Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Operon Model01:23

Operon Model

337
The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
337
Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

22.3K
Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
22.3K
Biosynthesis in Bacteria01:24

Biosynthesis in Bacteria

144
Biosynthesis in bacteria is a fundamental anabolic process that generates essential macromolecules, including proteins, nucleic acids, lipids, and polysaccharides. These macromolecules are critical for cellular growth, replication, and function. The process is tightly regulated and energetically linked to catabolic pathways to ensure optimal resource utilization.Biosynthetic pathways begin with precursor metabolites such as pyruvate, acetyl-CoA, and glucose-6-phosphate derived from glycolysis,...
144
Enzyme Kinetics01:19

Enzyme Kinetics

99.9K
Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
99.9K
Enzymes02:34

Enzymes

83.6K
Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
83.6K
Introduction to Metabolism01:30

Introduction to Metabolism

581
Metabolism encompasses all biochemical reactions in a living organism, facilitating both the breakdown and synthesis of biomolecules. These metabolic processes are categorized into catabolic and anabolic pathways, which operate in a coordinated manner to ensure energy balance and cellular function.Catabolic Pathways and Energy ReleaseCatabolic pathways involve the breakdown of complex macromolecules such as carbohydrates, lipids, and proteins into smaller structures like monosaccharides, fatty...
581

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Striatal functional connectivity alterations in mild cognitive impairment subtypes defined by CSF A/T biomarkers.

Frontiers in aging neuroscience·2026
Same author

Towards the construction of a virtual yeast.

Nature·2026
Same author

Mechanochemistry-driven acid-free strategy for synergistic recycling of mixed spent lithium-ion batteries.

Waste management (New York, N.Y.)·2026
Same author

Comparative transcriptome analysis of Qinchuan and Wagyu cattle reveals lnc11599 as a negative regulator of intramuscular fat deposition.

BMC genomics·2026
Same author

Deep learning for predicting lumbar segmental instability using neutral lateral lumbar radiographs: a retrospective study.

European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society·2026
Same author

Single-nucleus transcriptomics dissects beef quality variation: coordinated reprogramming of myofiber metabolism, FAPs Fate, and ECM-vascular signaling.

BMC genomics·2026

Related Experiment Video

Updated: Oct 6, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

17.9K

ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model.

Zhitao Mao1, Xin Zhao1, Xue Yang1

  • 1Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Biomolecules
|January 21, 2022
PubMed
Summary
This summary is machine-generated.

Enzyme-constrained metabolic models improve predictions of microbial behavior by incorporating enzyme limitations. This approach accurately models *Escherichia coli* metabolism, revealing insights into overflow metabolism and guiding metabolic engineering efforts.

Keywords:
Escherichia colienzyme kineticsenzyme-constrained modeloverflow metabolismprotein subunit

More Related Videos

Author Spotlight: Tackling Challenges in Synthetic Cell Engineering
10:56

Author Spotlight: Tackling Challenges in Synthetic Cell Engineering

Published on: April 12, 2024

1.3K
Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

10.3K

Related Experiment Videos

Last Updated: Oct 6, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

17.9K
Author Spotlight: Tackling Challenges in Synthetic Cell Engineering
10:56

Author Spotlight: Tackling Challenges in Synthetic Cell Engineering

Published on: April 12, 2024

1.3K
Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

10.3K

Area of Science:

  • Systems Biology
  • Metabolic Engineering
  • Computational Biology

Background:

  • Genome-scale metabolic models (GEMs) are crucial for predicting microbial phenotypes.
  • Traditional GEMs often lack constraints, leading to inaccurate predictions.
  • Incorporating enzyme capacity limitations can refine metabolic modeling.

Purpose of the Study:

  • To develop a simplified workflow (ECMpy) for constructing enzyme-constrained metabolic network models (ECMs).
  • To create an ECM for *Escherichia coli* (ec*i*ML1515) with enzyme constraints.
  • To enhance the predictive accuracy of metabolic models for *E. coli*.

Main Methods:

  • Developed a Python-based workflow (ECMpy) for building ECMs.
  • Constructed ec*i*ML1515 by adding enzyme amount constraints to a standard GEM.
  • Considered protein subunit composition and automated enzyme kinetic parameter calibration.

Main Results:

  • Accurately predicted *E. coli*'s overflow metabolism, identifying redox balance as a key factor differentiating it from *Saccharomyces cerevisiae*.
  • Significantly improved growth rate predictions on 24 single-carbon sources compared to other *E. coli* ECMs.
  • Revealed a trade-off between enzyme usage efficiency and biomass yield under varying substrate consumption rates.

Conclusions:

  • Enzyme-constrained models offer improved simulation accuracy for cellular phenotypes.
  • ECMs provide more precise predictions under genetic perturbations.
  • This approach offers reliable guidance for metabolic engineering applications.