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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...

Protein-Protein Interfaces

Protein-Protein Interfaces

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 Networks

Protein Networks

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Related Experiment Video

Updated: Apr 15, 2026

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Quantitative analysis of protein-protein interactions.

Ziad M Eletr¹, Keith D Wilkinson

¹Department of Biochemistry, Emory University School of Medicine, 4017 Rollins Research Building, 1510 Clifton Road, Atlanta, GA, 30083, USA.

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

|April 11, 2015

Summary

Detecting protein-protein interactions is now more accessible. This chapter covers essential design considerations, assumptions, and analytical methods for accurately quantifying these interactions.

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Area of Science:

Biochemistry
Molecular Biology
Proteomics

Background:

Protein-protein interactions (PPIs) are fundamental to cellular processes.
Numerous methods exist for detecting PPIs.
Accessibility of PPI detection techniques has increased due to core facilities and affordable instrumentation.

Purpose of the Study:

To discuss common design considerations for valid protein-protein interaction measurements.
To outline assumptions relevant to quantifying protein-protein interactions.
To review analytical methods for the quantitation of protein-protein interactions.

Main Methods:

This chapter focuses on conceptual and analytical aspects rather than specific experimental protocols.
It emphasizes the importance of experimental design for reliable data.
Discussion includes assumptions underlying various quantitation methods.

Main Results:

Valid measurements of protein-protein interactions require careful consideration of experimental design.
Understanding underlying assumptions is crucial for accurate quantitation.
Appropriate analytical methods are necessary for reliable results.

Conclusions:

Researchers can obtain valid measurements of protein-protein interactions with proper design.
Quantitation of protein-protein interactions necessitates awareness of assumptions and analytical techniques.
This chapter provides a foundational guide for investigators new to the field.