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Related Concept Videos

Ligand Binding Sites02:40

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...
Protein Networks02:26

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-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
Protein-protein Interfaces02:04

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...
The Equilibrium Binding Constant and Binding Strength02:18

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:
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Related Experiment Video

Updated: May 31, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Studying protein-protein affinity and immobilized ligand-protein affinity interactions using MS-based methods.

Jeroen Kool1, Niels Jonker, Hubertus Irth

  • 1BioMolecular Analysis, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands. j.kool@vu.nl

Analytical and Bioanalytical Chemistry
|July 15, 2011
PubMed
Summary

This review explores mass spectrometry (MS) methods for studying protein interactions, including protein-protein and protein-ligand binding. It highlights applications in drug discovery and understanding cellular processes.

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Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Proteomics

Background:

  • Protein interactions are fundamental to cellular processes.
  • Understanding these interactions is crucial for drug discovery and disease research.
  • Mass spectrometry (MS) offers powerful tools for analyzing these complex biological systems.

Purpose of the Study:

  • To provide a comprehensive overview of current mass spectrometry-based methods for studying protein affinity interactions.
  • To discuss the principles, recent developments, and applications of these techniques.
  • To highlight the relevance of these methods in drug discovery and elucidating cellular mechanisms.

Main Methods:

  • Direct and indirect MS-based analysis of intact protein complexes in the gas phase.
  • Pull-down assays for affinity-based protein-protein and protein-ligand interaction analysis.
  • Chemical proteomics for analyzing ligand selectivity profiles against multiple targets.
  • Surface Plasmon Resonance (SPR) coupled with MS for detailed interaction studies.

Main Results:

  • Detailed discussion of various MS-based techniques for protein interaction analysis.
  • Emphasis on methods applicable to interactomics, interaction proteomics, and chemical proteomics.
  • Exploration of recent advancements and practical applications of these MS approaches.

Conclusions:

  • Mass spectrometry is a versatile tool for dissecting complex protein affinity interactions.
  • These methods are vital for advancing lead compound generation in drug discovery.
  • MS-based interactomics contributes significantly to understanding the molecular basis of cellular functions and diseases.