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CLASSIFICATION OF ELEMENTARY FLUX MODES IN MITOCHONDRIAL ENERGETIC METABOLISM (« Physiopathologie Mitochondriale », INSERM U688 & Université de BORDEAUX.

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Présentation au sujet: "CLASSIFICATION OF ELEMENTARY FLUX MODES IN MITOCHONDRIAL ENERGETIC METABOLISM (« Physiopathologie Mitochondriale », INSERM U688 & Université de BORDEAUX."— Transcription de la présentation:

1 CLASSIFICATION OF ELEMENTARY FLUX MODES IN MITOCHONDRIAL ENERGETIC METABOLISM (« Physiopathologie Mitochondriale », INSERM U688 & Université de BORDEAUX 2) Marie BEURTON-AIMAR Charles LALÈS (Dcrt) Jean-Pierre MAZAT Nicolas PARISEY (Dcrt) Sabine PÉRÈS (Dcrte) - Bernard KORZENIEWSKI (Université de Krakow) - Christine NAZARET (ESTBB et MAB- Bordeaux 1) - Christine REDER (MAB- Bordeaux 1) (MAB- Bordeaux 1) - Pascal BALLET & Abdallah ZEMIRLINE (Université de Brest) (Université de Brest) - Frank MOLINA & Pierre MAZIÈRE (CNRS Montpellier) (CNRS Montpellier) MITOSCOPE

2 MITOCHONDRIA J.-P. Mazat Jena March 2005

3 SYMBIOTIC ORIGIN OF MITOCHONDRIA Mitochondria are ancient bacteria. They host their own genome, their own ribosomes and a metabolism of procaryotic origin. Ancient cell Bacteria ancestry of mitochondria DNA Nucleus mtDNA mitochondria J.-P. Mazat Jena March 2005

4 Different types of mitochondria Epithélium Spermatozoo Butterflys Adipose tissue Rat heart Mouse Heart Cortico-surrénales J.-P. Mazat Jena March 2005

5 Mitochondrial network Fragmentation J.-P. Mazat Jena March 2005

6 Oxidative Phosphorylation and mitochondrial genetics Complexe I Succinate Respiratory chain and ATP synthaseFunctions of mitochondria ATP synthesis. NADH reoxidation Metabolism Ca 2+ accumulation Heat production Free radicals production Apoptosis ADN mt ADN nucl. Complexe I7>30 Complexe II04 Complexe III110 Complexe IV310 Complexe V (ATPase)29 Double genetic origin Sous-unités codées par J.-P. Mazat Jena March 2005

7 DECOMPOSITION OF THE MITOCHONDRIAL ENERGETIC METABOLISM IN ELEMENTARY MODES J.-P. Mazat Jena March 2005

8 Succinate Fumarate H H H H n n n n S (André CASSAIGNE, Rachid OUHABI & Stéphane LUDINARD) FAMN FeS UQ b565, b566 FeS ; C1 Cu1 ; Cu2 a ; a3 F0 F1 C I C II C III C IV DHODH FAD Q G3-PDH NADH NAD Dihydrorotate Orotate FADH 2 3GP DHAP 2e Cyt c 2e O + 2H1/2 2 + H O 2 H H H H H H n n n n S ATP ADP Pi H H TP Mitochondrial Metabolism Citrate Isocitrate α-CÉtoglutarate Succinyl-CoA Succinate Fumarate Malate OxaloacÉtate Pyruvate AcÉtyl-CoA ADP + Pi 2 NAD NADH + CO 2 H O 2 NAD NADH + CO 2 NAD NADH + CO GDP + Pi GTP H O 2 FAD FADH 2 NAD NADH 2 H O 2 CitrateMalate GDP + Pi GTP Acyl-CoA (Cn) Trans enoyl CoA β-OH-acyl-CoA β-cÉtoacyl-CoA Acyl-CoA (n-2C) AcÉtyl-CoA Propionyl-CoA MÉthylmalonyl-CoA En fin dhÉlice, si nC est impair ATP + CO 2 AMP + PPi Hs-CoA Acyl-CoA (>12C) Acyl-CoA (<12C) Carnitine Hs-CoA AcÉtyl-CoA Carnitine AcÉtyl-CoA AcÉtoacÉtyl-CoA HO mÉthyl Glutaryl CoA AcÉtoacÉtate HO Butyrate Hs-CoA AcÉtyl-CoA α-CÉtoglutarate Glutamate NADNADH NH 3 Carbamyl-P Citrulline Ornithine 2 ATP + CO 2 2 ADP + Pi Argininosuccinate Arginine UrÉe Aspartate + ATP AMP + PPi Malate H O 2 Pi Fumarate Succinate Pi 2- α-CÉtoglutarate H + + H Malate Pi 2- Succinate Malate Glutamate Aspartate Ca 2+ + Cplx TIM22 Cplx OXA1 ATP E J.-P. Mazat Montpellier Fev 2005

9 WHY A DECOMPOSITION OF THIS NETWORK IN ELEMENTARY FLUX MODES ? -To compare mitochondrial metabolism in different tissues or organisms. How is it possible to obtain different types of mitochondria with the same metabolism ? J.-P. Mazat Jena March To point out specific prevailing pathways, which could be strongly represented in particular tissues and give them their specificity. - To unveil those mutations, which can be tolerated, those, which cannot and to understand why.

10 R6i : Pyr + CO2 + ATP = OAA + Pi + ADP. R7i : Pyr + NAD + CoA = ACoA + NADH2 + CO2. R8i : OAA + ACoA + H2O = Cit + CoA. R9 : Cit = Isocit. R10i : Isocit + NAD = Akg + NADH2 + CO2. R11i : Akg + NAD + CoA = SucCoA + NADH2 + CO2. R12 : SucCoA + Pi + ADP = Succ + CoA + ATP. R13 : Succ + FAD = Fum + FADH2. R14 : Fum + H2O = Mal. R15 : Mal + NAD = OAA + NADH2. R16 : Akg + NADH2 = Glu + NAD. R17 : Ala + NAD + H2O = Pyr + NH3 + NADH2. R18 : OAA + Glu = Asp + Akg. R20i : 2 ATP + NH3 + CO2 + H2O = 2 ADP + Pi + CarbamoylP. R21 : CarbamoylP + Ornit = Pi + Citrulline. R25i : 2 ACoA = CoA + AcetoACoA. R26 : ACoA + H2O + AcetoACoA = HmethylGlutCoA + CoA. R27 : HmethylGlutCoA = ACoA + Acetoacetate. R28 : Acetoacetate + NADH2 = Hbutanoate + NAD. R1i : NADH H = NAD + 10 H_ext. R2i : FADH2 + 6 H = FAD + 6 H. R3 : ADP + Pi + 3 H_ext = ATP + 3 H. R4i : H_ext = H. R30 : Acylcarnitine + CoA = Carnitine + AcylCoA. R31i : AcylCoA + 7 FAD + 7 NAD + 7 CoA + 7 H2O = 7 NADH2 + 7 FADH2 + 8 ACoA. T1 : Cit + H + Mal_ext = Mal + Cit_ext + H_ext. T2 : AKG_ext + Mal = Mal_ext + Akg. T3 : AcylC_ext + Carnitine = Carnitine_ext + Acylcarnitine. T4 : ADP_ext + ATP + H_ext = ADP + ATP_ext + H. T5 : Pi_ext + H_ext = Pi + H. T6 : Pyr_ext + H_ext = Pyr + H. T7 : Mal + Pi_ext = Pi + Mal_ext. T8 : Citrulline + Ornit_ext = Citru_ext + Ornit. T9 : Mal + Asp_ext = Mal_ext + Asp. T10 : Hbutanoate = HB_ext. T11 : AA_ext = Acetoacetate. T12 : Asp + Glu_ext + H_ext = Asp_ext + Glu + H. T13 : Mal + Succ_ext = Mal_ext + Succ. T14 : Asp + Succ_ext = Asp_ext + Succ. T15 : Asp + AKG_ext = Asp_ext + Akg. T16 : Asp + Pi_ext = Asp_ext + Pi. T17 : Succ + AKG_ext = Succ_ext + Akg. T18 : Succ + Pi_ext = Succ_ext + Pi. T19 : Akg + Pi_ext = AKG_ext + Pi. T20 : Glu_ext + H_ext = Glu + H. BIOCHEMICAL REACTIONS IN ENERGETIC MITOCHONDRIAL METABOLISM J.-P. Mazat Jena March reactions including 20 transporters 31 metabolites

11 ENERGETIC MITOCHONDRIAL METABOLIC NETWORK J.-P. Mazat Jena March 2005

12 [0, 0, 0, 1, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 1, -1, 0, 0, 0, -2, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, -1, 0; 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, -1, -1, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, 0, 0, -1, 0, -1, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 1, 0, 0, 0, 0, 2, 0, 0, -1, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, -1, 0, 0, 0, 0, -2, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, -1, 0, -1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0; 0, 0, 0, -1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; -1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 7, 0, 0, 0, 0, 0, 1, -1, 1, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, -1, 1, 0, -1, 0, 1, -7, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 1, 0, 0, 0, -1, 0, -1, -1, 0, 0, -7, 0, 0, 0, 0, 0, -1, 1, -1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, -7, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, -1, 0, -1, -1, -1, 0, 0, 0, 0; 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1; 10, 6, -1, 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, -1, -1, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, -1] STOICHIOMETRY MATRIX OF THE ENERGETIC MITOCHONDRIAL METABOLIC NETWORK matrix dimension r31 x c45 The following line indicates reversible (0) and irreversible reactions (1) rows and columns are sorted as declared in the inputfile N = J.-P. Mazat Jena March 2005

13 ELEMENTARY FLUX MODES elementary flux modes ! * How to make things clear ? Interest ? * With the help of Stefan Klamt J.-P. Mazat Jena March 2005 Why such a huge number ? - many exchangers - several non-equivalent way to maintain the steady-state of « currency metabolites ».

14 EXAMPLE OF ELEMENTARY FLUX MODE (1) T17 – T18 – T19 J.-P. Mazat Jena March 2005

15 EXEMPLE OF ELEMENTARY FLUX MODE (2) 8R8-8R10-8R11-4R20-16R25-5R31-8R9-8R12-(-35)R13-(-35)R14-8R15-(-43)R17-4R21-16-R26-16-R27-16R28-5R30-5T3-(-43)T5-4T8-(-43)T9-16T10-(- 43)T12-43T18-43T H+H J.-P. Mazat Jena March 2005 H+H+

16 TOP 10 OF REACTIONS R6 T20 R8 T3 R31 R30 T6 R14 R13 T4 Pyruvate carboxylase Glutamate carrier Citrate synthase Acylcarnitine translocase -oxydation of fatty acids Acylcarnitine transferase II Pyruvate carrier Fumarase Succinate deshydrogenase ATP/ADP Translocator STEPNAMENAMENUMBER of Elem. Modes J.-P. Mazat Jena March 2005

17 CLUSTERING ACCORDING TO « CURRENCY METABOLITE » (1) FAD/FADH 2 : R13 – R2 + 7 R31 = 0 NAD/NADH 2 : R7 + R10 + R11 + R15 – R16 + R17 – R28 – R1 + 7 R31 = 0 ADP/ATP : -R6 + R12 – 2 R20 + R3 – T4 = 0 CoA : R7 – R8 + R11 – R12 – R25 – R26 + R R31 = 0 P i : -R6 + R12 6 R20 – R21 + R3 – T5 – T7 – T16 – T18 – T19 = 0 H + : 10 R1 + 6 R2 – 3 R3 – R4 + T1 – T5 – T6 – T12 – T20 = 0 J.-P. Mazat Jena March 2005

18 CLUSTERING ACCORDING TO « CURRENCY METABOLITE » (2) FAD/FADH 2 : NAD/NADH 2 : ATP/ADP : CoA : P i : H : Motifs« Currency metabolite » J.-P. Mazat Jena March 2005

19 CONCLUSION Analysis of a network in terms of elementary flux modes modes : - Combinatory explosion of the number of elementary modes. - Usefulness ? -Thermodynamic considerations could decrease the number of elementary modes (metabolite concentrations outside mitochondria will give gradients) - Kinetic considerations could considerably decrease the number of elementary modes actually used in a given type of mitochondria. Metabolism organisation : -are in vivo only some elementary used depending on the cell type ? - or would the metabolism a functioning actually be this mess, whose the huge number of elementary flux modes give an idea ? J.-P. Mazat Jena March 2005 Important occurrence of some enzymes or exchangers : pyruvate carboxylase; glu and pyr carriers,… Implication for mitochondrial diseases

20 There are less molecule in the cell than elementary modes ….. Is it possible that one metabolite participate to all elementary modes in a mito ? elementary modes = true molecules A mitochondrion is a cube of 1 µm, which gives a volume of 1µm 3 = 1 dm 3. (10 -5 ) 3 = l true molecules = / moles = moles. Thus the concentration of this metabolite should have to be : moles / l = 1 mM

21 - Kacser, H., Burns, J.A., The control of flux, Symp. Soc. Exp. Biol. 32 (1973) Heinrich, R., Rapoport, T.A., A linear steady-state treatment of enzymatic chains. General properties, control and effector strength, Eur. J. Biochem. 42 (1974), Kacser, H. and Burns, J.A The molecular basis of dominance. Genetics 97: A seminal paper answering the long-standing riddle concerning the equivalence of heterozygote with the normal homozygote. - Reder, C., Metabolic control theory: a structural approach, J. Theor. Biol. 135 (1988) Groen AK, Wanders RJA, Westerhoff HV, Van der Meer R and Tager JM, Quantification of the contribution of various steps to the control of mitochondrial respiration, J. Biol. Chem. 257 : Tager JM, Wanders RJA, Groen AK, Kunz W, Bohnensack R, Kuster U, Letko, Bohme G, Duszynski J, Wojtczak L : Control of mitochondrial respiration FEBS Lett , David Fell : Understanding the control of metabolism Protland Press 1997, London and Miami. -Reinhart Heinrich and Stefan Schuster (1996) : The regulation of cellular systems Chapman & Hall. -Schuster S, Hilgetag C, Woods JH, Fell DA. Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism. J Math Biol. 2002;45: Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. Comparison of network-based pathway analysis methods. Trends Biotechnol. 2004;22: BIBLIOGRAPHIE

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23 mtDNA tRNA mRNA } Subunits of Respiratory Chain complexes VO2VATP MODEL OF mtDNA EXPRESSION Respiratory Complex VO2 WTmtDNA (WTmRNA) WTmRNA (Complex) WTmtDNA VO2 Seuil tARN mt + +

24 WTmtDNA (WTmRNA) WTmRNA (Complex) MODEL OF mtDNA and of mt-mRNA EXPRESSION WTmRNA = 2 * WTmtDNA KmtDNA + WTmtDNA (KmtDNA = 100) Complex = 2 * WTmRNA KmRNA + WTmRNA (KmRNA = 100)

25 THRESHOLD in tRNA WT-tRNA = 2 * WTmtDNA KmtDNA + WTmtDNA (KmtDNA = 100) Complex = 2 * WTmRNA KmRNA + WTmRNA (KmRNA = 100) If tRNA >= tRNA 0 Complex = 2 * WTmRNA KmRNA + WTmRNA (KmRNA = 100) If tRNA < tRNA 0 2 * WT-tRNA Km-tRNA + WT-tRNA (Km-tRNA = 100)

26 Respiratory Complex Cplxth VO2th VO 2 Slope = Control Coefficient MODEL OF COMPLEX EXPRESSION IN FLUX

27 WTmtDNA VO2 MODEL OF COMPLEX EXPRESSION IN FLUX

28 2ème Solution Traiter la synthèse des protéines et les régulations par des systèmes discrets multivalués : MetaReg par Ron Shamir & Gat-Viks (Tel-Aviv) : -Considèrent différents niveaux successifs en remontant de la voie métabolique (voie de biosynthèse de la lysine chez S. cerevisiae) : Ac. Am. Ext. / Ac. Am. Perméases / Ac. Am. Int. / Trpt. Comp. N / Trad. Prot. / Cont. Transcription / Enz. / Voie Métabolique -Les espèces à ces différents niveaux constituent les nœuds du réseau qui sont reliés par des interactions qui sont exprimées selon des tableaux comme ci-dessous : Etc.

29 3 - MULTI-AGENTS MODELS (FERBER) - Agents are entities, objects for which distinctive properties are described : Ex: enzymes, metabolites,…... - Roles : function representation. Ex : interactions between enzymes and metabolites, probability of reaction, etc….. - A group is defined by a set of roles between agents, a graph of interactions and a language or a protocol of interactions. Collaboration Pascal Ballet et Abdalla Zermiline Université de Brest. Example : Michaelis - Henri equation: S + E ES E + P - E, ES, S and P are agents. Roles : agent moving collision and reaction probabilities System free to evolve. S + E ES E + P

30 3ème Solution : Réseaux de Petri hybrides HFPN (Hybrid Functional Petri Net) H. Matsuno et al. : Biopathways Representation and Simulation on Hybrid Functional Petri Net. (http://www.GenomiObjet.Net) m1m1 3 Deux sortes de réseaux : Discontinus :Continus : m2m2 m3m3 2 1 T t =1.0 If m 1 2 and m 2 3 P1P1 P2P2 P3P3 m1m1 m2m2 m3m3 T v = m 1 - m 2 / 10 P1P1 P2P2 P3P3 Permet une modélisation mixte continu-discontinu avec le même type de représentation Permet la modélisation en même temps (de manière intégrée) des voies métaboliques (glycolyse) et des réseaux génétiques (opéron lactose).

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32 PROJET : MITOCHONDRIE VIRTUELLE Marie Beurton-Aimar, Jean-Pierre Mazat, Christine Nazaret, Nicolas Parisey et Sabine Pérès 1 - Analyse des modèles existant des ox-phos :.Article et mise sur le web juin 2002 avec aide à lutilisation des différents modèles.. Application aux courbes de seuil expériemntales (coll. TL) 2 - Modélisation du métabolisme mitochondrial global : Ox-phos, cycle de Krebs, oxydation des acides gras, cycle de l urée,…. 3 – Construction dune base de donnée mitochondrie à laide du langage dannotation des processus biologiques Bio. (Collaboration Frank Molina et Pierre Mazières, Montpellier) 4 – Exploration de différentes méthodes de modélisation. Modes élémentaires.. Réseaux hybrides ?

33 - MATRICE DE STOECHIOMÉTRIE - EXEMPLE 2 X1X1 V1V1 V3V3 V2V2 N = [ ] V1V1 V2V2 V3V3 = V 1 – V 2 – V 3 dX 1 dt et dX dt = N. V avec : dX dt = dX 1 dt V ==

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36 II LE CONTRÔLE DES OXYDATIONS PHOSPHORYLANTES

37 Complexe I CoQ FAD + 2 FeS centers Cyt b FeS Cyt c 1 (Rieske) Complexe III Complex II Cyt c Cyt a 3 Complexe IV ( Cytochrome c Oxidase) Rotenone Antimycine KCN CHAÎNE RESPIRATOIRE NADH FMN + 5 FeS centers PyruvateGlutamate Succinate, Fatty Acids O2O2O2O2 H2OH2OH2OH2O NAD J.-P. Mazat Montpellier Fev 2005

38 KCN µM Inhibition par le KCN de la Cytochrome- c-Oxidase et de la vitesse de respiration A Letellier et al. (1994) The kinetic basis of threshold effects observed in mitochondrial diseases Biochem. J % COX Activity or VO 2 % inhibition de la cytochrome c oxidase B % Respiratory rate (VO ) 2 J.-P. Mazat Montpellier Fev 2005

39 COEFFICIENTS DE CONTRÔLE DES OXYDATIVE PHOSPHORYLTION DANS LES MITOCHONDRIES DE MUSCLE Pyruvate transport Complex I Complex III Complex IV ATP Synthase Translocase Phosphate Carrier Somme : V ATP V O2 COEFFICIENTS DE CONTRÔLE J.-P. Mazat Montpellier Fev 2005

40 EFFET DE SEUIL MÉTABOLIQUE dans le cadre de la théorie du contrôle du métabolisme Le contrôle est partagé Le contrôle est partagé C i = 1 C i = 1 La plupart des coefficients La plupart des coefficients de contrôle sont faibles. de contrôle sont faibles. Effet de seuil. Effet de seuil. Flux Étape Inhibiteur Faible coefficient de contrôle C i = F/ v i i J.-P. Mazat Montpellier Fev 2005

41 GÉNÉTIQUE MITOCHONDRIALE hérédité maternelle. Hétéroplasmie de lADN mitochondrial La proportion (heteroplasmie) de lADNmt muté peut varier de 0 à 100 % J.-P. Mazat Montpellier Fev 2005

42

43 Activité COX (50 biopsies) Vitesse de respiration MISE EN ÉVIDENCE DUN SEUIL DANS LES PATHOLOGIES MITOCHONDRIALES J.-P. Mazat Montpellier Fev 2005

44 COURBES DEFFET DE SEUIL MÉTABOLIQUE Complexe I and III ROSSIGNOL, R., MALGAT, M., MAZAT, J.-P and.LETELLIER, T., :. (1999) J. Biol. Chem., 274: J.-P. Mazat Montpellier Fev 2005

45 COURBES DEFFET DE SEUIL MÉTABOLIQUE Complexe IV, ATP synt., Pi carrier, Pyr. Carrier, ANT ROSSIGNOL, R., LETELLIER, T., MALGAT, M., ROCHER, C. AND MAZAT, J.-P. (2000) : Biochem. J. 347 : J.-P. Mazat Montpellier Fev 2005

46 0,50,40,30,20,10, Complexe I Complexe III Complexe IV ATPase ANT Transport du Phosphate Coefficients de Contrôle Threshold value (% inhibition of isolated step activity) y = 90, ,42x R^2 = 0,805 RELATION ENTRE LES COEFFICIENTS DE CONTRÔLE ET LES VLEURS DE SEUIL J.-P. Mazat Montpellier Fev 2005


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