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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

11.9K
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...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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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:
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Protein Networks02:26

Protein Networks

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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,...
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Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

28.0K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
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Related Experiment Video

Updated: May 4, 2026

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

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Dynamic protein ligand interactions--insights from MS.

Carla Schmidt1, Carol V Robinson

  • 1Department of Chemistry, University of Oxford, UK.

The FEBS Journal
|January 8, 2014
PubMed
Summary

Mass spectrometry (MS) is a powerful tool for studying how proteins interact with various molecules like drugs and lipids. This review highlights MS methods for analyzing these dynamic protein-ligand interactions, revealing cellular functions.

Keywords:
MScrosslinkinghydrogen-deuterium exchangehydroxyl radical footprintingprotein complexesprotein-ligand interactionsproteomics

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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Area of Science:

  • Biochemistry and Molecular Biology
  • Analytical Chemistry
  • Structural Biology

Background:

  • Proteins interact dynamically with diverse ligands (carbohydrates, lipids, nucleotides) to perform cellular functions.
  • Understanding these protein-ligand interactions is crucial for deciphering biological systems.
  • Mass spectrometry (MS) has emerged as a key technique for studying both covalent and non-covalent protein-ligand assemblies.

Purpose of the Study:

  • To review and highlight Mass Spectrometry (MS) approaches for studying protein-ligand interactions.
  • To provide a broad definition of ligands, including protein subunits, drugs, oligonucleotides, carbohydrates, and lipids.
  • To showcase recent literature examples of MS applications in this field.

Main Methods:

  • Mass spectrometry (MS) and associated techniques.
  • Hydrogen-deuterium exchange (HDX) MS.
  • Proteomics.
  • Hydroxyl radical footprinting.
  • Intact mass analysis of protein complexes.
  • Crosslinking coupled with MS.

Main Results:

  • MS can determine the composition, heterogeneity, dynamics, structural arrangements, and binding affinities of protein-ligand interactions.
  • Various MS-based methods provide insights into conformational changes and modifications upon ligand binding.
  • These techniques are applicable to a wide range of protein-ligand complexes, including integral membrane proteins.

Conclusions:

  • Mass spectrometry is a versatile and powerful platform for investigating complex protein-ligand interactions.
  • The integration of multiple MS-based methodologies offers comprehensive insights into molecular mechanisms.
  • This review underscores the significance of MS in advancing the understanding of fundamental biological processes driven by protein-ligand binding.