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Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

Andreas Hoppe, Sabrina Hoffmann, Hermann-Georg Holzhütter
2007 BMC Systems Biology  
In recent years, constrained optimization -usually referred to as flux balance analysis (FBA) -has become a widely applied method for the computation of stationary fluxes in large-scale metabolic networks  ...  Conclusion: Our method incorporates the thermodynamic link between flux directions and metabolite concentrations into a practical computational algorithm.  ...  Here we go one step further to include information on metabolite concentrations directly into the calculation of the flux distribution.  ... 
doi:10.1186/1752-0509-1-23 pmid:17543097 pmcid:PMC1903363 fatcat:yswzcqjbebh77ettl4qxpq5bza

System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

Stefan J. Jol, Anne Kümmel, Marco Terzer, Jörg Stelling, Matthias Heinemann, Jason A. Papin
2012 PLoS Computational Biology  
One of the most obvious phenotypes of a cell is its metabolic activity, which is defined by the fluxes in the metabolic network.  ...  From the 71 million EFMs in a medium size metabolic network of S. cerevisiae, we classified 54% as thermodynamically feasible.  ...  Acknowledgments We would like to thank Barbara Bakker for the helpful comments and discussions regarding redox metabolism. Author Contributions  ... 
doi:10.1371/journal.pcbi.1002415 pmid:22416224 pmcid:PMC3296127 fatcat:gjfgiabbang3bc5gzx7zytgs6e

Removing both Internal and Unrealistic Energy-Generating Cycles in Flux Balance Analysis [article]

Elad Noor
2018 arXiv   pre-print
Constraint-based stoichiometric models are ubiquitous in metabolic research, with Flux Balance Analysis (FBA) being the most widely used method to describe metabolic phenotypes of cells growing in steady-state  ...  thermodynamic parameters as in the case of thermodynamic FBA.  ...  Including metabo- Quantitative assignment of reaction direction- lite concentrations into flux balance analysis: ality in constraint-based models of metabolism: thermodynamic  ... 
arXiv:1803.04999v1 fatcat:scjaqs27rzap5iviefq2v6b3vy

Use of Randomized Sampling for Analysis of Metabolic Networks

Jan Schellenberger, Bernhard Ø. Palsson
2008 Journal of Biological Chemistry  
These techniques have been applied extensively to the reaction rate (flux) space of networks, with more recent work focusing on dynamic/kinetic properties.  ...  Genome-scale metabolic network reconstructions in microorganisms have been formulated and studied for about 8 years.  ...  (34) used thermodynamic considerations to describe a set of constraints on the concentrations of metabolites.  ... 
doi:10.1074/jbc.r800048200 pmid:18940807 fatcat:dvewrdt42vgf5hbk5cygd6emu4

Flux balance analysis of biological systems: applications and challenges

K. Raman, N. Chandra
2009 Briefings in Bioinformatics  
In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used.  ...  matrix and a biologically relevant objective function to identify optimal reaction flux distributions.  ...  Holzhütter and co-workers have proposed a method to include metabolite concentrations into FBA, to ensure thermodynamic realisability [39] , overcoming the conventional reliance of FBA on the intuitive  ... 
doi:10.1093/bib/bbp011 pmid:19287049 fatcat:542cezsctjdmznnpwyfwpkdj3a

Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems

Christophe H. Schilling, Jeremy S. Edwards, David Letscher, Bernhard Ø. Palsson
2000 Biotechnology and Bioengineering  
A shift in emphasis from single metabolic reactions to systemically defined pathways is one consequence of such an integrative analysis of metabolic systems.  ...  The constraints of systemic stoichiometry, and limited thermodynamics have led to the definition of the flux space within the context of convex analysis.  ...  To complete the description of the metabolic network we must include the constraints that are placed on fluxes due to reaction thermodynamics and the systemic characteristics (input/output) of the network  ... 
doi:10.1002/1097-0290(2000)71:4<286::aid-bit1018>;2-r pmid:11291038 fatcat:nv23hyavsrfhncubc2if7kf4v4

Network design and analysis for multi-enzyme biocatalysis

Lisa Katharina Blaß, Christian Weyler, Elmar Heinzle
2017 BMC Bioinformatics  
In addition, a thermodynamic profile, the overall reactant balance and potential side reactions as well as an SBML file for visualization are generated for each pathway alternative.  ...  We implemented a path-finding algorithm based on a mixed-integer linear program (MILP) which takes into account both topology and stoichiometry of the underlying network.  ...  Availability of data and materials All data generated or analyzed during this study are included in this published article and its supplementary information files.  ... 
doi:10.1186/s12859-017-1773-y pmid:28797226 pmcid:PMC5553788 fatcat:ph72digepjdqfkh3kuyv4ylvou

Generic flux coupling analysis

Arne C. Reimers, Yaron Goldstein, Alexander Bockmayr
2015 Mathematical Biosciences  
Originally, it was introduced for constraint-based models of metabolic networks that are based on the steady-state assumption.  ...  We illustrate our method by thermodynamic flux coupling analysis (tFCA), which allows studying steady-state metabolic models with loop-law thermodynamic constraints.  ...  It contains all flux distributions v ∈ R R satisfying the stoichiometric and irreversibility constraints. A prominent example of a constraint-based method is flux balance analysis (FBA) [44] .  ... 
doi:10.1016/j.mbs.2015.01.003 pmid:25619608 fatcat:cngylawv7zbcrkjfajo3hljfk4

Pruning genome-scale metabolic models to consistent ad functionem networks

Sabrina Hoffmann, Andreas Hoppe, Hermann-Georg Holzhütter
2007 Genome Informatics Series  
Depending on the choice of the exchangeable metabolites, composition of the external medium, and type of thermodynamic constraints we obtain different reduced network variants that may serve as a basis  ...  for flux balance models.  ...  Obviously, these are compounds that do not represent metabolites in a strict sense and thus should not be included into the metabolic network.  ... 
pmid:18546498 fatcat:yxole3zrrbfllpxgsxxravvgni

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints

Anirikh Chakrabarti, Ljubisa Miskovic, Keng Cher Soh, Vassily Hatzimanikatis
2013 Biotechnology Journal  
Recent developments in the construction and analysis of stoichiometric models made it possible to define limits on steady-state metabolic behavior using flux balance analysis.  ...  Our results indicate that enzyme saturation is a necessary consideration in modeling metabolic networks and it extends the feasible ranges of the metabolic fluxes and metabolite concentrations.  ...  This is the set of mass balance constraints used in the Flux Balance Analysis.  ... 
doi:10.1002/biot.201300091 pmid:23868566 fatcat:2vd7a327e5feddz5wiwa2pxykm

Integration of metabolomics data into metabolic networks

Nadine Töpfer, Sabrina Kleessen, Zoran Nikoloski
2015 Frontiers in Plant Science  
However, while changes in transcript or to some extent protein levels can usually be traced back to one or several responsible genes, changes in fluxes and particularly changes in metabolite levels do  ...  to relate network structural properties to metabolite levels.  ...  METABOLITE DATA TO INFER THERMODYNAMIC REALIZABILITY INCLUDING METABOLITE CONCENTRATIONS INTO FLUX BALANCE ANALYSIS Metabolite concentrations in metabolic networks are intrinsically tied to the thermodynamic  ... 
doi:10.3389/fpls.2015.00049 pmid:25741348 pmcid:PMC4330704 fatcat:pte3apjxfrcxppdjf33pv3dtc4

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

Christoph Gille, Christian Bölling, Andreas Hoppe, Sascha Bulik, Sabrina Hoffmann, Katrin Hübner, Anja Karlstädt, Ramanan Ganeshan, Matthias König, Kristian Rother, Michael Weidlich, Jörn Behre (+1 others)
2010 Molecular Systems Biology  
The network comprises 777 metabolites in six intracellular and two extracellular compartments and 2539 reactions, including 1466 transport reactions.  ...  We present HepatoNet1, the first reconstruction of a comprehensive metabolic network of the human hepatocyte that is shown to accomplish a large canon of known metabolic liver functions.  ...  Acknowledgements We acknowledge the assistance of Thomas Handorf who performed a scope analysis on intermediate stages of the network to identify unconnected network clusters, Albert Gevorgyan who performed  ... 
doi:10.1038/msb.2010.62 pmid:20823849 pmcid:PMC2964118 fatcat:qvm2rcul5vcfxfmhbnve35cgmq

FASIMU: flexible software for flux-balance computation series in large metabolic networks

Andreas Hoppe, Sabrina Hoffmann, Andreas Gerasch, Christoph Gille, Hermann-Georg Holzhütter
2011 BMC Bioinformatics  
Flux-balance analysis based on linear optimization is widely used to compute metabolic fluxes in large metabolic networks and gains increasingly importance in network curation and structural analysis.  ...  Conclusions: We present a flux-balance optimization program whose main merits are the implementation of thermodynamics as a constraint, batch series of computations, free availability of sources, choice  ...  Acknowledgements and Funding The work of AH has been funded by HepatoSys, the Network Systems Biology, funded by Bundesministerium für Bildung und Forschung, Germany. Author details 1  ... 
doi:10.1186/1471-2105-12-28 pmid:21255455 pmcid:PMC3038154 fatcat:3rkqpmzf2rgcza7xmoo27fkqnq

Quantification of Microbial Phenotypes

Verónica Martínez, Jens Krömer
2016 Metabolites  
Better estimations of metabolic phenotypes will be obtained when further constraints are included in the analysis.  ...  Thermodynamics provides information on the direction in which a reversible reaction will operate under the given conditions.  ...  Thermodynamics-based metabolic flux analysis (TMFA) goes one step further, estimating metabolic flux distributions utilizing thermodynamic constraints directly by metabolic flux analysis (MFA) [20] .  ... 
doi:10.3390/metabo6040045 pmid:27941694 pmcid:PMC5192451 fatcat:neelu2q6orakpi5u2n4rwsi3bq

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

Elad Noor, Avi Flamholz, Arren Bar-Even, Dan Davidi, Ron Milo, Wolfram Liebermeister, Daniel A Beard
2016 PLoS Computational Biology  
It depends on enzyme parameters (such as kcat and KM constants), but also on metabolite concentrations.  ...  and computationally tractable way to include enzyme kinetics into constraint-based metabolic models, where kinetics have usually been ignored or oversimplified.  ...  In both cases, ECM is fully applicable as long as metabolic fluxes are predefined and loop-less (in order to be realizable by a thermodynamically consistent state [67] ).  ... 
doi:10.1371/journal.pcbi.1005167 pmid:27812109 pmcid:PMC5094713 fatcat:y55lbn2ghvbwbdv66srxnukfey
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