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Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations
2010
Biosystems (Amsterdam. Print)
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The good dynamic behavior and the powerful predictive capabilities obtained using the hybrid model composed of Michaelis-Menten and the approximate lin-log kinetics indicate that this is a possible suitable ...
The construction of dynamic metabolic models at reaction network level requires the use of mechanistic enzymatic rate equations that comprise a large number of parameters. ...
of improved microbial cell factories" (MIT-Pt/BS-BB/0082/2008). ...
doi:10.1016/j.biosystems.2010.03.001
pmid:20226228
fatcat:264ehzvevrhezfpuwaegntbglq
A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering
2018
Frontiers in Microbiology
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In this work, we review the state of the art of dynamic modeling and related methods used for metabolic engineering applications, including approaches based on hybrid modeling. ...
kinetic rate laws of metabolic processes. ...
AUTHOR CONTRIBUTIONS All authors participated in the preparation of this work. OK had a major role in writing and editing the manuscript. ...
doi:10.3389/fmicb.2018.01690
pmid:30108559
pmcid:PMC6079213
fatcat:dgs2tzysijevdbza7sga3fzi2m
Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling
2011
IET Systems Biology
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In this work, we provide a critical overview of specific limitations found during the reconstruction of the central carbon metabolism dynamic model from E. coli (based on kinetic data available). ...
Detailed kinetic models at the network reaction level are usually constructed using enzymatic mechanistic rate equations and the associated kinetic parameters. ...
A hybrid modelling approach combining approximated lin-log kinetics and Michaelis -Mentens equations are introduced in [65] . Another hybrid approach was developed by Yugi et al. [60] . ...
doi:10.1049/iet-syb.2009.0058
pmid:21639589
fatcat:6yuzpbanxbab3jj3plgnkp2oum
A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data
2018
npj Systems Biology and Applications
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Kinetic models rest on an explicit functional relationship connecting the rate of change 43 of a metabolite and the proteins and metabolites involved in the reaction (see Fig. 1 ): Michaelis-Menten kinetics ...
Approaches such as 48 ensemble modeling 39-43 tackle the parsity of known kinetic constants by producing an ensemble of models displaying different 49 combinations of randomly chosen kinetic parameters ...
Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. Biosystems 100, 150-157 (2010). ...
doi:10.1038/s41540-018-0054-3
pmid:29872542
pmcid:PMC5974308
fatcat:b67iumgdn5hqloaxevlerb7l5y
Modeling Cell-Free Protein Synthesis Systems—Approaches and Applications
2020
Frontiers in Bioengineering and Biotechnology
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Black-box models laid the foundation for understanding the production and degradation dynamics of macromolecule components such as mRNA, ribosomes, and proteins. ...
Currently, the scope of CFPS modeling has broadened to various applications, ranging from the screening of kinetic parameters to the stochastic analysis of liposome-encapsulated CFPS systems and the assessment ...
In structured models, kinetic models such as Michaelis-Menten or Hill are implemented in combination with larger ODE systems of up to 100 equations. ...
doi:10.3389/fbioe.2020.584178
pmid:33195146
pmcid:PMC7655533
fatcat:esynrf2ltbch3mfe4wihe5dt2e
Towards the engineering of in vitro systems
2009
Journal of the Royal Society Interface
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When looking at a comparatively simple system, such as a medium-sized enzymatic reaction network as it is represented by glycolysis, major issues such as a lack of comprehensive enzyme kinetics and of ...
Given the complexity of living systems and our current lack of understanding of many aspects of living cells, this is a major undertaking. ...
Michaelis -Menten kinetics. ...
doi:10.1098/rsif.2009.0110.focus
pmid:19474076
pmcid:PMC2843965
fatcat:nfrbtsp2zvhw5d4smkvycxsfte
Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data
2016
Frontiers in Molecular Biosciences
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In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. ...
the metabolic reaction network. ...
AUTHOR CONTRIBUTIONS All authors listed, have made substantial, direct and intellectual contribution to the work, and approved it for publication. ...
doi:10.3389/fmolb.2016.00015
pmid:27200361
pmcid:PMC4853375
fatcat:4ma6i74u7vgzzbni5agppwyabe
Exploring the gap between dynamic and constraint-based models of metabolism
2012
Metabolic Engineering
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We compare and analyze dynamic and constraint-based formulations of the same model of the central carbon metabolism of Escherichia coli. ...
Systems biology provides new approaches for metabolic engineering through the development of models and methods for simulation and optimization of microbial metabolism. ...
Discussion We have analyzed and compared dynamic and constraintbased formulations of the same model for the central carbon metabolism of E. coli (Chassagnole et al., 2002) . ...
doi:10.1016/j.ymben.2012.01.003
pmid:22306209
pmcid:PMC3465724
fatcat:utobsc22dzho7e3znriscpslja
Systems analysis of cellular networks under uncertainty
2009
FEBS Letters
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Besides the often-quoted complexity of cellular networks, the prevalence of uncertainties about components, interactions, and their quantitative features provides a largely underestimated hallmark of current ...
As a common denominator, the methods focus on structural, rather than more detailed, kinetic network properties. ...
Acknowledgements We gratefully acknowledge financial support by the EU FP7 Project UniCellSys and by the Swiss Initiative for Systems Biology (Sys-temsX.ch RTD Project YeastX). ...
doi:10.1016/j.febslet.2009.10.074
pmid:19879267
fatcat:w74siyswzjgxjicmc5sy7sacpu
Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis
2020
Metabolites
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Metabolic networks are regulated to ensure the dynamic adaptation of biochemical reaction fluxes to maintain cell homeostasis and optimal metabolic fitness in response to endogenous and exogenous perturbations ...
Constraint-based modelling and kinetic modelling are among the most widely used methods to study cell metabolism at different scales, ranging from cells to tissues and organisms. ...
(Michaelis-Menten laws). ...
doi:10.3390/metabo10080303
pmid:32722118
fatcat:g7aq4jrsebbqrcu2wh3jcei3jm
Current status and future perspectives of kinetic modeling for the cell metabolism with incorporation of the metabolic regulation mechanism
2015
Bioresources and Bioprocessing
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A brief overview is given for the current status of the kinetic modeling of the cell metabolism from the point of view of metabolic regulation focusing on Escherichia coli (but not limited to E. coli). ...
Among various modeling approaches, kinetic modeling is promising in the sense of realizing the essential feature of metabolic regulation. ...
Westerhoff of the University of Manchester, Prof. J. McFadden of the Surrey University in UK, and the UK-Japan systems biology project funded by JST (Japan) and BBSRC (UK). ...
doi:10.1186/s40643-014-0031-7
fatcat:ntvfw6teovavbilentqipcmwoi
Mathematical Modelling as a Tool for Optimized PHA Production
english
2015
Chemical and Biochemical Engineering Quarterly
english
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For this purpose, the complex enzyme kinetic was used: a reversible ping-pong BiBi mechanism, reversible sequential ordered BiBi mechanism, and Michaelis-Menten equation for nonreversible system corrected ...
Key words: cybernetic models, dynamic models, hybrid models, formal kinetic modelling, mathematical modelling, metabolic models, neuronal networks, poly(hydroxyalkanoate) (PHA) terns of product formation ...
Puchałka et al. 101 Pseudomonas putida KT2440 Genome-scale network reconstruction, FBA, FVA, C 13 ...
doi:10.15255/cabeq.2014.2101
fatcat:sbnabwlayvh6ji4qfgy3t33adq
In Silico Models for Dynamic Connected Cell Cultures Mimicking Hepatocyte-Endothelial Cell-Adipocyte Interaction Circle
2014
PLoS ONE
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The whole model was based on a modular approach and on a set of nonlinear differential equations implemented in Simulink, applying Michaelis-Menten kinetic laws and some energy balance considerations to ...
first model reproduced the metabolic behaviour of a hepatocyte, the second one represented an endothelial cell, and the third one described an adipocyte. ...
In physiological concentration conditions for total plasma fatty acids (bound and unbound, 0.45 mM), saturation kinetic prevails and it is well described by a Michaelis-Menten model equation: d S ½ dt~ ...
doi:10.1371/journal.pone.0111946
pmid:25502576
pmcid:PMC4266517
fatcat:fs67lgtfhjd5plbny3onpihfye
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
2010
The ISME Journal
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Here, we have created a dynamic genome-scale metabolic model of Geobacter sulfurreducens and Rhodoferax ferrireducens, the two primary iron-reducers in subsurface environments, in order to understand the ...
The dynamics of the community involved is complex and needs to be understood better for improving the bioremediation. ...
Michaelis-Menten kinetics can be used to incorporate kinetics measurements as dynamic constraints [50] . ...
doi:10.1038/ismej.2010.117
pmid:20668487
pmcid:PMC3105697
fatcat:l5scltqiyrflnnytpes2tp5iwa
Kinetic models in industrial biotechnology – Improving cell factory performance
2014
Metabolic Engineering
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Emphasis is on modeling methodology concepts, including model network structure, kinetic rate expressions, parameter estimation, optimization methods, identifiability analysis, model reduction, and model ...
Here we review the current status of kinetic cell factory modeling. ...
Though, the concepts of dynamic flux balance might become useful in hybrid strategies where stoichiometric models and kinetic models are combined. ...
doi:10.1016/j.ymben.2014.03.007
pmid:24747045
fatcat:7nankknr4batfkyvrgzx5mpl2m
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