Modeling of peptides connecting the ligand-binding and transmembrane domains in the GluR2 glutamate receptor.

Ligand-gated Glutamate receptors (GluR) mediate synaptic signals in the nervous system. Ionotropic GluRs of AMPA type, the subject of this study, are tetrameric assemblies of monomer subunits, each of which is constructed in a modular fashion from functional subdomains. The extracellular ligand-binding domain (LBD) changes its conformation upon binding of an agonist ligand followed by opening of a transmembrane (TM) ion channel. Peptides connecting the LBD and TM domains facilitate gating of the channel, and their structure and composition are important for the receptor functioning. In this study, we used replica exchange molecular dynamics (REMD) simulations to model S1M1 and S2M3 connecting peptides of the GluR2 receptor in two implicit solvents, water and interfacial water/lipid medium characterized by lower polarity. Propensity of these peptides to form helical structures was analyzed using helicity measure derived from the free energy of the simulated ensembles of structures. The S1M1 and S2M3 connecting peptides were not helical in our simulations in both dielectric environments in the absence of the rest of the protein. The structures of the LBD fragment with known high-resolution alpha-helical structure and of the TM3 helix were successfully predicted in the simulations, which in part validate our results. The S2M3 peptide, which is important in gating, formed a well-defined coil structure and salt-bridges with the S2 domain. The S1M1 peptide formed a loop structure via formation of internal salt-bridges. Potential implications of these structures on function of the receptor are discussed. 2008 Wiley-Liss, Inc.