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

Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

You might also read

Related Articles

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

Sort by
Same author

Suppressing the Aberrant Transcriptional Functionality of EWS::FLI1 Oncoprotein by Designer polyQ Fusions with Its Homologous Peptides.

Biomedicines·2026
Same author

[Ilizarov technique combined with segmented removal of bone cement for the treatment of composite defects of tibia and soft tissues of skin].

Zhongguo gu shang = China journal of orthopaedics and traumatology·2026
Same author

PolyQ Expansion Controls Biomolecular Condensation and Aggregation of the N-Terminal Fragments of Ataxin-2.

International journal of molecular sciences·2025
Same author

The CDK9-targeting degrader PO-8 alleviates LPS-induced inflammation by inhibiting JAK-STAT signaling in vitro and in vivo.

Biochemical pharmacology·2025
Same author

A designer polyQ fusion protein modulates NF-κB signaling by sequestering P65/RelA into aggregates.

Scientific reports·2025
Same author

Design, synthesis, and biological evaluation of quinolinyl-ureido-phenyl-hydrazide derivatives and quinolinyl-hydrazide derivatives as anticancer agents targeting Nur77-mediated ferroptosis.

European journal of medicinal chemistry·2025

Related Experiment Video

Updated: May 20, 2026

In Vitro Analysis of E3 Ubiquitin Ligase Function
06:06

In Vitro Analysis of E3 Ubiquitin Ligase Function

Published on: May 14, 2021

Structural aspects of ubiquitin binding specificities.

Qing-Shan Fu1, Ai-Xin Song, Hong-Yu Hu

  • 1Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

Current Protein & Peptide Science
|July 21, 2012
PubMed
Summary

Ubiquitin-binding domains (UBDs) recognize ubiquitin (Ub) and its related proteins, controlling cellular events. Understanding UBD structure-specificity is key to deciphering ubiquitination and deubiquitination processes.

More Related Videos

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
11:54

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Ubiquitin Chain Analysis by Parallel Reaction Monitoring
08:33

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Published on: June 17, 2020

Related Experiment Videos

Last Updated: May 20, 2026

In Vitro Analysis of E3 Ubiquitin Ligase Function
06:06

In Vitro Analysis of E3 Ubiquitin Ligase Function

Published on: May 14, 2021

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
11:54

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Ubiquitin Chain Analysis by Parallel Reaction Monitoring
08:33

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Published on: June 17, 2020

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Background:

  • Ubiquitin (Ub) and Ub-like proteins are crucial in eukaryotic cellular processes.
  • Numerous Ubiquitin-Binding Domains (UBDs) with varying affinities for Ub and its homologues have been identified.
  • These interactions are fundamental for cellular signaling and protein degradation pathways.

Purpose of the Study:

  • To review recent advancements in understanding the structure-based binding specificities of UBDs.
  • To highlight the importance of these specificities in regulating ubiquitination and deubiquitination.
  • To elucidate the intricate mechanisms of Ub recognition and cellular regulation.

Main Methods:

  • Literature review of recent structural biology studies.
  • Analysis of UBD-Ub complex structures.
  • Synthesis of data on binding specificities and affinities.

Main Results:

  • Detailed structural insights into various UBDs (UBA, CUE, UIM, ZnF, Pru) and their interactions with Ub.
  • Demonstration of how binding specificities dictate cellular functions and protein targeting.
  • Understanding of the molecular basis for Ub recognition by different UBDs.

Conclusions:

  • Structure-based specificities of UBDs are fundamental for orchestrating ubiquitination and deubiquitination.
  • Deciphering these specificities provides critical insights into cellular regulatory mechanisms.
  • This knowledge is essential for understanding diverse cellular events controlled by the Ub system.