Homology modeling and molecular dynamics simulations of the active state of the nociceptin receptor reveal new insights into agonist binding and activation

Proteins. 2012 Aug;80(8):1948-61. doi: 10.1002/prot.24077. Epub 2012 May 17.


The opioid receptor-like receptor, also known as the nociceptin receptor (NOP), is a class A G protein-coupled receptor (GPCR) in the opioid receptor family. Although NOP shares a significant homology with the other opioid receptors, it does not bind known opioid ligands and has been shown to have a distinct mechanism of activation compared to the closely related opioid receptors mu, delta, and kappa. Previously reported homology models of the NOP receptor, based on the inactive-state GPCR crystal structures, give limited information on the activation and selectivity features of this fourth member of the opioid receptor family. We report here the first active-state homology model of the NOP receptor based on the opsin GPCR crystal structure. An inactive-state homology model of NOP was also built using a multiple template approach. Molecular dynamics simulation of the active-state NOP model and comparison to the inactive-state model suggest that NOP activation involves movements of transmembrane (TM)3 and TM6 and several activation microswitches, consistent with GPCR activation. Docking of the selective nonpeptidic NOP agonist ligand Ro 64-6198 into the active-state model reveals active-site residues in NOP that play a role in the high selectivity of this ligand for NOP over the other opioid receptors. Docking the shortest active fragment of endogenous agonist nociceptin/orphaninFQ (residues 1-13) shows that the NOP extracellular loop 2 (EL2) loop interacts with the positively charged residues (8-13) of N/OFQ. Both agonists show extensive polar interactions with residues at the extracellular end of the TM domain and EL2 loop, suggesting agonist-induced reorganization of polar networks, during receptor activation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acids
  • Analgesics, Opioid / chemistry*
  • Animals
  • Binding Sites
  • Catalysis
  • Cattle
  • Hydrogen Bonding
  • Imidazoles / chemistry
  • Ligands
  • Lipid Bilayers / chemistry
  • Molecular Dynamics Simulation*
  • Opsins / chemistry*
  • Peptides / chemistry
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • Receptors, Opioid / agonists
  • Receptors, Opioid / chemistry*
  • Spiro Compounds / chemistry
  • Structural Homology, Protein
  • Water


  • Amino Acids
  • Analgesics, Opioid
  • Imidazoles
  • Ligands
  • Lipid Bilayers
  • Opsins
  • Peptides
  • Receptors, Opioid
  • Ro 64-6198
  • Spiro Compounds
  • Water
  • nociceptin receptor