Creation of a GPR18 homology model using conformational memories

UNCG Author/Contributor (non-UNCG co-authors, if there are any, appear on document)
Marianne G. Schmeisser (Creator)
Institution
The University of North Carolina at Greensboro (UNCG )
Web Site: http://library.uncg.edu/
Advisor
Patricia Reggio

Abstract: G-protein coupled receptors (GPCRs) make up the largest family of eukaryotic membrane receptors, covering a broad range of cellular responses in the body. This wide range of activity makes them important pharmacological targets. In general, all Class A GPCRs share a common structure that consists of seven transmembrane alpha helices, connected by extracellular and intracellular loops, an extracellular N-terminus, and an intracellular C-terminus. These similarities can be used to construct a model of an unknown receptor, which can then be used to help guide further studies of this receptor and its pharmacology. The orphan GPCR GPR18 is a member of the Class A subfamily of GPCRs. GPR18 binds both lipid-like and small molecule ligands, such as NAGly and abnormal-cannabidiol (Abn-CBD), leading to belief that GPR18 may be the Abnormal Cannabinoid Receptor. The goal of this project was to construct a model of GPR18 in its inactive state and to explore the binding site of a key antagonist already identified for this receptor. A model of the GPR18 inactive (R) state was created using the μ-Opioid receptor (MOR) crystal structure as template (PDB: 4DKL). The Monte Carlo/simulated annealing method, Conformational Memories (CM) was used to study the accessible conformations of three GPR18 transmembrane helices (TMHs) with important sequence divergences from the MOR template: TMH3, TMH4, and TMH7. CM was also used to calculate the accessible conformations for TMH6, which allowed the choice of TMH6 conformers appropriate for the GPR18 R and R* models. Docking studies were guided by the hypothesis that a positively charged residue (either R2.60 or R5.42) may be the primary ligand interaction site in the GPR18 binding pocket. The binding pocket of the antagonist, cannabidiol (CBD) was explored in the inactive state GPR18 model using Glide, an automatic docking program in the Schr√∂dinger modeling suite. These studies identified that both of these argenines are the primary interaction site for CBD. With the pocket determined, extracellular and intracellular loops were calculated using another Monte Carlo technique, Modeler. Once loops were attached, the N and C termini were modeled and added as well. Much like the S1PR1 receptor, and continuing the hypothesis that GPR18 used a lipid level access to the binding pocket, the N terminus displayed a small helical portion that lay atop the bundle, effectively blocking the extracellular side along with EC2. With the identification of key residues and a complete bundle, further mutation studies and dynamic simulations can be used to further refine and test these modeling results.

Additional Information

Publication
Thesis
Language: English
Date: 2013
Keywords
Molecular Modelling
Subjects
G proteins
Drug receptors

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