ABSTRACT
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.
Subject(s)
Peptides/chemistry , Peptides/metabolism , Receptors, AMPA/chemistry , Amino Acid Sequence , Binding Sites , Computer Simulation , Ligands , Models, Molecular , Molecular Sequence Data , Protein Conformation , Receptors, AMPA/metabolism , Water/metabolismABSTRACT
Field potentials recorded in the olfactory bulb glomerular layer (GL) are thought to result mainly from activation of mitral and tufted cells. The contribution of juxtaglomerular cells (JG) is unknown. We tested the hypothesis that JG are the main driving force to novel spontaneous glomerular layer field potentials (sGLFPs), which were recorded in rat olfactory bulb slices maintained in an interface chamber. We found that sGLFPs have comparable magnitudes, durations and frequencies both in standard horizontal slices, where all layers with all cell types were present, and in isolated GL slices, where only JG cells were preserved. Hence, the impact of mitral and deep/medium tufted cells to sGLFPs turned out to be minor. Therefore, we propose that the main generators of sGLFPs are JG neurons. We further explored the mechanism of generation of sGLFPs using a neuronal ensemble model comprising all types of cells associated with a single glomerulus. Random orientation and homogenous distribution of dendrites in the glomerular neuropil along with surrounding shell of cell bodies of JG neurons resulted in substantial spatial restriction of the generated field potential. The model predicts that less than 20% of sGLFP can spread from one glomerulus to an adjacent one. The contribution of JG cells to the total field in the center of the glomerulus is estimated as approximately 50% ( approximately 34% periglomerular and approximately 16% external tufted cells), whereas deep/medium tufted cells provide approximately 39% and mitral cells only approximately 10%. Occasionally, some sGLFPs recorded in adjacent or remote glomeruli were cross-correlated, suggesting involvement of interglomerular communication in information coding. These results demonstrate a leading role of JG cells in activation of the main olfactory bulb (MOB) functional modules. Finally, we hypothesize that the GL is not a set of independent modules, but it represents a subsystem in the MOB network, which can perform initial processing of odors.
Subject(s)
Evoked Potentials/physiology , Nerve Net/physiology , Neurons/physiology , Olfactory Bulb/cytology , 6-Cyano-7-nitroquinoxaline-2,3-dione/pharmacology , Animals , Animals, Newborn , Bicuculline/pharmacology , Electric Stimulation , Evoked Potentials/drug effects , Evoked Potentials/radiation effects , Excitatory Amino Acid Antagonists/pharmacology , Female , GABA Antagonists/pharmacology , In Vitro Techniques , Male , Models, Neurological , Nerve Net/drug effects , Neurons/drug effects , Neurons/radiation effects , Patch-Clamp Techniques/methods , Rats , Rats, Sprague-Dawley , Reaction Time/drug effects , Reaction Time/physiology , Reaction Time/radiation effects , Valine/analogs & derivatives , Valine/pharmacologyABSTRACT
A recently introduced real-space lattice methodology for solving the three-dimensional Poisson-Nernst-Planck equations is used to compute current-voltage relations for ion permeation through the gramicidin A ion channel embedded in membranes characterized by surface dipoles and/or surface charge. Comparisons to a variety of experimental results, presented herein, have proven largely successful. Strengths and weaknesses of the method are discussed.
Subject(s)
Cell Membrane/chemistry , Gramicidin/chemistry , Ion Channels/chemistry , Protein Structure, Tertiary , Static Electricity , Algorithms , Cell Membrane/metabolism , Computer Simulation , Ion Channels/metabolism , Ion Transport/physiology , Membranes, Artificial , Models, Chemical , Models, Molecular , Poisson DistributionABSTRACT
A lattice relaxation algorithm is developed to solve the Poisson-Nernst-Planck (PNP) equations for ion transport through arbitrary three-dimensional volumes. Calculations of systems characterized by simple parallel plate and cylindrical pore geometries are presented in order to calibrate the accuracy of the method. A study of ion transport through gramicidin A dimer is carried out within this PNP framework. Good agreement with experimental measurements is obtained. Strengths and weaknesses of the PNP approach are discussed.
