Monte Carlo loop refinement and virtual screening of the thyroid-stimulating hormone receptor transmembrane domain

Abstract

Metropolis Monte Carlo (MMC) loop refinement has been performed on the three extracellular loops (ECLs) of rhodopsin and opsin-based homology models of the thyroid-stimulating hormone receptor transmembrane domain, a class A type G protein-coupled receptor. The Monte Carlo sampling technique, employing torsion angles of amino acid side chains and local moves for the six consecutive backbone torsion angles, has previously reproduced the conformation of several loops with known crystal structures with accuracy consistently less than 2 Å. A grid-based potential map, which includes van der Waals, electrostatics, hydrophobic as well as hydrogen-bond potentials for bulk protein environment and the solvation effect, has been used to significantly reduce the computational cost of energy evaluation. A modified sigmoidal distance-dependent dielectric function has been implemented in conjunction with the desolvation and hydrogen-bonding terms. A long high-temperature simulation with 2 kcal/mol repulsion potential resulted in extensive sampling of the conformational space. The slow annealing leading to the low-energy structures predicted secondary structure by the MMC technique. Molecular docking with the reported agonist reproduced the binding site within 1.5 Å. Virtual screening performed on the three lowest structures showed that the ligand-binding mode in the inter-helical region is dependent on the ECL conformations.

Transmembrane Domains of Attraction on the TSH Receptor

“…The strong biochemical and biophysical evidence of TM1 as a potential regional interface for TSHR oligomerization was further supported by BD analysis based on our TMD structure developed from a rhodopsin-based model of the loop regions of the TSHR-TMD (23). While both the homology model and the BD protocol used involved serious approximations, earlier work showed that this technique was capable of predicting actual dimerization surfaces.…”

“…This led us to map the interfacial contacts on the TMD. To proceed with mapping and prediction of residues that may be involved in TSHR dimer/oligomer formation we generated a new model of the TSHR-TMD by constructing a TMD with extra and intracellular loops (23). Our modeling data predicted that constitutive oligomerization of the TSHR would involve multiple residues in one or more helices and the experimental data were also in favor of multiple interacting sites.…”

“…The ab initio method implemented in the program Modeler (24) was used to model the three extra and intracellular loops of the TSHR-TMD (23). The initial atomic coordinates for the TSH-TMD and residue sequences without the intra and extracellular loops were obtained from the Glycoprotein-hormone Receptors Information System (GRIS) database (http://gris.ulb.ac.be).…”

“…To be able to use BD, we have developed a model of the TSHR transmembrane helical structure by homology modeling based on rhodopsin as a template (21)(22)(23) using the Modeler program (24). This allowed us to study the dimer interfacial regions of the TMD within a membrane environment using BD (19,25,26).…”

New Small Molecule Agonists to the Thyrotropin Receptor

“…This template was chosen because of the low RMSD values between the backbone of the TM helices of the TSHR model and that of the rhodopsin x-ray crystal structure (33), and fits the experimental parameters previously described (34). The initial homology model of rhodopsin was obtained from the Uniprot server (www.uniprot.org).…”