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,...

You might also read

Related Articles

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

Sort by

Same author

NLRP3 haploinsufficiency unmasks a compensatory NLRP1-NLRP3 interaction that drives accelerated aging in mice.

Science advances·2026

Same author

A robotic and high-throughput X-ray micro-computed tomography workflow.

Journal of synchrotron radiation·2026

Same author

PANCS-spec-Binders: A system for rapidly discovering isoform- or epitope-specific binders.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Reverse-engineering amyloid strains with generative protein design.

bioRxiv : the preprint server for biology·2026

Same author

Phylogenetic Analysis and Structural Evaluation of <i>Staphylococcus aureus</i> Serine-Aspartate Repeat-Containing Protein D with a Focus on Periprosthetic Joint Infection.

bioRxiv : the preprint server for biology·2026

Same author

Cysteines are critical determinants of spontaneous and seeded tau aggregation in cells.

Research square·2026

Search research articles

Related Experiment Video

Updated: May 26, 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

Mapping Hsp104 interactions using cross-linking mass spectrometry.

Kinga Westphal^1,2, Karolina Michalska^3,4, Andrzej Joachimiak^3,4,5

¹Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.

|February 24, 2025

Summary

Cross-linking mass spectrometry reveals how Hsp104 molecular machines change shape with ATP and bind substrates like PCSK9. This method helps understand protein disaggregase function and interactions within their central channel.

Keywords:

Hsp104 PCSK9 XL‐MS protein–protein interactions

More Related Videos

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

Published on: September 24, 2012

Defining Hsp33's Redox-regulated Chaperone Activity and Mapping Conformational Changes on Hsp33 Using Hydrogen-deuterium Exchange Mass Spectrometry

Defining Hsp33's Redox-regulated Chaperone Activity and Mapping Conformational Changes on Hsp33 Using Hydrogen-deuterium Exchange Mass Spectrometry

Published on: June 7, 2018

Related Experiment Videos

Last Updated: May 26, 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

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

Published on: September 24, 2012

Defining Hsp33's Redox-regulated Chaperone Activity and Mapping Conformational Changes on Hsp33 Using Hydrogen-deuterium Exchange Mass Spectrometry

Defining Hsp33's Redox-regulated Chaperone Activity and Mapping Conformational Changes on Hsp33 Using Hydrogen-deuterium Exchange Mass Spectrometry

Published on: June 7, 2018

Area of Science:

Biochemistry
Structural Biology
Molecular Biophysics

Background:

AAA+ protein disaggregases, like Hsp104, are crucial for protein homeostasis, involving folding, disaggregation, and DNA processing.
Recent structural studies using cryo-electron microscopy (cryo-EM) reveal conformational changes critical for AAA+ machine function.
Understanding substrate interactions and ATP-induced conformational dynamics is key to elucidating their mechanisms.

Purpose of the Study:

To investigate ATP-dependent conformational changes in the Hsp104 disaggregase using cross-linking mass spectrometry (XL-MS).
To map substrate interactions, specifically with PCSK9, within the central channel of Hsp104.
To develop and apply robust XL-MS methods for analyzing homo-oligomeric protein machines.

Main Methods:

Application of various cross-linking reagents to Hsp104 from *Calcarisporiella thermophila*.
Integration of XL-MS data with existing X-ray and cryo-EM structures.
Development of an analysis pipeline to distinguish intra- and inter-subunit contacts in the hexameric Hsp104.

Main Results:

Identification of cross-links that distinguish ATP-hydrolysis competent conformations from defective mutants.
Mapping of inter-subunit contacts within the Hsp104 hexamer.
Detection of Hsp104-PCSK9 contacts along the central channel, suggesting translocation interactions.

Conclusions:

XL-MS provides a robust method for interpreting conformational dynamics and substrate binding in AAA+ molecular machines.
The study elucidates how ATP binding influences Hsp104 conformation and facilitates substrate interaction.
This approach enables the integration of experimental data with modeling for studying complex protein assemblies.