RRML - Three-dimensional model of ligand-binding domain from glucagon like peptide-1 receptor, molecular target of antidiabetic treatment
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Concept, Design & Programming
Dr. Adrian Man
   
 
Nr. 12(3)/2008
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Three-dimensional model of ligand-binding domain from glucagon like peptide-1 receptor, molecular target of antidiabetic treatment

Ştefan V. Hobai


Abstract:

Using the applications of Schrödinger library a 3D model of ligand-binding domain of the glucagon like peptide-1 receptor (LBD-GLP-1R) was created. The template structures were related receptors, worked out by X-ray/NMR, like GIPR, CRFR and PACAPR. The procedure starts with the graft of GLP-1R radicals on the GIPR backbone. This stage is justified by the fact that the best sequence homology is between these two receptors. The resulted raw structure, which is a GIPR backbone bearing GLP-1R aligned radicals, has some gaps because the GLP-1R chain is longer than the GIPR. These gaps were completed in the following stage by chain building. The dihedral adjustments were made concomitantly with the chain building, based on the Φ-Ψ-Ω torsion angle values of the aligned template residues from the other receptors (CRFR and PACAPR). The resulted model was statistically compared with some models received from 3D structure prediction servers and with the crystallographic solution model of LBD-GLP-1R from PDB. Secondary structure and disulfide analyses reveal in Model the conserved conformational elements (α-helix, β-sheets and the disulfide pattern). A more detailed analysis showed that the Model atomic topologies (Asp-Arg ion-pairs, Trp-Arg-Trp sandwich contacts) are very similar with those of solution model and of server released models.

Keywords: GLP-1 receptor,N-terminal domain,multiple sequence alignment,structure prediction

 
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How to cite
Hobai ŞV. Three-dimensional model of ligand-binding domain from glucagon like peptide-1 receptor, molecular target of antidiabetic treatment. Rev Romana Med Lab. 2008;12(3):7-15