Paper Citing NAMD - Abstract
Gonzalez, Angel; Perez-Acle, Tomas; Pardo, Leonardo; Deupi, Xavier
Molecular Basis of Ligand Dissociation in beta-Adrenergic Receptors
PLOS ONE, 6 Art. No. e23815, SEP 7 2011
The important and diverse biological functions of beta-adrenergic receptors (beta ARs) have promoted the search for compounds to stimulate or inhibit their activity. In this regard, unraveling the molecular basis of ligand binding/unbinding events is essential to understand the pharmacological properties of these G protein-coupled receptors. In this study, we use the steered molecular dynamics simulation method to describe, in atomic detail, the unbinding process of two inverse agonists, which have been recently co-crystallized with beta(1) and beta(2)ARs subtypes, along four different channels. Our results indicate that this type of compounds likely accesses the orthosteric binding site of bARs from the extracellular water environment. Importantly, reconstruction of forces and energies from the simulations of the dissociation process suggests, for the first time, the presence of secondary binding sites located in the extracellular loops 2 and 3 and transmembrane helix 7, where ligands are transiently retained by electrostatic and Van der Waals interactions. Comparison of the residues that form these new transient allosteric binding sites in both bARs subtypes reveals the importance of non-conserved electrostatic interactions as well as conserved aromatic contacts in the early steps of the binding process.
