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

Enzymes02:34

Enzymes

94.9K
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...
94.9K
Enzyme Kinetics01:19

Enzyme Kinetics

104.2K
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...
104.2K
Enzyme-linked Receptors01:00

Enzyme-linked Receptors

86.7K
Enzyme-linked receptors are proteins that act as both receptor and enzyme, activating multiple intracellular signals. This is a large group of receptors that include the receptor tyrosine kinase (RTK) family. Many growth factors and hormones bind to and activate the RTKs.
Neurotrophin (NT) receptors are a family of RTKs, including trkA, trkB, and trkC (tropomyosin-related kinase) receptors. TrkA is specific for nerve growth factor (NGF), neurotrophin-6, and neurotrophin-7. TrkB binds...
86.7K
Enzyme Inhibition01:30

Enzyme Inhibition

92.5K
Inhibitors are molecules that reduce enzyme activity by binding to the enzyme. In a normally functioning cell, enzymes are regulated by a variety of inhibitors. Drugs and other toxins can also inhibit enzymes. Some inhibitors bind to the enzyme’s active site, while others inhibit enzymatic activity by binding to other sites on the protein structure.
92.5K
Introduction to Enzymes01:22

Introduction to Enzymes

32.2K
The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that...
32.2K
Restriction Enzymes01:11

Restriction Enzymes

36.2K
Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
36.2K

You might also read

Related Articles

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

Sort by
Same author

Living bacterial reservoir computers for information processing and sensing.

Cell systems·2026
Same author

Active-learning-guided optimization of cell-free systems for genome-wide transcriptomic profiling reveals progressive layers of regulation.

Nature communications·2026
Same author

Living buildings with living electronics: towards biologically intelligent biohybrids.

Trends in biotechnology·2026
Same author

dAMN: a genome-scale neural-mechanistic hybrid model to predict bacterial growth dynamics.

Bioinformatics (Oxford, England)·2026
Same author

RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery.

Nucleic acids research·2025
Same author

Microbial computing: Review and Perspectives.

Biotechnology advances·2025
Same journal

Clinical Europium fluorescent based lectin assays for mucin O-glycomics.

Methods in enzymology·2026
Same journal

A dual-color FRET assay for detection and quantitative analysis of O-glycopeptidases.

Methods in enzymology·2026
Same journal

Evolutionary genetic approaches to analyze mucins.

Methods in enzymology·2026
Same journal

Ex vivo imaging and enzymatic analysis of intestinal mucus.

Methods in enzymology·2026
Same journal

Glyco-TRAPP: A real-time glycocalyx permeability assay for assessing transmembrane mucin barrier function in live and fixed tissues.

Methods in enzymology·2026
Same journal

Quantitative imaging approaches to capture structural and functional dynamics of colonic mucus in health and disease in situ.

Methods in enzymology·2026
See all related articles

Related Experiment Video

Updated: Feb 5, 2026

GENPLAT: an Automated Platform for Biomass Enzyme Discovery and Cocktail Optimization
11:38

GENPLAT: an Automated Platform for Biomass Enzyme Discovery and Cocktail Optimization

Published on: October 24, 2011

15.9K

Enzyme Discovery: Enzyme Selection and Pathway Design.

Pablo Carbonell1, Mathilde Koch2, Thomas Duigou2

  • 1Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.

Methods in Enzymology
|September 4, 2018
PubMed
Summary
This summary is machine-generated.

This study presents in silico methods for designing enzymatic pathways for chemical production. These protocols aid in automated synthetic biology, improving enzyme selection and pathway discovery for metabolic engineering.

Keywords:
Enzyme selectionPathway designRetrosynthesis

More Related Videos

Bacterial Peptide Display for the Selection of Novel Biotinylating Enzymes
10:43

Bacterial Peptide Display for the Selection of Novel Biotinylating Enzymes

Published on: October 3, 2019

6.4K
Multi-enzyme Screening Using a High-throughput Genetic Enzyme Screening System
08:10

Multi-enzyme Screening Using a High-throughput Genetic Enzyme Screening System

Published on: August 8, 2016

9.3K

Related Experiment Videos

Last Updated: Feb 5, 2026

GENPLAT: an Automated Platform for Biomass Enzyme Discovery and Cocktail Optimization
11:38

GENPLAT: an Automated Platform for Biomass Enzyme Discovery and Cocktail Optimization

Published on: October 24, 2011

15.9K
Bacterial Peptide Display for the Selection of Novel Biotinylating Enzymes
10:43

Bacterial Peptide Display for the Selection of Novel Biotinylating Enzymes

Published on: October 3, 2019

6.4K
Multi-enzyme Screening Using a High-throughput Genetic Enzyme Screening System
08:10

Multi-enzyme Screening Using a High-throughput Genetic Enzyme Screening System

Published on: August 8, 2016

9.3K

Area of Science:

  • Biotechnology
  • Synthetic Biology
  • Biochemistry

Background:

  • Engineering enzymatic pathways for chemical production is complex.
  • Selecting appropriate enzymes and viable pathways is a significant challenge.
  • Current methods lack automation and integration for iterative design.

Purpose of the Study:

  • To describe in silico design methods for engineering enzymatic production pathways.
  • To provide protocols for automated processes within a Design-Build-Test-Learn cycle.
  • To enhance synthetic biology and metabolic engineering for chemical production.

Main Methods:

  • Enzyme selection using a scoring approach considering sequence and reaction similarity.
  • Pathway design via retrosynthesis with selectable reaction rule specificity.
  • Clustering discovery and product identification for protocol reversal.

Main Results:

  • A method for identifying candidate enzyme sequences based on homology and reaction similarity.
  • A retrosynthesis-based method for discovering alternative biochemical pathways.
  • Integration of protocols into a pipeline for automated design.

Conclusions:

  • The described in silico methods facilitate automated synthetic biology design.
  • These protocols enhance metabolic engineering for efficient chemical production.
  • The developed toolbox supports iterative improvement of bioproduction pathways.