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

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

Tagging and Fusion Proteins

Tagging and Fusion Proteins

Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...

You might also read

Related Articles

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

Sort by

Same author

Protein phosphatase 2 phosphatase activator (PTPA) promotes oncogene-induced senescence and carboplatin response in human malignant pleural mesothelioma cells.

Cellular oncology (Dordrecht, Netherlands)·2026

Same author

Genetically encoding ε-N-methacryllysine into proteins in live cells.

Nature communications·2025

Same author

Intrinsic temperature increase drives lipid metabolism towards ferroptosis evasion and chemotherapy resistance in pancreatic cancer.

Nature communications·2024

Same author

K128 ubiquitination constrains RAS activity by expanding its binding interface with GAP proteins.

The EMBO journal·2024

Same author

TIPRL1 and its ATM-dependent phosphorylation promote radiotherapy resistance in head and neck cancer.

Cellular oncology (Dordrecht, Netherlands)·2023

Same author

Spatial Mechano-Signaling Regulation of GTPases through Non-Degradative Ubiquitination.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2023

Search research articles

Related Experiment Video

Updated: Sep 15, 2025

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Enrichable cross-linkers for mapping direct protein interactions.

Ting Wu^1,2,3, Hang-Xu Zhou^2,3, Jing Tian^4,5

¹Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China.

|July 15, 2025

Summary

This summary is machine-generated.

New cross-linkers, ePDES1 and ePDES2, enable efficient identification of hundreds of directly interacting proteins within cellular compartments like the nucleus and mitochondria using cross-linking mass spectrometry.

Keywords:

Cross-linking mass spectrometry Direct protein interaction IMAC Subcellular organelles Thioredoxin

More Related Videos

Isolation of Labile Multi-protein Complexes by in vivo Controlled Cellular Cross-Linking and Immuno-magnetic Affinity Chromatography

Isolation of Labile Multi-protein Complexes by in vivo Controlled Cellular Cross-Linking and Immuno-magnetic Affinity Chromatography

Published on: March 9, 2010

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Related Experiment Videos

Last Updated: Sep 15, 2025

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Isolation of Labile Multi-protein Complexes by in vivo Controlled Cellular Cross-Linking and Immuno-magnetic Affinity Chromatography

Isolation of Labile Multi-protein Complexes by in vivo Controlled Cellular Cross-Linking and Immuno-magnetic Affinity Chromatography

Published on: March 9, 2010

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Area of Science:

Biochemistry
Proteomics
Cell Biology

Background:

Investigating protein functions in specific subcellular environments is critical.
Cross-linking mass spectrometry (MS) maps protein interactomes by identifying inter-protein cross-links.
Identifying low-abundance inter-protein cross-linked peptides remains a significant challenge.

Purpose of the Study:

To develop novel chemical cross-linkers for enhanced enrichment of cross-linked peptides.
To improve the identification of direct protein-protein interactions in complex biological samples.

Main Methods:

Chemical synthesis of novel cross-linkers: ePDES1 and ePDES2.
Incorporation of alkyne and azide-phosphate functionalities for click chemistry-based enrichment.
Application of cross-linking mass spectrometry for interactome mapping.

Main Results:

Successful synthesis and application of ePDES1 and ePDES2 cross-linkers.
High-quality cross-linking spectra obtained using the novel methods.
Identification of hundreds of directly interacting proteins and substrates.

Conclusions:

The developed cross-linking methods significantly enhance the identification of protein interactions.
These methods enable the mapping of protein interactomes in specific subcellular locations, such as the nucleus and mitochondria.
The study successfully identified direct protein interactors and substrates of thioredoxins.