Monte Carlo Loop Refinement of Trans-Membrane Domain of the Thyroid Stimulating Hormone Receptor

Abstract

While the ectodomain structure of the Thyroid Stimulating Hormone Receptor (TSH-R) a GPCR, has been recently reported (Sanders, Chirgadze et al. 2007), for the transmembrane domain (TMD) only model structures exist. However, for virtual screen of small molecules targeting the TMD domain region reliable structure is a prerequisite. In this work we have used an ab initio method, that previously had reported to reproduce crystal structures within 2 A RMSD, to model 3 extra-cellular and 3 intra-cellular TSHR-TMD loops (Cui, Mezei et al. 2008). The method employs Modeller (Sali and Blundell 1993) to generate an initial loop structure. This is followed by a Metropolis Monte Carlo run in the torsion angle space of the of loop regions at high temperature for extensive sampling of the conformation space. Selected conformations are subjected to simulated annealing and the final structure with the lowest energy is chosen as the loop structure.The Charmm molecular mechanics force field is used for the VdW interactions between the protein atoms and for the torsion angles; water is represented by a sigmoidal distance dependent dielectric function and the Autodock desolvation term (Cui, Mezei et al. 2008). In addition, explicit hydrogen-bonding terms are used. We will present the computational and structural details of the methods used.