Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models
出版年份 2021 全文链接
标题
Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models
作者
关键词
Genome-scale metabolic network models, Thermodynamics, Enzymatic constraints, Escherichia coli, Pathway feasibility
出版物
METABOLIC ENGINEERING
Volume 67, Issue -, Pages 133-144
出版商
Elsevier BV
发表日期
2021-06-24
DOI
10.1016/j.ymben.2021.06.005
参考文献
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注意：仅列出部分参考文献，下载原文获取全部文献信息。- In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing
- (2021) Yu Wang et al. Nature Communications
- Automatic construction of metabolic models with enzyme constraints
- (2020) Pavlos Stephanos Bekiaris et al. BMC BIOINFORMATICS
- Growth of E. coli on formate and methanol via the reductive glycine pathway
- (2020) Seohyoung Kim et al. Nature Chemical Biology
- The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
- (2020) Pierre Salvy et al. Nature Communications
- An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli
- (2020) Hai He et al. METABOLIC ENGINEERING
- High-throughput enrichment of temperature-sensitive argininosuccinate synthetase for two-stage citrulline production in E. coli
- (2020) Thorben Schramm et al. METABOLIC ENGINEERING
- Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers
- (2020) David Heckmann et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- BRENDA, the ELIXIR core data resource in 2021: new developments and updates
- (2020) Antje Chang et al. NUCLEIC ACIDS RESEARCH
- Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains
- (2019) Ilaria Massaiu et al. Microbial Cell Factories
- Constructing a synthetic pathway for acetyl-coenzyme A from one-carbon through enzyme design
- (2019) Xiaoyun Lu et al. Nature Communications
- Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli
- (2019) Daniel Charlier et al. AMINO ACIDS
- Novel biosynthesis of L-malate based on overflow metabolism in Escherichia coli
- (2019) Jiangfeng Ma et al. BIOCHEMICAL ENGINEERING JOURNAL
- Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum
- (2019) Satyakam Dash et al. METABOLIC ENGINEERING
- Energy metabolism controls phenotypes by protein efficiency and allocation
- (2019) Yu Chen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Development of an engineered carbamoyl phosphate synthetase with released sensitivity to feedback inhibition by site-directed mutation and casting error-prone PCR
- (2019) Su Shen et al. ENZYME AND MICROBIAL TECHNOLOGY
- Metabolic control analysis of L-tryptophan production with Escherichia coli based on data from short-term perturbation experiments
- (2019) Julia Tröndle et al. JOURNAL OF BIOTECHNOLOGY
- Systematic design and in vitro validation of novel one-carbon assimilation pathways
- (2019) Xue Yang et al. METABOLIC ENGINEERING
- Exploring the combinatorial space of complete pathways to chemicals
- (2018) Lin Wang et al. BIOCHEMICAL SOCIETY TRANSACTIONS
- Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method
- (2018) Bin Du et al. BIOPHYSICAL JOURNAL
- Modeling the multi-scale mechanisms of macromolecular resource allocation
- (2018) Laurence Yang et al. CURRENT OPINION IN MICROBIOLOGY
- Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential
- (2018) Johannes Asplund-Samuelsson et al. METABOLIC ENGINEERING
- Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield
- (2018) Meike T. Wortel et al. PLoS Computational Biology
- COBRAme: A computational framework for genome-scale models of metabolism and gene expression
- (2018) Colton J. Lloyd et al. PLoS Computational Biology
- A Bird’s-Eye View of Enzyme Evolution: Chemical, Physicochemical, and Physiological Considerations
- (2018) Dan Davidi et al. CHEMICAL REVIEWS
- OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli
- (2018) Oliver Hädicke et al. PLoS Computational Biology
- Design and in vitro realization of carbon-conserving photorespiration
- (2018) Devin L. Trudeau et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Estimating Metabolic Equilibrium Constants: Progress and Future Challenges
- (2018) Bin Du et al. TRENDS IN BIOCHEMICAL SCIENCES
- Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
- (2018) David Heckmann et al. Nature Communications
- Engineering Escherichia coli for poly-(3-hydroxybutyrate) production guided by genome-scale metabolic network analysis
- (2017) Yangyang Zheng et al. ENZYME AND MICROBIAL TECHNOLOGY
- Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints
- (2017) Benjamín J Sánchez et al. Molecular Systems Biology
- iML1515, a knowledgebase that computes Escherichia coli traits
- (2017) Jonathan M Monk et al. NATURE BIOTECHNOLOGY
- Coupling between d-3-phosphoglycerate dehydrogenase and d-2-hydroxyglutarate dehydrogenase drives bacterial l-serine synthesis
- (2017) Wen Zhang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Metabolic Models of Protein Allocation Call for the Kinetome
- (2017) Avlant Nilsson et al. Cell Systems
- Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements
- (2016) Dan Davidi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization
- (2016) Elad Noor et al. PLoS Computational Biology
- Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes
- (2016) Jonathan M. Monk et al. Cell Systems
- Overflow metabolism in Escherichia coli results from efficient proteome allocation
- (2015) Markus Basan et al. NATURE
- Metabolic engineering ofCorynebacterium glutamicumfor the production of L-ornithine
- (2014) Seo Yun Kim et al. BIOTECHNOLOGY AND BIOENGINEERING
- Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
- (2014) Joanne K Liu et al. BMC Systems Biology
- Constraint-based models predict metabolic and associated cellular functions
- (2014) Aarash Bordbar et al. NATURE REVIEWS GENETICS
- Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
- (2014) Elad Noor et al. PLoS Computational Biology
- Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins
- (2013) Kaspar Valgepea et al. Molecular BioSystems
- Glycolytic strategy as a tradeoff between energy yield and protein cost
- (2013) A. Flamholz et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Biosynthesis of ethylene glycol in Escherichia coli
- (2012) Huaiwei Liu et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes
- (2012) Arren Bar-Even et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
- An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
- (2012) Elad Noor et al. BIOINFORMATICS
- PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life
- (2012) M. Wang et al. MOLECULAR & CELLULAR PROTEOMICS
- Systems metabolic engineering of microorganisms for natural and non-natural chemicals
- (2012) Jeong Wook Lee et al. Nature Chemical Biology
- Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters
- (2012) Roi Adadi et al. PLoS Computational Biology
- Recommendations for terminology and databases for biochemical thermodynamics
- (2011) Robert A. Alberty et al. BIOPHYSICAL CHEMISTRY
- Recent advances in reconstruction and applications of genome-scale metabolic models
- (2011) Tae Yong Kim et al. CURRENT OPINION IN BIOTECHNOLOGY
- eQuilibrator--the biochemical thermodynamics calculator
- (2011) A. Flamholz et al. NUCLEIC ACIDS RESEARCH
- Network thermodynamics in the post-genomic era
- (2010) Keng Cher Soh et al. CURRENT OPINION IN MICROBIOLOGY
- What is flux balance analysis?
- (2010) Jeffrey D Orth et al. NATURE BIOTECHNOLOGY
- Shifts in growth strategies reflect tradeoffs in cellular economics
- (2009) Douwe Molenaar et al. Molecular Systems Biology
- Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
- (2009) Bryson D Bennett et al. Nature Chemical Biology
- How mitochondria produce reactive oxygen species
- (2008) Michael P. Murphy BIOCHEMICAL JOURNAL
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