A model of the glycine receptor deduced from Brownian dynamics studies

Abstract

We have developed a three-dimensional model of the ␣1 homomeric glycine receptor by using Brownian dynamics simulations to account for its observed physiological properties. The model channel contains a large external vestibule and a shallow internal vestibule, connected by a narrow, cylindrical selectivity filter. Three rings of charged residues from the pore-lining M2 domain are modeled as point charges in the protein. Our simulations reproduce many of the key features of the channel, such as the currentvoltage profiles, permeability ratios, and ion selectivity. When we replace the ring of alanine residues lining the selectivity filter with glutamates, the mutant model channel becomes permeable to cations, as observed experimentally. In this mutation, anions act as chaperones for sodium ions in the extracellular vestibule, and together they penetrate deep inside the channel against a steep energy barrier encountered by unaccompanied ions. Two subsequent amino acid mutations increase the cation permeability, enabling monovalent cations to permeate through the channel unaided and divalent cations to permeate when chaperoned by anions. These results illustrate the key structural features and underlying mechanism for charge selectivity in the glycine receptor.ligand-gated ion channels ͉ conductance ͉ permeation I n recent years, enormous strides have been made in our understanding of the structure-function relationships in biological ion channels. The determination of the structures of several different classes of ion channels and concurrent advances in computational biophysics have prompted numerous theoretical investigations that have shed considerable light on mechanisms of permeation and selectivity. Among these are the thermodynamics of cation permeation through the selectivity filter (1), macroscopic studies of energy profiles in the pore (2-4), semimicroscopic simulations to elucidate the mechanisms of ion permeation and selectivity (4-7), and molecular dynamics calculations focusing on permeation (8)(9)(10)(11)(12)(13)(14). In addition, threedimensional Brownian dynamics simulations have been fruitfully used to construct a model of the L-type calcium channel (15, 16). These theoretical studies are reviewed in several recent articles (17)(18)(19)(20).One class of proteins that has been neglected in theoretical investigations is that of anion-selective channels. Important members of the ligand-gated anion channel family include the ␥-aminobutyric acid (GABA) and glycine receptors, which mediate hyperpolarizing synaptic potentials in response to neurotransmitters. Although the crystal structures of the glycine and GABA receptors are not yet determined, the experimental findings and the high similarity of these channels to the nicotinic acetylcholine receptor allow us to make a reasonable conjecture on their approximate shape and the locations of dipoles and charged residues lining the channel wall. Like the acetylcholine receptor (21), which belongs to the same superfamily, the glycine receptor (GlyR) is like...

Homology Model of the GABAA Receptor Examined Using Brownian Dynamics

“…This initiates ion conduction, resulting in the outermost ion being expelled from the pore, thus restoring the stable 10-ion equilibrium. This process has been noticed in previous Brownian dynamics simulations using all-atom and electrostatic models of other channels O'Mara et al, 2003).…”

Ligand-Gated Channels

“…This needs to be done in femtosecond time steps for all the ions in the channel and the calculations repeated millions of times, to determine the trajectories of the ions and subsequent ionic fluxes, for different voltages across the channel. This has now been done for WT and some cation-selective mutant GlyRs [37]. This study was able to simulate the key permeation features of these channels and particularly the basic role of charged residues in determining ion charge selectivity.…”

Anion currents in yeast K+ transporters (TRK) characterize a structural homologue of ligand-gated ion channels

“…9b are depicted in presumed closed states, which would be enforced by hydrophobic exclusion of water, and therefore exclusion of hydrated ions. For LGICs, elaborate machinery has evolved in the surrounding protein to control gating; and there is much discussion of how that might work, focusing on Arg/Lys-0′ and adjacent residues, on the center of the membrane adjacent to Leu-9′, and on changes in tilt of the M2 helices [11, 36, 62, 65, 82]. For the yeast TRK-Cl − conductance, no organic ligands, TRK segments, or β subunits are presently known to effect gating.…”