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

Ligand Binding Sites

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...

Ligand Binding Sites

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-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...

The Equilibrium Binding Constant and Binding Strength

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:

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-Drug Binding: Determination Methods

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...

You might also read

Related Articles

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

Sort by

Same author

A genomic and epigenomic lens into the biology of acute lymphoblastic leukaemia.

Nature reviews. Cancer·2026

Same author

FATP2-mediated lipid metabolism enhances chimeric antigen receptor T-cell therapy resistance in B-cell acute lymphoblastic leukemia.

Leukemia·2026

Same author

A Multidisciplinary Integrated Approach for the Identification and Characterization of the AMP Profile in <i>Hermetia illucens</i> Hemolymph.

Insects·2026

Same author

From Sea to Therapy: Development and Analytical Control of Recombinant Human CDKL5 Production in the Marine Bacterium <i>Pseudoalteromonas haloplanktis</i> TAC125.

Marine drugs·2026

Same author

Proteomic and degradomic signatures of extracellular matrix remodeling in calcific aortic valve stenosis.

Molecular medicine (Cambridge, Mass.)·2026

Same author

The ASH HematOmics Program supports integrative analysis of genomic and clinical data in hematologic diseases.

Blood·2026

Search research articles

Related Experiment Video

Updated: Jul 6, 2026

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

Methods for the Investigation of Protein-Ligands Interactions.

Ilaria Iacobucci¹, Flora Cozzolino¹, Irene Cipollone¹

¹Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.

Advances in Experimental Medicine and Biology

|July 4, 2026

Summary

This summary is machine-generated.

Mass spectrometry-based proteomics offers advanced methods to study biomolecular interactions. This review details techniques for mapping protein-protein, protein-nucleic acid, and protein-drug interactions for research and drug discovery.

Keywords:

Affinity purification Chemoproteomics Cross-linking ms Interactomics Mass spectrometry Protein–ligand interactions Protein–nucleic acid interactions Protein–protein interactions Proximity labeling Structural proteomics Systems biology Thermal proteome profiling

More Related Videos

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

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

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

Published on: October 15, 2018

Related Experiment Videos

Last Updated: Jul 6, 2026

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

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

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

Published on: October 15, 2018

Area of Science:

Biochemistry and Molecular Biology
Proteomics
Biophysics

Background:

Cellular functions rely on complex biomolecular interactions.
Mass spectrometry-based proteomics has revolutionized the study of these interactions.
Understanding these interactions is crucial for cellular regulation and therapeutic development.

Purpose of the Study:

To provide a comprehensive overview of state-of-the-art proteomics methodologies for studying biomolecular interactions.
To emphasize experimental design, sample preparation, and data quality control in interactomics.
To guide researchers in selecting and applying appropriate techniques for robust interactomics experiments.

Main Methods:

Protein-protein interactions: Affinity purification-mass spectrometry, proximity-dependent labeling, cross-linking mass spectrometry, Blue Native PAGE, SEC-MS.
Protein-nucleic acid interactions: Affinity capture, EMSA-MS, ChIP-MS, CRISPR-based enrichment, CLIP-based methods.
Protein-drug interactions: Chemoproteomics, thermal proteome profiling, label-free structural proteomics.

Main Results:

Discussion of targeted and untargeted proteomics strategies for interaction mapping.
Highlighting recent technological innovations and computational tools.
Evaluation of the strengths, limitations, and applications of various methodologies.

Conclusions:

Proteomics provides powerful tools for dissecting complex molecular networks.
Integrative multi-omics strategies enhance interaction mapping across biological scales.
This work offers practical guidance for basic and translational research in interactomics.