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Metabolic network

A metabolic network is the comprehensive system of interconnected biochemical reactions within a cell or organism that converts carbon and energy sources, along with electron donors and acceptors, into biomass, energy, and by-products essential for sustaining life.^[1] These networks encompass all enzymatic transformations of metabolites, forming a dynamic web that integrates physical processes, regulatory interactions, and physiological properties to maintain homeostasis.^[1] At its core, a metabolic network comprises metabolites as nodes—such as substrates, products, activators, and inhibitors—and directed edges representing chemical reactions catalyzed by enzymes, often organized into major pathways like glycolysis, the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation.^[2] These components enable the breakdown of nutrients (catabolism) to generate energy in the form of ATP and the synthesis of complex molecules (anabolism) for growth and repair, with fluxes regulated by environmental cues, genetic expression, and feedback mechanisms.^[3] Disruptions in network balance, such as enzyme deficiencies or pathway imbalances, underlie metabolic disorders like diabetes and contribute to phenomena like the Warburg effect in cancer cells, where glycolysis is upregulated even in oxygen-rich conditions.^[1] In systems biology, metabolic networks are modeled as graph structures exhibiting scale-free and small-world properties, where a few highly connected "hub" metabolites and enzymes link disparate pathways, conferring robustness and efficiency across organisms from bacteria to humans.^[4] Genome-scale reconstructions, such as the human Recon 2.2 model with 7,785 reactions and 1,675 genes or the Escherichia coli iJO1366 with 2,583 reactions and 1,366 genes, enable predictive simulations using techniques like flux balance analysis to forecast cellular behavior under varying conditions.^[1] These models have revolutionized applications in metabolic engineering for biofuel production, drug target identification in precision medicine, and synthetic biology for designing novel organisms.^[3] Evolutionarily, metabolic networks trace back over 3.5 billion years, with conserved core elements like the 146 protein families in the last bacterial common ancestor forming the foundational architecture that has adapted across domains of life while retaining universal structural motifs for error tolerance and evolvability.^[5] Ongoing research leverages high-throughput omics data and computational frameworks to map network rewiring in response to stress or disease, bridging fundamental biology with therapeutic innovation.^[6]

Fundamentals

Definition

A metabolic network is a biochemical system represented as a graph, in which nodes correspond to metabolites—small organic molecules such as amino acids, sugars, nucleotides, and lipids—and directed edges represent enzymatic reactions that transform one or more substrate metabolites into product metabolites.^[2]^[7] This graph-theoretic model captures the interconnected pathways of chemical conversions essential to cellular processes, with each edge denoting a specific biochemical reaction catalyzed by enzymes. Key characteristics of metabolic networks include their directed nature, reflecting the thermodynamic feasibility and directionality of reactions, where irreversible reactions form unidirectional edges and reversible ones allow bidirectional connections.^[8] Additionally, these networks are often weighted to account for stoichiometry, the quantitative coefficients in reaction equations that specify the molar ratios of reactants and products, enabling precise modeling of mass balance. Such structural features distinguish metabolic networks from undirected or unweighted graphs used in other contexts, emphasizing the flow of matter through stoichiometric constraints.^[9] Unlike signaling networks, which model information propagation through protein interactions and post-translational modifications, or gene regulatory networks, which depict transcriptional control among genes and transcription factors, metabolic networks exclusively focus on the catabolic breakdown and anabolic synthesis of small molecules via enzymatic catalysis.^[10]^[11] This delineation underscores the unique role of metabolic networks in representing material transformations rather than regulatory signaling or genetic control mechanisms.^[12]

Biological Significance

Metabolic networks play a central role in cellular energy production by orchestrating pathways such as glycolysis and oxidative phosphorylation, which generate adenosine triphosphate (ATP) to fuel essential life processes. In glycolysis, glucose is oxidized to pyruvate, yielding a net of two ATP molecules per glucose molecule under anaerobic conditions, providing rapid energy for cells in low-oxygen environments. Oxidative phosphorylation, occurring in the mitochondria of eukaryotic cells, couples the electron transport chain with ATP synthase to produce the majority of cellular ATP, approximately 30-32 molecules per glucose, through proton gradient-driven chemiosmosis. These interconnected pathways ensure efficient energy homeostasis across diverse physiological states.^[13]^[14] Beyond energy generation, metabolic networks facilitate biosynthesis, enabling the production of essential biomolecules like amino acids through dedicated pathways integrated within the broader network. For instance, the shikimate pathway and transamination reactions synthesize aromatic and non-essential amino acids, linking carbon skeletons from central metabolism to nitrogen assimilation for protein building blocks. This anabolic function supports growth, repair, and signaling, with disruptions leading to metabolic disorders.^[15] Metabolic networks maintain homeostasis by adapting to environmental perturbations via intricate feedback loops, including allosteric regulation of key enzymes. Allosteric effectors bind to sites distinct from the active site, modulating enzyme activity to balance metabolite levels; for example, phosphofructokinase in glycolysis is inhibited by high ATP or citrate, preventing overproduction during energy surplus. Such network-wide regulation enhances robustness, allowing cells to respond dynamically to nutrient availability or stress while preserving steady-state conditions.^[16] The evolutionary conservation of metabolic networks underscores their fundamental importance, with core pathways like the tricarboxylic acid (TCA) cycle present in both prokaryotes and eukaryotes, albeit with increasing complexity in higher organisms. The TCA cycle, comprising eight enzymes that oxidize acetyl-CoA to generate reducing equivalents for ATP production, originated early in evolution and remains highly preserved, reflecting selective pressure for efficient carbon metabolism. Variations, such as compartmentalization in eukaryotic mitochondria, have evolved to accommodate specialized functions without altering the core sequence.^[17]^[18]

Components and Structure

Metabolites and Reactions

Metabolites serve as the fundamental nodes in metabolic networks, representing small molecules that participate in biochemical transformations. They are broadly classified into substrates, which are the initial compounds consumed in reactions; products, the end compounds generated; intermediates, transient species formed and further processed within pathways; and cofactors, non-protein molecules that assist enzymes in catalysis and may undergo transient structural changes but are regenerated, such as ATP (hydrolyzed to ADP during energy transfer and regenerated) and NAD⁺ (reduced to NADH in redox reactions and reoxidized).^[19]^[20]^[21] Glucose exemplifies a central hub metabolite, acting as a primary substrate in carbon metabolism and connecting multiple pathways like glycolysis and the pentose phosphate pathway.^[22] Reactions form the directed edges connecting these metabolites, typically catalyzed by enzymes that lower activation energies and ensure specificity. Stoichiometry defines the quantitative relationships between reactants and products in these reactions, maintaining mass and charge balance across the network. For instance, the overall stoichiometry of glycolysis, a core catabolic pathway, is represented as:

\text{glucose} + 2\,\text{NAD}^{+} + 2\,\text{ADP} \rightarrow 2\,\text{pyruvate} + 2\,\text{NADH} + 2\,\text{ATP}

This equation highlights the conversion of one glucose molecule into two pyruvates, coupled with net energy gain in the form of ATP and reducing equivalents.^[13] Metabolic reactions are categorized into types such as transport reactions, which move metabolites across membranes without chemical alteration, and conversion reactions, which transform one metabolite into another through bond rearrangements or group transfers.^[19] Compartmentalization organizes metabolites and reactions within cellular organelles, enhancing efficiency and regulation by isolating incompatible processes. In eukaryotic cells, for example, oxidative respiration is confined to mitochondria, where metabolites like pyruvate are imported for Krebs cycle and electron transport chain activities, preventing interference with cytosolic glycolysis.^[23] This spatial segregation also facilitates cofactor recycling, such as NAD⁺/NADH shuttling across mitochondrial membranes.^[24]

Network Topology

Metabolic networks are typically represented as directed graphs, with metabolites serving as nodes and biochemical reactions as edges connecting substrates to products. These networks display a scale-free topology, where the degree distribution of nodes follows a power-law, meaning a few highly connected hubs dominate while most nodes have low connectivity. Prominent hubs include central metabolites like pyruvate, which participate in numerous reactions across pathways such as glycolysis, the tricarboxylic acid cycle, and amino acid synthesis, underscoring their pivotal role in network connectivity.^[25] A defining feature of metabolic network topology is its inherent modularity, organized into semi-independent functional modules corresponding to biochemical pathways, such as the glycolysis module that processes glucose to pyruvate. This modularity is hierarchical, with sub-modules nested within larger pathway clusters, enabling efficient information flow and functional specialization while integrating global connectivity. Scale-free properties and modularity coexist, as hubs often bridge modules, facilitating cross-pathway interactions.^[26] Key topological metrics reveal small-world characteristics in metabolic networks, including a high clustering coefficient—indicating dense local connections within modules—and a low average path length, typically around 2-4 in bacterial networks, which supports rapid metabolite propagation across the system. These properties contribute to robustness against perturbations, such as gene knockouts, where random removal of nodes minimally disrupts overall connectivity due to the scale-free design and redundant pathways. A notable structural motif enhancing this resilience is the bow-tie architecture observed in Escherichia coli metabolism, featuring a narrow "knot" of core intermediates flanked by broad input (nutrient uptake) and output (biomass production) layers, allowing the network to maintain function under varying conditions.^[27]^[28]^[29] Comparative analyses highlight topological distinctions between prokaryotic and eukaryotic metabolic networks. Prokaryotic networks, exemplified by bacteria like E. coli, are compact and unified within a single cytoplasmic compartment, resulting in shorter path lengths and higher interconnectivity among reactions. In contrast, eukaryotic networks are expanded and more fragmented due to subcellular compartmentalization into organelles such as mitochondria and peroxisomes, necessitating additional transport edges across membranes and increasing overall network diameter while amplifying modularity for specialized functions.^[30]^[31]

Reconstruction Methods

Genome-Scale Modeling

Genome-scale modeling refers to the process of constructing detailed computational representations of an organism's entire metabolic network, encompassing thousands of reactions derived primarily from genomic data. These models serve as structured knowledge bases that link genes to enzymes and biochemical transformations, enabling the simulation of metabolic behaviors at a systems level. The approach originated from efforts to map microbial metabolism comprehensively, evolving into a standardized methodology for diverse organisms. The reconstruction pipeline begins with an annotated genome, where open reading frames are identified and associated with enzymatic functions using databases like KEGG or BioCyc to infer potential reactions. This initial draft model, often automated, is then manually curated to ensure biochemical accuracy, including the addition of transport reactions and compartmentalization based on known cellular localization. Gap-filling addresses inconsistencies, such as missing reactions required for biomass production, by hypothesizing and validating alternative pathways through literature review or experimental data. This multi-step process typically involves iterative refinement to achieve a high-quality, predictive model. Key tools and frameworks facilitate this workflow, with the Constraint-Based Reconstruction and Analysis (COBRA) Toolbox being a cornerstone for building, curating, and validating genome-scale models in MATLAB or Python environments. For instance, the iJR904 model for Escherichia coli K-12, comprising 904 genes and 931 reactions, exemplifies early automated reconstruction followed by manual verification to predict metabolic fluxes accurately. Similarly, the human Recon3D model integrates 13,543 reactions, highlighting the scalability of these tools for complex eukaryotes. More recent efforts include the Human1 model (2020), unifying Recon and HMR series, and continued updates via community resources like the Metabolic Atlas as of 2025.^[32] Challenges in genome-scale modeling include handling incomplete genomic annotations, which can lead to gaps in pathway coverage, necessitating extensive literature mining for resolution. Organism-specific variations, such as tissue-specific isoforms in humans or strain differences in microbes, further complicate curation, often requiring community-driven updates to maintain model relevance and accuracy.

Data Integration Techniques

Data integration techniques play a crucial role in refining and validating metabolic network models by incorporating diverse biological datasets beyond initial genome-based reconstructions. These methods enhance model accuracy by constraining reaction fluxes and metabolite concentrations to align with experimental observations, thereby bridging the gap between static network structures and dynamic cellular behaviors. Omics data, in particular, provide quantitative insights into system states under specific conditions, allowing for context-specific adjustments to genome-scale metabolic models (GEMs).^[33] Incorporation of omics data involves mapping high-throughput measurements to network components. Metabolomics data, which quantify intracellular and extracellular metabolite concentrations, can be used to set bounds on reaction rates or identify active pathways by correlating metabolite levels with flux predictions. Transcriptomics data, capturing gene expression levels, inform enzyme availability by adjusting reaction upper limits proportional to mRNA abundances, assuming a correlation between transcription and catalytic capacity. Proteomics data offer direct measures of enzyme protein levels, enabling more precise flux constraints through integration with kinetic parameters or stoichiometric models; for instance, methods like large-scale Bayesian flux balance analysis (LBFBA) incorporate proteomic abundances to refine flux distributions in human models.^[34] These integrations often employ algorithms such as machine learning-based reconciliation or constraint-based optimization to reconcile multi-omics inputs, improving predictive power for phenotypic outcomes.^[33]^[34] Validation of integrated models relies on experimental benchmarks to ensure physiological relevance. Comparison with measured fluxes from 13C-labeling experiments, such as 13C-metabolic flux analysis (13C-MFA), tests model predictions against isotopomer distributions in key metabolites, quantifying intracellular fluxes with high resolution in microbial and mammalian systems; goodness-of-fit metrics, like chi-squared tests, confirm model fidelity when simulated labeling patterns match observed data. Thermodynamic constraints further validate spontaneity by enforcing negative Gibbs free energy changes (ΔG < 0) for irreversible reactions, using group contribution methods to estimate ΔG from metabolite concentrations and standard potentials, thus eliminating infeasible flux solutions in GEMs. These approaches collectively reduce solution spaces and enhance model robustness.^[35]^[36]^[37] Databases like KEGG, BioCyc, and MetaCyc serve as foundational resources for data integration by supplying curated reaction rules, pathway architectures, and stoichiometric coefficients. KEGG provides pathway maps and enzyme annotations that facilitate automated gap-filling in network reconstructions, integrating genomic and metabolomic data through its orthology-based mappings. BioCyc, encompassing organism-specific databases, offers detailed metabolic networks with evidence-linked reactions, enabling the import of omics data for flux prediction and validation via tools like the Metabolic Network Explorer. MetaCyc, as a non-redundant reference of experimentally verified pathways, supports de novo pathway prediction and integration by providing reaction directionality and thermodynamic data, aiding in the refinement of GEMs across diverse taxa. These resources ensure standardized, evidence-based inputs for multi-omics reconciliation.^[38]^[39]^[40]

Analysis Approaches

Flux Balance Analysis

Flux balance analysis (FBA) is a constraint-based computational method used to predict steady-state metabolic fluxes in genome-scale metabolic networks by solving a linear programming problem. It assumes that the metabolic system operates at quasi-steady state, where the concentrations of intracellular metabolites remain constant over time, leading to a balance of fluxes into and out of each metabolite. This approach relies on the stoichiometric matrix S, which represents the network's reactions and metabolites as derived from genome-scale reconstructions.^[41] The core of FBA involves optimizing an objective function, typically microbial growth rate or biomass production, subject to mass balance constraints and thermodynamic bounds on reaction fluxes. Mathematically, this is formulated as maximizing Z = c^T v, where v is the flux vector of dimension n (number of reactions), and c is a coefficient vector specifying the objective (e.g., c with 1 for the biomass reaction and 0 elsewhere). The primary constraint is the steady-state condition S v = 0, where S is the m \times n stoichiometric matrix (m metabolites). Additional constraints include lower and upper bounds on fluxes, lb \leq v \leq ub, often set to reflect reversibility, enzyme capacities, or experimental data (e.g., lb_i = 0 for irreversible reactions). The flux vector v quantifies the rates of metabolite transformation through the network, providing predictions of intracellular flows without requiring kinetic parameters. This formulation was first applied to quantitatively predict growth and by-product secretion in Escherichia coli.^[42]^[43] A key variant, parsimonious FBA (pFBA), extends standard FBA by incorporating a secondary objective to minimize total enzyme usage after maximizing the primary objective, assuming cellular economy in resource allocation. In pFBA, the optimization first maximizes growth \max c^T v subject to S v = 0 and bounds, then minimizes \min \sum |v_j| (or a weighted sum) over the optimal growth solutions, yielding a unique flux distribution closer to experimental observations. This hierarchical approach has been shown to align better with proteomic data in evolved E. coli strains.^[44] FBA is widely used for predicting the effects of genetic perturbations, such as gene knockouts, by setting the flux of associated reactions to zero and re-solving the optimization to assess impacts on the objective function. For instance, reactions whose knockout reduces growth to zero are deemed essential, enabling in silico essentiality analysis that matches experimental gene deletion phenotypes in E. coli with high accuracy. This capability has facilitated the identification of metabolic vulnerabilities across organisms.^[45] Recent advances (as of 2025) include hybrid approaches like NEXT-FBA, which integrate data-driven elements to enhance prediction accuracy with minimal input data requirements, and couplings of FBA with reactive transport modeling for simulating microbial metabolism in environmental contexts.^[46]^[47]

Dynamic Modeling

Dynamic modeling of metabolic networks employs kinetic approaches to capture the time-dependent evolution of metabolite concentrations and reaction fluxes, enabling simulations of how networks respond to perturbations such as changes in nutrient availability or enzyme activity. These models typically formulate the system using ordinary differential equations (ODEs) that describe the rate of change in metabolite concentrations as the net result of production and consumption rates across reactions. For a metabolite M_i, the governing equation is \frac{d[M_i]}{dt} = \sum v_{j \rightarrow i} - \sum v_{k \rightarrow i}, where v represents the reaction rates, aggregated over forward and reverse directions. Reaction rates are often derived from enzyme kinetics, with the Michaelis-Menten equation providing a foundational form: v = \frac{V_{\max} [S]}{K_m + [S]}, where V_{\max} is the maximum rate, [S] is substrate concentration, and K_m is the Michaelis constant. This framework allows for the prediction of transient behaviors, contrasting with steady-state methods by incorporating temporal dynamics and regulatory mechanisms like allosteric inhibition.^[48]^[49]^[50] Hybrid methods integrate kinetic ODEs with constraint-based approaches, such as flux balance analysis (FBA), to bridge multi-scale analyses where detailed kinetics are applied to subsystems while leveraging steady-state flux constraints for genome-scale coverage. In these hybrids, ODEs model dynamic compartments (e.g., signaling pathways), while FBA optimizes fluxes in larger metabolic networks, facilitating simulations of coupled processes like gene regulation and metabolism. A key challenge in developing such models is parameter estimation, which requires fitting kinetic constants (e.g., V_{\max}, K_m) to experimental time-course data; however, incomplete, noisy measurements often lead to identifiability issues and high computational demands for optimization. Techniques like ensemble modeling address this by generating parameter sets that fit data within statistical bounds, improving robustness.^[51]^[52]^[53] Applications of dynamic modeling include integrative simulations of insulin signaling and metabolic networks in diabetes, where ODE-based models capture how insulin receptor activation propagates through phosphorylation cascades to modulate glucose uptake and glycolysis. For instance, Sedaghat et al. developed an ODE model linking insulin binding to GLUT4 translocation and glycogen synthesis, revealing feedback loops that amplify insulin sensitivity. More recent extensions, such as those by Noguchi et al., incorporate metabolic fluxes to simulate insulin resistance states, predicting altered dynamics in hepatic gluconeogenesis under diabetic conditions. These models aid in understanding disease progression and testing therapeutic interventions by forecasting concentration trajectories over time.^[54]^[55] As of 2025, emerging developments include neural-mechanistic hybrid models that combine machine learning with ODE frameworks to improve phenotype predictions in metabolic networks, and integrations of multimodal large language models with mechanistic simulations for advanced glucose homeostasis modeling in diabetes.^[56]^[57]

Applications

Biotechnology and Engineering

Metabolic engineering leverages reconstructed metabolic networks to optimize microbial pathways for industrial production, enabling the redirection of carbon fluxes toward high-value biofuels and pharmaceuticals. In biofuel production, Saccharomyces cerevisiae has been extensively engineered to enhance ethanol yields from lignocellulosic feedstocks. For instance, strategies involving the overexpression of xylose transporters and isomerases, combined with evolutionary adaptation, have increased ethanol titers to over 50 g/L in engineered strains, surpassing wild-type capabilities on pentose sugars.^[58] Similarly, pathway optimization in Escherichia coli for artemisinin precursors, such as amorphadiene, has achieved production levels up to 25 g/L through mevalonate pathway engineering and cytochrome P450 integration, providing a scalable alternative to plant extraction for antimalarial drugs.^[59] Synthetic biology tools, particularly CRISPR-based genome editing, facilitate precise rerouting of metabolic fluxes by targeting key regulatory nodes in central carbon metabolism. For example, CRISPR-Cpf1 has been used to edit Corynebacterium glutamicum for succinate production from softwood hydrolysates, achieving titers of 39.67 g/L in fed-batch fermentation with a yield of 0.77 g succinate per g sugars consumed by deleting lactate dehydrogenase and overexpressing succinate export genes, reducing byproducts.^[60] These edits often integrate with flux balance analysis (FBA) to predict and validate flux redistributions, ensuring efficient resource allocation in industrial fermentations. Such approaches exemplify how synthetic designs can transform microbial chassis into tunable factories for organic acids used in bioplastics and chemicals. Recent advances as of 2024 include multi-omics integration in genome-scale models for engineering microbial consortia in biofuel production from lignocellulose, enhancing yields through host-microbe metabolic interactions.^[61] Case studies in industrial amino acid production highlight the impact of FBA-guided knockouts in Corynebacterium glutamicum, a cornerstone organism for L-lysine and L-glutamate manufacturing. Metabolic engineering strategies, including deletions to redirect flux in the aspartate pathway, have boosted L-lysine productivity to around 150 g/L with yields of approximately 0.5 g/g glucose in fed-batch processes.^[62] These optimizations, informed by genome-scale models, have scaled global production to millions of tons annually, demonstrating the translational power of metabolic network engineering from computational prediction to commercial bioreactors.^[63]

Biomedical Research

Metabolic network modeling has been instrumental in elucidating disease-specific alterations, particularly in cancer where the Warburg effect drives upregulated glycolysis even under aerobic conditions. This phenomenon, characterized by increased glucose uptake and lactate production, supports rapid proliferation and biosynthetic demands in tumor cells. Using flux balance analysis (FBA) within computational models, researchers have shown that a 20- to 40-fold increase in glycolytic flux (parameterized as p_G > 20) correlates with maximal tumor aggressiveness, enhanced acidity for immune evasion, and competitive glucose consumption in hypoxic microenvironments.^[64] In metabolic disorders like type 2 diabetes, FBA applied to genome-scale networks reveals flux imbalances, such as reduced glucose uptake and altered lipid oxidation in insulin-resistant states, as simulated in pancreatic and adipose tissue models. These imbalances highlight disrupted pathways in fed versus fasting conditions, aiding in biomarker identification for disease progression.^[65] Therapeutic applications leverage metabolic networks for drug target identification through simulated perturbations, exemplified by statins that inhibit 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) in the cholesterol biosynthesis pathway. Genome-scale reconstructions like Recon 1 integrate this enzyme into a coupled reaction network, predicting how statin inhibition reduces mevalonate production and downstream isoprenoid synthesis, thereby lowering cardiovascular risk while revealing potential side effects like myopathy.^[66] Pharmacometabolomics further advances personalized medicine by analyzing baseline metabolite profiles to forecast individual responses to drugs, linking variations in pathways like amino acid and lipid metabolism to efficacy and toxicity. For instance, pre-dose signatures in histidine and phenylalanine networks have predicted outcomes for therapies like acetaminophen, enabling tailored dosing to minimize adverse events.^[67] Human metabolic models, such as the Recon series, enable prediction of off-target drug effects by simulating gene knockouts or enzyme inhibitions within the network. In a renal context-specific Recon 1 model with 1,587 reactions, structural analysis via the SMAP algorithm identified off-targets for drugs like torcetrapib, such as PTGIS inhibition leading to prostaglandin imbalances and hypertension, validated against clinical data with high predictive accuracy (ROC analysis).^[68] Recent 2020s studies on COVID-19 have applied similar network approaches to uncover viral-induced rewiring, where SARS-CoV-2 reduces oxidative glutamine flux into the TCA cycle while boosting pyruvate carboxylase activity, enhancing mTORC1 signaling for replication. This metabolic shift, observed in infected cell lines and airway cultures, suggests vulnerabilities targetable by mTORC1 inhibitors like rapamycin, reducing viral loads without broad cytotoxicity.^[69] As of 2025, extensions of these models have been used to simulate metabolic changes in long COVID, identifying persistent flux alterations in energy metabolism for potential therapeutic targets.^[70]

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In this work, an incremental and iterative parameter estimation method is proposed that combines and iterates between two estimation phases.2 Methods · 3 Results · 3.2 The Glycolytic Pathway...
[50]
A mathematical model of metabolic insulin signaling pathways
We develop a mathematical model that explicitly represents many of the known signaling components mediating translocation of the insulin-responsive glucose ...
[51]
Mathematical Modeling of the Insulin Signal Transduction Pathway ...
Our current mathematical model of the insulin signal transduction pathway comprises a set of ordinary differential equations (ODEs) describing all known events ...
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From Saccharomyces cerevisiae to Ethanol: Unlocking the Power of ...
In this review, we focus on key examples of metabolic and evolutionary engineering for improved first- and second-generation S. cerevisiae bioethanol ...Missing: seminal | Show results with:seminal
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A Novel Semi-biosynthetic Route for Artemisinin Production Using ...
Mar 9, 2009 · The initial overexpression of wild-type P450BM3 in E. coli engineered to produce amorphadiene demonstrated no detectable oxidation activity ...
[54]
Combining orthogonal CRISPR and CRISPRi systems for genome ...
Jan 13, 2019 · The combination of orthogonal CRISPR/CRISPRi for metabolic engineering enhanced succinate production while inhibiting byproduct formation and ...2.2 Plasmid Construction · 2.5 Crispr-Mediated... · 3 Results
[55]
A new genome-scale metabolic model of Corynebacterium ...
Jun 30, 2017 · Corynebacterium glutamicum is an important platform organism for industrial biotechnology to produce amino acids, organic acids, bioplastic ...
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Metabolic engineering of Corynebacterium glutamicum aimed at ...
In this review we focus on the state of the art of metabolic engineering of C. glutamicum for utilization of alternative carbon sources.
[57]
Mathematical Modeling of the Function of Warburg Effect in Tumor ...
Jun 11, 2018 · A number of possible advantages of Warburg effect offered to cancer cells include enhanced biosynthetic activity, accelerated adenosine ...
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Network modeling approaches for metabolic diseases and diabetes
We present here a brief overview of network modeling methods applied to inborn errors of metabolism (IEM), systemic metabolic conditions (mainly diabetes),
[59]
Global reconstruction of the human metabolic network based on ...
3-Hydroxy-3-methylglutaryl-CoA reductase (Entrez Gene ID 3156), a primary metabolic target of the antilipidemic class of statin drugs, is in this coupled ...
[60]
Pharmacokinetics in Pharmacometabolomics - NIH
Nov 7, 2023 · Pharmacometabolomics is the most promising method for personalized medication. Within the domain of pharmacometabolomics, its synergy with ...
[61]
Drug Off-Target Effects Predicted Using Structural Analysis in the ...
Sep 23, 2010 · As well, the model predicts no effect on renal reabsorption or secretion for a number of other predicted off-target metabolic proteins.
[62]
SARS-CoV-2 infection rewires host cell metabolism and is ... - Nature
Mar 25, 2021 · We describe that SARS-CoV-2 infection rewires carbon entry into the TCA cycle, reducing oxidative glutamine metabolism and increasing pyruvate entry.