Using Pathway Tools & Matlab for Flux Balance Analysis. Kent Peterson 25 Aug. 2009
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1 Using Pathway Tools & Matlab for Flux Balance Analysis Kent Peterson 25 Aug. 2009
2 Summary Flux Balance Analysis (FBA) Workflow: from Ptools to Matlab, and back again A simple example What next? 2
3 Let s start at the very beginning... E 12 X 1 X 2 k 12 Krebs cycle in A. thaliana (from Widipedia) Bio Chemical Reaction Network
4
5
6 Flux Balance Analysis (FBA) Flux = rate at which chemicals are transformed or transported Balanced = input & output rates are equal (a.k.a. steady-state) Analysis = optimize (balanced) flux with constraints Example: maximize product synthesis per unit feedstock, while satisfying maintenance (biomass) requirements Biomass Feedstock Cell Product
7 Software components Pathway Tools 1 (PGDB for organism) SBML 2 Toolbox (export metabolic description files) COBRA 3 (setup the LP) GLPK 4 (solve the LP) Matlab 5 (math s programming & graphics) Palsson UCSD, 4. GNU Linear Programming Kit,
8 Workflow Load PGDB into PathwayTools Export metabolic network into SBML file Import SBML file into Matlab Compute FBA solution in Matlab Examine network & flux sol n, using Matlab GUIs Iterate Write FBA sol n to text file Import sol n to Pathway Tools Omics Viewer Export Pathway tools Import Matlab Iterate 8
9 Example Maximize anabolic biomass produced from a feedstock 9
10 Getting the data from Ptools to Matlab SBML export from Pathway Tools SBML import into Matlab 10
11 What a mess! (9) MET!0001 (25) NADP (2) (28) PHOSPHORIBULOKINASE DIHYDROXY!ACETONE!PHOSPHATE (11) (19) (10) RXN!0006 (3) RIBULP3EPIM CMP (14) RXN!0001 (18) MET!0006 (6) OXYGEN!MOLECULE (2) (33) CDP (34) BiomassFormation (15) RXN!0002 (3) PHOSPHO!ENOL!PYRUVATE (12) MET!0002 (36) D!SEDOHEPTULOSE!7!P (11) MET!0004 (31) CMPKIN (21) RXN!0008 (25) PSII (16) MET!0007 (1) PROTON C CO!THY!LUM!CYA (43) Biomass (10) TRIOSEPISOMERIZATION (30) ERYTHROSE!4P (23) PROTON (42) RIBULOSE!5P (26) NADPH (33) WATER (5) MET!0009 (8) PYRUVATE (4) SEDOHEPTULOSE!BISPHOSPHATASE (41) RIBOSE!5P (15) PPI (24) G3P (40) ADP (20) MET!0005 (1) RIB5PISOM (21) Reduced!ferredoxins (9) F16ALDOLASE (26) RXN!0010 (32) GAP (22) CARBON!DIOXIDE (17) MET!0008 (18) RXN!0005 (8) SEDOBISALDOL (27) DPG (29) FRUCTOSE!16!DIPHOSPHATE (23) (24) RXN490!3650 (37) XYLULOSE!5!PH (5) 2TRANSKETO (28) 2PGADEHYDRAT (4) 2!PG (13)(12) RUBISCO PHOSGLYPHOS (34) D!SEDOHEPTULOSE!1!7!P2 (16) RXN!0003 (13) CTP (7) E! (35) Pi (38) ATP (6) 1TRANSKETO (14) MET!0003 (19) Oxidized!ferredoxins (17) RXN!0004 (22) RXN!0009 Reaction Metabolite Substrate flux Product flux (39) D!RIBULOSE!15!P2 (31) FRUCTOSE!6P 0.1 (32) INORGPYROPHOSPHAT (30) CDPKIN (27) 3PGAREARR (29) PEPDEPHOS (7) F16BDEPHOS (20) RXN!
12 (15) PPI (38) ATP (40) ADP (26) NADPH (25) NADP (35) Pi Matlab tools (1): Met/Rxn graph (39) D!RIBULOSE!15!P2 (13) RUBISCO (30) CDPKIN (2) PHOSPHORIBULOKINASE (24) G3P (27) 3PGAREARR (42) RIBULOSE!5P (4) 2!PG (2) CDP (3) RIBULP3EPIM Calvin (12) PHOSGLYPHOS (28) 2PGADEHYDRAT (1) RIB5PISOM (3) PHOSPHO!ENOL!PYRUVATE (37) XYLULOSE!5!PHOSPHATE cycle (29) PEPDEPHOS (41) RIBOSE!5P (27) DPG (8) PYRUVATE (31) CMPKIN (6) 1TRANSKETO (11) (22) RXN!0009 (5) 2TRANSKETO (32) GAP (36) D!SEDOHEPTULOSE!7!P (9) MET!0001 (21) RXN!0008 (10) CMP (4) SEDOHEPTULOSE!BISPHOSPHATASE (12) MET!0002 (34) D!SEDOHEPTULOSE!1!7!P2 (10) TRIOSEPISOMERIZATION (18) RXN!0005 (30) ERYTHROSE!4P (14) MET!0003 (28) DIHYDROXY!ACETONE!PHOSPHATE (19) RXN!0006 (31) FRUCTOSE!6P (8) SEDOBISALDOL (9) F16ALDOLASE (11) MET!0004 (20) RXN!0007 (7) F16BDEPHOS (29) FRUCTOSE!16!DIPHOSPHATE (32) INORGPYROPHOSPHAT (33) (25) PSII (7) E! (23) PROTON (22) CARBON!DIOXIDE (33) WATER (23) (1) PROTON CO!THY!LUM!CYA C (6) OXYGEN!MOLECULE (20) MET!0005 (14) RXN!0001 (18) MET!0006 (16) RXN!0003 (15) RXN!0002 (16) MET!0007 (17) RXN!0004 (17) MET!0008 (13) CTP (26) RXN!0010 (19) Oxidized!ferredoxins (24) RXN490!3650 (5) MET!0009 (34) BiomassFormation (21) Reduced!ferredoxins (43) Biomass Reaction Metabolite Substrate flux Product flux 12
13 Matlab tools (2): Met/Rxn browser 13
14 (15) PPI (38) ATP (40) ADP (26) NADPH (25) NADP (35) Pi Final product: an FBA solution (39) D!RIBULOSE!15!P2 (13) RUBISCO (30) CDPKIN (2) PHOSPHORIBULOKINASE (24) G3P (27) 3PGAREARR (42) RIBULOSE!5P (4) 2!PG (2) CDP (3) RIBULP3EPIM (12) PHOSGLYPHOS (28) 2PGADEHYDRAT (1) RIB5PISOM (3) PHOSPHO!ENOL!PYRUVATE (37) XYLULOSE!5!PHOSPHATE (29) PEPDEPHOS (41) RIBOSE!5P (27) DPG (8) PYRUVATE (31) CMPKIN (6) 1TRANSKETO (11) (22) RXN!0009 (5) 2TRANSKETO (32) GAP (36) D!SEDOHEPTULOSE!7!P (9) MET!0001 (21) RXN!0008 (10) CMP (4) SEDOHEPTULOSE!BISPHOSPHATASE (12) MET!0002 (34) D!SEDOHEPTULOSE!1!7!P2 (10) TRIOSEPISOMERIZATION (18) RXN!0005 (30) ERYTHROSE!4P (14) MET!0003 (28) DIHYDROXY!ACETONE!PHOSPHATE (19) RXN!0006 (31) FRUCTOSE!6P (8) SEDOBISALDOL (9) F16ALDOLASE (11) MET!0004 (20) RXN!0007 (7) F16BDEPHOS (29) FRUCTOSE!16!DIPHOSPHATE (32) INORGPYROPHOSPHAT (33) (25) PSII (7) E! (23) PROTON (22) CARBON!DIOXIDE (33) WATER (23) (1) PROTON CO!THY!LUM!CYA C (6) OXYGEN!MOLECULE (20) MET!0005 (14) RXN!0001 (18) MET!0006 (16) RXN!0003 (15) RXN!0002 (16) MET!0007 (17) RXN!0004 (17) MET!0008 (13) CTP (26) RXN!0010 (19) Oxidized!ferredoxins (24) RXN490!3650 (5) MET!0009 (34) BiomassFormation (21) Reduced!ferredoxins (43) Biomass
15 Import to Omics Viewer 15
16 Recap What have we accomplished? From stoichiometry (structure) of reaction network... Steady-state flux subspace, v N (S) Conserved motifs, ẋ N (S T ) From flux constraints... Unique steady-state operating point (solution of LP) We used biomass optimization, but there are many variations on the theme (e.g., MOMA, ROOM) What is not represented? Quantity (Concentrations) Thermodynamics (chemical potentials) Dynamics (approach to steady-state, stability,...) Spatial inhomogeneities Regulation (neither metabolic nor transcriptional) 16
17 Network dynamics (1): Linearized 17
18 Network dynamics (2): Nonlinear 18
19 A network model can (should?) include: Structure (connections, stoichiometric weights) Flux (chemical flow) Concentration (chemical potential) Kinetics (flux/potential constitutive model) Regulatory feedback Ref: Krappmann, Lipscomb, Braus (2000) PNAS 97(25):
20 Example of Metabolic Control from EcoCyc Transcriptional control Modulatory control
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