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

Improving Translational Accuracy02:07

Improving Translational Accuracy

11.7K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
11.7K
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

10.7K
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
10.7K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

3.8K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
3.8K
Ribosome Profiling02:24

Ribosome Profiling

3.6K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.6K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

11.0K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
11.0K
Conservation of Protein Domains02:26

Conservation of Protein Domains

3.2K
3.2K

You might also read

Related Articles

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

Sort by
Same author

From structure to function: conformational dynamics and differential binding of substrates in tri18 acyltransferase during harzianum A biosynthesis.

Journal of biomolecular structure & dynamics·2026
Same author

Harnessing artificial intelligence in plant breeding: innovations in digital phenotyping and breeding methodologies.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·2026
Same author

Coexistence of cicatricial alopecia and alopecia areata: A case series.

JAAD case reports·2026
Same author

Genome-wide association mapping and haplotype analysis reveal the genetic architecture of sodicity tolerance in bread wheat (Triticum aestivum L.).

Scientific reports·2026
Same author

Rural-Urban Inequalities in Lifetime Tobacco Consumption Among Middle-Aged and Older Adults in India: A Decomposition Analysis Using Survey-Weighted National Data.

Substance use & addiction journal·2026
Same author

Phenotypic profiling of neutrophils in acute <i>Clostridioides difficile</i> infection identifies a TNF-induced activation signature associated with epithelial damage.

Gut microbes·2026

Related Experiment Video

Updated: Aug 12, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

3.7K

CoDe: a web-based tool for codon deoptimization.

Divya Sharma1, Tracey Baas2, Aitor Nogales3

  • 1Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India.

Bioinformatics Advances
|January 26, 2023
PubMed
Summary
This summary is machine-generated.

We created CoDe, a web tool for codon deoptimization, to reduce protein expression by altering genetic sequences. This tool offers flexible options for targeted sequence modification and analysis.

More Related Videos

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

9.3K
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

5.2K

Related Experiment Videos

Last Updated: Aug 12, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

3.7K
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

9.3K
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

5.2K

Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Synthetic Biology

Background:

  • Codon usage bias influences protein expression levels.
  • Controlling gene expression is crucial for synthetic biology applications.

Purpose of the Study:

  • To develop a user-friendly web tool, CoDe (Codon Deoptimization), for reducing protein expression.
  • To enable targeted deoptimization of genetic sequences based on codon usage bias.

Main Methods:

  • Developed a web-based application for codon deoptimization.
  • Implemented algorithms to alter genetic sequences according to specified codon usage bias.
  • Integrated functionality to identify restriction enzyme sites in modified sequences.

Main Results:

  • CoDe successfully deoptimizes genetic sequences to reduce protein expression.
  • The tool allows for specific regional or amino acid-based deoptimization.
  • Restriction enzyme target sites are clearly indicated in both wild-type and deoptimized sequences.

Conclusions:

  • CoDe provides a flexible and accessible platform for researchers to control protein expression through codon deoptimization.
  • The tool's user-friendly interface and downloadable results facilitate its integration into various research workflows.