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ABSTRACT lonotropic glutamate receptors are essential for fast synaptic nerve transmission. Recent x-ray structures for the ligand-binding (SiS2) region of the GluR2 a-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-sensitive receptor have suggested how differences in protein/ligand interactions may determine whether a ligand will behave as a full agonist. We have used multiple molecular dynamics simulations of 2-5 ns duration to explore the structural dynamics of GluR2 S1 S2 in the presence and absence of glutamate and in a complex with kainate. Our studies indicate that not only is the degree of domain closure dependent upon interactions with the ligand, but also that protein/ligand interactions influence the motion of the S2 domain with respect to Sl. Differences in domain mobility between the three states (apo-SlS2, glutamate-bound, and kainate-bound) are surprisingly clear-cut. We discuss how these changes in dynamics may provide an explanation relating the mechanism of transmission of the agonist-binding event to channel opening. We also show here how the glutamate may adopt an alternative mode of binding not seen in the x-ray structure, which involves a key threonine (T480) side chain flipping into a new conformation. This new conformation results in an altered pattern of hydrogen bonding at the agonist-binding site.
INTRODUCTION
Fast synaptic transmission between nerve cells in mammals is carried out predominantly by ionotropic glutamate receptors (iGluR). These receptors are a family of ligand-gated ion channels that open in response to the binding of glutamate (Dingledine et al., 1999; Sprengel et al., 2001). Glutamate is released presynaptically and binds to a postsynaptic receptor gating a cation-selective channel, thus depolarizing the post-synaptic cell. Although glutamate is the natural ligand, the various iGluRs identified by sequence comparisons may also be classified in terms of their agonist pharmacology (Hollmann and Heinemann, 1994). Those receptors (GluR1-4) that show greatest sensitivity to the synthetic agonist a-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) are termed AMPA receptors (Borges and Dingledine, 1998). Likewise, those that show greatest sensitivity to kainate (GluRS-7 and KAI-2) are referred to as kainate receptors (Lerma et al., 1997; Chittajallu et al., 1999). Receptors activated by the synthetic N-methyl-D-aspartate (NMDAR1 and NMDAR2a-d) are called NMDA receptors (Yamakura and Shimoji, 1999) and need glycine and glutamate as the natural agonist. In all of these GluRs the agonist/antagonist binding site is located within...