Related Experiment Video
Updated: May 13, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
Published on: July 19, 2024
Molecular dynamic simulation of mGluR5 amino terminal domain: essential dynamics analysis captures the agonist or
Alessandro Casoni1, Francesca Clerici, Alessandro Contini
1Dipartimento di Scienze Farmaceutiche - sezione di Chimica Generale e Organica Alessandro Marchesini, Università degli Studi di Milano, via Venezian, 21 20133 Milano, Italy.
Abstract:
We describe the application of molecular dynamics followed by principal component analysis to study the inter-domain movements of the ligand binding domain (LBD) of mGluR5 in response to the binding of selected agonists or antagonists. Our results suggest that the method is an attractive alternative to current approaches to predict the agonist-induced or antagonist-blocked LBD responses. The ratio between the eigenvalues of the first and second eigenvectors (R1,2) is also proposed as a numerical descriptor for discriminating the ligand behavior as a mGluR5 agonist or antagonist.
Related Concept Videos
The Two-State Receptor Model
The binding affinity of a drug determines its interaction with one...
Ligand Binding Sites
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
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...
Cooperative Allosteric Transitions
Activation and Inactivation of G Proteins
Drug-Receptor Interaction: Agonist
Agonists can bind to receptors in different ways. Some agonists bind directly to the receptor's active site, mimicking the endogenous ligand's action.
