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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 polypeptide...

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Related Experiment Video

Updated: May 8, 2026

Deacetylation Assays to Unravel the Interplay between Sirtuins (SIRT2) and Specific Protein-substrates

Deacetylation Assays to Unravel the Interplay between Sirtuins (SIRT2) and Specific Protein-substrates

Published on: February 27, 2016

Generating mammalian sirtuin tools for protein-interaction analysis.

Kathleen A Hershberger¹, Jonathan Motley, Matthew D Hirschey

¹Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA.

Methods in Molecular Biology (Clifton, N.J.)

|September 10, 2013

Summary

This summary is machine-generated.

Researchers developed a new method to identify sirtuin protein interactors. This technique helps pinpoint sirtuin targets, aiding research into aging, cancer, and metabolism.

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Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Published on: July 6, 2014

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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Last Updated: May 8, 2026

Deacetylation Assays to Unravel the Interplay between Sirtuins (SIRT2) and Specific Protein-substrates

Deacetylation Assays to Unravel the Interplay between Sirtuins (SIRT2) and Specific Protein-substrates

Published on: February 27, 2016

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Published on: July 6, 2014

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

Biochemistry
Molecular Biology
Genetics

Background:

Sirtuins are NAD(+)-dependent deacylases impacting aging, cancer, and metabolism.
Identifying specific sirtuin targets is challenging due to numerous acetylated proteins.
Sirtuin substrates are known to physically associate with their regulators.

Purpose of the Study:

To describe a novel method for identifying sirtuin protein interactors.
To facilitate the discovery of bona fide sirtuin substrates.
To aid in understanding sirtuin functions in biological processes.

Main Methods:

Utilizing molecular cloning to create mammalian sirtuin protein expression plasmids.
Employing immunochemistry techniques for overexpression and immunoprecipitation of sirtuins and interacting partners.
Applying the Database for Annotation, Visualization, and Integrated Discovery (DAVID) for data interpretation.

Main Results:

Successfully generated expression plasmids for sirtuin proteins.
Established a method to co-immunoprecipitate sirtuins with their interacting proteins.
Obtained data on sirtuin-protein interactions for further analysis.

Conclusions:

The described method effectively identifies sirtuin protein interactors.
This approach can aid in discovering novel sirtuin substrates.
The findings support the strategy of identifying interacting proteins to find sirtuin targets.