von Bertalanffy 1.0：一个 COBRA 工具箱扩展，用于对代谢模型进行热力学约束。
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.
机构信息
Science Institute, University of Iceland, Reykjavik, Iceland.
出版信息
Bioinformatics. 2011 Jan 1;27(1):142-3. doi: 10.1093/bioinformatics/btq607. Epub 2010 Nov 28.
Abstract
MOTIVATION
In flux balance analysis of genome scale stoichiometric models of metabolism, the principal constraints are uptake or secretion rates, the steady state mass conservation assumption and reaction directionality. Here, we introduce an algorithmic pipeline for quantitative assignment of reaction directionality in multi-compartmental genome scale models based on an application of the second law of thermodynamics to each reaction. Given experimental or computationally estimated standard metabolite species Gibbs energy and metabolite concentrations, the algorithms bounds reaction Gibbs energy, which is transformed to in vivo pH, temperature, ionic strength and electrical potential.
RESULTS
This cross-platform MATLAB extension to the COnstraint-Based Reconstruction and Analysis (COBRA) toolbox is computationally efficient, extensively documented and open source.
AVAILABILITY
摘要
动机
在基因组规模代谢物衡算模型的通量平衡分析中，主要的约束条件是摄取或分泌速率、稳态质量守恒假设和反应方向。在这里，我们基于热力学第二定律在每个反应中的应用，引入了一种用于多隔室基因组规模模型中定量分配反应方向的算法流程。给定实验或计算估计的标准代谢物种类吉布斯自由能和代谢物浓度，算法会限制反应吉布斯自由能，这会转化为体内 pH 值、温度、离子强度和电势能。
结果
这是一个跨平台的 MATLAB 扩展，用于基于约束的重构和分析 (COBRA) 工具箱，计算效率高，文档详尽，并且是开源的。
可用性
相似文献
1
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.von Bertalanffy 1.0：一个 COBRA 工具箱扩展，用于对代谢模型进行热力学约束。
Bioinformatics. 2011 Jan 1;27(1):142-3. doi: 10.1093/bioinformatics/btq607. Epub 2010 Nov 28.
2
Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli.基于约束的代谢模型中反应方向的定量分配：在大肠杆菌中的应用。
Biophys Chem. 2009 Dec;145(2-3):47-56. doi: 10.1016/j.bpc.2009.08.007. Epub 2009 Sep 1.
3
Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.在多隔室人体代谢重建中定量分配反应方向性。
Biophys J. 2012 Apr 18;102(8):1703-11. doi: 10.1016/j.bpj.2012.02.032.
4
COBRApy: COnstraints-Based Reconstruction and Analysis for Python.COBRApy：用于Python的基于约束的重建与分析
BMC Syst Biol. 2013 Aug 8;7:74. doi: 10.1186/1752-0509-7-74.
5
Elimination of thermodynamically infeasible loops in steady-state metabolic models.消除稳态代谢模型中的热力学不可行环。
Biophys J. 2011 Feb 2;100(3):544-553. doi: 10.1016/j.bpj.2010.12.3707.
6
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis.pyTFA 和 matTFA：基于热力学通量分析的 Python 包和 Matlab 工具箱。
Bioinformatics. 2019 Jan 1;35(1):167-169. doi: 10.1093/bioinformatics/bty499.
7
Cardinality optimization in constraint-based modelling: application to human metabolism.基于约束的建模中的基数优化：在人类代谢中的应用。
Bioinformatics. 2023 Sep 2;39(9). doi: 10.1093/bioinformatics/btad450.
8
Fast thermodynamically constrained flux variability analysis.快速热力学约束通量变异性分析。
Bioinformatics. 2013 Apr 1;29(7):903-9. doi: 10.1093/bioinformatics/btt059. Epub 2013 Feb 6.
9
Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.稳态代谢的综合化学计量学、热力学和动力学建模。
J Theor Biol. 2010 Jun 7;264(3):683-92. doi: 10.1016/j.jtbi.2010.02.044. Epub 2010 Mar 15.
10
FastMM: an efficient toolbox for personalized constraint-based metabolic modeling.FastMM：一个用于个性化约束代谢建模的高效工具包。
BMC Bioinformatics. 2020 Feb 21;21(1):67. doi: 10.1186/s12859-020-3410-4.
引用本文的文献
1
Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model.在体外多发性骨髓瘤模型中代谢网络的数学重建。
PLoS Comput Biol. 2023 Sep 15;19(9):e1011374. doi: 10.1371/journal.pcbi.1011374. eCollection 2023 Sep.
2
eQuilibrator 3.0: a database solution for thermodynamic constant estimation.eQuilibrator 3.0：热力学常数估算的数据库解决方案。
Nucleic Acids Res. 2022 Jan 7;50(D1):D603-D609. doi: 10.1093/nar/gkab1106.
3
Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of .使用基于最大熵的模拟预测代谢物浓度、速率常数和翻译后调控及其在……中心代谢中的应用
Processes (Basel). 2018 Jun;6(6). doi: 10.3390/pr6060063. Epub 2018 May 28.
4
Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions.适用于中温生长条件下基于热力学的计量衡算模型的物理化学和代谢约束。
PLoS Comput Biol. 2021 Jan 25;17(1):e1007694. doi: 10.1371/journal.pcbi.1007694. eCollection 2021 Jan.
5
iMet: A graphical user interface software tool to merge metabolic networks.iMet：一种用于合并代谢网络的图形用户界面软件工具。
Heliyon. 2019 Jun 19;5(6):e01766. doi: 10.1016/j.heliyon.2019.e01766. eCollection 2019 Jun.
6
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.使用 COBRA Toolbox v.3.0 创建和分析基于生化约束的模型。
Nat Protoc. 2019 Mar;14(3):639-702. doi: 10.1038/s41596-018-0098-2.
7
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis.pyTFA 和 matTFA：基于热力学通量分析的 Python 包和 Matlab 工具箱。
Bioinformatics. 2019 Jan 1;35(1):167-169. doi: 10.1093/bioinformatics/bty499.
8
Reply to "Challenges in modeling the human gut microbiome".对《人类肠道微生物群建模中的挑战》的回应
Nat Biotechnol. 2018 Aug 6;36(8):686-691. doi: 10.1038/nbt.4212.
9
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota.从网络分析到人类肠道微生物群的功能代谢建模
mSystems. 2018 Mar 27;3(3). doi: 10.1128/mSystems.00209-17. eCollection 2018 May-Jun.
10
Model-based metabolism design: constraints for kinetic and stoichiometric models.基于模型的代谢设计：动力学和计量模型的约束条件。
Biochem Soc Trans. 2018 Apr 17;46(2):261-267. doi: 10.1042/BST20170263. Epub 2018 Feb 22.
本文引用的文献
1
A protocol for generating a high-quality genome-scale metabolic reconstruction.生成高质量基因组尺度代谢重建的方案。
Nat Protoc. 2010 Jan;5(1):93-121. doi: 10.1038/nprot.2009.203. Epub 2010 Jan 7.
2
Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli.基于约束的代谢模型中反应方向的定量分配：在大肠杆菌中的应用。
Biophys Chem. 2009 Dec;145(2-3):47-56. doi: 10.1016/j.bpc.2009.08.007. Epub 2009 Sep 1.
3
Group contribution method for thermodynamic analysis of complex metabolic networks.复杂代谢网络热力学分析的基团贡献法
Biophys J. 2008 Aug;95(3):1487-99. doi: 10.1529/biophysj.107.124784.
4
LibSBML: an API library for SBML.LibSBML：一个用于系统生物学标记语言（SBML）的应用程序编程接口库。
Bioinformatics. 2008 Mar 15;24(6):880-1. doi: 10.1093/bioinformatics/btn051. Epub 2008 Feb 5.
5
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.针对大肠杆菌K-12 MG1655的全基因组规模代谢重建，该重建考虑了1260个开放阅读框和热力学信息。
Mol Syst Biol. 2007;3:121. doi: 10.1038/msb4100155. Epub 2007 Jun 26.
6
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.基于约束模型的细胞代谢定量预测：COBRA工具箱
Nat Protoc. 2007;2(3):727-38. doi: 10.1038/nprot.2007.99.
7
Biochemical thermodynamics: applications of Mathematica.生化热力学：Mathematica软件的应用
Methods Biochem Anal. 2006;48:1-458.
Zotero 插件