Molecular dynamic simulation of mGluR5 amino terminal domain: essential dynamics analysis captures the agonist or antagonist behaviour of ligands.

Alessandro Casoni, Francesca Clerici, Alessandro Contini

Dipartimento di Scienze Farmaceutiche - sezione di Chimica Generale e Organica Alessandro Marchesini, Università degli Studi di Milano, via Venezian, 21 20133 Milano, Italy.

Journal of molecular graphics & modelling 2013 Apr

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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. Copyright © 2013 Elsevier Inc. All rights reserved.

Citation

Alessandro Casoni, Francesca Clerici, Alessandro Contini. Molecular dynamic simulation of mGluR5 amino terminal domain: essential dynamics analysis captures the agonist or antagonist behaviour of ligands. Journal of molecular graphics & modelling. 2013 Apr;41:72-8