_2123_0__Kb * CaM_Ca4_2091_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_Ca3\_bind\_Ca\_2123\_0\_\_Kf}\mathrm{CaM\_Ca3\_2101\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_Ca3\_bind\_Ca\_2123\_0\_\_Kb}\mathrm{CaM\_Ca4\_2091\_0\_}$ Surprisingly, no direct info on rates from neurogranin at this time. These rates are based on GAP-43 binding studies. As GAP-43 and neurogranin share near identity in the CaM/PKC binding regions, and also similarity in phosph and dephosph rates, I am borrowing GAP-43 kinetic info. See Alexander et al JBC 262:13 6108-6113 1987 494.0 -210.023866348 white 10 kinetics_1676_0_ * neurogranin_bind_CaM_2125_0__Kf * neurogranin_2099_0_*CaM_2093_0_-kinetics_1676_0_ * neurogranin_bind_CaM_2125_0__Kb * neurogranin_CaM_2095_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{neurogranin\_bind\_CaM\_2125\_0\_\_Kf}\mathrm{neurogranin\_2099\_0\_}\mathrm{CaM\_2093\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{neurogranin\_bind\_CaM\_2125\_0\_\_Kb}\mathrm{neurogranin\_CaM\_2095\_0\_}$ This is put in to keep the basal levels of neurogranin* experimentally reasonable. From various papers, specially Ramakers et al JBC 270:23 1995 13892-13898, it looks like the basal level of phosph is between 20 and 40%. I est around 25 % The kf of 0.005 gives around this level at basal PKC activity levels of 0.1 uM active PKC. 508.9 -210.023866348 white 10 kinetics_1676_0_ * dephosph_neurogranin_2127_0__Kf * neurogranin_p_2097_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{dephosph\_neurogranin\_2127\_0\_\_Kf}\mathrm{neurogranin\_p\_2097\_0\_}$ Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer _and Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 523.9 -210.023866348 white 10 kinetics_1676_0_ * CaM_bind_Ca_2129_0__Kf * CaM_2093_0_*Ca_2413_0_-kinetics_1676_0_ * CaM_bind_Ca_2129_0__Kb * CaM_Ca_2121_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_bind\_Ca\_2129\_0\_\_Kf}\mathrm{CaM\_2093\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_bind\_Ca\_2129\_0\_\_Kb}\mathrm{CaM\_Ca\_2121\_0\_}$ K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10 538.0 -210.023866348 white 10 kinetics_1676_0_ * CaM_Ca2_bind_Ca_2131_0__Kf * Ca_2413_0_*CaM_Ca2_2119_0_-kinetics_1676_0_ * CaM_Ca2_bind_Ca_2131_0__Kb * CaM_Ca3_2101_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_Ca2\_bind\_Ca\_2131\_0\_\_Kf}\mathrm{Ca\_2413\_0\_}\mathrm{CaM\_Ca2\_2119\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_Ca2\_bind\_Ca\_2131\_0\_\_Kb}\mathrm{CaM\_Ca3\_2101\_0\_}$ Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer _and Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 552.8 -210.023866348 white 10 kinetics_1676_0_ * CaM_Ca_bind_Ca_2133_0__Kf * CaM_Ca_2121_0_*Ca_2413_0_-kinetics_1676_0_ * CaM_Ca_bind_Ca_2133_0__Kb * CaM_Ca2_2119_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_Ca\_bind\_Ca\_2133\_0\_\_Kf}\mathrm{CaM\_Ca\_2121\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_Ca\_bind\_Ca\_2133\_0\_\_Kb}\mathrm{CaM\_Ca2\_2119\_0\_}$ 567.9 -210.023866348 white 10 kinetics_1676_0_ * CaMKIII_bind_CaM_Ca4_2135_0__Kf * CaM_Ca4_2091_0_*CaMKIII_2686_0_-kinetics_1676_0_ * CaMKIII_bind_CaM_Ca4_2135_0__Kb * CaMKIII_CaM_Ca4_2688_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaMKIII\_bind\_CaM\_Ca4\_2135\_0\_\_Kf}\mathrm{CaM\_Ca4\_2091\_0\_}\mathrm{CaMKIII\_2686\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaMKIII\_bind\_CaM\_Ca4\_2135\_0\_\_Kb}\mathrm{CaMKIII\_CaM\_Ca4\_2688\_0\_}$ K inhib = 1nM from Cohen Ann Rev Bioch 1989, 4 nM from Foukes et al Assume 2 nM. kf /kb = 8.333e-4 596.8 -210.023866348 white 11 kinetics_1676_0_ * Inact_PP1_2164_0__Kf * PP1_active_2139_0_*I1_p_2158_0_-kinetics_1676_0_ * Inact_PP1_2164_0__Kb * PP1_I1_p_2160_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Inact\_PP1\_2164\_0\_\_Kf}\mathrm{PP1\_active\_2139\_0\_}\mathrm{I1\_p\_2158\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Inact\_PP1\_2164\_0\_\_Kb}\mathrm{PP1\_I1\_p\_2160\_0\_}$ Let us assume that the equil in this case is very far over to the right. This is probably safe. 611.0 -210.023866348 white 11 kinetics_1676_0_ * dissoc_PP1_I1_2166_0__Kf * PP1_I1_2162_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{dissoc\_PP1\_I1\_2166\_0\_\_Kf}\mathrm{PP1\_I1\_2162\_0\_}$ 626.2 -209.521416907 white black kinetics_1676_0_ * basal_phosph_I1_2168_0__Kf * I1_2156_0_-kinetics_1676_0_ * basal_phosph_I1_2168_0__Kb * I1_p_2158_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{basal\_phosph\_I1\_2168\_0\_\_Kf}\mathrm{I1\_2156\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{basal\_phosph\_I1\_2168\_0\_\_Kb}\mathrm{I1\_p\_2158\_0\_}$ This process is probably much more complicated and involves CaM. However, as I can't find detailed info I am bundling this into a single step. Based on Steemer and Klee pg 6863, the Kact is 0.5 uM. kf/kb = 1/(0.5 * 6e5)^2 = 1.11e-11 742.9 -210.023866348 white 12 kinetics_1676_0_ * Ca_bind_CaNAB_Ca2_2182_0__Kf * Ca_2413_0_^2*CaNAB_Ca2_2174_0_-kinetics_1676_0_ * Ca_bind_CaNAB_Ca2_2182_0__Kb * CaNAB_Ca4_2114_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Ca\_bind\_CaNAB\_Ca2\_2182\_0\_\_Kf}\mathrm{Ca\_2413\_0\_}^2\mathrm{CaNAB\_Ca2\_2174\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Ca\_bind\_CaNAB\_Ca2\_2182\_0\_\_Kb}\mathrm{CaNAB\_Ca4\_2114\_0\_}$ going on the experience with CaM, we put the fast (high affinity) sites first. We only know (Stemmer and Klee) that the affinity is _lessthan_ 70 nM. Assuming 10 nM at first, we get kf = 2.78e-8, kb = 1. Try 20 nM. kf = 7e-9, kb = 1 758.0 -210.023866348 white 12 kinetics_1676_0_ * Ca_bind_CaNAB_2184_0__Kf * CaNAB_2172_0_*Ca_2413_0_^2-kinetics_1676_0_ * Ca_bind_CaNAB_2184_0__Kb * CaNAB_Ca2_2174_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Ca\_bind\_CaNAB\_2184\_0\_\_Kf}\mathrm{CaNAB\_2172\_0\_}\mathrm{Ca\_2413\_0\_}^2-\mathrm{kinetics\_1676\_0\_}\mathrm{Ca\_bind\_CaNAB\_2184\_0\_\_Kb}\mathrm{CaNAB\_Ca2\_2174\_0\_}$ Disabled. See notes for PP2B7.g 771.9 -210.023866348 white 12 kinetics_1676_0_ * CaM_Ca2_bind_CaNAB_2186_0__Kf * CaNAB_Ca4_2114_0_*CaM_Ca2_2119_0_-kinetics_1676_0_ * CaM_Ca2_bind_CaNAB_2186_0__Kb * CaMCa2_CaNAB_2178_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_Ca2\_bind\_CaNAB\_2186\_0\_\_Kf}\mathrm{CaNAB\_Ca4\_2114\_0\_}\mathrm{CaM\_Ca2\_2119\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_Ca2\_bind\_CaNAB\_2186\_0\_\_Kb}\mathrm{CaMCa2\_CaNAB\_2178\_0\_}$ 786.9 -210.023866348 white 12 kinetics_1676_0_ * CaMCa3_bind_CaNAB_2188_0__Kf * CaNAB_Ca4_2114_0_*CaM_Ca3_2101_0_-kinetics_1676_0_ * CaMCa3_bind_CaNAB_2188_0__Kb * CaMCa3_CaNAB_2176_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaMCa3\_bind\_CaNAB\_2188\_0\_\_Kf}\mathrm{CaNAB\_Ca4\_2114\_0\_}\mathrm{CaM\_Ca3\_2101\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaMCa3\_bind\_CaNAB\_2188\_0\_\_Kb}\mathrm{CaMCa3\_CaNAB\_2176\_0\_}$ 802.0 -210.023866348 white 12 kinetics_1676_0_ * CaMCa4_bind_CaNAB_2190_0__Kf * CaNAB_Ca4_2114_0_*CaM_Ca4_2091_0_-kinetics_1676_0_ * CaMCa4_bind_CaNAB_2190_0__Kb * CaMCa4_CaNAB_2180_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaMCa4\_bind\_CaNAB\_2190\_0\_\_Kf}\mathrm{CaNAB\_Ca4\_2114\_0\_}\mathrm{CaM\_Ca4\_2091\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaMCa4\_bind\_CaNAB\_2190\_0\_\_Kb}\mathrm{CaMCa4\_CaNAB\_2180\_0\_}$ Hasler et al FASEB J 6:2734-2741 1992 say Kd =1e-7M for type II, 5.6e-8 M for type I. Take mean which comes to 2e-13 #/cell Smith et al PNAS USA 78:3 1591-1595 1981 have better data. First kf/kb=2.1e7/M = 3.5e-5 (#/cell). Ogreid and Doskeland Febs Lett 129:2 287-292 1981 have figs suggesting time course of complete assoc is _lessthan_ 1 min. 890.0 -210.023866348 white 13 kinetics_1676_0_ * cAMP_bind_site_B1_2223_0__Kf * R2C2_2205_0_*cAMP_2239_0_-kinetics_1676_0_ * cAMP_bind_site_B1_2223_0__Kb * R2C2_cAMP_2207_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{cAMP\_bind\_site\_B1\_2223\_0\_\_Kf}\mathrm{R2C2\_2205\_0\_}\mathrm{cAMP\_2239\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{cAMP\_bind\_site\_B1\_2223\_0\_\_Kb}\mathrm{R2C2\_cAMP\_2207\_0\_}$ For now let us set this to the same Km (1e-7M) as site B. This gives kf/kb = .7e-7M * 1e6 / (6e5^2) : 1/(6e5^2) = 2e-13:2.77e-12 Smith et al have better values. They say that this is cooperative, so the consts are now kf/kb =8.3e-4 903.9 -210.023866348 white 13 kinetics_1676_0_ * cAMP_bind_site_B2_2225_0__Kf * cAMP_2239_0_*R2C2_cAMP_2207_0_-kinetics_1676_0_ * cAMP_bind_site_B2_2225_0__Kb * R2C2_cAMP2_2209_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{cAMP\_bind\_site\_B2\_2225\_0\_\_Kf}\mathrm{cAMP\_2239\_0\_}\mathrm{R2C2\_cAMP\_2207\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{cAMP\_bind\_site\_B2\_2225\_0\_\_Kb}\mathrm{R2C2\_cAMP2\_2209\_0\_}$ 918.9 -210.023866348 white 13 kinetics_1676_0_ * cAMP_bind_site_A1_2227_0__Kf * R2C2_cAMP2_2209_0_*cAMP_2239_0_-kinetics_1676_0_ * cAMP_bind_site_A1_2227_0__Kb * R2C2_cAMP3_2211_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{cAMP\_bind\_site\_A1\_2227\_0\_\_Kf}\mathrm{R2C2\_cAMP2\_2209\_0\_}\mathrm{cAMP\_2239\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{cAMP\_bind\_site\_A1\_2227\_0\_\_Kb}\mathrm{R2C2\_cAMP3\_2211\_0\_}$ 934.0 -210.023866348 white 13 kinetics_1676_0_ * cAMP_bind_site_A2_2229_0__Kf * R2C2_cAMP3_2211_0_*cAMP_2239_0_-kinetics_1676_0_ * cAMP_bind_site_A2_2229_0__Kb * R2C2_cAMP4_2213_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{cAMP\_bind\_site\_A2\_2229\_0\_\_Kf}\mathrm{R2C2\_cAMP3\_2211\_0\_}\mathrm{cAMP\_2239\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{cAMP\_bind\_site\_A2\_2229\_0\_\_Kb}\mathrm{R2C2\_cAMP4\_2213\_0\_}$ This has to be fast, as the activation of PKA by cAMP is also fast. kf was 10 947.9 -210.023866348 white 13 kinetics_1676_0_ * Release_C1_2231_0__Kf * R2C2_cAMP4_2213_0_-kinetics_1676_0_ * Release_C1_2231_0__Kb * PKA_active_2194_0_*R2C_cAMP4_2215_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Release\_C1\_2231\_0\_\_Kf}\mathrm{R2C2\_cAMP4\_2213\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Release\_C1\_2231\_0\_\_Kb}\mathrm{PKA\_active\_2194\_0\_}\mathrm{R2C\_cAMP4\_2215\_0\_}$ 962.9 -210.023866348 white 13 kinetics_1676_0_ * Release_C2_2233_0__Kf * R2C_cAMP4_2215_0_-kinetics_1676_0_ * Release_C2_2233_0__Kb * R2_cAMP4_2217_0_*PKA_active_2194_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Release\_C2\_2233\_0\_\_Kf}\mathrm{R2C\_cAMP4\_2215\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Release\_C2\_2233\_0\_\_Kb}\mathrm{R2\_cAMP4\_2217\_0\_}\mathrm{PKA\_active\_2194\_0\_}$ This has to be set to zero for matching the expts in vitro. In vivo we need to consider the inhibition though. kf = 1e-5 kb = 1 977.0 -210.023866348 white 13 kinetics_1676_0_ * inhib_PKA_2235_0__Kf * PKA_active_2194_0_*PKA_inhibitor_2219_0_-kinetics_1676_0_ * inhib_PKA_2235_0__Kb * inhibited_PKA_2221_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{inhib\_PKA\_2235\_0\_\_Kf}\mathrm{PKA\_active\_2194\_0\_}\mathrm{PKA\_inhibitor\_2219\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{inhib\_PKA\_2235\_0\_\_Kb}\mathrm{inhibited\_PKA\_2221\_0\_}$ Half-max at 20 nM CaM (Tang et al JBC 266:13 8595-8603 1991 kb/kf = 20 nM = 12000 #/cell so kf = kb/12000 = kb * 8.333e-5 11.0 -401.256123603 white 14 kinetics_1676_0_ * CaM_bind_AC1_2289_0__Kf * CaM_Ca4_2091_0_*AC1_2247_0_-kinetics_1676_0_ * CaM_bind_AC1_2289_0__Kb * AC1_CaM_2243_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_bind\_AC1\_2289\_0\_\_Kf}\mathrm{CaM\_Ca4\_2091\_0\_}\mathrm{AC1\_2247\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_bind\_AC1\_2289\_0\_\_Kb}\mathrm{AC1\_CaM\_2243\_0\_}$ Random rate. 25.8 -401.256123603 white 14 kinetics_1676_0_ * dephosph_AC2_2291_0__Kf * AC2_p_2249_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{dephosph\_AC2\_2291\_0\_\_Kf}\mathrm{AC2\_p\_2249\_0\_}$ Half-max at around 3nM = kb/kf from fig 5 in Feinstein et al PNAS USA 88 10173-10177 1991 kf = kb/1800 = 5.56e-4 kb Ofer's thesis data indicates it is more like 2 nM. kf = kb/1200 = 8.33e-4 39.9 -401.256123603 white 14 kinetics_1676_0_ * Gs_bind_AC2_2293_0__Kf * AC2_2257_0_*Gs_alpha_2335_0_-kinetics_1676_0_ * Gs_bind_AC2_2293_0__Kb * AC2_Gs_2253_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Gs\_bind\_AC2\_2293\_0\_\_Kf}\mathrm{AC2\_2257\_0\_}\mathrm{Gs\_alpha\_2335\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Gs\_bind\_AC2\_2293\_0\_\_Kb}\mathrm{AC2\_Gs\_2253\_0\_}$ Half-max 8nM from Tang et al JBC266:13 8595-8603 kb/kf = 8 nM = 4800#/cell so kf = kb * 2.08e-4 55.0 -401.256123603 white 14 kinetics_1676_0_ * Gs_bind_AC1_2295_0__Kf * Gs_alpha_2335_0_*AC1_2247_0_-kinetics_1676_0_ * Gs_bind_AC1_2295_0__Kb * AC1_Gs_2259_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Gs\_bind\_AC1\_2295\_0\_\_Kf}\mathrm{Gs\_alpha\_2335\_0\_}\mathrm{AC1\_2247\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Gs\_bind\_AC1\_2295\_0\_\_Kb}\mathrm{AC1\_Gs\_2259\_0\_}$ kb/kf = 1.2 nM so kf = kb/720 = 1.3888 * kb. 69.8 -401.256123603 white 14 kinetics_1676_0_ * Gs_bind_AC2_p_2297_0__Kf * AC2_p_2249_0_*Gs_alpha_2335_0_-kinetics_1676_0_ * Gs_bind_AC2_p_2297_0__Kb * AC2_p_Gs_2263_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Gs\_bind\_AC2\_p\_2297\_0\_\_Kf}\mathrm{AC2\_p\_2249\_0\_}\mathrm{Gs\_alpha\_2335\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Gs\_bind\_AC2\_p\_2297\_0\_\_Kb}\mathrm{AC2\_p\_Gs\_2263\_0\_}$ The rates for this are poorly constrained. In adipocytes (probably a different PDE) the dephosphorylation is complete within 15 min, but there are no intermediate time points so it could be much faster. Identity of phosphatase etc is still unknown. 83.9 -401.256123603 white 14 kinetics_1676_0_ * dephosph_PDE_2299_0__Kf * cAMP_PDE_p_2272_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{dephosph\_PDE\_2299\_0\_\_Kf}\mathrm{cAMP\_PDE\_p\_2272\_0\_}$ For olf epi PDE1, affinity is 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec. Then kf = 5 / (0.007 * 6e5) = 1.2e-3 99.0 -401.256123603 white 14 kinetics_1676_0_ * CaM_bind_PDE1_2301_0__Kf * CaM_Ca4_2091_0_*PDE1_2277_0_-kinetics_1676_0_ * CaM_bind_PDE1_2301_0__Kb * CaM_dot_PDE1_2282_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_bind\_PDE1\_2301\_0\_\_Kf}\mathrm{CaM\_Ca4\_2091\_0\_}\mathrm{PDE1\_2277\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{CaM\_bind\_PDE1\_2301\_0\_\_Kb}\mathrm{CaM\_dot\_PDE1\_2282\_0\_}$ kf = kf from text = 1e7 / M / sec = 10 /uM/sec = 10 / 6e5 / # / sec = 1.67e-5 kb = kr from text = 60 / sec Note that we continue to use uM here since [phenylephrine] is also in uM. From Martin et al FEBS Lett 316:2 191-196 1993 we have Kd = 600 nM Assuming kb = 10/sec, we get kf = 10/(0.6 uM * 6e5) = 2.8e-5 1/sec/# 157.7 -401.256123603 white 15 kinetics_1676_0_ * RecLigandBinding_2315_0__Kf * Glutamate_2305_0_*mGluR_2307_0_-kinetics_1676_0_ * RecLigandBinding_2315_0__Kb * Rec_Glu_2309_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{RecLigandBinding\_2315\_0\_\_Kf}\mathrm{Glutamate\_2305\_0\_}\mathrm{mGluR\_2307\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{RecLigandBinding\_2315\_0\_\_Kb}\mathrm{Rec\_Glu\_2309\_0\_}$ This is the k1-k2 equivalent for enzyme complex formation in the binding of Rec-Glu to Gq. See Fay et al Biochem 30 5066-5075 1991. kf = 5e-5 which is nearly the same as calculated by Fay et al. (4.67e-5) kb = .04 June 1996: Closer reading of Fay et al suggests that kb _lessthan_= 0.0001, so kf = 1e-8 by detailed balance. This reaction appears to be neglible. 171.9 -401.256123603 white 15 kinetics_1676_0_ * Rec_Glu_bind_Gq_2317_0__Kf * Rec_Glu_2309_0_*G_GDP_2333_0_-kinetics_1676_0_ * Rec_Glu_bind_Gq_2317_0__Kb * Rec_Glu_Gq_2313_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Rec\_Glu\_bind\_Gq\_2317\_0\_\_Kf}\mathrm{Rec\_Glu\_2309\_0\_}\mathrm{G\_GDP\_2333\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Rec\_Glu\_bind\_Gq\_2317\_0\_\_Kb}\mathrm{Rec\_Glu\_Gq\_2313\_0\_}$ From Fay et al kb3 = kb = 1.06e-3 which is rather slow. k+1 = kf = 2.8e7 /M/sec= 4.67e-5/sec use 5e-5. However, the Kd from Martin et al may be more appropriate, as this is Glu not the system from Fay. kf = 2.8e-5, kb = 10 Let us compromise. since we have the Fay model, keep kf = k+1 = 2.8e-5. But kb (k-3) is .01 * k-1 from Fay. Scaling by .01, kb = .01 * 10 = 0.1 186.9 -401.256123603 white 15 kinetics_1676_0_ * Glu_bind_Rec_Gq_2319_0__Kf * Glutamate_2305_0_*Rec_Gq_2311_0_-kinetics_1676_0_ * Glu_bind_Rec_Gq_2319_0__Kb * Rec_Glu_Gq_2313_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Glu\_bind\_Rec\_Gq\_2319\_0\_\_Kf}\mathrm{Glutamate\_2305\_0\_}\mathrm{Rec\_Gq\_2311\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Glu\_bind\_Rec\_Gq\_2319\_0\_\_Kb}\mathrm{Rec\_Glu\_Gq\_2313\_0\_}$ This is the kcat==k3 stage of the Rec-Glu ezymatic activation of Gq. From Berstein et al actiation is at .35 - 0.7/min From Fay et al Biochem 30 5066-5075 1991 kf = .01/sec From Nakamura et al J physiol Lond 474:1 35-41 1994 see time courses. Also (Berstein) 15-40% of gprot is in GTP-bound form on stim. 202.0 -401.256123603 white 15 kinetics_1676_0_ * Activate_Gq_2321_0__Kf * Rec_Glu_Gq_2313_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Activate\_Gq\_2321\_0\_\_Kf}\mathrm{Rec\_Glu\_Gq\_2313\_0\_}$ Lets try out the same kinetics as the Rec-Glu-bind-Gq This is much too forward. We know that the steady-state amount of Rec-Gq should be 40% of the total amount of receptor. This is for a different receptor, still we can try to match the value. kf = 1e-6 and kb = 1 give 0.333:0.8 which is pretty close. 215.9 -401.256123603 white 15 kinetics_1676_0_ * Rec_bind_Gq_2323_0__Kf * mGluR_2307_0_*G_GDP_2333_0_-kinetics_1676_0_ * Rec_bind_Gq_2323_0__Kb * Rec_Gq_2311_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Rec\_bind\_Gq\_2323\_0\_\_Kf}\mathrm{mGluR\_2307\_0\_}\mathrm{G\_GDP\_2333\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Rec\_bind\_Gq\_2323\_0\_\_Kb}\mathrm{Rec\_Gq\_2311\_0\_}$ kf = kg1 = 0.01/sec, kb = 0. This is the basal exchange of GTP for GDP. 303.9 -401.256123603 white 16 kinetics_1676_0_ * Basal_Act_Gq_2337_0__Kf * G_GDP_2333_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Basal\_Act\_Gq\_2337\_0\_\_Kf}\mathrm{G\_GDP\_2333\_0\_}$ kf == kg3 = 1e-5 /cell/sec. As usual, there is no back-reaction kb = 0 318.9 -401.256123603 white 16 kinetics_1676_0_ * Trimerize_G_2339_0__Kf * G_pGDP_2331_0_*BetaGamma_2327_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Trimerize\_G\_2339\_0\_\_Kf}\mathrm{G\_pGDP\_2331\_0\_}\mathrm{BetaGamma\_2327\_0\_}$ From Berstein et al JBC 267:12 8081-8088 1992, kcat for GTPase activity of Gq is only 0.8/min 332.9 -401.256123603 white 16 kinetics_1676_0_ * Inact_Gq_2341_0__Kf * G_pGTP_2329_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Inact\_Gq\_2341\_0\_\_Kf}\mathrm{G\_pGTP\_2329\_0\_}$ kCa3 = 2 * Ca transporter rate since each step has 2 Ca++. = 0.5 uM/sec from Lauffenburger and Linderman 1993 Receptors pg200 The amount of the activated transporter is about 0.01 uM = 6e3#. from runs. So 0.01uM * kf * 2 = 0.5 uM/sec (no back reaction) so kf = 25, kb = 0 Alternatively, 6e3 * kf = 0.25 * 6e5, giving the same kf 590.74 -382.223338777 white darkgreen kinetics_1676_0_ * CaTraspATPase_2415_0__Kf * CaTransp_2Ca_2421_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaTraspATPase\_2415\_0\_\_Kf}\mathrm{CaTransp\_2Ca\_2421\_0\_}$ Rates from Lauffenburger abd Linderman 1993 Receptors pg 200. Kd = KCa2 = 0.2 uM 590.64 -382.826278106 white darkgreen kinetics_1676_0_ * Ca_bind_to_Transp_2425_0__Kf * Ca_2413_0_^2*CaTransp_2423_0_-kinetics_1676_0_ * Ca_bind_to_Transp_2425_0__Kb * CaTransp_2Ca_2421_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Ca\_bind\_to\_Transp\_2425\_0\_\_Kf}\mathrm{Ca\_2413\_0\_}^2\mathrm{CaTransp\_2423\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Ca\_bind\_to\_Transp\_2425\_0\_\_Kb}\mathrm{CaTransp\_2Ca\_2421\_0\_}$ Based on Lauffenburger and Linderman 1993 Receptors pg 200. The binding of IP3 on this reaction had a Hill coeff of 3. The eqns of Mahama and Linderman (cited in the book as 1993 a) are equivalent to the binding all occurring in a single step, so that is how I do it in this version. Their Ki1 is 0.07 uM. Lots of other data sources: Ramos-Franco et al, Biophys J 75, 1998: 834-39 have Ca sensitivity curves. At 250 nM free Ca, the EC50 for type1 is 58 nM and type 2 is 194 nM. Type 3 would be about 2 uM according to Newton et al, JBC 268(46), 1994: 28613-19. For the purposes of this model we use a Kd of 2.7 uM which is high but maybe OK at low calcium. The details of Ca interaction with the IP3R are not included in this model. 575.0 -410.400703429 white darkgreen kinetics_1676_0_ * IP3Rbind_2429_0__Kf * IP3_1817_0_^3*IP3R_2427_0_-kinetics_1676_0_ * IP3Rbind_2429_0__Kb * IP3R_p_2431_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{IP3Rbind\_2429\_0\_\_Kf}\mathrm{IP3\_1817\_0\_}^3\mathrm{IP3R\_2427\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{IP3Rbind\_2429\_0\_\_Kb}\mathrm{IP3R\_p\_2431\_0\_}$ The Kd is set at about 3 uM so that at resting Ca the capacitative Ca entry is almost blocked. A 2nd order response makes the response steep. 589.71 -382.926767994 white darkgreen kinetics_1676_0_ * inactivate_cap_Ca_2450_0__Kf * CaStores_2454_0_^2*capacitive_Ca_entry_p_2446_0_-kinetics_1676_0_ * inactivate_cap_Ca_2450_0__Kb * inact_cap_entry_2452_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{inactivate\_cap\_Ca\_2450\_0\_\_Kf}\mathrm{CaStores\_2454\_0\_}^2\mathrm{capacitive\_Ca\_entry\_p\_2446\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{inactivate\_cap\_Ca\_2450\_0\_\_Kb}\mathrm{inact\_cap\_entry\_2452\_0\_}$ 742.9 -401.256123603 white 19 kinetics_1676_0_ * bind_Gab1_2493_0__Kf * SHC_p_Grb2_clx_1995_0_*Gab1_2479_0_-kinetics_1676_0_ * bind_Gab1_2493_0__Kb * SHC_p_Grb2_Gab1_clx_2481_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{bind\_Gab1\_2493\_0\_\_Kf}\mathrm{SHC\_p\_Grb2\_clx\_1995\_0\_}\mathrm{Gab1\_2479\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{bind\_Gab1\_2493\_0\_\_Kb}\mathrm{SHC\_p\_Grb2\_Gab1\_clx\_2481\_0\_}$ 758.0 -401.256123603 white 19 kinetics_1676_0_ * PI3K_act_2495_0__Kf * PI3K_2472_0_*SHC_p_Grb2_Gab1_clx_2481_0_-kinetics_1676_0_ * PI3K_act_2495_0__Kb * SHC_p_Grb2_Gab1_PI3K_clx_2467_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PI3K\_act\_2495\_0\_\_Kf}\mathrm{PI3K\_2472\_0\_}\mathrm{SHC\_p\_Grb2\_Gab1\_clx\_2481\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PI3K\_act\_2495\_0\_\_Kb}\mathrm{SHC\_p\_Grb2\_Gab1\_PI3K\_clx\_2467\_0\_}$ 771.9 -401.256123603 white 19 kinetics_1676_0_ * basal_PI3K_act_2497_0__Kf * PI3K_2472_0_-kinetics_1676_0_ * basal_PI3K_act_2497_0__Kb * PI3K_basal_2474_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{basal\_PI3K\_act\_2497\_0\_\_Kf}\mathrm{PI3K\_2472\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{basal\_PI3K\_act\_2497\_0\_\_Kb}\mathrm{PI3K\_basal\_2474\_0\_}$ 824.0 -401.256123603 white 19 kinetics_1676_0_ * PI3K_bind_Ras_GTP_2499_0__Kf * PI3K_2472_0_*GTP_Ras_1922_0_-kinetics_1676_0_ * PI3K_bind_Ras_GTP_2499_0__Kb * Ras_GTP_PI3K_2488_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PI3K\_bind\_Ras\_GTP\_2499\_0\_\_Kf}\mathrm{PI3K\_2472\_0\_}\mathrm{GTP\_Ras\_1922\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PI3K\_bind\_Ras\_GTP\_2499\_0\_\_Kb}\mathrm{Ras\_GTP\_PI3K\_2488\_0\_}$ 890.0 -401.256123603 white 20 kinetics_1676_0_ * PIP3_bind_AKT_2527_0__Kf * PIP3_2460_0_*AKT_2525_0_-kinetics_1676_0_ * PIP3_bind_AKT_2527_0__Kb * PIP3_AKT_2503_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PIP3\_bind\_AKT\_2527\_0\_\_Kf}\mathrm{PIP3\_2460\_0\_}\mathrm{AKT\_2525\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PIP3\_bind\_AKT\_2527\_0\_\_Kb}\mathrm{PIP3\_AKT\_2503\_0\_}$ 903.9 -401.256123603 white 20 kinetics_1676_0_ * PIP3_bind_PDK1_2529_0__Kf * PIP3_2460_0_*PDK1_2462_0_-kinetics_1676_0_ * PIP3_bind_PDK1_2529_0__Kb * PIP3_PDK1_2505_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{PIP3\_bind\_PDK1\_2529\_0\_\_Kf}\mathrm{PIP3\_2460\_0\_}\mathrm{PDK1\_2462\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{PIP3\_bind\_PDK1\_2529\_0\_\_Kb}\mathrm{PIP3\_PDK1\_2505\_0\_}$ 6.9 -591.382992086 white 21 kinetics_1676_0_ * Autophos_TrKB_2551_0__Kf * BDNF_TrKB2_clx_2537_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Autophos\_TrKB\_2551\_0\_\_Kf}\mathrm{BDNF\_TrKB2\_clx\_2537\_0\_}$ 20.9 -591.382992086 white 21 kinetics_1676_0_ * Dimeriz_TrKB_2553_0__Kf * BDNF_TrKB_clx_2539_0_*TrKB_2535_0_-kinetics_1676_0_ * Dimeriz_TrKB_2553_0__Kb * BDNF_TrKB2_clx_2537_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Dimeriz\_TrKB\_2553\_0\_\_Kf}\mathrm{BDNF\_TrKB\_clx\_2539\_0\_}\mathrm{TrKB\_2535\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Dimeriz\_TrKB\_2553\_0\_\_Kb}\mathrm{BDNF\_TrKB2\_clx\_2537\_0\_}$ 35.9 -591.382992086 white 21 kinetics_1676_0_ * Ligand_binding_2555_0__Kf * BDNF_2682_0_*TrKB_2535_0_-kinetics_1676_0_ * Ligand_binding_2555_0__Kb * BDNF_TrKB_clx_2539_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Ligand\_binding\_2555\_0\_\_Kf}\mathrm{BDNF\_2682\_0\_}\mathrm{TrKB\_2535\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Ligand\_binding\_2555\_0\_\_Kb}\mathrm{BDNF\_TrKB\_clx\_2539\_0\_}$ 50.9 -591.382992086 white 21 kinetics_1676_0_ * LR_Internalize_2557_0__Kf * BDNF_TrKB2_p_clx_2541_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{LR\_Internalize\_2557\_0\_\_Kf}\mathrm{BDNF\_TrKB2\_p\_clx\_2541\_0\_}$ 64.9 -591.382992086 white 21 kinetics_1676_0_ * LR_cycling_2559_0__Kf * Int_BDNF_TrKB2_p_clx_2533_0_-kinetics_1676_0_ * LR_cycling_2559_0__Kb * TrKB_2535_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{LR\_cycling\_2559\_0\_\_Kf}\mathrm{Int\_BDNF\_TrKB2\_p\_clx\_2533\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{LR\_cycling\_2559\_0\_\_Kb}\mathrm{TrKB\_2535\_0\_}$ 110.0 -590.478583093 white black kinetics_1676_0_ * TrKB_basal_phospho_2561_0__Kf * TrKB_2535_0_-kinetics_1676_0_ * TrKB_basal_phospho_2561_0__Kb * basal_TrKB_p_2549_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{TrKB\_basal\_phospho\_2561\_0\_\_Kf}\mathrm{TrKB\_2535\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{TrKB\_basal\_phospho\_2561\_0\_\_Kb}\mathrm{basal\_TrKB\_p\_2549\_0\_}$ 166.655383481 -585.934682867 white 22 kinetics_1676_0_ * Rheb_GTP_bind_TORclx_2582_0__Kf * TOR_clx_2569_0_*Rheb_GTP_2565_0_-kinetics_1676_0_ * Rheb_GTP_bind_TORclx_2582_0__Kb * TOR_Rheb_GTP_clx_2571_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Rheb\_GTP\_bind\_TORclx\_2582\_0\_\_Kf}\mathrm{TOR\_clx\_2569\_0\_}\mathrm{Rheb\_GTP\_2565\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Rheb\_GTP\_bind\_TORclx\_2582\_0\_\_Kb}\mathrm{TOR\_Rheb\_GTP\_clx\_2571\_0\_}$ 180.855383481 -585.934682867 white 22 kinetics_1676_0_ * GDP_to_GTP_2584_0__Kf * Rheb_GDP_2567_0_-kinetics_1676_0_ * GDP_to_GTP_2584_0__Kb * Rheb_GTP_2565_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{GDP\_to\_GTP\_2584\_0\_\_Kf}\mathrm{Rheb\_GDP\_2567\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{GDP\_to\_GTP\_2584\_0\_\_Kb}\mathrm{Rheb\_GTP\_2565\_0\_}$ 500.665514381 -780.147764287 white 23 kinetics_1676_0_ * S6_dephosph_2610_0__Kf * _40S_2764_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{S6\_dephosph\_2610\_0\_\_Kf}\mathrm{\_40S\_2764\_0\_}$ 333.123385612 -590.581674587 white 23 kinetics_1676_0_ * basal_S6K_2612_0__Kf * S6K_2590_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{basal\_S6K\_2612\_0\_\_Kf}\mathrm{S6K\_2590\_0\_}$ 449.8 -591.382992086 white 24 kinetics_1676_0_ * eIF4E_bind_BP2_2628_0__Kf * _4E_BP_2616_0_*eIF4E_2704_0_-kinetics_1676_0_ * eIF4E_bind_BP2_2628_0__Kb * eIF4E_BP_2620_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4E\_bind\_BP2\_2628\_0\_\_Kf}\mathrm{\_4E\_BP\_2616\_0\_}\mathrm{eIF4E\_2704\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4E\_bind\_BP2\_2628\_0\_\_Kb}\mathrm{eIF4E\_BP\_2620\_0\_}$ 464.9 -591.382992086 white 24 kinetics_1676_0_ * eIF4E_BP2_disso_2630_0__Kf * eIF4E_BP_t37_46_s65_2624_0_-kinetics_1676_0_ * eIF4E_BP2_disso_2630_0__Kb * eIF4E_2704_0_*_4E_BP_t37_46_s65_2618_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4E\_BP2\_disso\_2630\_0\_\_Kf}\mathrm{eIF4E\_BP\_t37\_46\_s65\_2624\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4E\_BP2\_disso\_2630\_0\_\_Kb}\mathrm{eIF4E\_2704\_0\_}\mathrm{\_4E\_BP\_t37\_46\_s65\_2618\_0\_}$ 479.9 -591.382992086 white 24 kinetics_1676_0_ * eIF4E_BP_disso_2632_0__Kf * eIF4E_BP_thr37_46_2622_0_-kinetics_1676_0_ * eIF4E_BP_disso_2632_0__Kb * eIF4E_2704_0_*_4E_BP_t37_46_2626_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4E\_BP\_disso\_2632\_0\_\_Kf}\mathrm{eIF4E\_BP\_thr37\_46\_2622\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4E\_BP\_disso\_2632\_0\_\_Kb}\mathrm{eIF4E\_2704\_0\_}\mathrm{\_4E\_BP\_t37\_46\_2626\_0\_}$ 596.8 -591.382992086 white 25 kinetics_1676_0_ * Q_binds_R_2644_0__Kf * Quaternary_clx_2640_0_*_40S_2764_0_-kinetics_1676_0_ * Q_binds_R_2644_0__Kb * Q_dot_R_2636_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{Q\_binds\_R\_2644\_0\_\_Kf}\mathrm{Quaternary\_clx\_2640\_0\_}\mathrm{\_40S\_2764\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{Q\_binds\_R\_2644\_0\_\_Kb}\mathrm{Q\_dot\_R\_2636\_0\_}$ 611.0 -591.382992086 white 25 kinetics_1676_0_ * QR_binds_M_2646_0__Kf * eIF4F_mRNA_clx_2716_0_*Q_dot_R_2636_0_-kinetics_1676_0_ * QR_binds_M_2646_0__Kb * _43Scomplex_2642_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{QR\_binds\_M\_2646\_0\_\_Kf}\mathrm{eIF4F\_mRNA\_clx\_2716\_0\_}\mathrm{Q\_dot\_R\_2636\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{QR\_binds\_M\_2646\_0\_\_Kb}\mathrm{\_43Scomplex\_2642\_0\_}$ 626.0 -591.382992086 white 25 kinetics_1676_0_ * R_binds_M_2648_0__Kf * _40S_2764_0_*eIF4F_mRNA_clx_2716_0_-kinetics_1676_0_ * R_binds_M_2648_0__Kb * RM_2638_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{R\_binds\_M\_2648\_0\_\_Kf}\mathrm{\_40S\_2764\_0\_}\mathrm{eIF4F\_mRNA\_clx\_2716\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{R\_binds\_M\_2648\_0\_\_Kb}\mathrm{RM\_2638\_0\_}$ 640.8 -591.382992086 white 25 kinetics_1676_0_ * RM_binds_Q_2650_0__Kf * Quaternary_clx_2640_0_*RM_2638_0_-kinetics_1676_0_ * RM_binds_Q_2650_0__Kb * _43Scomplex_2642_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{RM\_binds\_Q\_2650\_0\_\_Kf}\mathrm{Quaternary\_clx\_2640\_0\_}\mathrm{RM\_2638\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{RM\_binds\_Q\_2650\_0\_\_Kb}\mathrm{\_43Scomplex\_2642\_0\_}$ 742.9 -591.382992086 white 26 kinetics_1676_0_ * pep_elongation_2670_0__Kf * peptide_2656_0_-kinetics_1676_0_ * pep_elongation_2670_0__Kb * protein_2660_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{pep\_elongation\_2670\_0\_\_Kf}\mathrm{peptide\_2656\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{pep\_elongation\_2670\_0\_\_Kb}\mathrm{protein\_2660\_0\_}$ 758.0 -591.382992086 white 26 kinetics_1676_0_ * protein_deg_2672_0__Kf * protein_2660_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{protein\_deg\_2672\_0\_\_Kf}\mathrm{protein\_2660\_0\_}$ 771.9 -591.382992086 white 26 kinetics_1676_0_ * rad_pep_elongation_2674_0__Kf * rad_peptide_2664_0_-kinetics_1676_0_ * rad_pep_elongation_2674_0__Kb * rad_protein_2666_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{rad\_pep\_elongation\_2674\_0\_\_Kf}\mathrm{rad\_peptide\_2664\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{rad\_pep\_elongation\_2674\_0\_\_Kb}\mathrm{rad\_protein\_2666\_0\_}$ 786.9 -591.382992086 white 26 kinetics_1676_0_ * rad_protein_deg_2676_0__Kf * rad_protein_2666_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{rad\_protein\_deg\_2676\_0\_\_Kf}\mathrm{rad\_protein\_2666\_0\_}$ 802.0 -591.382992086 white 26 kinetics_1676_0_ * labelling_2678_0__Kf * AA_2654_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{labelling\_2678\_0\_\_Kf}\mathrm{AA\_2654\_0\_}$ 11.0 -782.615249341 white 28 kinetics_1676_0_ * CaMKIII_dephospho_2700_0__Kf * CaMKIII_p_2698_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{CaMKIII\_dephospho\_2700\_0\_\_Kf}\mathrm{CaMKIII\_p\_2698\_0\_}$ 136.935847461 -798.31972508 white 29 kinetics_1676_0_ * eIF4F_clx_2720_0__Kf * eIF4E_2704_0_*eIF4G_A_clx_2706_0_-kinetics_1676_0_ * eIF4F_clx_2720_0__Kb * eIF4F_2712_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4F\_clx\_2720\_0\_\_Kf}\mathrm{eIF4E\_2704\_0\_}\mathrm{eIF4G\_A\_clx\_2706\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4F\_clx\_2720\_0\_\_Kb}\mathrm{eIF4F\_2712\_0\_}$ 147.135847461 -799.224134073 white 29 kinetics_1676_0_ * eIF4G_A_clx_formation_2722_0__Kf * eIF4A_2708_0_*eIF4G_2710_0_-kinetics_1676_0_ * eIF4G_A_clx_formation_2722_0__Kb * eIF4G_A_clx_2706_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4G\_A\_clx\_formation\_2722\_0\_\_Kf}\mathrm{eIF4A\_2708\_0\_}\mathrm{eIF4G\_2710\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4G\_A\_clx\_formation\_2722\_0\_\_Kb}\mathrm{eIF4G\_A\_clx\_2706\_0\_}$ 169.435847461 -799.626093626 white 29 kinetics_1676_0_ * eIF4F_mRNA_clx_formation_2724_0__Kf * eIF4F_2712_0_*mRNA_2714_0_-kinetics_1676_0_ * eIF4F_mRNA_clx_formation_2724_0__Kb * eIF4F_mRNA_clx_2716_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4F\_mRNA\_clx\_formation\_2724\_0\_\_Kf}\mathrm{eIF4F\_2712\_0\_}\mathrm{mRNA\_2714\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4F\_mRNA\_clx\_formation\_2724\_0\_\_Kb}\mathrm{eIF4F\_mRNA\_clx\_2716\_0\_}$ 188.125699122 -800.392236052 white black kinetics_1676_0_ * eIF4E_mRNA_eIF4F_clx_formation_2726_0__Kf * eIF4G_A_clx_2706_0_*eIF4E_mRNA_clx_2718_0_-kinetics_1676_0_ * eIF4E_mRNA_eIF4F_clx_formation_2726_0__Kb * eIF4F_mRNA_clx_2716_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4E\_mRNA\_eIF4F\_clx\_formation\_2726\_0\_\_Kf}\mathrm{eIF4G\_A\_clx\_2706\_0\_}\mathrm{eIF4E\_mRNA\_clx\_2718\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4E\_mRNA\_eIF4F\_clx\_formation\_2726\_0\_\_Kb}\mathrm{eIF4F\_mRNA\_clx\_2716\_0\_}$ 158.035847461 -798.822174521 white black kinetics_1676_0_ * eIF4E_mRNA_clx_formation_2728_0__Kf * eIF4E_2704_0_*mRNA_2714_0_-kinetics_1676_0_ * eIF4E_mRNA_clx_formation_2728_0__Kb * eIF4E_mRNA_clx_2718_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4E\_mRNA\_clx\_formation\_2728\_0\_\_Kf}\mathrm{eIF4E\_2704\_0\_}\mathrm{mRNA\_2714\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{eIF4E\_mRNA\_clx\_formation\_2728\_0\_\_Kb}\mathrm{eIF4E\_mRNA\_clx\_2718\_0\_}$ 303.9 -782.615249341 white 30 kinetics_1676_0_ * elongation_2756_0__Kf * _80S_ribos_clx_2746_0_*eEF2_2732_0_-kinetics_1676_0_ * elongation_2756_0__Kb * Translation_clx_2738_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{elongation\_2756\_0\_\_Kf}\mathrm{\_80S\_ribos\_clx\_2746\_0\_}\mathrm{eEF2\_2732\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{elongation\_2756\_0\_\_Kb}\mathrm{Translation\_clx\_2738\_0\_}$ 318.9 -782.615249341 white 30 kinetics_1676_0_ * activation_2758_0__Kf * _60S_R_2736_0_*_43Scomplex_2642_0_-kinetics_1676_0_ * activation_2758_0__Kb * _80S_ribos_clx_2746_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{activation\_2758\_0\_\_Kf}\mathrm{\_60S\_R\_2736\_0\_}\mathrm{\_43Scomplex\_2642\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{activation\_2758\_0\_\_Kb}\mathrm{\_80S\_ribos\_clx\_2746\_0\_}$ 596.8 -782.615249341 white 32 kinetics_1676_0_ * TSC1_TSC2_dephospho_2780_0__Kf * TSC1_TSC2_p_2773_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{TSC1\_TSC2\_dephospho\_2780\_0\_\_Kf}\mathrm{TSC1\_TSC2\_p\_2773\_0\_}$ 742.9 -782.615249341 white 33 kinetics_1676_0_ * L_dot_mGluR_HomerBinding_2797_0__Kf * Homer_2784_0_*Rec_Glu_2309_0_-kinetics_1676_0_ * L_dot_mGluR_HomerBinding_2797_0__Kb * L_dot_mGluR_p_dot_Homer_2786_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{L\_dot\_mGluR\_HomerBinding\_2797\_0\_\_Kf}\mathrm{Homer\_2784\_0\_}\mathrm{Rec\_Glu\_2309\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{L\_dot\_mGluR\_HomerBinding\_2797\_0\_\_Kb}\mathrm{L\_dot\_mGluR\_p\_dot\_Homer\_2786\_0\_}$ 758.0 -782.615249341 white 33 kinetics_1676_0_ * L_dot_mGluR_dot_Homer_PIKE_Binding_2799_0__Kf * L_dot_mGluR_p_dot_Homer_2786_0_*PIKE_L_2790_0_-kinetics_1676_0_ * L_dot_mGluR_dot_Homer_PIKE_Binding_2799_0__Kb * L_dot_mGluR_p_dot_Homer_dot_PIKE_L_2788_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{L\_dot\_mGluR\_dot\_Homer\_PIKE\_Binding\_2799\_0\_\_Kf}\mathrm{L\_dot\_mGluR\_p\_dot\_Homer\_2786\_0\_}\mathrm{PIKE\_L\_2790\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{L\_dot\_mGluR\_dot\_Homer\_PIKE\_Binding\_2799\_0\_\_Kb}\mathrm{L\_dot\_mGluR\_p\_dot\_Homer\_dot\_PIKE\_L\_2788\_0\_}$ 771.9 -782.615249341 white 33 kinetics_1676_0_ * L_dot_mGluR_dot_Homer_dot_PIKE_PI3K_Binding_2801_0__Kf * PI3K_2472_0_*L_dot_mGluR_p_dot_Homer_dot_PIKE_L_2788_0_-kinetics_1676_0_ * L_dot_mGluR_dot_Homer_dot_PIKE_PI3K_Binding_2801_0__Kb * L_dot_mGluR_p_dot_Homer_dot_PIKE_L_dot_PI3K_2792_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{L\_dot\_mGluR\_dot\_Homer\_dot\_PIKE\_PI3K\_Binding\_2801\_0\_\_Kf}\mathrm{PI3K\_2472\_0\_}\mathrm{L\_dot\_mGluR\_p\_dot\_Homer\_dot\_PIKE\_L\_2788\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{L\_dot\_mGluR\_dot\_Homer\_dot\_PIKE\_PI3K\_Binding\_2801\_0\_\_Kb}\mathrm{L\_dot\_mGluR\_p\_dot\_Homer\_dot\_PIKE\_L\_dot\_PI3K\_2792\_0\_}$ Heitzler,2012 890.0 -782.615249341 white 34 kinetics_1676_0_ * mGluR_barr2_assoc_2824_0__Kf * L_dot_mGluR_p_2810_0_*barr2_2812_0_-kinetics_1676_0_ * mGluR_barr2_assoc_2824_0__Kb * L_dot_mGluR_p_dot_barr2_2816_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{mGluR\_barr2\_assoc\_2824\_0\_\_Kf}\mathrm{L\_dot\_mGluR\_p\_2810\_0\_}\mathrm{barr2\_2812\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{mGluR\_barr2\_assoc\_2824\_0\_\_Kb}\mathrm{L\_dot\_mGluR\_p\_dot\_barr2\_2816\_0\_}$ Rate based on internalization time after beta-arrestin binding. According to Mundell SJ et al., 2001, t(1/2) ~ 1.9(+/-)0.4 min. Therefore, kf =0.005 to 0.0077/s 903.9 -782.615249341 white 34 kinetics_1676_0_ * mGluR_internalize_2826_0__Kf * mGluR_p_dot_barr2_2822_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{mGluR\_internalize\_2826\_0\_\_Kf}\mathrm{mGluR\_p\_dot\_barr2\_2822\_0\_}$ 918.9 -782.615249341 white 34 kinetics_1676_0_ * barr2_dissoc_2828_0__Kf * Internal_mGluR_p_dot_barr2_2814_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{barr2\_dissoc\_2828\_0\_\_Kf}\mathrm{Internal\_mGluR\_p\_dot\_barr2\_2814\_0\_}$ 934.0 -782.615249341 white 34 kinetics_1676_0_ * mGluR_recycling_2830_0__Kf * Internal_mGluR_2818_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{mGluR\_recycling\_2830\_0\_\_Kf}\mathrm{Internal\_mGluR\_2818\_0\_}$ Navarro DL et al., Amino Acids (2005). Kd for glutamte-mGluR for rat fetus is 599 (+/-) 89.7 nM and for mothers is 534.3 (+/-) 89.7 nM. Therefore, assuming Kd = 595nM 947.9 -782.615249341 white 34 kinetics_1676_0_ * ligand_dissoc_2832_0__Kf * L_dot_mGluR_p_dot_barr2_2816_0_-kinetics_1676_0_ * ligand_dissoc_2832_0__Kb * Glutamate_2305_0_*mGluR_p_dot_barr2_2822_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{ligand\_dissoc\_2832\_0\_\_Kf}\mathrm{L\_dot\_mGluR\_p\_dot\_barr2\_2816\_0\_}-\mathrm{kinetics\_1676\_0\_}\mathrm{ligand\_dissoc\_2832\_0\_\_Kb}\mathrm{Glutamate\_2305\_0\_}\mathrm{mGluR\_p\_dot\_barr2\_2822\_0\_}$ Rate consts from Chen et al Biochem 32, 1032 (1993) k3 = k2 = 4 k1 = 9e-5 recalculated gives 1.666e-5, which is not very different. Looks like k3 is rate-limiting in this case: there is a huge amount of craf locked up in the enz complex. Let us assume a 10x higher Km, ie, lower affinity. k1 drops by 10x. Also changed k2 to 4x k3. Lowerd k1 to 1e-6 to balance 10X DAG sensitivity of PKC PKC_active_1706_0_ craf_1_1865_0_ PKC_act_raf_cplx_1709_0_ PKC_act_raf_1708_0_ 1 69.8 -124.406481598 red yellow kinetics_1676_0_ * ( k1 * craf_1_1865_0_*PKC_active_1706_0_ - k2 * PKC_act_raf_cplx_1709_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{craf\_1\_1865\_0\_}\mathrm{PKC\_active\_1706\_0\_}-\mathrm{k2}\mathrm{PKC\_act\_raf\_cplx\_1709\_0\_})$ PKC_act_raf_cplx_1709_0_ PKC_active_1706_0_ craf_1_p_1867_0_ PKC_act_raf_1708_0_ 2 69.8 -124.406481598 red yellow kinetics_1676_0_ * k3*PKC_act_raf_cplx_1709_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PKC\_act\_raf\_cplx\_1709\_0\_}$ Rate consts copied from PCK-act-raf This reaction inactivates GAP. The idea is from the Boguski and McCormick review. PKC_active_1706_0_ GAP_1928_0_ PKC_inact_GAP_cplx_1712_0_ PKC_inact_GAP_1711_0_ 1 69.8 -114.457982665 red yellow kinetics_1676_0_ * ( k1 * GAP_1928_0_*PKC_active_1706_0_ - k2 * PKC_inact_GAP_cplx_1712_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{GAP\_1928\_0\_}\mathrm{PKC\_active\_1706\_0\_}-\mathrm{k2}\mathrm{PKC\_inact\_GAP\_cplx\_1712\_0\_})$ PKC_inact_GAP_cplx_1712_0_ PKC_active_1706_0_ GAP_p_1926_0_ PKC_inact_GAP_1711_0_ 2 69.8 -114.457982665 red yellow kinetics_1676_0_ * k3*PKC_inact_GAP_cplx_1712_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PKC\_inact\_GAP\_cplx\_1712\_0\_}$ Rate consts from PKC-act-raf. This reaction activates GEF. It can lead to at least 2X stim of ras, and a 2X stim of MAPK over and above that obtained via direct phosph of c-raf. Note that it is a push-pull reaction, and there is also a contribution through the phosphorylation and inactivation of GAPs. The original PKC-act-raf rate consts are too fast. We lower K1 by 10 X PKC_active_1706_0_ inact_GEF_1912_0_ PKC_act_GEF_cplx_1715_0_ PKC_act_GEF_1714_0_ 1 69.8 -105.514382615 red yellow kinetics_1676_0_ * ( k1 * inact_GEF_1912_0_*PKC_active_1706_0_ - k2 * PKC_act_GEF_cplx_1715_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{inact\_GEF\_1912\_0\_}\mathrm{PKC\_active\_1706\_0\_}-\mathrm{k2}\mathrm{PKC\_act\_GEF\_cplx\_1715\_0\_})$ PKC_act_GEF_cplx_1715_0_ PKC_active_1706_0_ GEF_p_1917_0_ PKC_act_GEF_1714_0_ 2 69.8 -105.514382615 red yellow kinetics_1676_0_ * k3*PKC_act_GEF_cplx_1715_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PKC\_act\_GEF\_cplx\_1715\_0\_}$ Rates from Huang et al ABB 305:2 570-580 1993 PKC_active_1706_0_ neurogranin_2099_0_ PKC_phosph_neurogranin_cplx_1718_0_ PKC_phosph_neurogranin_1717_0_ 1 69.8 -95.565883683 red red kinetics_1676_0_ * ( k1 * PKC_active_1706_0_*neurogranin_2099_0_ - k2 * PKC_phosph_neurogranin_cplx_1718_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PKC\_active\_1706\_0\_}\mathrm{neurogranin\_2099\_0\_}-\mathrm{k2}\mathrm{PKC\_phosph\_neurogranin\_cplx\_1718\_0\_})$ PKC_phosph_neurogranin_cplx_1718_0_ PKC_active_1706_0_ neurogranin_p_2097_0_ PKC_phosph_neurogranin_1717_0_ 2 69.8 -95.565883683 red red kinetics_1676_0_ * k3*PKC_phosph_neurogranin_cplx_1718_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PKC\_phosph\_neurogranin\_cplx\_1718\_0\_}$ Rates are 60% those of PKC-phosph-neurogranin. See Huang et al ABB 305:2 570-580 1993 PKC_active_1706_0_ neurogranin_CaM_2095_0_ PKC_phosph_ng_CaM_cplx_1721_0_ PKC_phosph_ng_CaM_1720_0_ 1 69.8 -86.6222836327 red red kinetics_1676_0_ * ( k1 * PKC_active_1706_0_*neurogranin_CaM_2095_0_ - k2 * PKC_phosph_ng_CaM_cplx_1721_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PKC\_active\_1706\_0\_}\mathrm{neurogranin\_CaM\_2095\_0\_}-\mathrm{k2}\mathrm{PKC\_phosph\_ng\_CaM\_cplx\_1721\_0\_})$ PKC_phosph_ng_CaM_cplx_1721_0_ PKC_active_1706_0_ neurogranin_p_2097_0_ CaM_2093_0_ PKC_phosph_ng_CaM_1720_0_ 2 69.8 -86.6222836327 red red kinetics_1676_0_ * k3*PKC_phosph_ng_CaM_cplx_1721_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PKC\_phosph\_ng\_CaM\_cplx\_1721\_0\_}$ Phorbol esters have little effect on AC1 or on the Gs-stimulation of AC2. So in this model we are only dealing with the increase in basal activation of AC2 induced by PKC k1 = 1.66e-6 k2 = 16 k3 =4 PKC_active_1706_0_ AC2_2257_0_ phosph_AC2_cplx_1724_0_ phosph_AC2_1723_0_ 1 69.8 -76.6737847004 red red kinetics_1676_0_ * ( k1 * AC2_2257_0_*PKC_active_1706_0_ - k2 * phosph_AC2_cplx_1724_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{AC2\_2257\_0\_}\mathrm{PKC\_active\_1706\_0\_}-\mathrm{k2}\mathrm{phosph\_AC2\_cplx\_1724\_0\_})$ phosph_AC2_cplx_1724_0_ PKC_active_1706_0_ AC2_p_2249_0_ phosph_AC2_1723_0_ 2 69.8 -76.6737847004 red red kinetics_1676_0_ * k3*phosph_AC2_cplx_1724_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{phosph\_AC2\_cplx\_1724\_0\_}$ 10 x raise oct22 12 x oct 24, set k2 = 4 * k3 PLA2_Ca_p_1750_0_ APC_1770_0_ kenz_cplx_1753_0_ kenz_1752_0_ 1 164.8 -18.8920989825 red yellow kinetics_1676_0_ * ( k1 * APC_1770_0_*PLA2_Ca_p_1750_0_ - k2 * kenz_cplx_1753_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{APC\_1770\_0\_}\mathrm{PLA2\_Ca\_p\_1750\_0\_}-\mathrm{k2}\mathrm{kenz\_cplx\_1753\_0\_})$ kenz_cplx_1753_0_ PLA2_Ca_p_1750_0_ Arachidonic_Acid_1779_0_ kenz_1752_0_ 2 164.8 -18.8920989825 red yellow kinetics_1676_0_ * k3*kenz_cplx_1753_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{kenz\_cplx\_1753\_0\_}$ 10 X raise oct 22 12 X further raise oct 24 to allow for correct conc of enzyme PIP2_PLA2_p_1755_0_ APC_1770_0_ kenz_cplx_1758_0_ kenz_1757_0_ 1 179.7 -18.8920989825 red cyan kinetics_1676_0_ * ( k1 * APC_1770_0_*PIP2_PLA2_p_1755_0_ - k2 * kenz_cplx_1758_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{APC\_1770\_0\_}\mathrm{PIP2\_PLA2\_p\_1755\_0\_}-\mathrm{k2}\mathrm{kenz\_cplx\_1758\_0\_})$ kenz_cplx_1758_0_ PIP2_PLA2_p_1755_0_ Arachidonic_Acid_1779_0_ kenz_1757_0_ 2 179.7 -18.8920989825 red cyan kinetics_1676_0_ * k3*kenz_cplx_1758_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{kenz\_cplx\_1758\_0\_}$ 10 x raise oct 22 12 x and rescale for k2 = 4 * k3 convention oct 24 Increase further to get the match to expt, which was spoilt due to large accumulation of PLA2 in the enzyme complexed forms. Lets raise k3, leaving the others at k1 = 1.5e-5 and k2 = 144 since they are large already. PIP2_Ca_PLA2_p_1760_0_ APC_1770_0_ kenz_cplx_1763_0_ kenz_1762_0_ 1 193.8 -18.8920989825 red cyan kinetics_1676_0_ * ( k1 * PIP2_Ca_PLA2_p_1760_0_*APC_1770_0_ - k2 * kenz_cplx_1763_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PIP2\_Ca\_PLA2\_p\_1760\_0\_}\mathrm{APC\_1770\_0\_}-\mathrm{k2}\mathrm{kenz\_cplx\_1763\_0\_})$ kenz_cplx_1763_0_ PIP2_Ca_PLA2_p_1760_0_ Arachidonic_Acid_1779_0_ kenz_1762_0_ 2 193.8 -18.8920989825 red cyan kinetics_1676_0_ * k3*kenz_cplx_1763_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{kenz\_cplx\_1763\_0\_}$ 10 X raise oct 22 12 X raise oct 24 + conversion to k2 =4 * k3 DAG_Ca_PLA2_p_1765_0_ APC_1770_0_ kenz_cplx_1768_0_ kenz_1767_0_ 1 208.9 -18.8920989825 red pink kinetics_1676_0_ * ( k1 * APC_1770_0_*DAG_Ca_PLA2_p_1765_0_ - k2 * kenz_cplx_1768_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{APC\_1770\_0\_}\mathrm{DAG\_Ca\_PLA2\_p\_1765\_0\_}-\mathrm{k2}\mathrm{kenz\_cplx\_1768\_0\_})$ kenz_cplx_1768_0_ DAG_Ca_PLA2_p_1765_0_ Arachidonic_Acid_1779_0_ kenz_1767_0_ 2 208.9 -18.8920989825 red pink kinetics_1676_0_ * k3*kenz_cplx_1768_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{kenz\_cplx\_1768\_0\_}$ This form should be 3 to 6 times as fast as the Ca-only form. I have scaled by 4x which seems to give a 5x rise. 10x raise Oct 22 12 x oct 24, changed k2 = 4 * k3 PLA2_p_Ca_1772_0_ APC_1770_0_ kenz_cplx_1775_0_ kenz_1774_0_ 1 237.9 -18.8920989825 red orange kinetics_1676_0_ * ( k1 * APC_1770_0_*PLA2_p_Ca_1772_0_ - k2 * kenz_cplx_1775_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{APC\_1770\_0\_}\mathrm{PLA2\_p\_Ca\_1772\_0\_}-\mathrm{k2}\mathrm{kenz\_cplx\_1775\_0\_})$ kenz_cplx_1775_0_ PLA2_p_Ca_1772_0_ Arachidonic_Acid_1779_0_ kenz_1774_0_ 2 237.9 -18.8920989825 red orange kinetics_1676_0_ * k3*kenz_cplx_1775_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{kenz\_cplx\_1775\_0\_}$ From Sternweis et al Phil Trans R Soc Lond 1992, also matched by Homma et al. k1 = 1.5e-5, now 4.2e-6 k2 = 70/sec; now 40/sec k3 = 17.5/sec; now 10/sec Note that the wording in Sternweis et al is ambiguous re the Km. PLC_Ca_1801_0_ PIP2_1819_0_ PLC_Ca_cplx_1804_0_ PLC_Ca_1803_0_ 1 325.9 -18.8920989825 red cyan kinetics_1676_0_ * ( k1 * PLC_Ca_1801_0_*PIP2_1819_0_ - k2 * PLC_Ca_cplx_1804_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PLC\_Ca\_1801\_0\_}\mathrm{PIP2\_1819\_0\_}-\mathrm{k2}\mathrm{PLC\_Ca\_cplx\_1804\_0\_})$ PLC_Ca_cplx_1804_0_ PLC_Ca_1801_0_ IP3_1817_0_ DAG_1815_0_ PLC_Ca_1803_0_ 2 325.9 -18.8920989825 red cyan kinetics_1676_0_ * k3*PLC_Ca_cplx_1804_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PLC\_Ca\_cplx\_1804\_0\_}$ From Sternweis et al, Phil Trans R Soc Lond 1992, and the values from other refs eg Homma et al JBC 263(14) pp6592 1988 match. k1 = 5e-5/sec k2 = 240/sec; now 120/sec k3 = 60/sec; now 30/sec Note that the wording in Sternweis et al is ambiguous wr. to the Km for Gq vs non-Gq states of PLC. K1 is still a bit too low. Raise to 7e-5 9 Jun 1996: k1 was 0.0002, changed to 5e-5 PLC_Ca_Gq_1806_0_ PIP2_1819_0_ PLCb_Ca_Gq_cplx_1809_0_ PLCb_Ca_Gq_1808_0_ 1 340.9 -18.8920989825 red cyan kinetics_1676_0_ * ( k1 * PIP2_1819_0_*PLC_Ca_Gq_1806_0_ - k2 * PLCb_Ca_Gq_cplx_1809_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PIP2\_1819\_0\_}\mathrm{PLC\_Ca\_Gq\_1806\_0\_}-\mathrm{k2}\mathrm{PLCb\_Ca\_Gq\_cplx\_1809\_0\_})$ PLCb_Ca_Gq_cplx_1809_0_ PLC_Ca_Gq_1806_0_ IP3_1817_0_ DAG_1815_0_ PLCb_Ca_Gq_1808_0_ 2 340.9 -18.8920989825 red cyan kinetics_1676_0_ * k3*PLCb_Ca_Gq_cplx_1809_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PLCb\_Ca\_Gq\_cplx\_1809\_0\_}$ Km = 25uM @ 50 uM ATP and 1mg/ml MBP (huge XS of substrate) Vmax = 4124 pmol/min/ml at a conc of 125 pmol/ml of enz, so: k3 = .5/sec (rate limiting) k1 = (k2 + k3)/Km = (.5 + 0)/(25*6e5) = 2e-8 (#/cell)^-1 #s from Sanghera et al JBC 265 pp 52 , 1990. From Nemenoff et al JBC 268(3):1960-1964 - using Sanghera's 1e-4 ratio of MAPK to protein, we get k3 = 7/sec from 1000 pmol/min/mg fig 5 MAPK_p_p_1845_0_ PLA2_cytosolic_1748_0_ MAPK_p_p_cplx_1848_0_ MAPK_p_p_1847_0_ 1 589.9 -18.8920989825 red orange kinetics_1676_0_ * ( k1 * PLA2_cytosolic_1748_0_*MAPK_p_p_1845_0_ - k2 * MAPK_p_p_cplx_1848_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PLA2\_cytosolic\_1748\_0\_}\mathrm{MAPK\_p\_p\_1845\_0\_}-\mathrm{k2}\mathrm{MAPK\_p\_p\_cplx\_1848\_0\_})$ MAPK_p_p_cplx_1848_0_ MAPK_p_p_1845_0_ PLA2_p_1777_0_ MAPK_p_p_1847_0_ 2 589.9 -18.8920989825 red orange kinetics_1676_0_ * k3*MAPK_p_p_cplx_1848_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MAPK\_p\_p\_cplx\_1848\_0\_}$ Ueki et al JBC 269(22):15756-15761 show the presence of this step, but not the rate consts, which are derived from Sanghera et al JBC 265(1):52-57, 1990, see the deriv in the MAPK* notes. MAPK_p_p_1845_0_ craf_1_p_1867_0_ MAPK_p_p_feedback_cplx_1851_0_ MAPK_p_p_feedback_1850_0_ 1 589.9 -28.941087803 red orange kinetics_1676_0_ * ( k1 * craf_1_p_1867_0_*MAPK_p_p_1845_0_ - k2 * MAPK_p_p_feedback_cplx_1851_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{craf\_1\_p\_1867\_0\_}\mathrm{MAPK\_p\_p\_1845\_0\_}-\mathrm{k2}\mathrm{MAPK\_p\_p\_feedback\_cplx\_1851\_0\_})$ MAPK_p_p_feedback_cplx_1851_0_ MAPK_p_p_1845_0_ craf_1_p_p_1879_0_ MAPK_p_p_feedback_1850_0_ 2 589.9 -28.941087803 red orange kinetics_1676_0_ * k3*MAPK_p_p_feedback_cplx_1851_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MAPK\_p\_p\_feedback\_cplx\_1851\_0\_}$ See Porfiri and McCormick JBC 271:10 pp5871 1996 for the existence of this step. We'll take the rates from the ones used for the phosph of Raf by MAPK. Sep 17 1997: The transient activation curve matches better with k1 up by 10 x. MAPK_p_p_1845_0_ Sos_1993_0_ phosph_Sos_cplx_1854_0_ phosph_Sos_1853_0_ 1 589.9 -38.8895867353 red orange kinetics_1676_0_ * ( k1 * Sos_1993_0_*MAPK_p_p_1845_0_ - k2 * phosph_Sos_cplx_1854_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{Sos\_1993\_0\_}\mathrm{MAPK\_p\_p\_1845\_0\_}-\mathrm{k2}\mathrm{phosph\_Sos\_cplx\_1854\_0\_})$ phosph_Sos_cplx_1854_0_ MAPK_p_p_1845_0_ Sos_p_1991_0_ phosph_Sos_1853_0_ 2 589.9 -38.8895867353 red orange kinetics_1676_0_ * k3*phosph_Sos_cplx_1854_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{phosph\_Sos\_cplx\_1854\_0\_}$ MAPK_p_p_1845_0_ S6K_2590_0_ cluster_phospho_S6K_cplx_1857_0_ cluster_phospho_S6K_1856_0_ 1 589.9 -47.8331867856 red red kinetics_1676_0_ * ( k1 * MAPK_p_p_1845_0_*S6K_2590_0_ - k2 * cluster_phospho_S6K_cplx_1857_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{MAPK\_p\_p\_1845\_0\_}\mathrm{S6K\_2590\_0\_}-\mathrm{k2}\mathrm{cluster\_phospho\_S6K\_cplx\_1857\_0\_})$ cluster_phospho_S6K_cplx_1857_0_ MAPK_p_p_1845_0_ S6K_p_2588_0_ cluster_phospho_S6K_1856_0_ 2 589.9 -47.8331867856 red red kinetics_1676_0_ * k3*cluster_phospho_S6K_cplx_1857_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{cluster\_phospho\_S6K\_cplx\_1857\_0\_}$ MAPK_p_p_1845_0_ _4E_BP_t37_46_2626_0_ MAPK_4E_BP_p_p_cplx_1860_0_ MAPK_4E_BP_p_p_1859_0_ 1 589.9 -57.7816857179 orange red kinetics_1676_0_ * ( k1 * _4E_BP_t37_46_2626_0_*MAPK_p_p_1845_0_ - k2 * MAPK_4E_BP_p_p_cplx_1860_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{\_4E\_BP\_t37\_46\_2626\_0\_}\mathrm{MAPK\_p\_p\_1845\_0\_}-\mathrm{k2}\mathrm{MAPK\_4E\_BP\_p\_p\_cplx\_1860\_0\_})$ MAPK_4E_BP_p_p_cplx_1860_0_ MAPK_p_p_1845_0_ _4E_BP_t37_46_s65_2618_0_ MAPK_4E_BP_p_p_1859_0_ 2 589.9 -57.7816857179 orange red kinetics_1676_0_ * k3*MAPK_4E_BP_p_p_cplx_1860_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MAPK\_4E\_BP\_p\_p\_cplx\_1860\_0\_}$ MAPK_p_p_1845_0_ eIF4E_BP_thr37_46_2622_0_ MAPK_4E_BP_phospho_cplx_1863_0_ MAPK_4E_BP_phospho_1862_0_ 1 589.9 -66.7252857681 47 red kinetics_1676_0_ * ( k1 * MAPK_p_p_1845_0_*eIF4E_BP_thr37_46_2622_0_ - k2 * MAPK_4E_BP_phospho_cplx_1863_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{MAPK\_p\_p\_1845\_0\_}\mathrm{eIF4E\_BP\_thr37\_46\_2622\_0\_}-\mathrm{k2}\mathrm{MAPK\_4E\_BP\_phospho\_cplx\_1863\_0\_})$ MAPK_4E_BP_phospho_cplx_1863_0_ MAPK_p_p_1845_0_ eIF4E_BP_t37_46_s65_2624_0_ MAPK_4E_BP_phospho_1862_0_ 2 589.9 -66.7252857681 47 red kinetics_1676_0_ * k3*MAPK_4E_BP_phospho_cplx_1863_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MAPK\_4E\_BP\_phospho\_cplx\_1863\_0\_}$ craf_1_p_1867_0_ MAPKK_1875_0_ MEK_phospho_cplx_1870_0_ MEK_phospho_1869_0_ 1 618.8 -18.8920989825 black 0 kinetics_1676_0_ * ( k1 * MAPKK_1875_0_*craf_1_p_1867_0_ - k2 * MEK_phospho_cplx_1870_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{MAPKK\_1875\_0\_}\mathrm{craf\_1\_p\_1867\_0\_}-\mathrm{k2}\mathrm{MEK\_phospho\_cplx\_1870\_0\_})$ MEK_phospho_cplx_1870_0_ craf_1_p_1867_0_ MAPKK_p_1891_0_ MEK_phospho_1869_0_ 2 618.8 -18.8920989825 black 0 kinetics_1676_0_ * k3*MEK_phospho_cplx_1870_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MEK\_phospho\_cplx\_1870\_0\_}$ craf_1_p_1867_0_ MAPKK_p_1891_0_ MEKp_phospho_cplx_1873_0_ MEKp_phospho_1872_0_ 1 618.8 -28.941087803 black 63 kinetics_1676_0_ * ( k1 * MAPKK_p_1891_0_*craf_1_p_1867_0_ - k2 * MEKp_phospho_cplx_1873_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{MAPKK\_p\_1891\_0\_}\mathrm{craf\_1\_p\_1867\_0\_}-\mathrm{k2}\mathrm{MEKp\_phospho\_cplx\_1873\_0\_})$ MEKp_phospho_cplx_1873_0_ craf_1_p_1867_0_ MAPKK_p_p_1883_0_ MEKp_phospho_1872_0_ 2 618.8 -28.941087803 black 63 kinetics_1676_0_ * k3*MEKp_phospho_cplx_1873_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MEKp\_phospho\_cplx\_1873\_0\_}$ The actual MAPKK is 2 forms from Seger et al JBC 267:20 14373(1992) Vmax = 150nmol/min/mg From Haystead et al FEBS 306(1):17-22 we get Km=46.6nM for at least one of the phosphs. Putting these together: k3=0.15/sec, scale to get k2=0.6. k1=0.75/46.6nM=2.7e-5 MAPKK_p_p_1883_0_ MAPK_1877_0_ MAPKKtyr_cplx_1886_0_ MAPKKtyr_1885_0_ 1 692.0 -18.8920989825 red pink kinetics_1676_0_ * ( k1 * MAPKK_p_p_1883_0_*MAPK_1877_0_ - k2 * MAPKKtyr_cplx_1886_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{MAPKK\_p\_p\_1883\_0\_}\mathrm{MAPK\_1877\_0\_}-\mathrm{k2}\mathrm{MAPKKtyr\_cplx\_1886\_0\_})$ MAPKKtyr_cplx_1886_0_ MAPKK_p_p_1883_0_ MAPK_p_1881_0_ MAPKKtyr_1885_0_ 2 692.0 -18.8920989825 red pink kinetics_1676_0_ * k3*MAPKKtyr_cplx_1886_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MAPKKtyr\_cplx\_1886\_0\_}$ Rate consts same as for MAPKKtyr. MAPKK_p_p_1883_0_ MAPK_p_1881_0_ MAPKKthr_cplx_1889_0_ MAPKKthr_1888_0_ 1 692.0 -28.941087803 red pink kinetics_1676_0_ * ( k1 * MAPK_p_1881_0_*MAPKK_p_p_1883_0_ - k2 * MAPKKthr_cplx_1889_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{MAPK\_p\_1881\_0\_}\mathrm{MAPKK\_p\_p\_1883\_0\_}-\mathrm{k2}\mathrm{MAPKKthr\_cplx\_1889\_0\_})$ MAPKKthr_cplx_1889_0_ MAPKK_p_p_1883_0_ MAPK_p_p_1845_0_ MAPKKthr_1888_0_ 2 692.0 -28.941087803 red pink kinetics_1676_0_ * k3*MAPKKthr_cplx_1889_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MAPKKthr\_cplx\_1889\_0\_}$ Kinetics are the same as for the craf-1* activity, ie., k1=1.1e-6, k2=.42, k3 =0.105 These are based on Force et al PNAS USA 91 1270-1274 1994. These parms cannot reach the observed 4X stim of MAPK. So lets increase the affinity, ie, raise k1 10X to 1.1e-5 Lets take it back down to where it was. Back up to 5X: 5.5e-6 Raf_p_GTP_Ras_1893_0_ MAPKK_1875_0_ Raf_p_GTP_Ras_dot_1_cplx_1896_0_ Raf_p_GTP_Ras_dot_1_1895_0_ 1 596.8 -124.406481598 red red kinetics_1676_0_ * ( k1 * MAPKK_1875_0_*Raf_p_GTP_Ras_1893_0_ - k2 * Raf_p_GTP_Ras_dot_1_cplx_1896_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{MAPKK\_1875\_0\_}\mathrm{Raf\_p\_GTP\_Ras\_1893\_0\_}-\mathrm{k2}\mathrm{Raf\_p\_GTP\_Ras\_dot\_1\_cplx\_1896\_0\_})$ Raf_p_GTP_Ras_dot_1_cplx_1896_0_ Raf_p_GTP_Ras_1893_0_ MAPKK_p_1891_0_ Raf_p_GTP_Ras_dot_1_1895_0_ 2 596.8 -124.406481598 red red kinetics_1676_0_ * k3*Raf_p_GTP_Ras_dot_1_cplx_1896_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Raf\_p\_GTP\_Ras\_dot\_1\_cplx\_1896\_0\_}$ Same kinetics as other c-raf activated forms. See Force et al PNAS 91 1270-1274 1994. k1 = 1.1e-6, k2 = .42, k3 = 1.05 raise k1 to 5.5e-6 Raf_p_GTP_Ras_1893_0_ MAPKK_p_1891_0_ Raf_p_GTP_Ras_dot_2_cplx_1899_0_ Raf_p_GTP_Ras_dot_2_1898_0_ 1 596.8 -114.457982665 red red kinetics_1676_0_ * ( k1 * MAPKK_p_1891_0_*Raf_p_GTP_Ras_1893_0_ - k2 * Raf_p_GTP_Ras_dot_2_cplx_1899_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{MAPKK\_p\_1891\_0\_}\mathrm{Raf\_p\_GTP\_Ras\_1893\_0\_}-\mathrm{k2}\mathrm{Raf\_p\_GTP\_Ras\_dot\_2\_cplx\_1899\_0\_})$ Raf_p_GTP_Ras_dot_2_cplx_1899_0_ Raf_p_GTP_Ras_1893_0_ MAPKK_p_p_1883_0_ Raf_p_GTP_Ras_dot_2_1898_0_ 2 596.8 -114.457982665 red red kinetics_1676_0_ * k3*Raf_p_GTP_Ras_dot_2_cplx_1899_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Raf\_p\_GTP\_Ras\_dot\_2\_cplx\_1899\_0\_}$ Kinetics based on the activation of Gq by the receptor complex in the Gq model (in turn based on the Mahama and Linderman model) k1 = 2e-5, k2 = 1e-10, k3 = 10 (I do not know why they even bother with k2). Lets put k1 at 2e-6 to get a reasonable equilibrium More specific values from, eg.g: Orita et al JBC 268(34) 25542-25546 from rasGRF and smgGDS: k1=3.3e-7; k2 = 0.08, k3 = 0.02 GEF_Gprot_bg_1907_0_ GDP_Ras_1924_0_ GEF_bg_act_Ras_cplx_1910_0_ GEF_bg_act_Ras_1909_0_ 1 736.0 -18.8920989825 red hotpink kinetics_1676_0_ * ( k1 * GEF_Gprot_bg_1907_0_*GDP_Ras_1924_0_ - k2 * GEF_bg_act_Ras_cplx_1910_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{GEF\_Gprot\_bg\_1907\_0\_}\mathrm{GDP\_Ras\_1924\_0\_}-\mathrm{k2}\mathrm{GEF\_bg\_act\_Ras\_cplx\_1910\_0\_})$ GEF_bg_act_Ras_cplx_1910_0_ GEF_Gprot_bg_1907_0_ GTP_Ras_1922_0_ GEF_bg_act_Ras_1909_0_ 2 736.0 -18.8920989825 red hotpink kinetics_1676_0_ * k3*GEF_bg_act_Ras_cplx_1910_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{GEF\_bg\_act\_Ras\_cplx\_1910\_0\_}$ inact_GEF_1912_0_ GDP_Ras_1924_0_ basal_GEF_activity_cplx_1915_0_ basal_GEF_activity_1914_0_ 1 751.0 -18.8920989825 hotpink red kinetics_1676_0_ * ( k1 * inact_GEF_1912_0_*GDP_Ras_1924_0_ - k2 * basal_GEF_activity_cplx_1915_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{inact\_GEF\_1912\_0\_}\mathrm{GDP\_Ras\_1924\_0\_}-\mathrm{k2}\mathrm{basal\_GEF\_activity\_cplx\_1915\_0\_})$ basal_GEF_activity_cplx_1915_0_ inact_GEF_1912_0_ GTP_Ras_1922_0_ basal_GEF_activity_1914_0_ 2 751.0 -18.8920989825 hotpink red kinetics_1676_0_ * k3*basal_GEF_activity_cplx_1915_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{basal\_GEF\_activity\_cplx\_1915\_0\_}$ Kinetics same as GEF-bg-act-ras GEF_p_1917_0_ GDP_Ras_1924_0_ GEF_p_act_Ras_cplx_1920_0_ GEF_p_act_Ras_1919_0_ 1 764.9 -18.8920989825 red hotpink kinetics_1676_0_ * ( k1 * GDP_Ras_1924_0_*GEF_p_1917_0_ - k2 * GEF_p_act_Ras_cplx_1920_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{GDP\_Ras\_1924\_0\_}\mathrm{GEF\_p\_1917\_0\_}-\mathrm{k2}\mathrm{GEF\_p\_act\_Ras\_cplx\_1920\_0\_})$ GEF_p_act_Ras_cplx_1920_0_ GEF_p_1917_0_ GTP_Ras_1922_0_ GEF_p_act_Ras_1919_0_ 2 764.9 -18.8920989825 red hotpink kinetics_1676_0_ * k3*GEF_p_act_Ras_cplx_1920_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{GEF\_p\_act\_Ras\_cplx\_1920\_0\_}$ From Eccleston et al JBC 268(36)pp27012-19 get Kd _lessthan_ 2uM, kcat - 10/sec From Martin et al Cell 63 843-849 1990 get Kd ~ 250 nM, kcat = 20/min I will go with the Eccleston figures as there are good error bars (10%). In general the values are reasonably close. k1 = 1.666e-3/sec, k2 = 1000/sec, k3 = 10/sec (note k3 is rate-limiting) 5 Nov 2002: Changed ratio term to 4 from 100. Now we have k1=8.25e-5; k2=40, k3=10. k3 is still rate-limiting. GAP_1928_0_ GTP_Ras_1922_0_ GAP_inact_Ras_cplx_1931_0_ GAP_inact_Ras_1930_0_ 1 824.0 -18.8920989825 red red kinetics_1676_0_ * ( k1 * GAP_1928_0_*GTP_Ras_1922_0_ - k2 * GAP_inact_Ras_cplx_1931_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{GAP\_1928\_0\_}\mathrm{GTP\_Ras\_1922\_0\_}-\mathrm{k2}\mathrm{GAP\_inact\_Ras\_cplx\_1931\_0\_})$ GAP_inact_Ras_cplx_1931_0_ GAP_1928_0_ GDP_Ras_1924_0_ GAP_inact_Ras_1930_0_ 2 824.0 -18.8920989825 red red kinetics_1676_0_ * k3*GAP_inact_Ras_cplx_1931_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{GAP\_inact\_Ras\_cplx\_1931\_0\_}$ Kinetics same as GEF-bg_act-ras CaM_GEF_1935_0_ GDP_Ras_1924_0_ CaM_GEF_act_Ras_cplx_1938_0_ CaM_GEF_act_Ras_1937_0_ 1 852.9 -18.8920989825 red pink kinetics_1676_0_ * ( k1 * GDP_Ras_1924_0_*CaM_GEF_1935_0_ - k2 * CaM_GEF_act_Ras_cplx_1938_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{GDP\_Ras\_1924\_0\_}\mathrm{CaM\_GEF\_1935\_0\_}-\mathrm{k2}\mathrm{CaM\_GEF\_act\_Ras\_cplx\_1938\_0\_})$ CaM_GEF_act_Ras_cplx_1938_0_ CaM_GEF_1935_0_ GTP_Ras_1922_0_ CaM_GEF_act_Ras_1937_0_ 2 852.9 -18.8920989825 red pink kinetics_1676_0_ * k3*CaM_GEF_act_Ras_cplx_1938_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{CaM\_GEF\_act\_Ras\_cplx\_1938\_0\_}$ Hsu et al JBC 266:1 603-608 1991 Km = 385 +- 100 uM, Vm = 5.1 +-1 pmol/min/ug for PLC-771. Other sites have similar range, but are not stim as much by EGF. k1 = 2.8e-2/385/6e5 = 1.2e-10. Phenomenally slow. But Sherrill and Kyte say turnover # for angiotensin II is 5/min for cell extt, and 2/min for placental. Also see Okada et al for Shc rates which are much faster. L_dot_EGFR_1958_0_ Ca_dot_PLC_g_2020_0_ Ca_dot_PLC_g_phospho_cplx_1961_0_ Ca_dot_PLC_g_phospho_1960_0_ 1 896.9 -18.8920989825 red red kinetics_1676_0_ * ( k1 * Ca_dot_PLC_g_2020_0_*L_dot_EGFR_1958_0_ - k2 * Ca_dot_PLC_g_phospho_cplx_1961_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{Ca\_dot\_PLC\_g\_2020\_0\_}\mathrm{L\_dot\_EGFR\_1958\_0\_}-\mathrm{k2}\mathrm{Ca\_dot\_PLC\_g\_phospho\_cplx\_1961\_0\_})$ Ca_dot_PLC_g_phospho_cplx_1961_0_ L_dot_EGFR_1958_0_ Ca_dot_PLC_g_p_2024_0_ Ca_dot_PLC_g_phospho_1960_0_ 2 896.9 -18.8920989825 red red kinetics_1676_0_ * k3*Ca_dot_PLC_g_phospho_cplx_1961_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Ca\_dot\_PLC\_g\_phospho\_cplx\_1961\_0\_}$ Rates from Okada et al JBC 270:35 pp 20737 1995 Km = 0.70 to 0.85 uM, Vmax = 4.4 to 5.0 pmol/min. Unfortunately the amount of enzyme is not known, the prep is only partially purified. Time course of phosph is max within 30 sec, falls back within 20 min. Ref: Sasaoka et al JBC 269:51 32621 1994. Use k3 = 0.1 based on this tau. L_dot_EGFR_1958_0_ SHC_1981_0_ SHC_phospho_cplx_1964_0_ SHC_phospho_1963_0_ 1 896.9 -28.941087803 red red kinetics_1676_0_ * ( k1 * SHC_1981_0_*L_dot_EGFR_1958_0_ - k2 * SHC_phospho_cplx_1964_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{SHC\_1981\_0\_}\mathrm{L\_dot\_EGFR\_1958\_0\_}-\mathrm{k2}\mathrm{SHC\_phospho\_cplx\_1964\_0\_})$ SHC_phospho_cplx_1964_0_ L_dot_EGFR_1958_0_ SHC_p_1983_0_ SHC_phospho_1963_0_ 2 896.9 -28.941087803 red red kinetics_1676_0_ * k3*SHC_phospho_cplx_1964_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{SHC\_phospho\_cplx\_1964\_0\_}$ SHC_p_dot_Sos_dot_Grb2_1976_0_ GDP_Ras_1924_0_ Sos_dot_Ras_GEF_cplx_1979_0_ Sos_dot_Ras_GEF_1978_0_ 1 4.5 -356.136163799 red brown kinetics_1676_0_ * ( k1 * SHC_p_dot_Sos_dot_Grb2_1976_0_*GDP_Ras_1924_0_ - k2 * Sos_dot_Ras_GEF_cplx_1979_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{SHC\_p\_dot\_Sos\_dot\_Grb2\_1976\_0\_}\mathrm{GDP\_Ras\_1924\_0\_}-\mathrm{k2}\mathrm{Sos\_dot\_Ras\_GEF\_cplx\_1979\_0\_})$ Sos_dot_Ras_GEF_cplx_1979_0_ SHC_p_dot_Sos_dot_Grb2_1976_0_ GTP_Ras_1922_0_ Sos_dot_Ras_GEF_1978_0_ 2 4.5 -356.136163799 red brown kinetics_1676_0_ * k3*Sos_dot_Ras_GEF_cplx_1979_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Sos\_dot\_Ras\_GEF\_cplx\_1979\_0\_}$ SHC_basal_1997_0_ SHC_1981_0_ Enz_cplx_2000_0_ Enz_1999_0_ 1 9.5 -356.538123351 27 23 kinetics_1676_0_ * ( k1 * SHC_basal_1997_0_*SHC_1981_0_ - k2 * Enz_cplx_2000_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{SHC\_basal\_1997\_0\_}\mathrm{SHC\_1981\_0\_}-\mathrm{k2}\mathrm{Enz\_cplx\_2000\_0\_})$ Enz_cplx_2000_0_ SHC_basal_1997_0_ SHC_p_1983_0_ Enz_1999_0_ 2 9.5 -356.538123351 27 23 kinetics_1676_0_ * k3*Enz_cplx_2000_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Enz\_cplx\_2000\_0\_}$ Mainly Homma et al JBC 263:14 1988 pp 6592, but these parms are the Ca-stimulated form. It is not clear whether the enzyme is activated by tyrosine phosphorylation at this point or not. Wahl et al JBC 267:15 10447-10456 1992 say that the Ca_stim and phosph form has 7X higher affinity for substrate than control. This is close to Wahl's figure 7, which I am using as reference. 179.7 -210.023866348 red pink kinetics_1676_0_ * ( kcat * PIP2_1819_0_ * Ca_dot_PLC_g_2020_0_ / ( Km + PIP2_1819_0_)) $\mathrm{kinetics\_1676\_0\_}\frac{\mathrm{kcat}\mathrm{PIP2\_1819\_0\_}\mathrm{Ca\_dot\_PLC\_g\_2020\_0\_}}{\mathrm{Km}+\mathrm{PIP2\_1819\_0\_}}$ Mainly Homma et al JBC 263:14 1988 pp 6592, but these parms are the Ca-stimulated form. It is not clear whether the enzyme is activated by tyrosine phosphorylation at this point or not. Wahl et al JBC 267:15 10447-10456 1992 say that this has 7X higher affinity for substrate than control. 193.8 -210.023866348 red pink kinetics_1676_0_ * ( kcat * PIP2_1819_0_ * Ca_dot_PLC_g_p_2024_0_ / ( Km + PIP2_1819_0_)) $\mathrm{kinetics\_1676\_0\_}\frac{\mathrm{kcat}\mathrm{PIP2\_1819\_0\_}\mathrm{Ca\_dot\_PLC\_g\_p\_2024\_0\_}}{\mathrm{Km}+\mathrm{PIP2\_1819\_0\_}}$ PLCg_basal_2028_0_ PLC_g_2016_0_ PLC_g_phospho_cplx_2031_0_ PLC_g_phospho_2030_0_ 1 208.9 -210.023866348 33 red kinetics_1676_0_ * ( k1 * PLC_g_2016_0_*PLCg_basal_2028_0_ - k2 * PLC_g_phospho_cplx_2031_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PLC\_g\_2016\_0\_}\mathrm{PLCg\_basal\_2028\_0\_}-\mathrm{k2}\mathrm{PLC\_g\_phospho\_cplx\_2031\_0\_})$ PLC_g_phospho_cplx_2031_0_ PLCg_basal_2028_0_ PLC_g_p_2018_0_ PLC_g_phospho_2030_0_ 2 208.9 -210.023866348 33 red kinetics_1676_0_ * k3*PLC_g_phospho_cplx_2031_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PLC\_g\_phospho\_cplx\_2031\_0\_}$ Rates from autocamtide phosphorylation, from Hanson and Schulman JBC 267:24 17216-17224 1992. Jan 1 1998: Speed up 12x to match fig 5. tot_CaM_CaMKII_2055_0_ CaMKII_thr286_2051_0_ CaM_act_305_cplx_2058_0_ CaM_act_305_2057_0_ 1 330.0 -255.746765482 red green kinetics_1676_0_ * ( k1 * CaMKII_thr286_2051_0_*tot_CaM_CaMKII_2055_0_ - k2 * CaM_act_305_cplx_2058_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{CaMKII\_thr286\_2051\_0\_}\mathrm{tot\_CaM\_CaMKII\_2055\_0\_}-\mathrm{k2}\mathrm{CaM\_act\_305\_cplx\_2058\_0\_})$ CaM_act_305_cplx_2058_0_ tot_CaM_CaMKII_2055_0_ CaMKII_p_p_p_2049_0_ CaM_act_305_2057_0_ 2 330.0 -255.746765482 red green kinetics_1676_0_ * k3*CaM_act_305_cplx_2058_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{CaM\_act\_305\_cplx\_2058\_0\_}$ tot_CaM_CaMKII_2055_0_ CaMKII_CaM_2045_0_ CaM_act_286_cplx_2061_0_ CaM_act_286_2060_0_ 1 317.1 -255.746765482 red green kinetics_1676_0_ * ( k1 * CaMKII_CaM_2045_0_*tot_CaM_CaMKII_2055_0_ - k2 * CaM_act_286_cplx_2061_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{CaMKII\_CaM\_2045\_0\_}\mathrm{tot\_CaM\_CaMKII\_2055\_0\_}-\mathrm{k2}\mathrm{CaM\_act\_286\_cplx\_2061\_0\_})$ CaM_act_286_cplx_2061_0_ tot_CaM_CaMKII_2055_0_ CaMKII_thr286_CaM_2047_0_ CaM_act_286_2060_0_ 2 317.1 -255.746765482 red green kinetics_1676_0_ * k3*CaM_act_286_cplx_2061_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{CaM\_act\_286\_cplx\_2061\_0\_}$ tot_CaM_CaMKII_2055_0_ CaMKII_2043_0_ CaM_act_autoph_cplx_2064_0_ CaM_act_autoph_2063_0_ 1 333.8 -151.538751413 47 red kinetics_1676_0_ * ( k1 * CaMKII_2043_0_*tot_CaM_CaMKII_2055_0_ - k2 * CaM_act_autoph_cplx_2064_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{CaMKII\_2043\_0\_}\mathrm{tot\_CaM\_CaMKII\_2055\_0\_}-\mathrm{k2}\mathrm{CaM\_act\_autoph\_cplx\_2064\_0\_})$ CaM_act_autoph_cplx_2064_0_ tot_CaM_CaMKII_2055_0_ CaMKII_thr286_2051_0_ CaM_act_autoph_2063_0_ 2 333.8 -151.538751413 47 red kinetics_1676_0_ * k3*CaM_act_autoph_cplx_2064_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{CaM\_act\_autoph\_cplx\_2064\_0\_}$ tot_auto_2066_0_ CaMKII_2043_0_ auton_autoph_cplx_2069_0_ auton_autoph_2068_0_ 1 346.7 -210.224846125 29 red kinetics_1676_0_ * ( k1 * tot_auto_2066_0_*CaMKII_2043_0_ - k2 * auton_autoph_cplx_2069_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{tot\_auto\_2066\_0\_}\mathrm{CaMKII\_2043\_0\_}-\mathrm{k2}\mathrm{auton\_autoph\_cplx\_2069\_0\_})$ auton_autoph_cplx_2069_0_ tot_auto_2066_0_ CaMKII_thr286_2051_0_ auton_autoph_2068_0_ 2 346.7 -210.224846125 29 red kinetics_1676_0_ * k3*auton_autoph_cplx_2069_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{auton\_autoph\_cplx\_2069\_0\_}$ tot_auto_2066_0_ CaMKII_CaM_2045_0_ auton_286_cplx_2072_0_ auton_286_2071_0_ 1 356.4 -210.023866348 29 red kinetics_1676_0_ * ( k1 * tot_auto_2066_0_*CaMKII_CaM_2045_0_ - k2 * auton_286_cplx_2072_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{tot\_auto\_2066\_0\_}\mathrm{CaMKII\_CaM\_2045\_0\_}-\mathrm{k2}\mathrm{auton\_286\_cplx\_2072\_0\_})$ auton_286_cplx_2072_0_ tot_auto_2066_0_ CaMKII_thr286_CaM_2047_0_ auton_286_2071_0_ 2 356.4 -210.023866348 29 red kinetics_1676_0_ * k3*auton_286_cplx_2072_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{auton\_286\_cplx\_2072\_0\_}$ tot_auto_2066_0_ CaMKII_thr286_2051_0_ auton_305_cplx_2075_0_ auton_305_2074_0_ 1 367.2 -210.124356237 29 red kinetics_1676_0_ * ( k1 * tot_auto_2066_0_*CaMKII_thr286_2051_0_ - k2 * auton_305_cplx_2075_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{tot\_auto\_2066\_0\_}\mathrm{CaMKII\_thr286\_2051\_0\_}-\mathrm{k2}\mathrm{auton\_305\_cplx\_2075\_0\_})$ auton_305_cplx_2075_0_ tot_auto_2066_0_ CaMKII_p_p_p_2049_0_ auton_305_2074_0_ 2 367.2 -210.124356237 29 red kinetics_1676_0_ * k3*auton_305_cplx_2075_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{auton\_305\_cplx\_2075\_0\_}$ From Seki et al ABB 316(2):673-679 CaM_bo_Ca_bc_n_CaNAB_2103_0_ neurogranin_p_2097_0_ dephosph_neurogranin_cplx_2106_0_ dephosph_neurogranin_2105_0_ 1 645.6 -229.016455219 red darkblue kinetics_1676_0_ * ( k1 * neurogranin_p_2097_0_*CaM_bo_Ca_bc_n_CaNAB_2103_0_ - k2 * dephosph_neurogranin_cplx_2106_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{neurogranin\_p\_2097\_0\_}\mathrm{CaM\_bo\_Ca\_bc\_n\_CaNAB\_2103\_0\_}-\mathrm{k2}\mathrm{dephosph\_neurogranin\_cplx\_2106\_0\_})$ dephosph_neurogranin_cplx_2106_0_ CaM_bo_Ca_bc_n_CaNAB_2103_0_ neurogranin_2099_0_ dephosph_neurogranin_2105_0_ 2 645.6 -229.016455219 red darkblue kinetics_1676_0_ * k3*dephosph_neurogranin_cplx_2106_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{dephosph\_neurogranin\_cplx\_2106\_0\_}$ CaM_bo_Ca_bc_n_CaNAB_2103_0_ I1_p_2158_0_ dephosph_inhib1_cplx_2109_0_ dephosph_inhib1_2108_0_ 1 645.6 -238.964954151 red darkblue kinetics_1676_0_ * ( k1 * I1_p_2158_0_*CaM_bo_Ca_bc_n_CaNAB_2103_0_ - k2 * dephosph_inhib1_cplx_2109_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{I1\_p\_2158\_0\_}\mathrm{CaM\_bo\_Ca\_bc\_n\_CaNAB\_2103\_0\_}-\mathrm{k2}\mathrm{dephosph\_inhib1\_cplx\_2109\_0\_})$ dephosph_inhib1_cplx_2109_0_ CaM_bo_Ca_bc_n_CaNAB_2103_0_ I1_2156_0_ dephosph_inhib1_2108_0_ 2 645.6 -238.964954151 red darkblue kinetics_1676_0_ * k3*dephosph_inhib1_cplx_2109_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{dephosph\_inhib1\_cplx\_2109\_0\_}$ CaM_bo_Ca_bc_n_CaNAB_2103_0_ PP1_I1_p_2160_0_ dephosph_PP1_I_p_cplx_2112_0_ dephosph_PP1_I_p_2111_0_ 1 645.6 -247.908554202 2 darkblue kinetics_1676_0_ * ( k1 * PP1_I1_p_2160_0_*CaM_bo_Ca_bc_n_CaNAB_2103_0_ - k2 * dephosph_PP1_I_p_cplx_2112_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP1\_I1\_p\_2160\_0\_}\mathrm{CaM\_bo\_Ca\_bc\_n\_CaNAB\_2103\_0\_}-\mathrm{k2}\mathrm{dephosph\_PP1\_I\_p\_cplx\_2112\_0\_})$ dephosph_PP1_I_p_cplx_2112_0_ CaM_bo_Ca_bc_n_CaNAB_2103_0_ PP1_I1_2162_0_ dephosph_PP1_I_p_2111_0_ 2 645.6 -247.908554202 2 darkblue kinetics_1676_0_ * k3*dephosph_PP1_I_p_cplx_2112_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{dephosph\_PP1\_I\_p\_cplx\_2112\_0\_}$ The rates here are so slow I do not know if we should even bother with this enz reacn. These numbers are from Liu and Storm. Other refs suggest that the Km stays the same but the Vmax goes to 10% of the CaM stim levels. Prev: k1=2.2e-9, k2 = 0.0052, k3 = 0.0013 New : k1=5.7e-8, k2=.136, k3=.034 CaNAB_Ca4_2114_0_ I1_p_2158_0_ dephosph_inhib1_noCaM_cplx_2117_0_ dephosph_inhib1_noCaM_2116_0_ 1 560.0 -210.023866348 red tan kinetics_1676_0_ * ( k1 * CaNAB_Ca4_2114_0_*I1_p_2158_0_ - k2 * dephosph_inhib1_noCaM_cplx_2117_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{CaNAB\_Ca4\_2114\_0\_}\mathrm{I1\_p\_2158\_0\_}-\mathrm{k2}\mathrm{dephosph\_inhib1\_noCaM\_cplx\_2117\_0\_})$ dephosph_inhib1_noCaM_cplx_2117_0_ CaNAB_Ca4_2114_0_ I1_2156_0_ dephosph_inhib1_noCaM_2116_0_ 2 560.0 -210.023866348 red tan kinetics_1676_0_ * k3*dephosph_inhib1_noCaM_cplx_2117_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{dephosph\_inhib1\_noCaM\_cplx\_2117\_0\_}$ The rates are from Stralfors et al Eur J Biochem 149 295-303 giving Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14. Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so k1 becomes 5.72e-6 Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10 to 5.72e-7, 1.4, 0.35 PP1_active_2139_0_ CaMKII_thr286_CaM_2047_0_ Deph_thr286_cplx_2142_0_ Deph_thr286_2141_0_ 1 589.9 -210.023866348 red cyan kinetics_1676_0_ * ( k1 * PP1_active_2139_0_*CaMKII_thr286_CaM_2047_0_ - k2 * Deph_thr286_cplx_2142_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP1\_active\_2139\_0\_}\mathrm{CaMKII\_thr286\_CaM\_2047\_0\_}-\mathrm{k2}\mathrm{Deph\_thr286\_cplx\_2142\_0\_})$ Deph_thr286_cplx_2142_0_ PP1_active_2139_0_ CaMKII_CaM_2045_0_ Deph_thr286_2141_0_ 2 589.9 -210.023866348 red cyan kinetics_1676_0_ * k3*Deph_thr286_cplx_2142_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Deph\_thr286\_cplx\_2142\_0\_}$ PP1_active_2139_0_ CaMKII_p_p_p_2049_0_ Deph_thr305_cplx_2145_0_ Deph_thr305_2144_0_ 1 589.9 -219.972365281 red cyan kinetics_1676_0_ * ( k1 * CaMKII_p_p_p_2049_0_*PP1_active_2139_0_ - k2 * Deph_thr305_cplx_2145_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{CaMKII\_p\_p\_p\_2049\_0\_}\mathrm{PP1\_active\_2139\_0\_}-\mathrm{k2}\mathrm{Deph\_thr305\_cplx\_2145\_0\_})$ Deph_thr305_cplx_2145_0_ PP1_active_2139_0_ CaMKII_thr286_2051_0_ Deph_thr305_2144_0_ 2 589.9 -219.972365281 red cyan kinetics_1676_0_ * k3*Deph_thr305_cplx_2145_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Deph\_thr305\_cplx\_2145\_0\_}$ See Cohen et al PP1_active_2139_0_ CaMKII_thr306_2053_0_ Deph_thr306_cplx_2148_0_ Deph_thr306_2147_0_ 1 589.9 -228.915965331 red cyan kinetics_1676_0_ * ( k1 * PP1_active_2139_0_*CaMKII_thr306_2053_0_ - k2 * Deph_thr306_cplx_2148_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP1\_active\_2139\_0\_}\mathrm{CaMKII\_thr306\_2053\_0\_}-\mathrm{k2}\mathrm{Deph\_thr306\_cplx\_2148\_0\_})$ Deph_thr306_cplx_2148_0_ PP1_active_2139_0_ CaMKII_2043_0_ Deph_thr306_2147_0_ 2 589.9 -228.915965331 red cyan kinetics_1676_0_ * k3*Deph_thr306_cplx_2148_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Deph\_thr306\_cplx\_2148\_0\_}$ PP1_active_2139_0_ CaMKII_p_p_p_2049_0_ Deph_thr286c_cplx_2151_0_ Deph_thr286c_2150_0_ 1 589.9 -238.864464263 red cyan kinetics_1676_0_ * ( k1 * CaMKII_p_p_p_2049_0_*PP1_active_2139_0_ - k2 * Deph_thr286c_cplx_2151_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{CaMKII\_p\_p\_p\_2049\_0\_}\mathrm{PP1\_active\_2139\_0\_}-\mathrm{k2}\mathrm{Deph\_thr286c\_cplx\_2151\_0\_})$ Deph_thr286c_cplx_2151_0_ PP1_active_2139_0_ CaMKII_thr306_2053_0_ Deph_thr286c_2150_0_ 2 589.9 -238.864464263 red cyan kinetics_1676_0_ * k3*Deph_thr286c_cplx_2151_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Deph\_thr286c\_cplx\_2151\_0\_}$ PP1_active_2139_0_ CaMKII_thr286_2051_0_ Deph_thr286b_cplx_2154_0_ Deph_thr286b_2153_0_ 1 589.9 -247.808064314 red cyan kinetics_1676_0_ * ( k1 * CaMKII_thr286_2051_0_*PP1_active_2139_0_ - k2 * Deph_thr286b_cplx_2154_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{CaMKII\_thr286\_2051\_0\_}\mathrm{PP1\_active\_2139\_0\_}-\mathrm{k2}\mathrm{Deph\_thr286b\_cplx\_2154\_0\_})$ Deph_thr286b_cplx_2154_0_ PP1_active_2139_0_ CaMKII_2043_0_ Deph_thr286b_2153_0_ 2 589.9 -247.808064314 red cyan kinetics_1676_0_ * k3*Deph_thr286b_cplx_2154_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Deph\_thr286b\_cplx\_2154\_0\_}$ This pathway inhibits Ras when cAMP is elevated. See: Hordijk et al JBC 269:5 3534-3538 1994 Burgering et al EMBO J 12:11 4211-4220 1993 The rates are the same as used in PKA-phosph-I1 PKA_active_2194_0_ inact_GEF_1912_0_ PKA_phosph_GEF_cplx_2197_0_ PKA_phosph_GEF_2196_0_ 1 881.9 -210.023866348 red yellow kinetics_1676_0_ * ( k1 * inact_GEF_1912_0_*PKA_active_2194_0_ - k2 * PKA_phosph_GEF_cplx_2197_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{inact\_GEF\_1912\_0\_}\mathrm{PKA\_active\_2194\_0\_}-\mathrm{k2}\mathrm{PKA\_phosph\_GEF\_cplx\_2197\_0\_})$ PKA_phosph_GEF_cplx_2197_0_ PKA_active_2194_0_ inact_GEF_p_1933_0_ PKA_phosph_GEF_2196_0_ 2 881.9 -210.023866348 red yellow kinetics_1676_0_ * k3*PKA_phosph_GEF_cplx_2197_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PKA\_phosph\_GEF\_cplx\_2197\_0\_}$ #s from Bramson et al CRC crit rev Biochem 15:2 93-124. They have a huge list of peptide substrates and I have chosen high-ish rates. These consts give too much PKA activity, so lower Vmax 1/3. Now, k1 = 3e-5, k2 = 36, k3 = 9 (still pretty fast). Also lower Km 1/3 so k1 = 1e-5 Cohen et al FEBS Lett 76:182-86 1977 say rate =30% PKA act on phosphokinase beta. PKA_active_2194_0_ I1_2156_0_ PKA_phosph_I1_cplx_2200_0_ PKA_phosph_I1_2199_0_ 1 881.9 -219.972365281 red yellow kinetics_1676_0_ * ( k1 * PKA_active_2194_0_*I1_2156_0_ - k2 * PKA_phosph_I1_cplx_2200_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PKA\_active\_2194\_0\_}\mathrm{I1\_2156\_0\_}-\mathrm{k2}\mathrm{PKA\_phosph\_I1\_cplx\_2200\_0\_})$ PKA_phosph_I1_cplx_2200_0_ PKA_active_2194_0_ I1_p_2158_0_ PKA_phosph_I1_2199_0_ 2 881.9 -219.972365281 red yellow kinetics_1676_0_ * k3*PKA_phosph_I1_cplx_2200_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PKA\_phosph\_I1\_cplx\_2200\_0\_}$ Same rates as PKA-phosph-I1 PKA_active_2194_0_ cAMP_PDE_2267_0_ phosph_PDE_cplx_2203_0_ phosph_PDE_2202_0_ 1 881.9 -228.915965331 red yellow kinetics_1676_0_ * ( k1 * PKA_active_2194_0_*cAMP_PDE_2267_0_ - k2 * phosph_PDE_cplx_2203_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PKA\_active\_2194\_0\_}\mathrm{cAMP\_PDE\_2267\_0\_}-\mathrm{k2}\mathrm{phosph\_PDE\_cplx\_2203\_0\_})$ phosph_PDE_cplx_2203_0_ PKA_active_2194_0_ cAMP_PDE_p_2272_0_ phosph_PDE_2202_0_ 2 881.9 -228.915965331 red yellow kinetics_1676_0_ * k3*phosph_PDE_cplx_2203_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{phosph\_PDE\_cplx\_2203\_0\_}$ 33.0 -401.256123603 red orange kinetics_1676_0_ * ( kcat * ATP_2241_0_ * AC1_CaM_2243_0_ / ( Km + ATP_2241_0_)) $\mathrm{kinetics\_1676\_0\_}\frac{\mathrm{kcat}\mathrm{ATP\_2241\_0\_}\mathrm{AC1\_CaM\_2243\_0\_}}{\mathrm{Km}+\mathrm{ATP\_2241\_0\_}}$ Reduced Km to match expt data for basal activation of AC2 by PKC. Now k1 = 2.9e-6, k2 = 72, k3 = 18 61.9 -401.256123603 red yellow kinetics_1676_0_ * ( kcat * ATP_2241_0_ * AC2_p_2249_0_ / ( Km + ATP_2241_0_)) $\mathrm{kinetics\_1676\_0\_}\frac{\mathrm{kcat}\mathrm{ATP\_2241\_0\_}\mathrm{AC2\_p\_2249\_0\_}}{\mathrm{Km}+\mathrm{ATP\_2241\_0\_}}$ 77.0 -401.256123603 red yellow kinetics_1676_0_ * ( kcat * ATP_2241_0_ * AC2_Gs_2253_0_ / ( Km + ATP_2241_0_)) $\mathrm{kinetics\_1676\_0\_}\frac{\mathrm{kcat}\mathrm{ATP\_2241\_0\_}\mathrm{AC2\_Gs\_2253\_0\_}}{\mathrm{Km}+\mathrm{ATP\_2241\_0\_}}$ 105.9 -401.256123603 red orange kinetics_1676_0_ * ( kcat * ATP_2241_0_ * AC1_Gs_2259_0_ / ( Km + ATP_2241_0_)) $\mathrm{kinetics\_1676\_0\_}\frac{\mathrm{kcat}\mathrm{ATP\_2241\_0\_}\mathrm{AC1\_Gs\_2259\_0\_}}{\mathrm{Km}+\mathrm{ATP\_2241\_0\_}}$ 121.0 -401.256123603 red green kinetics_1676_0_ * ( kcat * ATP_2241_0_ * AC2_p_Gs_2263_0_ / ( Km + ATP_2241_0_)) $\mathrm{kinetics\_1676\_0\_}\frac{\mathrm{kcat}\mathrm{ATP\_2241\_0\_}\mathrm{AC2\_p\_Gs\_2263\_0\_}}{\mathrm{Km}+\mathrm{ATP\_2241\_0\_}}$ Best rates are from Conti et al Biochem 34 7979-7987 1995. Though these are for the Sertoli cell form, it looks like they carry nicely into alternatively spliced brain form. See Sette et al JBC 269:28 18271-18274 Km ~2 uM, Vmax est ~ 10 umol/min/mg for pure form. Brain protein is 93 kD but this was 67. So k3 ~10, k2 ~40, k1 ~4.2e-6 cAMP_PDE_2267_0_ cAMP_2239_0_ PDE_cplx_2270_0_ PDE_2269_0_ 1 11.0 -505.765607336 red green kinetics_1676_0_ * ( k1 * cAMP_PDE_2267_0_*cAMP_2239_0_ - k2 * PDE_cplx_2270_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{cAMP\_PDE\_2267\_0\_}\mathrm{cAMP\_2239\_0\_}-\mathrm{k2}\mathrm{PDE\_cplx\_2270\_0\_})$ PDE_cplx_2270_0_ cAMP_PDE_2267_0_ AMP_2287_0_ PDE_2269_0_ 2 11.0 -505.765607336 red green kinetics_1676_0_ * k3*PDE_cplx_2270_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PDE\_cplx\_2270\_0\_}$ This form has about twice the activity of the unphosphorylated form. See Sette et al JBC 269:28 18271-18274 1994. We'll ignore cGMP effects for now. cAMP_PDE_p_2272_0_ cAMP_2239_0_ PDE_p_cplx_2275_0_ PDE_p_2274_0_ 1 25.8 -505.765607336 red green kinetics_1676_0_ * ( k1 * cAMP_PDE_p_2272_0_*cAMP_2239_0_ - k2 * PDE_p_cplx_2275_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{cAMP\_PDE\_p\_2272\_0\_}\mathrm{cAMP\_2239\_0\_}-\mathrm{k2}\mathrm{PDE\_p\_cplx\_2275\_0\_})$ PDE_p_cplx_2275_0_ cAMP_PDE_p_2272_0_ AMP_2287_0_ PDE_p_2274_0_ 2 25.8 -505.765607336 red green kinetics_1676_0_ * k3*PDE_p_cplx_2275_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PDE\_p\_cplx\_2275\_0\_}$ Rate is 1/6 of the CaM stim form. We'll just reduce all lf k1, k2, k3 so that the Vmax goes down 1/6. PDE1_2277_0_ cAMP_2239_0_ PDE1_cplx_2280_0_ PDE1_2279_0_ 1 39.9 -505.765607336 red green kinetics_1676_0_ * ( k1 * PDE1_2277_0_*cAMP_2239_0_ - k2 * PDE1_cplx_2280_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PDE1\_2277\_0\_}\mathrm{cAMP\_2239\_0\_}-\mathrm{k2}\mathrm{PDE1\_cplx\_2280\_0\_})$ PDE1_cplx_2280_0_ PDE1_2277_0_ AMP_2287_0_ PDE1_2279_0_ 2 39.9 -505.765607336 red green kinetics_1676_0_ * k3*PDE1_cplx_2280_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PDE1\_cplx\_2280\_0\_}$ Max activity ~10umol/min/mg in presence of lots of CaM. Affinity is low, 40 uM. k3 = 10, k2 = 40, k1 = (50/40) / 6e5. CaM_dot_PDE1_2282_0_ cAMP_2239_0_ CaM_dot_PDE1_cplx_2285_0_ CaM_dot_PDE1_2284_0_ 1 55.0 -505.765607336 red green kinetics_1676_0_ * ( k1 * CaM_dot_PDE1_2282_0_*cAMP_2239_0_ - k2 * CaM_dot_PDE1_cplx_2285_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{CaM\_dot\_PDE1\_2282\_0\_}\mathrm{cAMP\_2239\_0\_}-\mathrm{k2}\mathrm{CaM\_dot\_PDE1\_cplx\_2285\_0\_})$ CaM_dot_PDE1_cplx_2285_0_ CaM_dot_PDE1_2282_0_ AMP_2287_0_ CaM_dot_PDE1_2284_0_ 2 55.0 -505.765607336 red green kinetics_1676_0_ * k3*CaM_dot_PDE1_cplx_2285_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{CaM\_dot\_PDE1\_cplx\_2285\_0\_}$ The original kinetics have been modified to obey the k2 = 4 * k3 rule, while keeping kcat and Km fixed. As noted in the NOTES, the only constraining data point is the time course of MAPK dephosphorylation, which this model satisfies. It would be nice to have more accurate estimates of rate consts and MKP-1 levels from the literature. Effective Km : 67 nM kcat = 1.43 umol/min/mg MKP_1_2345_0_ MAPK_p_1881_0_ MKP1_tyr_deph_cplx_2348_0_ MKP1_tyr_deph_2347_0_ 1 442.9 -401.256123603 red hotpink kinetics_1676_0_ * ( k1 * MKP_1_2345_0_*MAPK_p_1881_0_ - k2 * MKP1_tyr_deph_cplx_2348_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{MKP\_1\_2345\_0\_}\mathrm{MAPK\_p\_1881\_0\_}-\mathrm{k2}\mathrm{MKP1\_tyr\_deph\_cplx\_2348\_0\_})$ MKP1_tyr_deph_cplx_2348_0_ MKP_1_2345_0_ MAPK_1877_0_ MKP1_tyr_deph_2347_0_ 2 442.9 -401.256123603 red hotpink kinetics_1676_0_ * k3*MKP1_tyr_deph_cplx_2348_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MKP1\_tyr\_deph\_cplx\_2348\_0\_}$ See MKP1-tyr-deph MKP_1_2345_0_ MAPK_p_p_1845_0_ MKP1_thr_deph_cplx_2351_0_ MKP1_thr_deph_2350_0_ 1 442.9 -410.199723653 red hotpink kinetics_1676_0_ * ( k1 * MKP_1_2345_0_*MAPK_p_p_1845_0_ - k2 * MKP1_thr_deph_cplx_2351_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{MKP\_1\_2345\_0\_}\mathrm{MAPK\_p\_p\_1845\_0\_}-\mathrm{k2}\mathrm{MKP1\_thr\_deph\_cplx\_2351\_0\_})$ MKP1_thr_deph_cplx_2351_0_ MKP_1_2345_0_ MAPK_p_1881_0_ MKP1_thr_deph_2350_0_ 2 442.9 -410.199723653 red hotpink kinetics_1676_0_ * k3*MKP1_thr_deph_cplx_2351_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MKP1\_thr\_deph\_cplx\_2351\_0\_}$ See parent PPhosphatase2A for parms PPhosphatase2A_2353_0_ craf_1_p_1867_0_ craf_dephospho_cplx_2356_0_ craf_dephospho_2355_0_ 1 457.9 -401.256123603 red hotpink kinetics_1676_0_ * ( k1 * PPhosphatase2A_2353_0_*craf_1_p_1867_0_ - k2 * craf_dephospho_cplx_2356_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PPhosphatase2A\_2353\_0\_}\mathrm{craf\_1\_p\_1867\_0\_}-\mathrm{k2}\mathrm{craf\_dephospho\_cplx\_2356\_0\_})$ craf_dephospho_cplx_2356_0_ PPhosphatase2A_2353_0_ craf_1_1865_0_ craf_dephospho_2355_0_ 2 457.9 -401.256123603 red hotpink kinetics_1676_0_ * k3*craf_dephospho_cplx_2356_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{craf\_dephospho\_cplx\_2356\_0\_}$ See: Kyriakis et al Nature 358 pp 417-421 1992 Ahn et al Curr Op Cell Biol 4:992-999 1992 for this pathway. See parent PPhosphatase2A for parms. PPhosphatase2A_2353_0_ MAPKK_p_p_1883_0_ MAPKK_dephospho_cplx_2359_0_ MAPKK_dephospho_2358_0_ 1 457.9 -410.199723653 red hotpink kinetics_1676_0_ * ( k1 * PPhosphatase2A_2353_0_*MAPKK_p_p_1883_0_ - k2 * MAPKK_dephospho_cplx_2359_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PPhosphatase2A\_2353\_0\_}\mathrm{MAPKK\_p\_p\_1883\_0\_}-\mathrm{k2}\mathrm{MAPKK\_dephospho\_cplx\_2359\_0\_})$ MAPKK_dephospho_cplx_2359_0_ PPhosphatase2A_2353_0_ MAPKK_p_1891_0_ MAPKK_dephospho_2358_0_ 2 457.9 -410.199723653 red hotpink kinetics_1676_0_ * k3*MAPKK_dephospho_cplx_2359_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MAPKK\_dephospho\_cplx\_2359\_0\_}$ PPhosphatase2A_2353_0_ MAPKK_p_1891_0_ MAPKK_dephospho_ser_cplx_2362_0_ MAPKK_dephospho_ser_2361_0_ 1 457.9 -420.148222585 red hotpink kinetics_1676_0_ * ( k1 * PPhosphatase2A_2353_0_*MAPKK_p_1891_0_ - k2 * MAPKK_dephospho_ser_cplx_2362_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PPhosphatase2A\_2353\_0\_}\mathrm{MAPKK\_p\_1891\_0\_}-\mathrm{k2}\mathrm{MAPKK\_dephospho\_ser\_cplx\_2362\_0\_})$ MAPKK_dephospho_ser_cplx_2362_0_ PPhosphatase2A_2353_0_ MAPKK_1875_0_ MAPKK_dephospho_ser_2361_0_ 2 457.9 -420.148222585 red hotpink kinetics_1676_0_ * k3*MAPKK_dephospho_ser_cplx_2362_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{MAPKK\_dephospho\_ser\_cplx\_2362\_0\_}$ Ueki et al JBC 269(22) pp 15756-15761 1994 show hyperphosphorylation of craf, so this is there to dephosphorylate it. Identity of phosphatase is not known to me, but it may be PP2A like the rest, so I have made it so. PPhosphatase2A_2353_0_ craf_1_p_p_1879_0_ craf_p_p_dephospho_cplx_2365_0_ craf_p_p_dephospho_2364_0_ 1 457.9 -428.991332747 red hotpink kinetics_1676_0_ * ( k1 * PPhosphatase2A_2353_0_*craf_1_p_p_1879_0_ - k2 * craf_p_p_dephospho_cplx_2365_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PPhosphatase2A\_2353\_0\_}\mathrm{craf\_1\_p\_p\_1879\_0\_}-\mathrm{k2}\mathrm{craf\_p\_p\_dephospho\_cplx\_2365\_0\_})$ craf_p_p_dephospho_cplx_2365_0_ PPhosphatase2A_2353_0_ craf_1_p_1867_0_ craf_p_p_dephospho_2364_0_ 2 457.9 -428.991332747 red hotpink kinetics_1676_0_ * k3*craf_p_p_dephospho_cplx_2365_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{craf\_p\_p\_dephospho\_cplx\_2365\_0\_}$ PPhosphatase2A_2353_0_ craf_1_p_ser259_1901_0_ deph_raf_ser259_cplx_2368_0_ deph_raf_ser259_2367_0_ 1 457.9 -391.30762467 hotpink red kinetics_1676_0_ * ( k1 * PPhosphatase2A_2353_0_*craf_1_p_ser259_1901_0_ - k2 * deph_raf_ser259_cplx_2368_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PPhosphatase2A\_2353\_0\_}\mathrm{craf\_1\_p\_ser259\_1901\_0\_}-\mathrm{k2}\mathrm{deph\_raf\_ser259\_cplx\_2368\_0\_})$ deph_raf_ser259_cplx_2368_0_ PPhosphatase2A_2353_0_ craf_1_1865_0_ deph_raf_ser259_2367_0_ 2 457.9 -391.30762467 hotpink red kinetics_1676_0_ * k3*deph_raf_ser259_cplx_2368_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{deph\_raf\_ser259\_cplx\_2368\_0\_}$ PP2A does most of the dephosph of I1 at basal Ca levels. See the review by Cohen in Ann Rev Biochem 1989. For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6 PP2A_2370_0_ I1_p_2158_0_ PP2A_dephospho_I1_cplx_2373_0_ PP2A_dephospho_I1_2372_0_ 1 472.0 -401.256123603 red red kinetics_1676_0_ * ( k1 * PP2A_2370_0_*I1_p_2158_0_ - k2 * PP2A_dephospho_I1_cplx_2373_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP2A\_2370\_0\_}\mathrm{I1\_p\_2158\_0\_}-\mathrm{k2}\mathrm{PP2A\_dephospho\_I1\_cplx\_2373\_0\_})$ PP2A_dephospho_I1_cplx_2373_0_ PP2A_2370_0_ I1_2156_0_ PP2A_dephospho_I1_2372_0_ 2 472.0 -401.256123603 red red kinetics_1676_0_ * k3*PP2A_dephospho_I1_cplx_2373_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PP2A\_dephospho\_I1\_cplx\_2373\_0\_}$ k1 changed from 3.3e-6 to 6.6e-6 PP2A_2370_0_ PP1_I1_p_2160_0_ PP2A_dephospho_PP1_I_p_cplx_2376_0_ PP2A_dephospho_PP1_I_p_2375_0_ 1 472.0 -410.199723653 red red kinetics_1676_0_ * ( k1 * PP1_I1_p_2160_0_*PP2A_2370_0_ - k2 * PP2A_dephospho_PP1_I_p_cplx_2376_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP1\_I1\_p\_2160\_0\_}\mathrm{PP2A\_2370\_0\_}-\mathrm{k2}\mathrm{PP2A\_dephospho\_PP1\_I\_p\_cplx\_2376\_0\_})$ PP2A_dephospho_PP1_I_p_cplx_2376_0_ PP2A_2370_0_ PP1_I1_2162_0_ PP2A_dephospho_PP1_I_p_2375_0_ 2 472.0 -410.199723653 red red kinetics_1676_0_ * k3*PP2A_dephospho_PP1_I_p_cplx_2376_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PP2A\_dephospho\_PP1\_I\_p\_cplx\_2376\_0\_}$ PP2A_2370_0_ S6K_p_2588_0_ dephos_clus_S6K_cplx_2379_0_ dephos_clus_S6K_2378_0_ 1 472.0 -420.148222585 25 red kinetics_1676_0_ * ( k1 * PP2A_2370_0_*S6K_p_2588_0_ - k2 * dephos_clus_S6K_cplx_2379_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP2A\_2370\_0\_}\mathrm{S6K\_p\_2588\_0\_}-\mathrm{k2}\mathrm{dephos\_clus\_S6K\_cplx\_2379\_0\_})$ dephos_clus_S6K_cplx_2379_0_ PP2A_2370_0_ S6K_2590_0_ dephos_clus_S6K_2378_0_ 2 472.0 -420.148222585 25 red kinetics_1676_0_ * k3*dephos_clus_S6K_cplx_2379_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{dephos\_clus\_S6K\_cplx\_2379\_0\_}$ PP2A_2370_0_ S6K_thr_412_2592_0_ dephos_S6K_cplx_2382_0_ dephos_S6K_2381_0_ 1 472.0 -428.991332747 25 red kinetics_1676_0_ * ( k1 * S6K_thr_412_2592_0_*PP2A_2370_0_ - k2 * dephos_S6K_cplx_2382_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{S6K\_thr\_412\_2592\_0\_}\mathrm{PP2A\_2370\_0\_}-\mathrm{k2}\mathrm{dephos\_S6K\_cplx\_2382\_0\_})$ dephos_S6K_cplx_2382_0_ PP2A_2370_0_ S6K_p_2588_0_ dephos_S6K_2381_0_ 2 472.0 -428.991332747 25 red kinetics_1676_0_ * k3*dephos_S6K_cplx_2382_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{dephos\_S6K\_cplx\_2382\_0\_}$ PP2A_2370_0_ S6K_thr_252_2597_0_ dephosp_S6K_cplx_2385_0_ dephosp_S6K_2384_0_ 1 472.0 -439.040321568 25 red kinetics_1676_0_ * ( k1 * PP2A_2370_0_*S6K_thr_252_2597_0_ - k2 * dephosp_S6K_cplx_2385_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP2A\_2370\_0\_}\mathrm{S6K\_thr\_252\_2597\_0\_}-\mathrm{k2}\mathrm{dephosp\_S6K\_cplx\_2385\_0\_})$ dephosp_S6K_cplx_2385_0_ PP2A_2370_0_ S6K_thr_412_2592_0_ dephosp_S6K_2384_0_ 2 472.0 -439.040321568 25 red kinetics_1676_0_ * k3*dephosp_S6K_cplx_2385_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{dephosp\_S6K\_cplx\_2385\_0\_}$ PP2A_2370_0_ PIP3_AKT_t308_s473_2517_0_ Dephos_AKTser473_cplx_2388_0_ Dephos_AKTser473_2387_0_ 1 472.0 -448.9888205 46 red kinetics_1676_0_ * ( k1 * PP2A_2370_0_*PIP3_AKT_t308_s473_2517_0_ - k2 * Dephos_AKTser473_cplx_2388_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP2A\_2370\_0\_}\mathrm{PIP3\_AKT\_t308\_s473\_2517\_0\_}-\mathrm{k2}\mathrm{Dephos\_AKTser473\_cplx\_2388\_0\_})$ Dephos_AKTser473_cplx_2388_0_ PP2A_2370_0_ PIP3_AKT_thr308_2515_0_ Dephos_AKTser473_2387_0_ 2 472.0 -448.9888205 46 red kinetics_1676_0_ * k3*Dephos_AKTser473_cplx_2388_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Dephos\_AKTser473\_cplx\_2388\_0\_}$ PP2A_2370_0_ PIP3_AKT_thr308_2515_0_ Dephosph_AKTthr308_cplx_2391_0_ Dephosph_AKTthr308_2390_0_ 1 472.0 -457.93242055 46 red kinetics_1676_0_ * ( k1 * PP2A_2370_0_*PIP3_AKT_thr308_2515_0_ - k2 * Dephosph_AKTthr308_cplx_2391_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP2A\_2370\_0\_}\mathrm{PIP3\_AKT\_thr308\_2515\_0\_}-\mathrm{k2}\mathrm{Dephosph\_AKTthr308\_cplx\_2391\_0\_})$ Dephosph_AKTthr308_cplx_2391_0_ PP2A_2370_0_ PIP3_AKT_2503_0_ Dephosph_AKTthr308_2390_0_ 2 472.0 -457.93242055 46 red kinetics_1676_0_ * k3*Dephosph_AKTthr308_cplx_2391_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Dephosph\_AKTthr308\_cplx\_2391\_0\_}$ PP2A_2370_0_ eEFthr_56_2734_0_ eEF2thr_56_dephospho_cplx_2394_0_ eEF2thr_56_dephospho_2393_0_ 1 472.0 -467.981409371 4 red kinetics_1676_0_ * ( k1 * PP2A_2370_0_*eEFthr_56_2734_0_ - k2 * eEF2thr_56_dephospho_cplx_2394_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP2A\_2370\_0\_}\mathrm{eEFthr\_56\_2734\_0\_}-\mathrm{k2}\mathrm{eEF2thr\_56\_dephospho\_cplx\_2394\_0\_})$ eEF2thr_56_dephospho_cplx_2394_0_ PP2A_2370_0_ eEF2_2732_0_ eEF2thr_56_dephospho_2393_0_ 2 472.0 -467.981409371 4 red kinetics_1676_0_ * k3*eEF2thr_56_dephospho_cplx_2394_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{eEF2thr\_56\_dephospho\_cplx\_2394\_0\_}$ PP2A_2370_0_ _4E_BP_t37_46_s65_2618_0_ PP2A_4E_BP_p_p_cplx_2397_0_ PP2A_4E_BP_p_p_2396_0_ 1 472.0 -476.925009421 4 red kinetics_1676_0_ * ( k1 * PP2A_2370_0_*_4E_BP_t37_46_s65_2618_0_ - k2 * PP2A_4E_BP_p_p_cplx_2397_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP2A\_2370\_0\_}\mathrm{\_4E\_BP\_t37\_46\_s65\_2618\_0\_}-\mathrm{k2}\mathrm{PP2A\_4E\_BP\_p\_p\_cplx\_2397\_0\_})$ PP2A_4E_BP_p_p_cplx_2397_0_ PP2A_2370_0_ _4E_BP_t37_46_2626_0_ PP2A_4E_BP_p_p_2396_0_ 2 472.0 -476.925009421 4 red kinetics_1676_0_ * k3*PP2A_4E_BP_p_p_cplx_2397_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PP2A\_4E\_BP\_p\_p\_cplx\_2397\_0\_}$ PP2A_2370_0_ _4E_BP_t37_46_2626_0_ PP2A_4E_BP_p_cplx_2400_0_ PP2A_4E_BP_p_2399_0_ 1 472.0 -486.873508353 4 red kinetics_1676_0_ * ( k1 * PP2A_2370_0_*_4E_BP_t37_46_2626_0_ - k2 * PP2A_4E_BP_p_cplx_2400_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP2A\_2370\_0\_}\mathrm{\_4E\_BP\_t37\_46\_2626\_0\_}-\mathrm{k2}\mathrm{PP2A\_4E\_BP\_p\_cplx\_2400\_0\_})$ PP2A_4E_BP_p_cplx_2400_0_ PP2A_2370_0_ _4E_BP_2616_0_ PP2A_4E_BP_p_2399_0_ 2 472.0 -486.873508353 4 red kinetics_1676_0_ * k3*PP2A_4E_BP_p_cplx_2400_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PP2A\_4E\_BP\_p\_cplx\_2400\_0\_}$ PP2A_2370_0_ eIF4E_BP_t37_46_s65_2624_0_ PP2A_4E_BP_cplx_2403_0_ PP2A_4E_BP_2402_0_ 1 472.0 -496.822007286 62 red kinetics_1676_0_ * ( k1 * eIF4E_BP_t37_46_s65_2624_0_*PP2A_2370_0_ - k2 * PP2A_4E_BP_cplx_2403_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{eIF4E\_BP\_t37\_46\_s65\_2624\_0\_}\mathrm{PP2A\_2370\_0\_}-\mathrm{k2}\mathrm{PP2A\_4E\_BP\_cplx\_2403\_0\_})$ PP2A_4E_BP_cplx_2403_0_ PP2A_2370_0_ eIF4E_BP_thr37_46_2622_0_ PP2A_4E_BP_2402_0_ 2 472.0 -496.822007286 62 red kinetics_1676_0_ * k3*PP2A_4E_BP_cplx_2403_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PP2A\_4E\_BP\_cplx\_2403\_0\_}$ PP2A_2370_0_ eIF4E_BP_thr37_46_2622_0_ PP2A_4EBP_cplx_2406_0_ PP2A_4EBP_2405_0_ 1 472.0 -505.765607336 62 red kinetics_1676_0_ * ( k1 * PP2A_2370_0_*eIF4E_BP_thr37_46_2622_0_ - k2 * PP2A_4EBP_cplx_2406_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP2A\_2370\_0\_}\mathrm{eIF4E\_BP\_thr37\_46\_2622\_0\_}-\mathrm{k2}\mathrm{PP2A\_4EBP\_cplx\_2406\_0\_})$ PP2A_4EBP_cplx_2406_0_ PP2A_2370_0_ eIF4E_BP_2620_0_ PP2A_4EBP_2405_0_ 2 472.0 -505.765607336 62 red kinetics_1676_0_ * k3*PP2A_4EBP_cplx_2406_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PP2A\_4EBP\_cplx\_2406\_0\_}$ PP2A_2370_0_ Internal_mGluR_p_2820_0_ mGluR_dephosph_cplx_2409_0_ mGluR_dephosph_2408_0_ 1 472.0 -515.714106268 black 23 kinetics_1676_0_ * ( k1 * PP2A_2370_0_*Internal_mGluR_p_2820_0_ - k2 * mGluR_dephosph_cplx_2409_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PP2A\_2370\_0\_}\mathrm{Internal\_mGluR\_p\_2820\_0\_}-\mathrm{k2}\mathrm{mGluR\_dephosph\_cplx\_2409\_0\_})$ mGluR_dephosph_cplx_2409_0_ PP2A_2370_0_ Internal_mGluR_2818_0_ mGluR_dephosph_2408_0_ 2 472.0 -515.714106268 black 23 kinetics_1676_0_ * k3*mGluR_dephosph_cplx_2409_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{mGluR\_dephosph\_cplx\_2409\_0\_}$ From McBurney and Neering, TINS 10(4), 1987, 164-169 1987. We are using the high-affinity pump here. Their numbers exceed M_andL so I am reducing the rates by 10X. Need to check. k1 = 3e-3, k2 = 288, k3 = 72, n = 1000. This comes to a Km of 0.2 for Ca, and a Vmax of 72. CaEPump_2435_0_ Ca_2413_0_ Ca_pump_out_cplx_2438_0_ Ca_pump_out_2437_0_ 1 590.71 -382.987061927 pink red kinetics_1676_0_ * ( k1 * CaEPump_2435_0_*Ca_2413_0_ - k2 * Ca_pump_out_cplx_2438_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{CaEPump\_2435\_0\_}\mathrm{Ca\_2413\_0\_}-\mathrm{k2}\mathrm{Ca\_pump\_out\_cplx\_2438\_0\_})$ Ca_pump_out_cplx_2438_0_ CaEPump_2435_0_ Ca_ext_2440_0_ Ca_pump_out_2437_0_ 2 590.71 -382.987061927 pink red kinetics_1676_0_ * k3*Ca_pump_out_cplx_2438_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Ca\_pump\_out\_cplx\_2438\_0\_}$ PDK1_2462_0_ S6K_thr_412_2592_0_ S6K_phospho_cplx_2465_0_ S6K_phospho_2464_0_ 1 795.0 -401.256123603 37 red kinetics_1676_0_ * ( k1 * S6K_thr_412_2592_0_*PDK1_2462_0_ - k2 * S6K_phospho_cplx_2465_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{S6K\_thr\_412\_2592\_0\_}\mathrm{PDK1\_2462\_0\_}-\mathrm{k2}\mathrm{S6K\_phospho\_cplx\_2465\_0\_})$ S6K_phospho_cplx_2465_0_ PDK1_2462_0_ S6K_thr_252_2597_0_ S6K_phospho_2464_0_ 2 795.0 -401.256123603 37 red kinetics_1676_0_ * k3*S6K_phospho_cplx_2465_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{S6K\_phospho\_cplx\_2465\_0\_}$ SHC_p_Grb2_Gab1_PI3K_clx_2467_0_ PIP2_1819_0_ Phospho_cplx_2470_0_ Phospho_2469_0_ 1 808.9 -401.256123603 brown red kinetics_1676_0_ * ( k1 * PIP2_1819_0_*SHC_p_Grb2_Gab1_PI3K_clx_2467_0_ - k2 * Phospho_cplx_2470_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PIP2\_1819\_0\_}\mathrm{SHC\_p\_Grb2\_Gab1\_PI3K\_clx\_2467\_0\_}-\mathrm{k2}\mathrm{Phospho\_cplx\_2470\_0\_})$ Phospho_cplx_2470_0_ SHC_p_Grb2_Gab1_PI3K_clx_2467_0_ PIP3_2460_0_ Phospho_2469_0_ 2 808.9 -401.256123603 brown red kinetics_1676_0_ * k3*Phospho_cplx_2470_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Phospho\_cplx\_2470\_0\_}$ PI3K_basal_2474_0_ PIP2_1819_0_ basal_phosp_cplx_2477_0_ basal_phosp_2476_0_ 1 837.9 -401.256123603 10 red kinetics_1676_0_ * ( k1 * PI3K_basal_2474_0_*PIP2_1819_0_ - k2 * basal_phosp_cplx_2477_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PI3K\_basal\_2474\_0\_}\mathrm{PIP2\_1819\_0\_}-\mathrm{k2}\mathrm{basal\_phosp\_cplx\_2477\_0\_})$ basal_phosp_cplx_2477_0_ PI3K_basal_2474_0_ PIP3_2460_0_ basal_phosp_2476_0_ 2 837.9 -401.256123603 10 red kinetics_1676_0_ * k3*basal_phosp_cplx_2477_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{basal\_phosp\_cplx\_2477\_0\_}$ PTEN_2483_0_ PIP3_2460_0_ PIP3_dephosp_cplx_2486_0_ PIP3_dephosp_2485_0_ 1 758.0 -505.765607336 37 red kinetics_1676_0_ * ( k1 * PTEN_2483_0_*PIP3_2460_0_ - k2 * PIP3_dephosp_cplx_2486_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PTEN\_2483\_0\_}\mathrm{PIP3\_2460\_0\_}-\mathrm{k2}\mathrm{PIP3\_dephosp\_cplx\_2486\_0\_})$ PIP3_dephosp_cplx_2486_0_ PTEN_2483_0_ PIP2_1819_0_ PIP3_dephosp_2485_0_ 2 758.0 -505.765607336 37 red kinetics_1676_0_ * k3*PIP3_dephosp_cplx_2486_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PIP3\_dephosp\_cplx\_2486\_0\_}$ Ras_GTP_PI3K_2488_0_ PIP2_1819_0_ PIP2_phospho_Ras_GTP_cplx_2491_0_ PIP2_phospho_Ras_GTP_2490_0_ 1 795.0 -505.765607336 31 red kinetics_1676_0_ * ( k1 * Ras_GTP_PI3K_2488_0_*PIP2_1819_0_ - k2 * PIP2_phospho_Ras_GTP_cplx_2491_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{Ras\_GTP\_PI3K\_2488\_0\_}\mathrm{PIP2\_1819\_0\_}-\mathrm{k2}\mathrm{PIP2\_phospho\_Ras\_GTP\_cplx\_2491\_0\_})$ PIP2_phospho_Ras_GTP_cplx_2491_0_ Ras_GTP_PI3K_2488_0_ PIP3_2460_0_ PIP2_phospho_Ras_GTP_2490_0_ 2 795.0 -505.765607336 31 red kinetics_1676_0_ * k3*PIP2_phospho_Ras_GTP_cplx_2491_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PIP2\_phospho\_Ras\_GTP\_cplx\_2491\_0\_}$ PIP3_PDK1_2505_0_ PIP3_AKT_2503_0_ phospho_thr308_cplx_2508_0_ phospho_thr308_2507_0_ 1 896.9 -401.256123603 9 red kinetics_1676_0_ * ( k1 * PIP3_PDK1_2505_0_*PIP3_AKT_2503_0_ - k2 * phospho_thr308_cplx_2508_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PIP3\_PDK1\_2505\_0\_}\mathrm{PIP3\_AKT\_2503\_0\_}-\mathrm{k2}\mathrm{phospho\_thr308\_cplx\_2508\_0\_})$ phospho_thr308_cplx_2508_0_ PIP3_PDK1_2505_0_ PIP3_AKT_thr308_2515_0_ phospho_thr308_2507_0_ 2 896.9 -401.256123603 9 red kinetics_1676_0_ * k3*phospho_thr308_cplx_2508_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{phospho\_thr308\_cplx\_2508\_0\_}$ PIP3_PDK2_2510_0_ PIP3_AKT_thr308_2515_0_ phosp_AKTser473_cplx_2513_0_ phosp_AKTser473_2512_0_ 1 912.0 -401.256123603 39 red kinetics_1676_0_ * ( k1 * PIP3_AKT_thr308_2515_0_*PIP3_PDK2_2510_0_ - k2 * phosp_AKTser473_cplx_2513_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PIP3\_AKT\_thr308\_2515\_0\_}\mathrm{PIP3\_PDK2\_2510\_0\_}-\mathrm{k2}\mathrm{phosp\_AKTser473\_cplx\_2513\_0\_})$ phosp_AKTser473_cplx_2513_0_ PIP3_PDK2_2510_0_ PIP3_AKT_t308_s473_2517_0_ phosp_AKTser473_2512_0_ 2 912.0 -401.256123603 39 red kinetics_1676_0_ * k3*phosp_AKTser473_cplx_2513_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{phosp\_AKTser473\_cplx\_2513\_0\_}$ PIP3_AKT_t308_s473_2517_0_ TSC1_TSC2_2775_0_ TSC2_phospho_cplx_2520_0_ TSC2_phospho_2519_0_ 1 940.9 -401.256123603 25 red kinetics_1676_0_ * ( k1 * PIP3_AKT_t308_s473_2517_0_*TSC1_TSC2_2775_0_ - k2 * TSC2_phospho_cplx_2520_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PIP3\_AKT\_t308\_s473\_2517\_0\_}\mathrm{TSC1\_TSC2\_2775\_0\_}-\mathrm{k2}\mathrm{TSC2\_phospho\_cplx\_2520\_0\_})$ TSC2_phospho_cplx_2520_0_ PIP3_AKT_t308_s473_2517_0_ TSC1_TSC2_p_2773_0_ TSC2_phospho_2519_0_ 2 940.9 -401.256123603 25 red kinetics_1676_0_ * k3*TSC2_phospho_cplx_2520_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{TSC2\_phospho\_cplx\_2520\_0\_}$ PIP3_AKT_t308_s473_2517_0_ craf_1_1865_0_ Enz_cplx_2523_0_ Enz_2522_0_ 1 940.9 -410.199723653 19 black kinetics_1676_0_ * ( k1 * craf_1_1865_0_*PIP3_AKT_t308_s473_2517_0_ - k2 * Enz_cplx_2523_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{craf\_1\_1865\_0\_}\mathrm{PIP3\_AKT\_t308\_s473\_2517\_0\_}-\mathrm{k2}\mathrm{Enz\_cplx\_2523\_0\_})$ Enz_cplx_2523_0_ PIP3_AKT_t308_s473_2517_0_ craf_1_p_ser259_1901_0_ Enz_2522_0_ 2 940.9 -410.199723653 19 black kinetics_1676_0_ * k3*Enz_cplx_2523_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Enz\_cplx\_2523\_0\_}$ BDNF_TrKB2_p_clx_2541_0_ PLC_g_2016_0_ PLC_g_phospho_cplx_2544_0_ PLC_g_phospho_2543_0_ 1 57.9 -591.382992086 red red kinetics_1676_0_ * ( k1 * PLC_g_2016_0_*BDNF_TrKB2_p_clx_2541_0_ - k2 * PLC_g_phospho_cplx_2544_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{PLC\_g\_2016\_0\_}\mathrm{BDNF\_TrKB2\_p\_clx\_2541\_0\_}-\mathrm{k2}\mathrm{PLC\_g\_phospho\_cplx\_2544\_0\_})$ PLC_g_phospho_cplx_2544_0_ BDNF_TrKB2_p_clx_2541_0_ PLC_g_p_2018_0_ PLC_g_phospho_2543_0_ 2 57.9 -591.382992086 red red kinetics_1676_0_ * k3*PLC_g_phospho_cplx_2544_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{PLC\_g\_phospho\_cplx\_2544\_0\_}$ BDNF_TrKB2_p_clx_2541_0_ SHC_1981_0_ SHC_phospho_cplx_2547_0_ SHC_phospho_2546_0_ 1 57.9 -601.431980907 red red kinetics_1676_0_ * ( k1 * BDNF_TrKB2_p_clx_2541_0_*SHC_1981_0_ - k2 * SHC_phospho_cplx_2547_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{BDNF\_TrKB2\_p\_clx\_2541\_0\_}\mathrm{SHC\_1981\_0\_}-\mathrm{k2}\mathrm{SHC\_phospho\_cplx\_2547\_0\_})$ SHC_phospho_cplx_2547_0_ BDNF_TrKB2_p_clx_2541_0_ SHC_p_1983_0_ SHC_phospho_2546_0_ 2 57.9 -601.431980907 red red kinetics_1676_0_ * k3*SHC_phospho_cplx_2547_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{SHC\_phospho\_cplx\_2547\_0\_}$ TOR_Rheb_GTP_clx_2571_0_ S6K_p_2588_0_ S6K_phospho_cplx_2574_0_ S6K_phospho_2573_0_ 1 202.755383481 -585.934682867 42 red kinetics_1676_0_ * ( k1 * TOR_Rheb_GTP_clx_2571_0_*S6K_p_2588_0_ - k2 * S6K_phospho_cplx_2574_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{TOR\_Rheb\_GTP\_clx\_2571\_0\_}\mathrm{S6K\_p\_2588\_0\_}-\mathrm{k2}\mathrm{S6K\_phospho\_cplx\_2574\_0\_})$ S6K_phospho_cplx_2574_0_ TOR_Rheb_GTP_clx_2571_0_ S6K_thr_412_2592_0_ S6K_phospho_2573_0_ 2 202.755383481 -585.934682867 42 red kinetics_1676_0_ * k3*S6K_phospho_cplx_2574_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{S6K\_phospho\_cplx\_2574\_0\_}$ TOR_Rheb_GTP_clx_2571_0_ eIF4E_BP_2620_0_ TOR_4E_BP_phospho_cplx_2577_0_ TOR_4E_BP_phospho_2576_0_ 1 202.755383481 -595.983671687 44 red kinetics_1676_0_ * ( k1 * TOR_Rheb_GTP_clx_2571_0_*eIF4E_BP_2620_0_ - k2 * TOR_4E_BP_phospho_cplx_2577_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{TOR\_Rheb\_GTP\_clx\_2571\_0\_}\mathrm{eIF4E\_BP\_2620\_0\_}-\mathrm{k2}\mathrm{TOR\_4E\_BP\_phospho\_cplx\_2577\_0\_})$ TOR_4E_BP_phospho_cplx_2577_0_ TOR_Rheb_GTP_clx_2571_0_ eIF4E_BP_thr37_46_2622_0_ TOR_4E_BP_phospho_2576_0_ 2 202.755383481 -595.983671687 44 red kinetics_1676_0_ * k3*TOR_4E_BP_phospho_cplx_2577_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{TOR\_4E\_BP\_phospho\_cplx\_2577\_0\_}$ TOR_Rheb_GTP_clx_2571_0_ _4E_BP_2616_0_ TOR_4E_BP_p_cplx_2580_0_ TOR_4E_BP_p_2579_0_ 1 202.755383481 -604.927271737 44 red kinetics_1676_0_ * ( k1 * _4E_BP_2616_0_*TOR_Rheb_GTP_clx_2571_0_ - k2 * TOR_4E_BP_p_cplx_2580_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{\_4E\_BP\_2616\_0\_}\mathrm{TOR\_Rheb\_GTP\_clx\_2571\_0\_}-\mathrm{k2}\mathrm{TOR\_4E\_BP\_p\_cplx\_2580\_0\_})$ TOR_4E_BP_p_cplx_2580_0_ TOR_Rheb_GTP_clx_2571_0_ _4E_BP_t37_46_2626_0_ TOR_4E_BP_p_2579_0_ 2 202.755383481 -604.927271737 44 red kinetics_1676_0_ * k3*TOR_4E_BP_p_cplx_2580_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{TOR\_4E\_BP\_p\_cplx\_2580\_0\_}$ S6K_thr_412_2592_0_ _40S_inact_2762_0_ S6_phos_cplx_2595_0_ S6_phos_2594_0_ 1 340.123385612 -590.581674587 48 red kinetics_1676_0_ * ( k1 * S6K_thr_412_2592_0_*_40S_inact_2762_0_ - k2 * S6_phos_cplx_2595_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{S6K\_thr\_412\_2592\_0\_}\mathrm{\_40S\_inact\_2762\_0\_}-\mathrm{k2}\mathrm{S6\_phos\_cplx\_2595\_0\_})$ S6_phos_cplx_2595_0_ S6K_thr_412_2592_0_ _40S_2764_0_ S6_phos_2594_0_ 2 340.123385612 -590.581674587 48 red kinetics_1676_0_ * k3*S6_phos_cplx_2595_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{S6\_phos\_cplx\_2595\_0\_}$ S6K_thr_252_2597_0_ CaMKIII_2686_0_ CaMKIII_phospho_cplx_2600_0_ CaMKIII_phospho_2599_0_ 1 355.123385612 -590.581674587 6 red kinetics_1676_0_ * ( k1 * S6K_thr_252_2597_0_*CaMKIII_2686_0_ - k2 * CaMKIII_phospho_cplx_2600_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{S6K\_thr\_252\_2597\_0\_}\mathrm{CaMKIII\_2686\_0\_}-\mathrm{k2}\mathrm{CaMKIII\_phospho\_cplx\_2600\_0\_})$ CaMKIII_phospho_cplx_2600_0_ S6K_thr_252_2597_0_ CaMKIII_p_2698_0_ CaMKIII_phospho_2599_0_ 2 355.123385612 -590.581674587 6 red kinetics_1676_0_ * k3*CaMKIII_phospho_cplx_2600_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{CaMKIII\_phospho\_cplx\_2600\_0\_}$ S6K_thr_252_2597_0_ _40S_inact_2762_0_ S6_phospho_cplx_2603_0_ S6_phospho_2602_0_ 1 355.123385612 -600.630663408 4 red kinetics_1676_0_ * ( k1 * _40S_inact_2762_0_*S6K_thr_252_2597_0_ - k2 * S6_phospho_cplx_2603_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{\_40S\_inact\_2762\_0\_}\mathrm{S6K\_thr\_252\_2597\_0\_}-\mathrm{k2}\mathrm{S6\_phospho\_cplx\_2603\_0\_})$ S6_phospho_cplx_2603_0_ S6K_thr_252_2597_0_ _40S_2764_0_ S6_phospho_2602_0_ 2 355.123385612 -600.630663408 4 red kinetics_1676_0_ * k3*S6_phospho_cplx_2603_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{S6\_phospho\_cplx\_2603\_0\_}$ S6K_basal_2605_0_ CaMKIII_2686_0_ CaMKIII_basal_cplx_2608_0_ CaMKIII_basal_2607_0_ 1 369.123385612 -590.581674587 45 red kinetics_1676_0_ * ( k1 * S6K_basal_2605_0_*CaMKIII_2686_0_ - k2 * CaMKIII_basal_cplx_2608_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{S6K\_basal\_2605\_0\_}\mathrm{CaMKIII\_2686\_0\_}-\mathrm{k2}\mathrm{CaMKIII\_basal\_cplx\_2608\_0\_})$ CaMKIII_basal_cplx_2608_0_ S6K_basal_2605_0_ CaMKIII_p_2698_0_ CaMKIII_basal_2607_0_ 2 369.123385612 -590.581674587 45 red kinetics_1676_0_ * k3*CaMKIII_basal_cplx_2608_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{CaMKIII\_basal\_cplx\_2608\_0\_}$ CaMKIII_CaM_Ca4_2688_0_ eEF2_2732_0_ phospho_cplx_2691_0_ phospho_2690_0_ 1 18.8 -782.615249341 58 red kinetics_1676_0_ * ( k1 * CaMKIII_CaM_Ca4_2688_0_*eEF2_2732_0_ - k2 * phospho_cplx_2691_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{CaMKIII\_CaM\_Ca4\_2688\_0\_}\mathrm{eEF2\_2732\_0\_}-\mathrm{k2}\mathrm{phospho\_cplx\_2691\_0\_})$ phospho_cplx_2691_0_ CaMKIII_CaM_Ca4_2688_0_ eEFthr_56_2734_0_ phospho_2690_0_ 2 18.8 -782.615249341 58 red kinetics_1676_0_ * k3*phospho_cplx_2691_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{phospho\_cplx\_2691\_0\_}$ CaMKIII_basal_2693_0_ eEF2_2732_0_ eEF2thr56_basal_cplx_2696_0_ eEF2thr56_basal_2695_0_ 1 33.0 -782.615249341 45 red kinetics_1676_0_ * ( k1 * eEF2_2732_0_*CaMKIII_basal_2693_0_ - k2 * eEF2thr56_basal_cplx_2696_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{eEF2\_2732\_0\_}\mathrm{CaMKIII\_basal\_2693\_0\_}-\mathrm{k2}\mathrm{eEF2thr56\_basal\_cplx\_2696\_0\_})$ eEF2thr56_basal_cplx_2696_0_ CaMKIII_basal_2693_0_ eEFthr_56_2734_0_ eEF2thr56_basal_2695_0_ 2 33.0 -782.615249341 45 red kinetics_1676_0_ * k3*eEF2thr56_basal_cplx_2696_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{eEF2thr56\_basal\_cplx\_2696\_0\_}$ Translation_clx_2738_0_ AA_2654_0_ pro_syn_cplx_2741_0_ pro_syn_2740_0_ 1 340.9 -782.615249341 52 red kinetics_1676_0_ * ( k1 * Translation_clx_2738_0_*AA_2654_0_ - k2 * pro_syn_cplx_2741_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{Translation\_clx\_2738\_0\_}\mathrm{AA\_2654\_0\_}-\mathrm{k2}\mathrm{pro\_syn\_cplx\_2741\_0\_})$ pro_syn_cplx_2741_0_ Translation_clx_2738_0_ peptide_2656_0_ pro_syn_2740_0_ 2 340.9 -782.615249341 52 red kinetics_1676_0_ * k3*pro_syn_cplx_2741_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{pro\_syn\_cplx\_2741\_0\_}$ Translation_clx_2738_0_ rad_AA_2662_0_ rad_pro_syn_cplx_2744_0_ rad_pro_syn_2743_0_ 1 340.9 -792.563748273 52 red kinetics_1676_0_ * ( k1 * Translation_clx_2738_0_*rad_AA_2662_0_ - k2 * rad_pro_syn_cplx_2744_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{Translation\_clx\_2738\_0\_}\mathrm{rad\_AA\_2662\_0\_}-\mathrm{k2}\mathrm{rad\_pro\_syn\_cplx\_2744\_0\_})$ rad_pro_syn_cplx_2744_0_ Translation_clx_2738_0_ rad_peptide_2664_0_ rad_pro_syn_2743_0_ 2 340.9 -792.563748273 52 red kinetics_1676_0_ * k3*rad_pro_syn_cplx_2744_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{rad\_pro\_syn\_cplx\_2744\_0\_}$ Basal_Translation_2748_0_ AA_2654_0_ basal_syn_cplx_2751_0_ basal_syn_2750_0_ 1 369.9 -782.615249341 53 red kinetics_1676_0_ * ( k1 * Basal_Translation_2748_0_*AA_2654_0_ - k2 * basal_syn_cplx_2751_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{Basal\_Translation\_2748\_0\_}\mathrm{AA\_2654\_0\_}-\mathrm{k2}\mathrm{basal\_syn\_cplx\_2751\_0\_})$ basal_syn_cplx_2751_0_ Basal_Translation_2748_0_ peptide_2656_0_ basal_syn_2750_0_ 2 369.9 -782.615249341 53 red kinetics_1676_0_ * k3*basal_syn_cplx_2751_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{basal\_syn\_cplx\_2751\_0\_}$ Basal_Translation_2748_0_ rad_AA_2662_0_ rad_basal_syn_cplx_2754_0_ rad_basal_syn_2753_0_ 1 369.9 -792.563748273 53 red kinetics_1676_0_ * ( k1 * Basal_Translation_2748_0_*rad_AA_2662_0_ - k2 * rad_basal_syn_cplx_2754_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{Basal\_Translation\_2748\_0\_}\mathrm{rad\_AA\_2662\_0\_}-\mathrm{k2}\mathrm{rad\_basal\_syn\_cplx\_2754\_0\_})$ rad_basal_syn_cplx_2754_0_ Basal_Translation_2748_0_ peptide_2656_0_ rad_basal_syn_2753_0_ 2 369.9 -792.563748273 53 red kinetics_1676_0_ * k3*rad_basal_syn_cplx_2754_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{rad\_basal\_syn\_cplx\_2754\_0\_}$ _40S_basal_2766_0_ _40S_inact_2762_0_ basal_cplx_2769_0_ basal_2768_0_ 1 472.0 -782.615249341 44 red kinetics_1676_0_ * ( k1 * _40S_inact_2762_0_*_40S_basal_2766_0_ - k2 * basal_cplx_2769_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{\_40S\_inact\_2762\_0\_}\mathrm{\_40S\_basal\_2766\_0\_}-\mathrm{k2}\mathrm{basal\_cplx\_2769\_0\_})$ basal_cplx_2769_0_ _40S_basal_2766_0_ _40S_2764_0_ basal_2768_0_ 2 472.0 -782.615249341 44 red kinetics_1676_0_ * k3*basal_cplx_2769_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{basal\_cplx\_2769\_0\_}$ TSC1_TSC2_2775_0_ Rheb_GTP_2565_0_ TSC2phospho_cplx_2778_0_ TSC2phospho_2777_0_ 1 604.0 -782.615249341 51 red kinetics_1676_0_ * ( k1 * Rheb_GTP_2565_0_*TSC1_TSC2_2775_0_ - k2 * TSC2phospho_cplx_2778_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{Rheb\_GTP\_2565\_0\_}\mathrm{TSC1\_TSC2\_2775\_0\_}-\mathrm{k2}\mathrm{TSC2phospho\_cplx\_2778\_0\_})$ TSC2phospho_cplx_2778_0_ TSC1_TSC2_2775_0_ Rheb_GDP_2567_0_ TSC2phospho_2777_0_ 2 604.0 -782.615249341 51 red kinetics_1676_0_ * k3*TSC2phospho_cplx_2778_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{TSC2phospho\_cplx\_2778\_0\_}$ L_dot_mGluR_p_dot_Homer_dot_PIKE_L_dot_PI3K_2792_0_ PIP2_1819_0_ Enz_cplx_2795_0_ Enz_2794_0_ 1 795.0 -782.615249341 23 27 kinetics_1676_0_ * ( k1 * L_dot_mGluR_p_dot_Homer_dot_PIKE_L_dot_PI3K_2792_0_*PIP2_1819_0_ - k2 * Enz_cplx_2795_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{L\_dot\_mGluR\_p\_dot\_Homer\_dot\_PIKE\_L\_dot\_PI3K\_2792\_0\_}\mathrm{PIP2\_1819\_0\_}-\mathrm{k2}\mathrm{Enz\_cplx\_2795\_0\_})$ Enz_cplx_2795_0_ L_dot_mGluR_p_dot_Homer_dot_PIKE_L_dot_PI3K_2792_0_ PIP3_2460_0_ Enz_2794_0_ 2 795.0 -782.615249341 23 27 kinetics_1676_0_ * k3*Enz_cplx_2795_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{Enz\_cplx\_2795\_0\_}$ GRK_2805_0_ Rec_Glu_2309_0_ GRK_binding_cplx_2808_0_ GRK_binding_2807_0_ 1 881.9 -782.615249341 black 20 kinetics_1676_0_ * ( k1 * GRK_2805_0_*Rec_Glu_2309_0_ - k2 * GRK_binding_cplx_2808_0_ ) $\mathrm{kinetics\_1676\_0\_}(\mathrm{k1}\mathrm{GRK\_2805\_0\_}\mathrm{Rec\_Glu\_2309\_0\_}-\mathrm{k2}\mathrm{GRK\_binding\_cplx\_2808\_0\_})$ GRK_binding_cplx_2808_0_ GRK_2805_0_ L_dot_mGluR_p_2810_0_ GRK_binding_2807_0_ 2 881.9 -782.615249341 black 20 kinetics_1676_0_ * k3*GRK_binding_cplx_2808_0_ $\mathrm{kinetics\_1676\_0\_}\mathrm{k3}\mathrm{GRK\_binding\_cplx\_2808\_0\_}$ kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics darkgreen kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue kinetics blue