Abstract
The β2-adrenergic receptor (β2-AR), a G protein-coupled receptor (GPCR), is a physiologically important transmembrane protein that is a target for drugs used for treatment of asthma and cardiovascular diseases. Study of the first steps of ligand recognition and the molecular basis of ligand binding to the orthosteric site is essential for understanding the pharmacological properties of the receptor. In this work we investigated the characteristic features of the agonist association–dissociation process to and from the different conformational forms of β2-AR by use of advanced molecular modeling techniques. The investigation was focused on estimating the free energy profiles (FEPs) corresponding to the process of a full agonist ((R,R)-fenoterol) and an inverse agonist (carazolol) binding and unbinding to and from β2-AR. The two different conformational forms of β2-AR, i.e. active β2-AR–PDB: 3P0G and inactive β2-AR–PDB: 2RH1 were included in this stage of the study. We revealed several significant qualitative differences between FEPs characteristic of both conformational forms. Both FEPs suggest the existence of three transient binding sites in the extracellular domain of β2-AR. Comparison of the residues surrounding these transient binding sites in both β2-AR states revealed the importance of the aromatic residues F194, H932.64, H2966.58, and H178 (extracellular part of β2-AR) in the early stages of the binding process. In addition, slightly different exit and entry paths are preferred by the ligand molecule in the extracellular part of β2-AR, depending on the conformation of the receptor.Electronic supplementary materialThe online version of this article (doi:10.1007/s00249-015-1010-4) contains supplementary material, which is available to authorized users.
Highlights
G protein-coupled receptors (GPCRs) are a family of seven-transmembrane receptors that, upon activation by extracellular signals, couple with trimeric G proteins or β-arrestins to transduce signals from the cellular environment into the cell
In theory, one cannot distinguish between the association and dissociation processes on the basis of free energy profiles (FEPs) expressed in terms of the accepted reaction coordinate, because this coordinate can describe both association and dissociation
Enhanced sampling MD simulations have been performed to calculate the free energy profiles associated with the full agonist ((R,R)-fenoterol) and inverse agonist association–dissociation process to and from the β2-adrenergic receptor (β2-AR)
Summary
G protein-coupled receptors (GPCRs) are a family of seven-transmembrane receptors that, upon activation by extracellular signals, couple with trimeric G proteins or β-arrestins to transduce signals from the cellular environment into the cell. GPCRs are activated by a variety of species ranging from photons to small-molecular-weight molecules and peptides. The β2 adrenergic receptor (β2-AR) is a well-studied GPCR that mediates natural responses to the catecholamine hormones adrenaline and noradrenaline. It is crucial for physiological regulation of cardiovascular and pulmonary functions. Β2-AR, similar to other GPCRs, consists of seven-transmembrane α-helices (TMs I–VII) connected by three extracellular (ECLs I–III) and three intracellular (ICLs I–III) loops, with an extracellular N-terminus and an intracellular C-terminus (Rosenbaum et al 2009). The interactions between β2-AR and ligands, and the mechanism of receptor activation have been intensively studied
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