Neurotransmitter Funneling Optimizes Glutamate Receptor Kinetics

Abstract

SummaryIonotropic glutamate receptors (iGluRs) mediate neurotransmission at the majority of excitatory synapses in the brain. Little is known, however, about how glutamate reaches the recessed binding pocket in iGluR ligand-binding domains (LBDs). Here we report the process of glutamate binding to a prototypical iGluR, GluA2, in atomistic detail using unbiased molecular simulations. Charged residues on the LBD surface form pathways that facilitate glutamate binding by effectively reducing a three-dimensional diffusion process to a spatially constrained, two-dimensional one. Free energy calculations identify residues that metastably bind glutamate and help guide it into the binding pocket. These simulations also reveal that glutamate can bind in an inverted conformation and also reorient while in its pocket. Electrophysiological recordings demonstrate that eliminating these transient binding sites slows activation and deactivation, consistent with slower glutamate binding and unbinding. These results suggest that binding pathways have evolved to optimize rapid responses of AMPA-type iGluRs at synapses.

Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP 6 )

“…Instead, to investigate how IP 6 stabilizes the capsid, we simulated individual hexamer and pentamer components of the capsid [Protein Data Bank (PDB) ID: 3H47, 5HGL, and 5MCY] using unbiased, microsecond time scale AA MD simulations on the special-purpose computer hardware, Anton 2, at the Pittsburgh Supercomputing Center ( 14 ). Similar to prior studies, IP 6 was initially added to the bulk solvent, approximately 10 Å away from any nonwater molecules ( 15 , 16 ). Four systems each for the CA hexamer and pentamer were prepared with IP 6 in randomized positions in bulk solvent and selected for longer time scale simulations on Anton 2 (see Materials and Methods for a complete description).…”

Population Shift Mechanism for Partial Agonism of AMPA Receptor

“…The LBDs form dimer of dimers, and it is believed that the dimer interface matters for the change in state from active to desensitized. However, a recent work including simulations shows that the ligand-binding process and LBD closure in the dimer are very similar to those in the monomer (46). In addition, cryo-EM structures suggest that the displacement of LBD-TMD linkers would be a main driving force for opening the ion channel (10,12).…”

“…By combining long, unbiased MD simulations, Yu et al (46) recently proposed that charged residues on the LBD surface form a ligand-binding pathway, which funnels a ligand into the binding site via a series of metastable interactions. Their model of ligand binding and cleft closing is as follows: 1) the ligand binds to R661 on D2; 2) the ligand's a-carboxylate interacts with R485 on D1, allowing a metastable interaction to form between D1 and D2; 3) the ligand shifts into the binding pocket while adjusting its interactions with D2; and 4) the ligand's amine interacts with E705 on D2, resulting in the cleft closure.…”

Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP6)

“…The β-hairpin regions were quite flexible, suggesting that opening or closing of the proposed gate is driven more by small changes in the conformational ensembles adopted by the β-hairpin rather than abrupt structural changes. binding pockets [21][22][23] , the flipping of ligand configurations between several bound poses 18,24 , and metastable electrostatic interactions that guide ligands into the binding pocket 18,19,25,26 . To assess the protein-ligand interactions that form during our simulations, we computed the spatial distribution occupied by the ligand's non-hydrogen atoms, or in other words a three-dimensional map of the ligand density ( Figure 4).…”

“…Free energy calculations demonstrate that IP 6 preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly.These results elucidate the molecular role of IP 6 in stabilizing and assembling the retroviral capsid.Pittsburgh Supercomputing Center 17 . Similar to prior studies, IP 6 was initially added to the bulk solvent, approximately 10 Å away from any non-water molecules 18,19 . Four systems each for the CA hexamer and pentamer were prepared with IP 6 in randomized positions in bulk solvent, and selected for longer timescale simulations on Anton 2 (see: Materials and Methods for a complete description).…”