Supplement to: How Robust are Switches in Intracellular Signaling Cascades? Nils Blüthgen and Hanspeter Herzel Institute for Theoretical Biology, Invalidenstrasse 43, D-10115 Berlin, Germany (Dated: January 10, 2005. Journal of Theoretical Biology 225 (2003), 293-300) Corrections There is a typo in the Methods section: Eqn. 3 should read k 1 = Vmax K m (1 + r) instead of k 1 = Vmax K m(1+r). Thanks to Keng-Hwee Chiam and Xinglai Ji who both pointed this out! I. MODELS FOR THE MAPK-CASCADE A. Parameters Concentrations taken from Bhalla & Iyengar (1999) (B/I), Huang & Ferrell (1996) (H/F). Total concentration [µm] (the corresponding parameter names are in brackets) protein B/I H/F Input-enzyme 0.1 (E 1,tot ) 0.0003 (PKC tot ) MAPKKK 0.2 (KKK tot ) 0.003 (KKK tot ) MAPKK 0.18 (KK tot ) 1.2 (KK tot ) MAPK 0.36 (K tot ) 1.2 (K tot ) MAPKKK-Phosphatase 0.224 (KKKS tot ) 0.0003 (PP2A tot ) MAPKK-Phosphatase 0.224 (KKS tot ) 0.0003 (PP2A tot ) MAPK-Phosphatase 0.0032 (KS tot ) 0.12 (MKP1 tot ) V max -values taken from Bhalla & Iyengar (1999) (B/I), Huang & Ferrell (1996) (H/F).
V max [min 1 ] (the corresponding parameter names are in brackets) reaction B/I H/F MAPKKK MAPKKK* (V max,1 ) 240 150 MAPKKK MAPKKK* (V max,2 ) 360 150 MAPKKK* MAPKKK** (V max,3 ) 600 - MAPKKK* MAPKKK** (V max,4 ) 360 - MAPKK MAPKK* (V max,5 ) 6.3 150 MAPKK* MAPKK** (V max,6 ) 6.3 150 MAPKK MAPKK* (V max,7 ) 360 150 MAPKK* MAPKK** (V max,8 ) 360 150 MAPK MAPK* (V max,9 ) 9 150 MAPK* MAPK** (V max,10 ) 9 150 MAPK MAPK* (V max,11 ) 60 150 MAPK* MAPK** (V max,12 ) 60 150 2
k m values taken from Bhalla & Iyengar (1999) (B/I), Huang & Ferrell (1996) (H/F). k m [µm] (the corresponding parameter names are in brackets) reaction B/I H/F MAPKKK MAPKKK* (k m,1 ) 66.6 0.3 MAPKKK MAPKKK* (k m,2 ) 15.65 0.3 MAPKKK* MAPKKK** (k m,3 ) 25.64 - MAPKKK* MAPKKK** (k m,4 ) 15.65 - MAPKK MAPKK* (k m,5 ) 0.159 0.3 MAPKK* MAPKK** (k m,6 ) 0.159 0.3 MAPKK MAPKK* (k m,7 ) 15.65 0.3 MAPKK* MAPKK** (k m,8 ) 15.65 0.3 MAPK MAPK* (k m,9 ) 0.046 0.3 MAPK* MAPK** (k m,10 ) 0.046 0.3 MAPK MAPK* (k m,11 ) 0.066 0.3 MAPK* MAPK** (k m,12 ) 0.066 0.3 In the model according to (Bhalla & Iyengar, 1999), Raf is only active, if it binds to the complex of GTP and RAS, which assumed as a constant here. The concentration of GTP-RAS complex is set to GR tot = 0.2µM. The rate constants are k b = 24min 1 µm 1 for binding and k d = 0.5min 1 for dissotiation. In order to keep variable names short, MAPK is abbreviated as K. An S at the end indicates phosphotases, wherever it is neccessary, a underscore indicates a complex. Stars show the phosphorylation states. B. Model According to Huang and Ferrell The parameters k 1,n, k 1,n and k 2,n were choosen in order to fullfill the Michaelis-Menten constants (k m, n) and maximal velocities (V max,n ) values in Tables above. The ratio of k 1,n and k 2,n (r) was choosen as 4 as in Huang & Ferrell (1996). k 1,n = V max,n (1 + r) k m,n (1) k 1,n = V max,n r (2) k 2,n = V max,n. (3) d [KKK ] = k 2,1 [KKK E 1 ] + k 1,2 [KKK E 2 ] k 1,2 [KKK ] [E 2 ] (4) d [KKK E 1 ] = k 1,1 [KKK] [E 1 ] (k 1,1 + k 2,1 ) [KKK E 1 ] (5) d [KKK E 2 ] = k 1,2 [KKK ] [E 2 ] (k 1,2 + k 2,2 ) [KKK E 2 ] (6) [E 2 ] = [E 2,tot ] [KKK E 2 ] (7) [E 1 ] = [E 1,tot ] [KKK E 1 ] (8) [KKK] = [KKK tot ] [KKK ] [KKK E 1 ] [KKK E 2 ] (9) [KK KKK ] [KK KKK ] d [KK KKK ] = k 1,5 [KK] [KKK ] (k 1,5 + k 2,5 ) [KK KKK ] (10) d [KK ] = k 2,5 [KK KKK ] + k 2,8 [KK KKS] (11) 3
+k 1,7 [KK KKK ] + k 1,6 [KK KKS] k 1,7 [KK ] [KKK ] k 1,6 [KK ] [KKS] d [KK KKK ] = k 1,7 [KK ] [KKK ] (k 2,7 + k 1,7 ) [KK KKK ] (12) d [KK ] = k 2,7 [KK KKK ] + k 1,8 [KK KKS] (13) k 1,8 [KK ] [KKS] d [KK KKS] = k 1,8 [KK ] [KKS] (k 2,8 + k 1,8 ) [KK KKS] (14) d [KK KKS] = k 1,6 [KK ] [KKS] (k 2,6 + k 1,6 ) [KK KKS] (15) [KKS] = [KKS tot ] [KK KKS] [KK KKS] (16) [KK] = [KK tot ] [KK ] [KK KKK ] (17) [KK KKK ] [KK ] [KK KKS] [KK KKS] [K KK ] [K KK ] d [K KK ] = k 1,9 [K] [KK ] (k 2,9 + k 1,9 ) [K KK ] (18) d [K ] = k 2,9 [K KK ] + V 10 [K KS] + k 1,11 [K KK ] (19) +k 1,10 [K KS] k 1,11 [K ] [KK ] k 1,10 [K ] [KS] d [K KK ] = k 1,11 [K ] [KK ] (k 2,11 + k 1,11 ) [K KK ] (20) d [K ] = k 2,11 [K KK ] + k 1,12 [K KS] k 1,12 [K ] [KS] (21) d [K KS] = k 1,12 [K ] [KS] (k 1,12 + k 2,12 ) [K KS] (22) d [K KS] = k 1,10 [K ] [KS] (k 1,10 + k 2,10 ) [K KS] (23) [KS] = [KS tot ] [K KS] [K KS] (24) [K] = [K tot ] [K ] [K ] [K KK ] (25) [K KK ] [K KS] [K KS] C. Model According to Bhalla and Iyengar The parameters k 1,n, k 1,n and k 2,n were calculated like in the Huang/Ferrell model. d [PKC KKK] d [KKK ] d [GR KKK ] = k 1,1 [KKK] [PKC] (k 1,1 + k 2,1 ) [PKC KKK] (26) = k 2,1 [PKC KKK] + k 2,4 [PP2A KKK ] (27) +k 1,2 [K KKK ] + k 1,3 [PP2A KKK ] (k 1,3 [PP2A] + k 1,2 [K ]) [KKK ] k b [GR] [KKK ] + k d [GR KKK ] = k b [GR] [KKK ] k d [GR KKK ] (28) k 1,5 [KK] [GR KKK ] k 1,6 [KK ] [GR KKK ] + (k 1,5 + k 2,5 ) [GR KKK KK] + (k 1,6 + k 2,6 ) [GR KKK KK ] 4
d [K KKK ] d [KKK ] d [PP2A KKK ] d [PP2A KKK ] d [KK] d [GR KKK KK] d [PP2A KK ] d [KK ] d [GR KKK KK ] d [PP2A KK ] d [KK K] d [K ] d [KK K ] d [K ] = k 1,2 [KKK ] [K ] (29) (k 1,2 + k 2,2 ) [K KKK ] = k 2,2 [K KKK ] + k 1,4 [PP2A KKK ] (30) k 1,4 [KKK ] [PP2A] = k 1,4 [PP2A] [KKK ] (31) (k 1,4 + k 2,4 ) [PP2A KKK ] = k 1,3 [PP2A] [KKK ] (32) (k 1,3 + k 2,3 ) [PP2A KKK ] = k 1,5 [GR KKK ] [KK] (33) +k 1,5 [GR KKK KK] + k 2,7 [PP2A KK ] = k 1,5 [GR KKK ] [KK] (34) (k 1,5 + k 2,5 ) [GR KKK KK] = k 1,7 [PP2A] [KK ] (k 1,7 + k 2,7 ) [PP2A KK ] (35) = k 2,5 [GR KKK KK] + k 2,8 [PP2A KK ] (36) +k 1,6 [GR KKK ] [KK ] + k 1,7 [PP2A KK ] (k 1,6 [GR KKK ] + k 1,7 [PP2A]) [KK ] = k 1,6 [KK ] [GR KKK ] (37) (k 1,6 + k 2,6 ) [GR KKK KK ] = k 1,8 [KK ] [PP2A] (k 1,8 + k 2,8 ) [PP2A KK ] (38) = k 1,9 [K] [KK ] (k 1,9 + k 2,9 ) [KK K] (39) = k 2,9 [KK K] + k 2,12 [MKP1 K ] (40) +k 1,11 [MKP1 K ] + k 1,10 [KK K ] (k 1,10 [KK ] + k 1,11 [MKP1]) [K ] = k 1,10 [K ] [KK ] (k 1,10 + k 2,10 ) [KK K ] (41) = k 2,10 [KK K ] + k 1,12 [MKP1 K ] (42) k 1,12 [MKP1] [K ] k 1,2 [K ] [KKK ] + (k 1,2 + k 2,2 ) [K KKK ] d [MKP1 K ] = k 1,12 [MKP1] [K ] (k 1,12 + k 2,12 ) [MKP1 K ] (43) d [MKP1 K ] = k 1,11 [MKP1] [K ] (k 1,11 + k 2,11 ) [MKP1 K ] (44) [KK ] = [KK tot ] ([KK ] + [GR KKK KK] (45) + [KK] + [GR KKK KK ] + [PP2A KK ] + [PP2A KK ] + [KK K] + [KK K ]) [PP2A] = [PP2A tot ] ([PP2A KK ] (46) + [PP2A KK ] + [PP2A K ] + [PP2A K ]) [GR] = [GR tot ] ([GR KKK KK] (47) 5
+ [GR KKK KK ] + [GR KKK ]) [MKP1] = [MKP1 tot ] [MKP1 K ] [MKP1 K ] (48) [K] = [K tot ] [KK K] [KK K ] (49) [MKP1 K ] [MKP1 K ] [K ] [K ] [K KKK ] [PKC] = [PKC tot ] [PKC KKK] (50) [KKK] = [KKK tot ] ([PKC KKK] + [KKK ] (51) + [K KKK ] + [KKK ] + [PP2A KKK ] + [PP2A KKK ] + [GR KKK ] + [GR KKK KK ] + [GR KKK KK]) II. MODEL FOR THE GOLBETER-KOSHLAND SWITCH Goldbeter & Koshland (1981) A. Parameters Parameter value total substrate concentration (A tot ) 1µM total phosphatase concentration (E 2,tot ) 0.01µM V max of kinase (V max,1 ) 1min 1 V max of phosphatase (V max,2 ) 1min 1 k m of kinase (k m,1 ) 0.1µM k m of phosphatase (k m,2 ) 0.1µM B. Equations d [A E 1 ] = k 1,1 [A] [E 1 ] (k 1,1 + k 2,1 ) [A E 1 ] (52) d [A ] = k 2,1 [A E 1 ] k 1,2 [A ] [E 2 ] + k 1,2 [A E 2 ] (53) d [A E 2 ] = k 1,2 [A ] [E 2 ] (k 1,2 + k 2,2 ) [A E 2 ] (54) [A] = [A tot ] [A E 1 ] [A E 2 ] [A ] (55) [E 1 ] = [E 1,tot ] [A E 1 ] (56) [E 2 ] = [E 2,tot ] [A E 2 ] (57) Bhalla, U. & Iyengar, R. (1999) Emergent properties of networks of biological signaling pathways. Science 283, 381 7. Goldbeter, A. & Koshland, D. (1981) An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl. Acad. Sci. USA 78, 6840 4. Huang, C. & Ferrell, J. (1996) Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc. Natl. Acad. Sci. USA 93, 10078 83. 6