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Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations

Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira
2010 Biosystems (Amsterdam. Print)  
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

Osvaldo D. Kim, Miguel Rocha, Paulo Maia
2018 Frontiers in Microbiology  
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

R.S. Costa, I. Rocha, E.C. Ferreira, D. Machado
2011 IET Systems Biology  
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

Zak Costello, Hector Garcia Martin
2018 npj Systems Biology and Applications  
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

Jan Müller, Martin Siemann-Herzberg, Ralf Takors
2020 Frontiers in Bioengineering and Biotechnology  
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

C. Hold, S. Panke
2009 Journal of the Royal Society Interface  
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

Kansuporn Sriyudthsak, Fumihide Shiraishi, Masami Yokota Hirai
2016 Frontiers in Molecular Biosciences  
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

Daniel Machado, Rafael S. Costa, Eugénio C. Ferreira, Isabel Rocha, Bruce Tidor
2012 Metabolic Engineering  
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

Hans-Michael Kaltenbach, Sotiris Dimopoulos, Jörg Stelling
2009 FEBS Letters  
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

Svetlana Volkova, Marta R. A. Matos, Matthias Mattanovich, Igor Marín de Mas
2020 Metabolites  
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

Yu Matsuoka, Kazuyuki Shimizu
2015 Bioresources and Bioprocessing  
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

M. Novak
2015 Chemical and Biochemical Engineering Quarterly  
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

Chiara Andreoni, Gianni Orsi, Carmelo De Maria, Francesca Montemurro, Giovanni Vozzi, Jonathan A. Coles
2014 PLoS ONE  
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

Kai Zhuang, Mounir Izallalen, Paula Mouser, Hanno Richter, Carla Risso, Radhakrishnan Mahadevan, Derek R Lovley
2010 The ISME Journal  
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

Joachim Almquist, Marija Cvijovic, Vassily Hatzimanikatis, Jens Nielsen, Mats Jirstrand
2014 Metabolic Engineering  
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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