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

Ligand Binding and Linkage

Ligand Binding and Linkage

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...

Structure-Activity Relationships and Drug Design

Structure-Activity Relationships and Drug Design

Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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:

You might also read

Related Articles

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

Sort by

Same author

D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Structural mechanism for noncanonical GPCR signaling in the Hedgehog pathway.

Nature structural & molecular biology·2026

Same author

A fold switch regulates conformation of an alphavirus RNA-dependent RNA polymerase.

Nucleic acids research·2026

Same author

Asymmetric isopeptide bond steers directional genomic RNA egress from icosahedral virus.

Science advances·2025

Same author

A fold switch regulates conformation of an alphavirus virus RNA-dependent RNA polymerase.

bioRxiv : the preprint server for biology·2025

Same author

Multiplicity of Regulatory Subunit Conformations Defines Structural Ensemble of Reset Protein Kinase A Holoenzyme.

Journal of the American Chemical Society·2025

Search research articles

Related Experiment Video

Updated: Feb 28, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Dissecting Orthosteric Contacts for a Reverse-Fragment-Based Ligand Design.

Arun Chandramohan¹, Nikhil K Tulsian¹, Ganesh S Anand¹

¹Department of Biological Sciences, National University of Singapore , 14 Science Drive 4, Singapore 117543.

Analytical Chemistry

|June 20, 2017

Summary

This study introduces a novel method using urea-induced protein unfolding to precisely measure the energetic contributions of individual ligand functional groups. This approach aids fragment-based drug discovery by ranking interactions within protein binding sites.

More Related Videos

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

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Related Experiment Videos

Last Updated: Feb 28, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

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

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Area of Science:

Biochemistry and Structural Biology
Computational Chemistry and Drug Design

Background:

Orthosteric protein binding sites involve complex, synergistic interactions between ligands and proteins.
Quantifying the energetic contribution of individual functional groups within these interactions is challenging.
Understanding these contributions is crucial for advancing iterative fragment-based drug discovery (FBDD).

Purpose of the Study:

To develop and validate a method for deconstructing protein-ligand interactions to determine individual functional group contributions.
To apply this method to protein-ligand systems, specifically cAMP-bound Protein Kinase A regulatory subunit (RIα) and IBMX-bound phosphodiesterase 8 (PDE8).
To provide a rational basis for optimizing ligand design in drug discovery.

Main Methods:

Utilized a gradient of urea to induce progressive unfolding of target proteins.
Monitored protein structural changes and ligand binding site integrity using amide hydrogen-deuterium exchange mass spectrometry (HDX-MS).
Analyzed two model systems: RIα-cAMP and PDE8-IBMX.

Main Results:

Successfully ranked the energetic contributions of individual functional groups within the ligands.
In RIα-cAMP interactions, exocyclic phosphate oxygens of cAMP showed stronger binding than ribose 2'-OH.
Determined the relative contributions of IBMX functional groups to PDE8 binding.

Conclusions:

The progressive unfolding strategy effectively deconstructs complex protein-ligand interactions.
This method enables the identification of key functional group interactions critical for ligand affinity.
Offers a valuable starting point for rational ligand design in fragment-based drug discovery.