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

Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

7.2K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
7.2K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

2.5K
No description available
2.5K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

8.7K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
8.7K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

3.0K
No description available
3.0K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

2.6K
No description available
2.6K
Conserved Binding Sites01:49

Conserved Binding Sites

5.1K
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...
5.1K

You might also read

Related Articles

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

Sort by
Same author

A Chromatin Biology Assessment of AlphaFold3.

bioRxiv : the preprint server for biology·2026
Same author

Mechanism of USP21 autoinhibition and histone H2AK119 deubiquitination.

Science advances·2025
Same author

A needed nomenclature for nucleosomes.

Molecular cell·2025
Same author

An intrinsically disordered region of Ubp10 regulates its binding and activity on ubiquitinated histone substrates.

Protein science : a publication of the Protein Society·2025
Same author

Haspin kinase binds to a nucleosomal DNA supergroove.

Nature structural & molecular biology·2025
Same author

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Nucleic acids research·2024

Related Experiment Video

Updated: Jan 24, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.5K

Arm-domain interactions can provide high binding cooperativity.

Robert Schleif1, Cynthia Wolberger

  • 1Biology Department, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA. schleif@jhu.edu

Protein Science : a Publication of the Protein Society
|September 25, 2004
PubMed
Summary
This summary is machine-generated.

Protein arms mediate crucial biological interactions. A thermodynamic analysis shows these arms increase DNA binding affinity without requiring allosteric conformational changes, simplifying interaction models.

More Related Videos

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain
14:25

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Published on: December 12, 2017

18.8K
Polyelectrolyte Complex for Heparin Binding Domain Osteogenic Growth Factor Delivery
12:27

Polyelectrolyte Complex for Heparin Binding Domain Osteogenic Growth Factor Delivery

Published on: August 22, 2016

8.1K

Related Experiment Videos

Last Updated: Jan 24, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.5K
Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain
14:25

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Published on: December 12, 2017

18.8K
Polyelectrolyte Complex for Heparin Binding Domain Osteogenic Growth Factor Delivery
12:27

Polyelectrolyte Complex for Heparin Binding Domain Osteogenic Growth Factor Delivery

Published on: August 22, 2016

8.1K

Area of Science:

  • Molecular biology
  • Biophysics
  • Protein-protein interactions

Background:

  • Peptidyl arms linking protein domains are vital for biological interactions.
  • Yeast homeodomain proteins MAT alpha2 and MAT a1 form a high-affinity DNA-bound heterodimer.
  • A carboxyl-terminal arm from MAT alpha2 to MAT a1 was hypothesized to allosterically enhance MAT a1 DNA binding affinity.

Purpose of the Study:

  • To thermodynamically explain the large increase in DNA binding affinity observed in the MAT alpha2-MAT a1 interaction.
  • To challenge the necessity of allosteric conformational changes in mediating this binding affinity enhancement.

Main Methods:

  • Thermodynamic analysis of protein-protein and protein-DNA interactions.
  • Re-evaluation of existing experimental data in light of new structural information.

Main Results:

  • A thermodynamic model successfully accounts for the observed binding behavior without invoking allosteric conformational changes.
  • The proposed model explains the significant increase in DNA binding affinity through non-allosteric mechanisms.

Conclusions:

  • Allosteric conformational changes are not required to explain the enhanced DNA binding affinity in the MAT alpha2-MAT a1 system.
  • The thermodynamic framework provides a simpler explanation for arm-mediated binding affinity increases.
  • This analysis offers a valuable approach for studying similar arm interactions in other biological systems.