Simulations of a G protein-coupled receptor homology model predict dynamic features and a ligand binding site.
A computational approach to predict structures of rhodopsin-like G protein-coupled receptors (GPCRs) is presented and evaluated by comparison to the X-ray structural models. By combining sequence alignment, the rhodopsin crystal structure, and point mutation data on the beta2 adrenoreceptor (b2ar), we predict a (-)-epinephrine-bound computational model of the beta2 adrenoreceptor. The model is evaluated by molecular dynamics simulations and by comparison with the recent X-ray structures of b2ar. The overall correspondence between the predicted and the X-ray structural model is high. Especially the prediction of the ligand binding site is accurate. This shows that the proposed dynamic homology modelling approach can be used to create reasonable models for the understanding of structure and dynamics of other rhodopsin-like GPCRs.
Wolf
Steffen
S
Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany.
Böckmann
Marcus
M
Höweler
Udo
U
Schlitter
Jürgen
J
Gerwert
Klaus
K
D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004837:Epinephrine / Q000737:chemistry; D008024:Ligands; D008958:Models, Molecular; D017354:Point Mutation; D018343:Receptors, Adrenergic, beta-2 / Q000737:chemistry / Q000235:genetics; D012243:Rhodopsin / Q000737:chemistry* / Q000235:genetics; D040681:Structural Homology, Protein
D008024:Ligands; D018343:Receptors, Adrenergic, beta-2; D012243:Rhodopsin; D004837:Epinephrine