One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue

Abstract

Recently discovered bacterial homologues of eukaryotic pentameric ligand-gated ion channels, such as the Gloeobacter violaceus receptor (GLIC), are increasingly used as structural and functional models of signal transduction in the nervous system. Here we present a one-microsecond-long molecular dynamics simulation of the GLIC channel pH stimulated gating mechanism. The crystal structure of GLIC obtained at acidic pH in an open-channel form is equilibrated in a membrane environment and then instantly set to neutral pH. The simulation shows a channel closure that rapidly takes place at the level of the hydrophobic furrow and a progressively increasing quaternary twist. Two major events are captured during the simulation. They are initiated by local but large fluctuations in the pore, taking place at the top of the M2 helix, followed by a global tertiary relaxation. The two-step transition of the first subunit starts within the first 50 ns of the simulation and is followed at 450 ns by its immediate neighbor in the pentamer, which proceeds with a similar scenario. This observation suggests a possible two-step domino-like tertiary mechanism that takes place between adjacent subunits. In addition, the dynamical properties of GLIC described here offer an interpretation of the paradoxical properties of a permeable A13′F mutant whose crystal structure determined at 3.15 Å shows a pore too narrow to conduct ions.allosteric transition | hydrophobic gate | cys-loop receptor family N eurotransmitter receptors mediate chemical communication in the nervous systems. In the case of ligand-gated ion channels typified by the nAChR (1, 2), the receptor is a transmembrane pentamer carrying the neurotransmitter binding sites and the ion channel on distinct extracellular (ECD) and transmembrane (TMD) domains, respectively, and acetylcholine binding elicits channel opening through a global conformational transition, creating a flux of cations along their electrochemical gradient.nAChRs belong to the cys-loop receptors family (CLRs) that includes serotonin, glycine, and GABA receptors (3), and their gating plausibly involves an allosteric pathway that links the neurotransmitter sites to the channel (4), the interface between TMD and ECD playing a critical role in this process (4). Furthermore, intermediate priming states in the gating process have recently been suggested (5, 6).The structural data of eukaryotic CLRs is limited to x-ray structures of the ECD (7,8) and to a model of Torpedo nAChR derived from cryo-EM data at 4-Å resolution (9). The discovery of CLR sequences in bacteria (10) and the demonstration that a Gloeobacter violaceus homologue (called GLIC), functions as a proton-gated cationic channel (11) were incentive to the resolution at 3.3 Å of the crystallographic structure of a full CLR from Erwinia chrysanthemi (12) in a closed conformation (called ELIC) and of GLIC at 2.9 Å resolution after crystallization at pH 4.6 in an open conformation (13,14). ELIC and GLIC structures resemble that of nAChRs but lack the unconser...

Crystal Structures of a Cysteine-modified Mutant in Loop D of Acetylcholine-binding Protein

“…This result suggests a functional role of the extracellular domain of ␣1 GlyR in selection and permeation of anions. Our observation fits with molecular dynamics simulations of the nAChR (51) and the bacterial homolog GLIC (52), which demonstrated the existence of one or more cation reservoirs in the extracellular domain of these cationselective Cys-loop receptors.…”

Structural basis for alcohol modulation of a pentameric ligand-gated ion channel

“…Early in the 200-ns simulation, the 14′ substitution caused a structural change with a dramatic increase in the kink angle of the M2 helix (Fig. 5A), around the level of the hydrophobic gate at the 9′ position (43). Over the second half of the simulation the kink angle was consistently larger in the F(14′)A mutant than in the wild-type channel (Fig.…”

Charge and Geometry of Residues in the Loop 2 β Hairpin Differentially Affect Agonist and Ethanol Sensitivity in Glycine Receptors

“…Loop 2 in GLIC is essentially identical to the corresponding loop 2 in the X-ray structure of the glutamate chloride channel (Hibbs and Gouaux, 2011). We chose to prepare a homology model based on GLIC because long time-scale molecular dynamics studies in GLIC (Nury et al, 2010(Nury et al, , 2011Zhu and Hummer, 2010) have allowed us to interpret interactions of salt bridges between the ligand-binding extracellular and TM domains of GlyR (Kash et al, 2003) in terms of dynamic interactions on the microsecond time scale (Murail et al, 2011).…”