Molecular Modeling of the M3 Acetylcholine Muscarinic Receptor and Its Binding Site

Abstract

The present study reports the results of a combined computational and site mutagenesis study designed to provide new insights into the orthosteric binding site of the human M3 muscarinic acetylcholine receptor. For this purpose a three-dimensional structure of the receptor at atomic resolution was built by homology modeling, using the crystallographic structure of bovine rhodopsin as a template. Then, the antagonist N-methylscopolamine was docked in the model and subsequently embedded in a lipid bilayer for its refinement using molecular dynamics simulations. Two different lipid bilayer compositions were studied: one component palmitoyl-oleyl phosphatidylcholine (POPC) and two-component palmitoyl-oleyl phosphatidylcholine/palmitoyl-oleyl phosphatidylserine (POPC-POPS). Analysis of the results suggested that residues F222 and T235 may contribute to the ligand-receptor recognition. Accordingly, alanine mutants at positions 222 and 235 were constructed, expressed, and their binding properties determined. The results confirmed the role of these residues in modulating the binding affinity of the ligand.

Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling

“…To that end we conducted the refinement process of the M3 model using the M2 muscarinic as template with tiotropium or N-methylscopolamine (NMS) docked in the orthosteric site and compared with the results obtained with a model refined without any ligand bound. Preliminary results of this work have been already reported (Lupala, Rasaeifar, Gomez-Gutierrez, & Perez, 2015;Martinez-Archundia, Cordomi, Garriga, & Perez, 2012).…”

Targeting Inhibition of SmpB by Peptide Aptamer Attenuates the Virulence to Protect Zebrafish against Aeromonas veronii Infection

“…PA-1 showed stronger interaction with SmpB than those controls of SN and BSA. The binding curve of PA-1 interacting with SmpB was plotted, and equilibrium dissociation constant ( K d ) was calculated by employing a model of one site binding-saturation analysis ( Martinez-Archundia et al, 2012 ). The results showed that the binding of PA-1 to SmpB was stronger with K d of 0.691 μM, in contrast to the binding of SN to SmpB with K d of 1.380 μM ( Figure 2C ).…”

Diphlorethohydroxycarmalol Isolated from Ishige okamurae Exerts Vasodilatory Effects via Calcium Signaling and PI3K/Akt/eNOS Pathway

“…Accordingly, having found that DPHC can effectively raise [Ca 2+ ] cytol and [Ca 2+ ] ER levels, we further focused on investigating how DPHC affects calcium regulation via cell membrane receptors (VEGFR2 and AchR). The muscarinic AchR family is divided into 5 subtypes: M1, M2, M3, M4, and M5 [ 32 ]. The activation of M3 receptors in vascular endothelial cells induces potent vasodilatation, and this process occurs via the release of an endothelium-derived relaxing factor, such as NO [ 33 ].…”