Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

Ligand Binding Sites

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...

Conserved Binding Sites

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...

Ligand Binding and Linkage

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...

Nuclear Binding Energy

Nuclear Binding Energy

The difference between the calculated and experimentally measured masses is known as the mass defect of the atom. In the case of helium-4, the mass defect indicates a “loss” in mass of 4.0331 amu – 4.0026 amu = 0.0305 amu. The loss in mass accompanying the formation of an atom from protons, neutrons, and electrons is due to the conversion of that mass into energy that is evolved as the atom forms. The nuclear binding energy is the energy produced when the atoms’ nucleons are bound...

You might also read

Related Articles

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

Sort by

Same author

Refinement of amino-acid conformation vs. difference density maps in time-resolved serial femtosecond crystallography data analysis.

FEBS open bio·2026

Same author

Hypoxia Upregulation of BACH1 Aggravates Pulmonary Hypertension Through TGFBR2/SMAD Pathways.

Circulation·2026

Same author

Label free multimodal optical imaging of metabolic heterogeneity in aging by integrating SRS, MPF, FLIM, and SHG.

bioRxiv : the preprint server for biology·2026

Same author

Metabolic thermodynamics: pertinent reference state and energy potentials.

The FEBS journal·2026

Same author

USP10 Deubiquitinates MTX2 to Suppress cGAS-STING Signaling in MI.

Circulation research·2026

Same author

Paeonol alleviates pulmonary arterial hypertension by activation of BRCC3.

Phytomedicine : international journal of phytotherapy and phytopharmacology·2026

Search research articles

Related Experiment Video

Updated: Feb 3, 2026

Pull-down of Calmodulin-binding Proteins

Pull-down of Calmodulin-binding Proteins

Published on: January 23, 2012

Binding and Enhanced Binding between Key Immunity Proteins TRAF6 and TIFA.

Wei-Cheng Huang¹, Jiahn-Haur Liao¹, Tzu-Chun Hsiao¹

¹Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan.

Chembiochem : a European Journal of Chemical Biology

|November 1, 2018

Summary

Tumor necrosis factor receptor associated factor (TRAF)-interacting protein (TIFA) directly binds TRAF6, a key regulator of innate immunity. This study reveals the structural basis for TIFA-TRAF6 interaction, enhancing our understanding of immune response pathways.

Keywords:

biological activity mutagenesis noncovalent interactions protein-protein interactions structure elucidation

More Related Videos

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Related Experiment Videos

Last Updated: Feb 3, 2026

Pull-down of Calmodulin-binding Proteins

Pull-down of Calmodulin-binding Proteins

Published on: January 23, 2012

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Area of Science:

Molecular Biology
Immunology
Structural Biology

Background:

TIFA is a critical regulator of NF-κB activation and innate immunity.
Its precise mechanism, particularly interaction with TRAF6, remains largely uncharacterized.

Purpose of the Study:

To investigate and provide structural evidence for the direct interaction between TIFA and TRAF6.
To elucidate how this interaction can be modulated.

Main Methods:

Co-immunoprecipitation assays to confirm TIFA-TRAF6 binding.
Site-directed mutagenesis to create TIFA double mutant (S174Q/M179D).
X-ray crystallography to determine the structure of TRAF6-TIFA peptide complexes.

Main Results:

Direct, albeit weak, binding was observed between TIFA and the TRAF domain of TRAF6.
A TIFA double mutant (S174Q/M179D) showed enhanced binding to TRAF6.
Structural analysis revealed salt-bridge formation crucial for the TIFA-TRAF6 interaction.

Conclusions:

This study provides direct evidence and a structural basis for the TIFA-TRAF6 interaction.
The findings highlight a mechanism for modulating TIFA-TRAF6 binding, impacting innate immune signaling.