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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 the...

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 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...

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...

Metal-Ligand Bonds

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

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Related Experiment Video

Updated: May 13, 2026

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Published on: January 14, 2020

Molecular recognition and ligand association.

Riccardo Baron¹, J Andrew McCammon

¹Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112-5820, USA. r.baron@utah.edu

Annual Review of Physical Chemistry

|March 12, 2013

Summary

This summary is machine-generated.

This review explores molecular recognition and ligand binding, detailing physical insights and computational methods. Advances in computational approaches offer dynamic, microscopic views complementing experimental data in pharmacology.

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Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

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Last Updated: May 13, 2026

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Published on: January 14, 2020

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

Area of Science:

Biochemistry
Computational Chemistry
Pharmacology

Background:

Molecular recognition and ligand binding are crucial in biological processes and drug development.
Understanding the driving forces behind these interactions is complex due to enthalpic-entropic compensation and solvation effects.

Purpose of the Study:

To review recent advancements in understanding molecular recognition and ligand association.
To highlight new physical insights and methodological progress in protein-ligand binding.
To discuss challenges and the expanding role of computational approaches in pharmacology.

Main Methods:

Review of studies focusing on physical insights into molecular recognition.
Analysis of methodological advances in computational approaches for protein-ligand binding.
Examination of challenges including compensating terms and configurational ensembles.

Main Results:

New physical insights into the driving forces of molecular recognition.
Methodological advances enhancing computational applications to protein-ligand binding.
Computational methods provide microscopic, dynamic views complementing experimental data.

Conclusions:

Physics-based computational approaches are increasingly powerful for pharmacology.
Addressing complex factors like solvation and configurational ensembles improves predictive power.
These advancements enhance the synergy between computational and experimental studies in drug discovery.