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Molecular modeling of the M3 acetylcholine muscarinic receptor and its binding site.

Martinez-Archundia M, Cordomi A, Garriga P, Perez JJ - J. Biomed. Biotechnol. (2012)

Bottom Line: 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.Analysis of the results suggested that residues F222 and T235 may contribute to the ligand-receptor recognition.The results confirmed the role of these residues in modulating the binding affinity of the ligand.

View Article: PubMed Central - PubMed

Affiliation: Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, 08028 Barcelona, Spain.

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.

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(a) Time evolution of the root mean square deviation (RMSD) of the of the α-carbon atoms of the protein along the different simulations. (b) Average root mean square deviation (rmsd) of the Cα atoms of each residues of the protein through the last 25 ns of each simulations computed from an average of the last 25 ns.
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fig2: (a) Time evolution of the root mean square deviation (RMSD) of the of the α-carbon atoms of the protein along the different simulations. (b) Average root mean square deviation (rmsd) of the Cα atoms of each residues of the protein through the last 25 ns of each simulations computed from an average of the last 25 ns.

Mentions: Deviations from the initial 7TM homology-based structure were monitored through the time evolution of the root-mean-square deviation (rmsd) of the α-carbon atoms as displayed in Figure 2(a). Smaller deviations are observed when the protein is embedded in the two-component lipid bilayer (POPS-POPC) than when the protein is embedded in the one-lipid environment (POPC) (Figure 2(a)). This behavior is probably due to the presence of the anionic lipid (POPS) in the cytoplasmic area of the receptor, neutralizing the cluster of positive charges located in that region, and it is consistent with the experimental finding that this part of the protein is difficult to crystallize due to its flexibility, as previously found in MD simulations of bovine rhodopsin [43]. The time evolution of the RMSD also permits to assess the influence of the ligand on the protein structure. The evolution of the α-carbon rmsd shows that the trajectories with the ligand bound display lower deviations in comparison to those simulations of the protein alone.


Molecular modeling of the M3 acetylcholine muscarinic receptor and its binding site.

Martinez-Archundia M, Cordomi A, Garriga P, Perez JJ - J. Biomed. Biotechnol. (2012)

(a) Time evolution of the root mean square deviation (RMSD) of the of the α-carbon atoms of the protein along the different simulations. (b) Average root mean square deviation (rmsd) of the Cα atoms of each residues of the protein through the last 25 ns of each simulations computed from an average of the last 25 ns.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3303834&req=5

fig2: (a) Time evolution of the root mean square deviation (RMSD) of the of the α-carbon atoms of the protein along the different simulations. (b) Average root mean square deviation (rmsd) of the Cα atoms of each residues of the protein through the last 25 ns of each simulations computed from an average of the last 25 ns.
Mentions: Deviations from the initial 7TM homology-based structure were monitored through the time evolution of the root-mean-square deviation (rmsd) of the α-carbon atoms as displayed in Figure 2(a). Smaller deviations are observed when the protein is embedded in the two-component lipid bilayer (POPS-POPC) than when the protein is embedded in the one-lipid environment (POPC) (Figure 2(a)). This behavior is probably due to the presence of the anionic lipid (POPS) in the cytoplasmic area of the receptor, neutralizing the cluster of positive charges located in that region, and it is consistent with the experimental finding that this part of the protein is difficult to crystallize due to its flexibility, as previously found in MD simulations of bovine rhodopsin [43]. The time evolution of the RMSD also permits to assess the influence of the ligand on the protein structure. The evolution of the α-carbon rmsd shows that the trajectories with the ligand bound display lower deviations in comparison to those simulations of the protein alone.

Bottom Line: 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.Analysis of the results suggested that residues F222 and T235 may contribute to the ligand-receptor recognition.The results confirmed the role of these residues in modulating the binding affinity of the ligand.

View Article: PubMed Central - PubMed

Affiliation: Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, 08028 Barcelona, Spain.

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.

Show MeSH