E-Cell System Abstract TCA 6 E-Cell 1 10 ( ) 6 TCA 11 TCA ([35]) Figure 1. 2

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1 E-Cell System Abstract TCA 6 E-Cell 1 10 ( ) 6 TCA 11 TCA ([35]) Figure 1. 2

2 (Plain E-Cell ) [13] E-Cell System [4] Q RNA RNA d[rna] k T [E 0 ][S 0 ] = dt K M +[S 0 ](1 + K H [RNA]) 8 >< >: 1 k T = P n j=2 K M = k T 1 k k FPj + k 1 PR + k 1 D5 0 1+K k k 3 SB n = [S0] k AS1[S 1 ] 1+ (kfp2+kds2)kds1 k FP2k AS2[S 2 ] K = k D3 0 k A5 0 k A3 0 k D5 0 + k D3 0 1 k 3 SB = P n j=2 K H = kpi k PR k T k D5 0 k A3 0 [DNA] k FPj +k DSj [S 0] k FPJ k ASj [S j ] n 1+ k A5 0 k A k A5 0 k A3 0 o 1+ k D3 0 k 3 12 [S0] o + 1 k A3 0 [DNA] 2.3 mtdna 1 polycistronic rrna mrna trna 1 1 trna mtrnase P trna trna trna 1 ([24][25][22]) mrna poly (A) trna CCA RNACleavageReactor(mtRNase P RNA [3]) AAtRNAReactor(tRNA [1]) RNA cleavage B. subtilis trna E. coli RNA CleavageRate = A[S]+B[S]2 C + D[S]+E[S] 2

3 4 Vol.6 8 >< >: A = k 2 k 3 k 4 (k 1 k 5 + k 5b k 6 ) B = k 1 k 2 k 3 k 4 k 6 C = k 2 k 3 k 4 (k 5 + k 5b ) D = k 4 (k 3 (k 1 k 5 + k 1 k 2 + k 5b k 6 + k 1b k 6 )+k 1 k 2 k 5 + k 2 k 5b k 6 )+k 2 k 3 (k 1 k 5 + k 5b k 6 ) E = k 1 k 6 (k 2 k 4 + k 2 k 3 + k 3 k 4 ) v = h D 1 C21 C32 C 12 C 23 C [E tot ] i + D2 C 23 C32 C D3 C 31 8>< >: D 1 = 1+[A] K 1 D 2 = 1+[PPi] K 4 D 3 = 1+[PP i] C 12 = C 21 = C 23 = C 32 = 1+[S] 1+[R] K 2 K R 1+[R] K 5 1+[AMP ] K PP C 31 = k 8 K 7 k 3fa + k 3fb[R] [A][S] K R K 1K 2 k 3ra + k3rb[r] [PPi] K 5 K 4 k 6fa + k 6fb[PP i] [R] K 4 K 5 k 6ra + k6rb3[ppi] K PP [AMP ] K ([26][32]) E. coli v = k cat[s]([e tot ] 0 [P ]) K m +[S] =length 1 v = k cat[s]([e tot ] 0 [P ]) K m +[S] 1 length 2.5 1

4 5 Figure ( )

5 6 Vol.6 3 Pyruvate dehydrogenase Acetyl-CoA TCA Figure 3 Palmitoyl-CoA ( =16 Acyl- CoA) CPT I II / 3 Palmitoyl-CoA 4 7 Acyl-CoA 1 1. Acetyl-CoA 1 (7 2 ) 2. Acyl-CoA 2 3. Ubiquinone 1 Figure 3. Table 1

6 7 Table 1. ( ETF: Electron Transfer Flavoprotein ox: red: IMS: MAT: ) Acyl-CoA Acyl-CoA + ETF ox Ordered Bi Bi ([27])? dehydrogenase 0! Enoyl-CoA + ETF red Enoyl-CoA Enoyl-CoA + H 2O Uni Uni Reversible ([34]) Bovine Liver hydratase 0! 3-hydroxyacyl-CoA 3-hydroxyacyl-CoA 3-hydroxyacyl-CoA + NAD + Michaelis-Menten ([34]) Pig Heart dehydrogenase 0! 3-oxoacyl-CoA + NADH 3-ketoacyl-CoA 3-oxoacyl-CoA + CoA Ping-Pong Bi Bi ([21]) Rat Liver Mitochondria thiolase 0! Acyl-CoA + Acetyl-CoA ETF-Q: ETF red +Q Ping-Pong Bi Bi ([5],[6]) Pig Liver Mitochondria oxidoreductase 0! ETF ox +QH 2 CPT I Hexadecanoyl-CoA + Carnitine Rapid Equilibrium Bovine Liver Mitochondria 0! CoA + Palmitoylcarnitine Random Bi Bi ([23]) CPT II CoA + Palmitoylcarnitine Ordered Bi Bi ([19]) Rat Liver Mitochondria! Palmitoyl-CoA(Acyl-CoA) + Carnitine Carnitine Carrier Palmitoylcarnitine IMS + Carnitine MAT Ping-Pong Bi Bi ([18]) Rat Liver Mitochondria! Palmitoylcarnitine MAT + Carnitine IMS 4 mtdna TCA Roise [28] Figure 4. ([28]) [28]

7 8 Vol.6 5 ( TCA ) Table 2 5 Oxoglutarate Carrier Asp/Glu Carrier - TCA Carnitine Carrier Table 2. ( IMS: MAT: ) Oxoglutarate Oxoglutarate IMS + Malate MAT Rapid Equilibrium Bovine Heart Mitochondria ([16]) Carrier (OGC) 0! Oxoglutarate MAT + Malate IMS Random Bi Bi ([16][31]) Rat Heart Mitochondria ([31]) Dicarboxylate Malate IMS +Pi MAT Rapid Equilibrium Rat Liver Mitochondria Carrier (DIC) 0! Malate MAT +Pi IMS Random Bi Bi ([17]) Tricarboxylate Citrate IMS + Malate MAT Rapid Equilibrium Rat Liver Mitochondria Carrier (CIC) 0! Citrate MAT + Malate IMS Random Bi Bi ([7]) Asp/Glu Asp IMS +Glu MAT Rapid Equilibrium Rat Heart Mitochondria Carrier (AGC) 0! Asp MAT +Glu IMS Random Bi Bi ([30]) Carnitine Palmitoylcarnitine IMS + Carnitine MAT Ping-Pong Bi Bi ([18]) Rat Liver Mitochondria Carrier (CAC)! Palmitoylcarnitine MAT + Carnitine IMS Dead-end Rapid Equilibrium Random Bi Bi ([29] pp.309) v = 1+ [A] K ia + [B] K ib + [P ] K ip [A][B] K iak ib k f cat[e] total 0 + [Q] K iq + [A][B] K iak ib + [P ][Q] K ip K k r iq cat[e] total [P ][Q] K ip K iq + [B][Q] K ibk iq + [A][P ] K iak ip 6 TCA 6.1 Wright Wright Dictyostelium discoideum TCA ([33]) 1. Succinyl-CoA synthase 2. Aconitase 3. Pyruvate carboxylase Figure 5. Wright TCA

8 9 2 TCA 8 Pyruvate carboxylase TCA (Oxaloacetate) 1 [33] Oxoglutarate Succinate Succinyl-CoA Oxoglutarate Succinyl- CoA Succinate Succinyl-CoA synthethase (Succinyl-CoA Succinate ) GDP GTP TCA Wright 6.2 [33] Dictyostelium discoideum TCA Table 3. TCA Pyruvate Pyruvate + NAD + + CoA See [14] Pig Heart Mitochondria dehydrogenase 0! Acetyl-CoA + NADH + CO 2 Pyruvate Pyruvate+ATP + CO 2 See [2] Chicken Liver carboxylase 0! Oxaloacetate + ADP + P i Malic Malate + NAD(P) + Ordered Bi Bi ([10]) Rabbit Heart Mitochondria enzyme 0! Pyruvate + NAD(P)H + CO 2 Transaminase Asp + Oxoglutarate Ping-Pong Bi Bi ([15]) Pig Heart (Asp/Glu) 0! Oxaloacetate + Glu Citrate Oxaloacetate + Acetyl-CoA Random Bi Bi ([20]) Rat Kidney, Rat Brain([20]) synthase 0! Citrate + CoA Aconitase Citrate 0! Isocitrate Uni Uni Reversible ([12]) Rat Liver Mitochondria Isocitrate Isocitrate + NAD(P) + Now Searching dehydrogenase 0! Oxoglutarate + NAD(P)H Oxoglutarate Oxoglutarate + NAD + + CoA See [14] Pig Heart Mitochondria dehydrogenase 0! Succinyl-CoA + NADH + CO 2 Succinyl-CoA Succinyl-CoA + GDP + P i See [8] Pig Heart synthetase 0! Succinate + CoA + GTP Succinate Succinate + Q Ping-Pong Bi Bi ([11]) Bovine Heart Mitochondria dehydrogenase 0! Fumarate + QH 2 Fumarase Fumarate 0! Malate Uni Uni Reversible Malate Malate + NAD + Ordered Bi Bi ([9]) Human Liver Cytosol dehydrogenase 0! Oxaloacetate + NADH

9 10 Vol ATP ( 50 ) (10633) Palmitoyl-CoA (477802) ADP (10275) P i (186534) ATP (339725) Palmitoyl-CoA ATP ADP P i ATP 7.2 ATP ADP P i Figure 6 Figure 6 50 ATP ADP P i ATP ADP P i 200 ATP ATP ADP P i Figure 6. ATP ADP P i

10 11 8 TCA Table 4. ATP synthase (Table 3 ) Acyl-CoA dehydrogenase 4 (ATP/ADP P i ) 1 1 E-Cell Manager ( ) ( )

11 [1] Airas, R.K., Analysis of the isoleucyl-trna synthetase reaction by total rate equations : Magnesium and spermidine in the trna kinetics, Eur. J. Biochem. 210(2):443-50, (trna ) [2] Barden, R.E., Fung, C.H., Utter, M.F. and Scrutton, M.C., Pyruvate carboxylase from chicken liver, J. Biol. Chem. 247(4): , (Pyruvate carboxylase ) [3] Beebe, J.A. and Fierke, C.A., A Kinetic Mechanism for Cleavage of Precursor trna Asp Catalyzed by the RNA Component ofbacillus subtilis Ribonuclease P, Biochemistry 33(34): , (RNA cleavage ) [4] Biebricher, C.K., Eigen, M. and Gardiner Jr., W.C., Kinetics of RNA Replication, Biochemistry 22(10): , (Q RNA ) [5] Beckmann, J.D. and Frerman, F.E., Electron-Transfer Flavoprotein-Ubiquinone Oxidoreductase from Pig Liver: Purication and Molecular, Redox, and Catalytic Properties, Biochemistry 24(15): , (ETF-Q:oxidoreductase ) [6] Beckmann, J.D. and Frerman, F.E., Reaction of Electron-Transfer Flavoprotein-Ubiquinone Oxidoreductase, Biochemistry 24(15):3922-5, (ETF-Q:oxidoreductase ) [7] Bisaccia, F., De Palma, A., Dierks, T., Kramer, R. and Palmieri, F., Reaction mechanism of the reconstituted tricarboxylate carrier from rat liver mitochondria, Biochim. Biophys. Acta 1142(1-2):139-45, (Tricarboxylate Carrier ) [8] Cha, S. and Parks Jr., R.E., Succinic Thiokinase II. Kinetic studies: initial velocity, product inhibition, and eect of arsenate, J. Biol. Chem. 239(6): , (Succinyl-CoA synthetase ) [9] Crow, K.E., Braggins, T.J. and Hardman, M.J., Human liver malate dehydrogenase: purication, kinetic properties, and role in ethanol metabolism, Arch. Biochem. Biophys. 225(2):621-9, (Malate dehydrogenase ) [10] Davisson, V.J., Schulz, A.R., The purication and steady-state kinetic behaviour of rabbit heart mitochondrial NAD(P)+ malic enzyme, Biochem. J. 225(2):335-42, (Malic enzyme ) 12

12 13 [11] Grivennikova, V.G., Gavrikova, E.V., Timoshin, A.A. and Vinogradov, A.D., Fumarate reductase activity ofbovine heart succinate-ubiquinone reductase. New assay system and overall properties of the reaction, Biochim. Biophys. Acta 1140(3):282-92, (Succninate dehydrogenase ) [12] Guarriero-Bobyleva, V., Masini, A., Volpi-Becchi, M.A. and Cennamo, C., Kinetic studies of cytoplasmic and mitochondrial aconitate hydratases from rat liver, Ital. J. Biochem. 27(5):287-99, (Aconitase ) [13], E-Cell System, ( ) 5: ,1998. ( ) [14] Hamada, M., Koike, K., Kakaula, Y., Hiraoka, T., Koike, M. and Hashimoto, T., A Kinetic Study of the -Keto Acid Dehdrogenase Complexes from Pig Heart Mitochondria, J. Biochem.(Tokyo) 77(5): ,1975. (Pyruvate dehydrogenase complex Oxoglutarate dehydrogenase complex ) [15] Henson, C.P. and Cleland, W.W., Kinetic studies of glutamic oxaloacetic transaminase isozymes, Biochemistry 3(3):338-45, (Transaminase ) [16] Indiveri, C., Dierks, T., Kramer, R. and Palmieri, F., Reaction mechanism of the reconstituted oxoglutarate carrier from bovine heart mitochondria, Eur. J. Biochem. 198(2):339-47, (Oxoglutarate Carrier ) [17] Indiveri, C., Prezioso, G., Dierks, T., Kramer, R. and Palmieri, F., Kinetic characterization of the reconstituted dicarboxylate carrier from mitochondria: a four-binding-site sequential transport system, Biochim. Biophys. Acta 1143(3):310-8, (Dicarboxylate Carrier ) [18] Indiveri, C., Tonazzi, A. and Palmieri, F., The reconstituted carnitine carrier from rat liver mitochondria: evidence for a transport mechanism dierent from that of the other mitochondrial translocators, Biochim. Biophys. Acta 1189(1):65-73, ( / ) [19] Mann, W.R., Yan, B., Dragland, C.J. and Bell, P.A., Kinetic, circular dichroism and uorescence studies on heterologously expressed carnitine palmitoyltransferase II, J. Enzyme. Inhib. 9(4):303-8, (CPT II ) [20] Matsuoka, Y. and Srere, P.A., Kinetic studies of citrate synthase from rat kidney and rat brain, J. Biol. Chem. 248(33): , (Citrate synthase ) [21] Miyazawa, S., Furuta, S., Osumi, T., Hashimoto, T. and Ui, N., Properties of peroxisomal 3- ketoacyl-coa thiolase from rat liver, J. Biochem.(Tokyo) 90(2):511-9, (3-ketoacyl-CoA thiolase )

13 14 Vol.6 [22] Montoya, J., Ojala, D. and Attardi, G., Distinctive features of the 50-terminal sequences of the human mitochondrial mrnas, Nature 290(5806):465-70, 1981 (1 ) [23] Ramsay, R.R., Derrick, J.P., Friend, A.S. and Tubbs, P.K., Purication and properties of the soluble carnitine palmitoyltransferase from bovine liver mitochondria, Biochem. J. 244(2):271-8, (CPT I ) [24] Rossmanith, W., Tullo, A., Potuschak, T., Karwan, R. and Sbisa, Human Mitochondrial trna Processing, J. Biol. Chem. 270(21): , (1 ) [25] Ojala, D., Montoya, J. and Attardi, G., trna punctuation model of RNA processing in human mitochondria, Nature 290(5806):470-4, (1 ) [26] Pape, T., Wintermeyer, W. and Rodnina, M.V., Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-trna to the A site of the E. coli ribosome, EMBO J. 17(24):7490-7, ( ) [27] Reinsch, J., Rojas, C. and McFarland, J.T., Kinetic Methods for the Study of the Enzyme Systems of -Oxidation, Arch. Biochem. Biophys. 227(1):21-30, (Acyl-CoA dehydrogenase ) [28] Roise, D., Interaction of a synthetic mitochondrial presequence with isolated yeast mitochondria: Mechanism of binding and kinetics of import, Proc. Natl. Acad. Sci. U.S.A. 89(2):608-12, ( ) [29] Segel, I.W. Enzyme kinetics, John Wiley & Sons, Inc., ( ) [30] Sluse, F.E., Evens, A., Dierks, T., Duyckaerts, C., Sluse-Goart, C.M. and Kramer, R., Kinetic study of the aspartate / glutamate carrier in intact rat heart mitochondria and comparison with a reconstituted system, Biochim. Biophys. Acta 1058(3):329-38, (Asp/Glu Carrier ) [31] Sluse, F.E., Ranson, M. and Liebecq, C., Mechanism of the exchanges catalysed by the oxoglutarate translocator of rat-heart mitochondria. Kinetics of the exchange reactions between 2-oxoglutarate, malate and malonate, Eur. J. Biochem. 25(2):207-17, (Oxoglutarate Carrier ) [32] Synetos, D. and Coutsogeorgopoulos, C., Studies on the catalytic rate constant of ribosomal peptidyltransferase, Biochim. Biophys. Acta 923(2):275-85, (Peptidyltransferase ) [33] Wright, B.E., Butler, M.H. and Albe, K.R., Systems analysis of the tricarboxylic acid cycle in Dictyostelium discoideum. I. The basis for model construction, J. Biol. Chem. 267(5):3101-5, ( Dictyostelium discoideum TCA )

14 15 [34] Yang, S.Y. and Schulz, H., Kinetics of Coupled Enzyme Reactions, Biochemistry 26(17): , (Enoyl-CoA hydratase Hydroxyl-CoA dehydrogenase ) [35], E-Cell System, ( ) 5:232-42,1998. ( )

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