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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...

Ligand Binding and Linkage

Ligand Binding and Linkage

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Related Experiment Video

Updated: Nov 5, 2025

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

Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics.

Mitsugu Araki¹, Shigeyuki Matsumoto², Gert-Jan Bekker³

¹Graduate School of Medicine, Kyoto University, Kyoto, Japan. araki.mitsugu.6w@kyoto-u.ac.jp.

Nature Communications

|May 15, 2021

Summary

This summary is machine-generated.

High-frequency ultrasound accelerates molecular dynamics (MD) simulations of slow biomolecular processes. This novel method enhances the speed of observing protein-inhibitor binding events by 10-20 times, revealing new kinetic details.

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Area of Science:

Biophysics
Computational Biology
Pharmacology

Background:

Atomistic-level simulation of biomolecular dynamics is limited by computational speed for slow processes (submillisecond timescales).
Conventional molecular dynamics (MD) struggles to capture rare events like protein-inhibitor binding within feasible simulation times.

Purpose of the Study:

To develop and validate a method for accelerating MD simulations using high-frequency ultrasound perturbation.
To investigate the binding kinetics and pathways of small-molecule inhibitors to the protein CDK2.

Main Methods:

Development of hypersound-accelerated MD simulations.
Application of the method to study the binding of inhibitors to CDK2, comparing results with conventional MD.

Main Results:

Accelerated MD simulations increased the observation rate of protein-inhibitor binding events by 10-20 times compared to conventional MD.
Revealed diverse microscopic kinetic features and binding pathways of inhibitors on the protein surface.
Enabled estimation of kinetic parameters and exploration of druggable pockets.

Conclusions:

Hypersound-accelerated MD is a powerful technique to overcome timescale limitations in biomolecular simulations.
Provides deeper insights into the molecular interactions governing biomolecular processes and drug discovery.