G Protein-coupled receptor-bioligand interactions modeled in a phospholipid bilayer

Abstract

The arginine vasopressin (AVP) V2 receptor (V2R), a member of the G protein-coupled receptor (GPCR) superfamily, mediates the regulation of renal water absorption whose disorders cause nephrogenic diabetes insipidus. A complete molecular model of V2R embedded in a fully hydrated dimyristoylphosphatidylcholine (DMPC) bilayer was developed. Both free and AVP-bound states of V2R were studied. An initial V2R was built using a rule-based automated method for GPCR modeling, implementing both the low-resolution structure of bovine rhodopsin and the multisequence analysis of the GPCR superfamily. The loops were added using homology modeling as implemented in SYBYL. The docking site of AVP was selected and justified upon consideration of ligand–receptor interactions versus structure–activity data. The model was initially relaxed using constrained simulated annealing in vacuo. Subsequently, it was placed in the relaxed fully hydrated DMPC bilayer and submitted to ∼1.5 ns molecular dynamics using the AMBER 4.1 package upon constant number–pressure–temperature (NPT) conditions on parallel computers: Cray T3E and/or IBM SP2. Physical properties of the system were evaluated and compared with a pure hydrated DMPC bilayer. The receptor–ligand interactions, solvation interactions, individual lipid–protein interactions, and fluctuations of the protein, the lipid, and water were analyzed in detail. Receptor residues likely to be involved in the ligand binding were selected. As expected, the membrane-spanning helices of the protein fluctuate less than do the peripheral loops. The protein locally disturbs the lipid structure. A contiguous network of polar residues, extending from the bottom of the docked ligand to the intracellular domain, is observed inside the receptor in the AVP-bound V2R, while a similar network is broken in the empty V2R. This observation may suggest possible active and resting states of V2R, respectively. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 61–70, 1999