Pore loops: an emerging theme in ion channel structure

Solute translocation probability, lifetime, and "rectification" in membrane channels with localized constriction

We study the translocation probability and lifetime of a solute molecule in a cylindrical membrane channel that contains a localized constriction at an arbitrary location. Using a one-dimensional continuous diffusion description of solute dynamics in the channel, we explore two models. The first one describes a molecule's interaction with the constriction in terms of a narrow rectangular barrier in the potential of mean force. The second novel model proposed here represents this interaction by introducing an infinitely thin permeable partition. It is shown that when the parameters of the two models are chosen to warrant the same translocation probability, both models predict the same mean lifetime of the molecule in the channel. While the translocation probability is independent of the constriction location, the mean lifetime is a function of the location. The benefit of the thin partition model is that it allows one to lump together the height and length of the potential barrier into a single parameter, which is the partition's permeability. It is shown that in the case of an asymmetric location of the localized constriction and strong repulsion between the solutes, the solute flux through the channel is a function of the direction in which it goes, analogous to the phenomenon known in ion channel electrophysiology as rectification.

Inhibitory effect of aloperine on transient outward potassium currents in rat cardiac myocytes

Objective

Aloperine (ALO) is an effective quinolizidine alkaloid. Previous research has demonstrated its antiarrhythmic effect by inhibiting voltage-gated sodium currents in rat ventricular myocytes. This study explored its effect on transient outward potassium currents (Ito) in rat atrial myocytes to identify potential targets in the context of ion channel currents.

Methods

The Ito characteristics in rat atrial myocytes were recorded using a whole-cell patch-clamp technique. Molecular docking was performed to validate ligand-protein binding interactions.

Results

ALO at concentrations of 3 and 10 μM significantly reduced Ito current densities. Gating kinetics analysis revealed ALO's ability to slow Ito activation, hasten inactivation, and prolong transition from inactive to resting state. Molecular docking revealed that ALO could stably bind to KCND2.

Conclusion

ALO may inhibit Ito by slowing the activation process, accelerating inactivation, and delaying the recovery time after inactivation, potentially preventing acetylcholine-induced AF.

Genome-wide identification of glutamate receptor genes in adzuki bean and the roles of these genes in light and rust fungal response

Plant glutamate receptor proteins (GLRs) are involved in plant development, biotic stress, and light-signal transduction. Vigna angularis is a traditional crop with important economic value in China, and the identification of functional genes can facilitate the breeding of stress resistant varieties. Here, we identified the members of the GLR gene family in the adzuki bean genome and investigated gene expression under light and rust fungal (Uromyces vignae) stimuli. Sixteen GLR genes were identified in V. angularis (VaGLRs), and these genes clustered in a single clade (clade III) with two groups. Evolutionary analysis showed that three VaGLRs result from tandem duplications and four result from whole genome/segmental duplications. To understand the regulation of expression of VaGLRs, cis-acting elements were analyzed in the promoter regions of the VaGLRs including cis-acting elements associated with light and stress responsiveness. Expression analysis by qRT-PCR revealed transcripts of eight and 10 VaGLRs in response to light stimuli and rust infection, respectively. For light responsiveness, the expression levels of XP_017430569.1 and XP_017425299.1 were higher under light condition than in darkness, while the expression levels of XP_017406996.1, XP_017425763.1, and XP_017423557.1 gradually recovered during dark treatment. Additionally, the relative expression levels of XP_017413816.1, XP_017436268.1, and XP_017425299.1 were significantly elevated during U. vignae infection in a resistant cultivar compared to the expression levels in a susceptible cultivar. XP_017425299.1 expression was induced both by light and rust infection, suggesting this gene may link light and disease resistance signaling pathways. Our results provide insight into how the VaGLRs contribute to adzuki bean response to light stimulus and pathogen attack. These identified VaGLRs also provide important reference to improve adzuki bean germplasm resources.

Personalized structural biology reveals the molecular mechanisms underlying heterogeneous epileptic phenotypes caused by de novo KCNC2 variants

Whole-exome sequencing (WES) in the clinic has identified several rare monogenic developmental and epileptic encephalopathies (DEE) caused by ion channel variants. However, WES often fails to provide actionable insight for rare diseases, such as DEEs, due to the challenges of interpreting variants of unknown significance (VUS). Here, we describe a "personalized structural biology" (PSB) approach that leverages recent innovations in the analysis of protein 3D structures to address this challenge. We illustrate this approach in an Undiagnosed Diseases Network (UDN) individual with DEE symptoms and a de novo VUS in KCNC2 (p.V469L), the Kv3.2 voltage-gated potassium channel. A nearby KCNC2 variant (p.V471L) was recently suggested to cause DEE-like phenotypes. Computational structural modeling suggests that both affect protein function. However, despite their proximity, the p.V469L variant is likely to sterically block the channel pore, while the p.V471L variant is likely to stabilize the open state. Biochemical and electrophysiological analyses demonstrate heterogeneous loss-of-function and gain-of-function effects, as well as differential response to 4-aminopyridine treatment. Molecular dynamics simulations illustrate that the pore of the p.V469L variant is more constricted, increasing the energetic barrier for K+ permeation, whereas the p.V471L variant stabilizes the open conformation. Our results implicate variants in KCNC2 as causative for DEE and guide the interpretation of a UDN individual. They further delineate the molecular basis for the heterogeneous clinical phenotypes resulting from two proximal pathogenic variants. This demonstrates how the PSB approach can provide an analytical framework for individualized hypothesis-driven interpretation of protein-coding VUS.

Genome-Wide Identification, Characterization, and Expression Analysis of Glutamate Receptor-like Gene (GLR) Family in Sugarcane

The plant glutamate receptor-like gene (GLR) plays a vital role in development, signaling pathways, and in its response to environmental stress. However, the GLR gene family has not been comprehensively and systematically studied in sugarcane. In this work, 43 GLR genes, including 34 in Saccharum spontaneum and 9 in the Saccharum hybrid cultivar R570, were identified and characterized, which could be divided into three clades (clade I, II, and III). They had different evolutionary mechanisms, the former was mainly on the WGD/segmental duplication, while the latter mainly on the proximal duplication. Those sugarcane GLR proteins in the same clade had a similar gene structure and motif distribution. For example, 79% of the sugarcane GLR proteins contained all the motifs, which proved the evolutionary stability of the sugarcane GLR gene family. The diverse cis-acting regulatory elements indicated that the sugarcane GLRs may play a role in the growth and development, or under the phytohormonal, biotic, and abiotic stresses. In addition, GO and KEGG analyses predicted their transmembrane transport function. Based on the transcriptome data, the expression of the clade III genes was significantly higher than that of the clade I and clade II. Furthermore, qRT-PCR analysis demonstrated that the expression of the SsGLRs was induced by salicylic acid (SA) treatment, methyl jasmonic acid (MeJA) treatment, and abscisic acid (ABA) treatment, suggesting their involvement in the hormone synthesis and signaling pathway. Taken together, the present study should provide useful information on comparative genomics to improve our understanding of the GLR genes and facilitate further research on their functions.

Structural Plasticity of the Selectivity Filter in Cation Channels

Ion channels allow for the passage of ions across biological membranes, which is essential for the functioning of a cell. In pore loop channels the selectivity filter (SF) is a conserved sequence that forms a constriction with multiple ion binding sites. It is becoming increasingly clear that there are several conformations and dynamic states of the SF in cation channels. Here we outline specific modes of structural plasticity observed in the SFs of various pore loop channels: disorder, asymmetry, and collapse. We summarize the multiple atomic structures with varying SF conformations as well as asymmetric and more dynamic states that were discovered recently using structural biology, spectroscopic, and computational methods. Overall, we discuss here that structural plasticity within the SF is a key molecular determinant of ion channel gating behavior.

Proteomic and Transcriptomic Analyses Reveal Pathological Changes in the Entorhinal Cortex Region that Correlate Well with Dysregulation of Ion Transport in Patients with Alzheimer's Disease

Alzheimer's disease (AD) is the most common neurodegenerative disorder. The earliest neuropathology of AD appears in entorhinal cortex (EC) regions. Therapeutic strategies and preventive measures to protect against entorhinal degeneration would be of substantial value in the early stages of AD. In this study, transcriptome based on the Illumina RNA-seq and proteome based on TMT-labelling were performed for RNA and protein profiling on AD EC samples and non-AD control EC samples. Immunohistochemistry was used to validate proteins expressions. After integrated analysis, 57 genes were detected both in transcriptome and proteome data, including 51 in similar altering trends (7 upregulated, 44 downregulated) and 6 in inverse trends when compared AD vs. control. The top 6 genes (GABRG2, CACNG3, CACNB4, GABRB2, GRIK2, and SLC17A6) within the 51 genes were selected and related to "ion transport". Correlation analysis demonstrated negative relationship of protein expression level with the neuropathologic changes. In conclusion, the integrate transcriptome and proteome analysis provided evidence for dysregulation of ion transport across brain regions in AD, which might be a critical signaling pathway that initiates pathology. This study might provide new insight into the earliest changes occurring in the EC of AD and novel targets for AD prevention and treatment.

Determination of the membrane topology of PORCN, an O-acyl transferase that modifies Wnt signalling proteins

Wnt gradients elicit distinct cellular responses, such as proliferation, specification, differentiation and survival in a dose-dependent manner. Porcupine (PORCN), a membrane-bound O-acyl transferase (MBOAT) that resides in the endoplasmic reticulum, catalyses the addition of monounsaturated palmitate to Wnt proteins and is required for Wnt gradient formation and signalling. In humans, PORCN mutations are causal for focal dermal hypoplasia (FDH), an X-linked dominant syndrome characterized by defects in mesodermal and endodermal tissues. PORCN is also an emerging target for cancer therapeutics. Despite the importance of this enzyme, its structure remains poorly understood. Recently, the crystal structure of DltB, an MBOAT family member from bacteria, was solved. In this report, we use experimental data along with homology modelling to DltB to determine the membrane topology of PORCN. Our studies reveal that PORCN has 11 membrane domains, comprising nine transmembrane spanning domains and two reentrant domains. The N-terminus is oriented towards the lumen while the C-terminus is oriented towards the cytosol. Like DltB, PORCN has a funnel-like structure that is encapsulated by multiple membrane-spanning helices. This new model for PORCN topology allows us to map residues that are important for biological activity (and implicated in FDH) onto its three-dimensional structure.

Molecular Mechanism of Autosomal Recessive Long QT-Syndrome 1 without Deafness

KCNQ1 encodes the voltage-gated potassium (Kv) channel KCNQ1, also known as KvLQT1 or Kv7.1. Together with its ß-subunit KCNE1, also denoted as minK, this channel generates the slowly activating cardiac delayed rectifier current I_Ks, which is a key regulator of the heart rate dependent adaptation of the cardiac action potential duration (APD). Loss-of-function mutations in KCNQ1 cause congenital long QT1 (LQT1) syndrome, characterized by a delayed cardiac repolarization and a prolonged QT interval in the surface electrocardiogram. Autosomal dominant loss-of-function mutations in KCNQ1 result in long QT syndrome, called Romano–Ward Syndrome (RWS), while autosomal recessive mutations lead to Jervell and Lange-Nielsen syndrome (JLNS), associated with deafness. Here, we identified a homozygous KCNQ1 mutation, c.1892_1893insC (p.P631fs*20), in a patient with an isolated LQT syndrome (LQTS) without hearing loss. Nevertheless, the inheritance trait is autosomal recessive, with heterozygous family members being asymptomatic. The results of the electrophysiological characterization of the mutant, using voltage-clamp recordings in Xenopus laevis oocytes, are in agreement with an autosomal recessive disorder, since the I_Ks reduction was only observed in homomeric mutants, but not in heteromeric I_Ks channel complexes containing wild-type channel subunits. We found that KCNE1 rescues the KCNQ1 loss-of-function in mutant I_Ks channel complexes when they contain wild-type KCNQ1 subunits, as found in the heterozygous state. Action potential modellings confirmed that the recessive c.1892_1893insC LQT1 mutation only affects the APD of homozygous mutation carriers. Thus, our study provides the molecular mechanism for an atypical autosomal recessive LQT trait that lacks hearing impairment.

Highlighting membrane protein structure and function: A celebration of the Protein Data Bank

Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.

Conserved biophysical features of the CaV2 presynaptic Ca2+ channel homologue from the early-diverging animal Trichoplax adhaerens

The dominant role of CaV2 voltage-gated calcium channels for driving neurotransmitter release is broadly conserved. Given the overlapping functional properties of CaV2 and CaV1 channels, and less so CaV3 channels, it is unclear why there have not been major shifts toward dependence on other CaV channels for synaptic transmission. Here, we provide a structural and functional profile of the CaV2 channel cloned from the early-diverging animal Trichoplax adhaerens, which lacks a nervous system but possesses single gene homologues for CaV1-CaV3 channels. Remarkably, the highly divergent channel possesses similar features as human CaV2.1 and other CaV2 channels, including high voltage-activated currents that are larger in external Ba2+ than in Ca2+; voltage-dependent kinetics of activation, inactivation, and deactivation; and bimodal recovery from inactivation. Altogether, the functional profile of Trichoplax CaV2 suggests that the core features of presynaptic CaV2 channels were established early during animal evolution, after CaV1 and CaV2 channels emerged via proposed gene duplication from an ancestral CaV1/2 type channel. The Trichoplax channel was relatively insensitive to mammalian CaV2 channel blockers ω-agatoxin-IVA and ω-conotoxin-GVIA and to metal cation blockers Cd2+ and Ni2+ Also absent was the capacity for voltage-dependent G-protein inhibition by co-expressed Trichoplax Gβγ subunits, which nevertheless inhibited the human CaV2.1 channel, suggesting that this modulatory capacity evolved via changes in channel sequence/structure, and not G proteins. Last, the Trichoplax channel was immunolocalized in cells that express an endomorphin-like peptide implicated in cell signaling and locomotive behavior and other likely secretory cells, suggesting contributions to regulated exocytosis.

TRP ion channels: Proteins with conformational flexibility

Ion channels display conformational changes in response to binding of their agonists and antagonists. The study of the relationships between the structure and the function of these proteins has witnessed considerable advances in the last two decades using a combination of techniques, which include electrophysiology, optical approaches (i.e. patch clamp fluorometry, incorporation of non-canonic amino acids, etc.), molecular biology (mutations in different regions of ion channels to determine their role in function) and those that have permitted the resolution of their structures in detail (X-ray crystallography and cryo-electron microscopy). The possibility of making correlations among structural components and functional traits in ion channels has allowed for more refined conclusions on how these proteins work at the molecular level. With the cloning and description of the family of Transient Receptor Potential (TRP) channels, our understanding of several sensory-related processes has also greatly moved forward. The response of these proteins to several agonists, their regulation by signaling pathways as well as by protein-protein and lipid-protein interactions and, in some cases, their biophysical characteristics have been studied thoroughly and, recently, with the resolution of their structures, the field has experienced a new boom. This review article focuses on the conformational changes in the pores, concentrating on some members of the TRP family of ion channels (TRPV and TRPA subfamilies) that result in changes in their single-channel conductances, a phenomenon that may lead to fine-tuning the electrical response to a given agonist in a cell.

Revealing the ultrastructure of the membrane pores of intact Serratia marcescens cells by atomic force microscopy

This study aimed to characterize the surface ultrastructure of intact Serratia marcescens cells under physiological conditions. Topographic information of membrane pores of the cells was obtained by atomic force microscope (AFM). Three types of membrane pores (CH-1-Pore A, CH-1-Pore B and CH-1-Pore C) were observed and the spatial arrangements of membrane-spanning subunits in membranes were defined. High-resolution images revealed that the doughnut-shaped structures of CH-1-Pore A and CH-1-Pore B were composed of six-to-eight and four transmembrane subunits. The inverted teepee-shaped structure of CH-1-Pore C was segmented into two transmembrane subunits straddling a single funnel-like pore. This study, to the best of authors' knowledge, represents the first direct characterization of the surface ultrastructure of the membrane pores of Serratia marcescens CH-1 cells at the nanometer scale and offers new prospects of mapping membrane pores on intact prokaryotic cells.

Permeation Mechanism of Potassium Ions through the Large Conductance Ca2+-Activated Potassium Channel

The permeation of the potassium ion (K⁺) through the selectivity filter (SF) of the large conductance Ca²⁺-activated potassium (Slo1) channel remains an interesting question to study. Although the mode of K⁺ entering and leaving the SF has been revealed, the mechanism of K⁺ passing through the SF is still not clear. In the present study, the pattern of K⁺ permeation through the SF is investigated by chemical computation and data mining based on the molecular structure of Slo1 from Aplysia californica. Both bond configurations and the free energy of K⁺s inside the SF was studied using Discovery Studio software. The results suggested that, to accommodate increasing energy levels and to tolerate more K⁺s, 4-fold symmetric subunits of SF can only move at one direction that is perpendicular to the center axis. In addition, two configurations of chemical bonds between K⁺s and the SF are usually employed including the chelate configuration under low free energy and the complex configuration under high free energy conditions. Moreover, three patterns of bond configurations for multiple K⁺s within the SF are used to accommodate the energetic changes of the SF, and each pattern is composed of one or two subconformations. These findings likely resulted from the evolutionary optimization of the protein function of Slo1. The specific conductance and the voltage-gating of the Slo1 channel can be reinterpreted with the permeation mechanism of K⁺s found in the current study. The permeation mechanism of K⁺s through the SF can be used to understand the interaction between various toxins and the Slo1 channel, and can be employed to develop new drugs targeting relevant ion channels.

Membranes with Functionalized Nanopores for Aromaticity-Based Separation of Small Molecules

Membranes that can separate molecules of similar size based on chemical features could transform chemical manufacturing. We demonstrate membranes with functional, 1-3 nm pores prepared using a simple and scalable approach: coating a porous support with random copolymer micelles in alcohol, followed by precipitation in water and functionalization of pore surfaces. This approach was used to prepare membranes that can separate two hormones of similar size and charge, differentiated by aromaticity, mediated through π-π interactions between the aromatic solute and pore walls functionalized with phenol groups. The aromatic molecule permeates more slowly in single-solute experiments. In competitive diffusion experiments, however, it permeates 7.1 times faster than its nonaromatic analogue. This approach can be used to manufacture membranes for complex separations based on various intermolecular interactions.

Thick Ascending Limb Sodium Transport in the Pathogenesis of Hypertension

The thick ascending limb plays a key role in maintaining water and electrolyte balance. The importance of this segment in regulating blood pressure is evidenced by the effect of loop diuretics or local genetic defects on this parameter. Hormones and factors produced by thick ascending limbs have both autocrine and paracrine effects, which can extend prohypertensive signaling to other structures of the nephron. In this review, we discuss the role of the thick ascending limb in the development of hypertension, not as a sole participant, but one that works within the rich biological context of the renal medulla. We first provide an overview of the basic physiology of the segment and the anatomical considerations necessary to understand its relationship with other renal structures. We explore the physiopathological changes in thick ascending limbs occurring in both genetic and induced animal models of hypertension. We then discuss the racial differences and genetic defects that affect blood pressure in humans through changes in thick ascending limb transport rates. Throughout the text, we scrutinize methodologies and discuss the limitations of research techniques that, when overlooked, can lead investigators to make erroneous conclusions. Thus, in addition to advancing an understanding of the basic mechanisms of physiology, the ultimate goal of this work is to understand our research tools, to make better use of them, and to contextualize research data. Future advances in renal hypertension research will require not only collection of new experimental data, but also integration of our current knowledge.

Polyamine-mediated channel block of ionotropic glutamate receptors and its regulation by auxiliary proteins

Most excitatory neurotransmission in the mammalian brain is mediated by a family of plasma membrane-bound signaling proteins called ionotropic glutamate receptors (iGluRs). iGluRs assemble at central synapses as tetramers, forming a central ion-channel pore whose primary function is to rapidly transport Na⁺ and Ca²⁺ in response to binding the neurotransmitter l-glutamic acid. The pore of iGluRs is also accessible to bulkier cytoplasmic cations, such as the polyamines spermine, spermidine, and putrescine, which are drawn into the permeation pathway, but get stuck and block the movement of other ions. The degree of this polyamine-mediated channel block is highly regulated by processes that control the free cytoplasmic polyamine concentration, the membrane potential, or the iGluR subunit composition. Recently, an additional regulation by auxiliary proteins, most notably transmembrane AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor regulatory proteins (TARPs), cornichons, and neuropilin and tolloid-like proteins (NETOs), has been identified. Here, I review what we have learned of polyamine block of iGluRs and its regulation by auxiliary subunits. TARPs, cornichons, and NETOs attenuate the channel block by enabling polyamines to exit the pore. As a result, polyamine permeation occurs at more negative and physiologically relevant membrane potentials. The structural basis for enhanced polyamine transport remains unresolved, although alterations in both channel architecture and charge-screening mechanisms have been proposed. That auxiliary subunits can attenuate the polyamine block reveals an unappreciated impact of polyamine permeation in shaping the signaling properties of neuronal AMPA- and kainate-type iGluRs. Moreover, enhanced polyamine transport through iGluRs may have a role in regulating cellular polyamine levels.

Cardiac Potassium Channels: Physiological Insights for Targeted Therapy

The development of novel drugs specifically directed at the ion channels underlying particular features of cardiac action potential (AP) initiation, recovery, and refractoriness would contribute to an optimized approach to antiarrhythmic therapy that minimizes potential cardiac and extracardiac toxicity. Of these, K⁺ channels contribute numerous and diverse currents with specific actions on different phases in the time course of AP repolarization. These features and their site-specific distribution make particular K⁺ channel types attractive therapeutic targets for the development of pharmacological agents attempting antiarrhythmic therapy in conditions such as atrial fibrillation. However, progress in the development of such temporally and spatially selective antiarrhythmic drugs against particular ion channels has been relatively limited, particularly in view of our incomplete understanding of the complex physiological roles and interactions of the various ionic currents. This review summarizes the physiological properties of the main cardiac potassium channels and the way in which they modulate cardiac electrical activity and then critiques a number of available potential antiarrhythmic drugs directed at them.

Arthropod toxins acting on neuronal potassium channels

Arthropod venoms are a rich mixture of biologically active compounds exerting different physiological actions across diverse phyla and affecting multiple organ systems including the central nervous system. Venom compounds can inhibit or activate ion channels, receptors and transporters with high specificity and affinity providing essential insights into ion channel function. In this review, we focus on arthropod toxins (scorpions, spiders, bees and centipedes) acting on neuronal potassium channels. A brief description of the K⁺ channels classification and structure is included and a compendium of neuronal K⁺ channels and the arthropod toxins that modify them have been listed. This article is part of the Special Issue entitled 'Venom-derived Peptides as Pharmacological Tools.'

Physiology and Evolution of Voltage-Gated Calcium Channels in Early Diverging Animal Phyla: Cnidaria, Placozoa, Porifera and Ctenophora

Voltage-gated calcium (Ca_v) channels serve dual roles in the cell, where they can both depolarize the membrane potential for electrical excitability, and activate transient cytoplasmic Ca²⁺ signals. In animals, Ca_v channels play crucial roles including driving muscle contraction (excitation-contraction coupling), gene expression (excitation-transcription coupling), pre-synaptic and neuroendocrine exocytosis (excitation-secretion coupling), regulation of flagellar/ciliary beating, and regulation of cellular excitability, either directly or through modulation of other Ca²⁺-sensitive ion channels. In recent years, genome sequencing has provided significant insights into the molecular evolution of Ca_v channels. Furthermore, expanded gene datasets have permitted improved inference of the species phylogeny at the base of Metazoa, providing clearer insights into the evolution of complex animal traits which involve Ca_v channels, including the nervous system. For the various types of metazoan Ca_v channels, key properties that determine their cellular contribution include: Ion selectivity, pore gating, and, importantly, cytoplasmic protein-protein interactions that direct sub-cellular localization and functional complexing. It is unclear when these defining features, many of which are essential for nervous system function, evolved. In this review, we highlight some experimental observations that implicate Ca_v channels in the physiology and behavior of the most early-diverging animals from the phyla Cnidaria, Placozoa, Porifera, and Ctenophora. Given our limited understanding of the molecular biology of Ca_v channels in these basal animal lineages, we infer insights from better-studied vertebrate and invertebrate animals. We also highlight some apparently conserved cellular functions of Ca_v channels, which might have emerged very early on during metazoan evolution, or perhaps predated it.

A Novel Method for the Description of Voltage-Gated Ionic Currents Based on Action Potential Clamp Results-Application to Hippocampal Mossy Fiber Boutons

Action potential clamp (AP-clamp) recordings of the delayed rectifier K(+) current I K and the fast-activated Na(+) current I Na in rat hippocampal mossy fiber boutons (MFBs) are analyzed using a computational technique recently reported. The method is implemented using a digitized AP from an MFB and computationally applying that data set to published models of I K and I Na. These numerical results are compared with experimental AP-clamp recordings. The I Na result is consistent with experiment; the I K result is not. The difficulty with the I K model concerns the fully activated current-voltage relation, which is described here by the Goldman-Hodgkin-Katz dependence on the driving force (V-E K) rather than (V-E K) itself, the standard model for this aspect of ion permeation. That revision leads to the second-a much steeper voltage dependent activation curve for I K than the one obtained from normalization of a family of I K records by (V-E K). The revised model provides an improved description of the AP-clamp measurement of I K in MFBs compared with the standard approach. The method described here is general. It can be used to test models of ionic currents in any excitable cell. In this way it provides a novel approach to the relationship between ionic current and membrane excitability in neurons.

Modular Design of the Selectivity Filter Pore Loop in a Novel Family of Prokaryotic 'Inward Rectifier' (NirBac) channels

Potassium channels exhibit a modular design with distinct structural and functional domains; in particular, a highly conserved pore-loop sequence that determines their ionic selectivity. We now report the functional characterisation of a novel group of functionally non-selective members of the prokaryotic 'inward rectifier' subfamily of K(+) channels. These channels share all the key structural domains of eukaryotic and prokaryotic Kir/KirBac channels, but instead possess unique pore-loop selectivity filter sequences unrelated to any other known ionic selectivity filter. The strikingly unusual architecture of these 'NirBac' channels defines a new family of functionally non-selective ion channels, and also provides important insights into the modular design of ion channels, as well as the evolution of ionic selectivity within this superfamily of tetrameric cation channels.

Voltage gating by molecular subunits of Na+ and K+ ion channels: higher-dimensional cubic kinetics, rate constants, and temperature

The structural similarity between the primary molecules of voltage-gated Na and K channels (alpha subunits) and activation gating in the Hodgkin-Huxley model is brought into full agreement by increasing the model's sodium kinetics to fourth order (m(3) → m(4)). Both structures then virtually imply activation gating by four independent subprocesses acting in parallel. The kinetics coalesce in four-dimensional (4D) cubic diagrams (16 states, 32 reversible transitions) that show the structure to be highly failure resistant against significant partial loss of gating function. Rate constants, as fitted in phase plot data of retinal ganglion cell excitation, reflect the molecular nature of the gating transitions. Additional dimensions (6D cubic diagrams) accommodate kinetically coupled sodium inactivation and gating processes associated with beta subunits. The gating transitions of coupled sodium inactivation appear to be thermodynamically irreversible; response to dielectric surface charges (capacitive displacement) provides a potential energy source for those transitions and yields highly energy-efficient excitation. A comparison of temperature responses of the squid giant axon (apparently Arrhenius) and mammalian channel gating yields kinetic Q10 = 2.2 for alpha unit gating, whose transitions are rate-limiting at mammalian temperatures; beta unit kinetic Q10 = 14 reproduces the observed non-Arrhenius deviation of mammalian gating at low temperatures; the Q10 of sodium inactivation gating matches the rate-limiting component of activation gating at all temperatures. The model kinetics reproduce the physiologically large frequency range for repetitive firing in ganglion cells and the physiologically observed strong temperature dependence of recovery from inactivation.

In silico ionomics segregates parasitic from free-living eukaryotes

Ion transporters are fundamental to life. Due to their ancient origin and conservation in sequence, ion transporters are also particularly well suited for comparative genomics of distantly related species. Here, we perform genome-wide ion transporter profiling as a basis for comparative genomics of eukaryotes. From a given predicted proteome, we identify all bona fide ion channels, ion porters, and ion pumps. Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand. This surprising finding indicates strong convergent evolution of the parasites regarding the acquisition and homeostasis of inorganic ions. Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites. Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism. This finding is in agreement with the phenomenon of iron withholding as a primordial antimicrobial strategy of infected mammals.

Large conductance, calcium- and voltage-gated potassium (BK) channels: regulation by cholesterol

Cholesterol (CLR) is an essential component of eukaryotic plasma membranes. CLR regulates the membrane physical state, microdomain formation and the activity of membrane-spanning proteins, including ion channels. Large conductance, voltage- and Ca²⁺-gated K⁺ (BK) channels link membrane potential to cell Ca²⁺ homeostasis. Thus, they control many physiological processes and participate in pathophysiological mechanisms leading to human disease. Because plasmalemma BK channels cluster in CLR-rich membrane microdomains, a major driving force for studying BK channel-CLR interactions is determining how membrane CLR controls the BK current phenotype, including its pharmacology, channel sorting, distribution, and role in cell physiology. Since both BK channels and CLR tissue levels play a pathophysiological role in human disease, identifying functional and structural aspects of the CLR-BK channel interaction may open new avenues for therapeutic intervention. Here, we review the studies documenting membrane CLR-BK channel interactions, dissecting out the many factors that determine the final BK current response to changes in membrane CLR content. We also summarize work in reductionist systems where recombinant BK protein is studied in artificial lipid bilayers, which documents a direct inhibition of BK channel activity by CLR and builds a strong case for a direct interaction between CLR and the BK channel-forming protein. Bilayer lipid-mediated mechanisms in CLR action are also discussed. Finally, we review studies of BK channel function during hypercholesterolemia, and underscore the many consequences that the CLR-BK channel interaction brings to cell physiology and human disease.

Sodium leak channels in neuronal excitability and rhythmic behaviors

Extracellular K⁺, Na⁺, and Ca²⁺ ions all influence the resting membrane potential of the neuron. However, the mechanisms by which extracellular Na⁺ and Ca²⁺ regulate basal neuronal excitability are not well understood. Recent findings suggest that NALCN, in association with UNC79 and UNC80, contributes a basal Na⁺ leak conductance in neurons. Mutations in Nalcn, Unc79, or Unc80 lead to severe phenotypes that include neonatal lethality and disruption in rhythmic behaviors. This review discusses the properties of the NALCN complex, its regulation, and its contribution to neuronal function and animal behavior.

Potassium-channel mutations and cardiac arrhythmias--diagnosis and therapy

The coordinated generation and propagation of action potentials within cardiomyocytes creates the intrinsic electrical stimuli that are responsible for maintaining the electromechanical pump function of the human heart. The synchronous opening and closing of cardiac Na(+), Ca(2+), and K(+) channels corresponds with the activation and inactivation of inward depolarizing (Na(+) and Ca(2+)) and outward repolarizing (K(+)) currents that underlie the various phases of the cardiac action potential (resting, depolarization, plateau, and repolarization). Inherited mutations in pore-forming α subunits and accessory β subunits of cardiac K(+) channels can perturb the atrial and ventricular action potential and cause various cardiac arrhythmia syndromes, including long QT syndrome, short QT syndrome, Brugada syndrome, and familial atrial fibrillation. In this Review, we summarize the current understanding of the molecular and cellular mechanisms that underlie K(+)-channel-mediated arrhythmia syndromes. We also describe translational advances that have led to the emerging role of genetic testing and genotype-specific therapy in the diagnosis and clinical management of individuals who harbor pathogenic mutations in genes that encode α or β subunits of cardiac K(+) channels.

Characterisation of 13 glutamate receptor-like genes encoded in the tomato genome by structure, phylogeny and expression profiles

Glutamate receptor-like genes (GLRs) are intimately associated with plant development, defence responses and signalling pathways. Structural and expression analyses of SlGLRs were performed to better characterise their roles in fruit development and metabolism. Utilising recently released tomato genomic sequence data, 15 GLRs were identified in the tomato genome (SlGLRs). Thirteen of these genes were represented by full-length sequences. Phylogenetic analysis of the SlGLRs and the AtGLRs indicates the occurrence of a tomato-specific clade (Clade I) that may have diverged prior to the evolving of other clades. Among the Clade II genes, five (SlGLR2.1, SlGLR2.2, SlGLR2.3, SlGLR2.4, and SlGLR2.5) were located proximally on chromosome 6, indicating possible gene duplication events. The expression level of four of these genes was low in all analysed samples. However, SlGLR2.2 expression level was notably higher, indicating that this gene may be functionally important. The results of this study may provide clues to the functions of the SlGLRs and enable future detailed characterisations of each gene.

Mutagenesis mapping of the presenilin 1 calcium leak conductance pore

Missense mutations in presenilin 1 (PS1) and presenilin 2 (PS2) proteins are a major cause of familial Alzheimer disease. Presenilins are proteins with nine transmembrane (TM) domains that function as catalytic subunits of the γ-secretase complex responsible for the cleavage of the amyloid precursor protein and other type I transmembrane proteins. The water-filled cavity within presenilin is necessary to mediate the intramembrane proteolysis reaction. Consistent with this idea, cysteine-scanning mutagenesis and NMR studies revealed a number of water-accessible residues within TM7 and TM9 of mouse PS1. In addition to γ-secretase function, presenilins also demonstrate a low conductance endoplasmic reticulum Ca(2+) leak function, and many familial Alzheimer disease presenilin mutations impair this function. To map the potential Ca(2+) conductance pore in PS1, we systematically evaluated endoplasmic reticulum Ca(2+) leak activity supported by a series of cysteine point mutants in TM6, TM7, and TM9 of mouse PS1. The results indicate that TM7 and TM9, but not TM6, could play an important role in forming the conductance pore of PS1. These results are consistent with previous cysteine-scanning mutagenesis and NMR analyses of PS1 and provide further support for our hypothesis that the hydrophilic catalytic cavity of presenilins may also constitute a Ca(2+) conductance pore.

Gated access to the pore of a P2X receptor: structural implications for closed-open transitions

P2X receptors are ligand-gated cation channels that transition from closed to open states upon binding ATP. The crystal structure of the closed zebrafish P2X4.1 receptor directly reveals that the ion-conducting pathway is formed by three transmembrane domain 2 (TM2) alpha-helices, each being provided by the three subunits of the trimer. However, the transitions in TM2 that accompany channel opening are incompletely understood and remain unresolved. In this study, we quantified gated access to Cd(2+) at substituted cysteines in TM2 of P2X2 receptors in the open and closed states. Our data for the closed state are consistent with the zebrafish P2X4.1 structure, with isoleucines and threonines (Ile-332 and Thr-336) positioned one helical turn apart lining the channel wall on approach to the gate. Our data for the open state reveal gated access to deeper parts of the pore (Thr-339, Val-343, Asp-349, and Leu-353), suggesting the closed channel gate is between Thr-336 and Thr-339. We also found unexpected interactions between native Cys-348 and D349C that result in tight Cd(2+) binding deep within the intracellular vestibule in the open state. Interpreted with a P2X2 receptor structural model of the closed state, our data suggest that the channel gate opens near Thr-336/Thr-339 and is accompanied by movement of the pore-lining regions, which narrow toward the cytosolic end of TM2 in the open state. Such transitions would relieve the barrier to ion flow and render the intracellular vestibule less splayed during channel opening in the presence of ATP.

Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting

We describe here a novel footprinting technique to probe the in vivo structural dynamics of membrane protein. This method utilized in situ generation of hydroxyl radicals to oxidize and covalently modify biomolecules on living Escherichia coli cell surface. After enriching and purifying the membrane proteome, the modified amino acid residues of the protein were identified with tandem mass spectrometry to map the solvent-accessible surface of the protein that will form the footprint of in vivo structure of the protein. Of about 100 outer membrane proteins identified, we investigated the structure details of a typical beta-barrel structure, the porin OmpF. We found that six modified tryptic peptides of OmpF were reproducibly detected with 19 amino acids modified under the physiological condition. The modified amino acid residues were widely distributed in the external loop area, beta-strands, and periplasmic turning area, and all of them were validated as solvent-accessible according to the crystallography data. We further extended this method to study the dynamics of the voltage gating of OmpF in vivo using mimic changes of physiological circumstance either by pH or by ionic strength. Our data showed the voltage gating of porin OmpF in vivo for the first time and supported the proposed mechanism that the local electrostatic field changes in the eyelet region may alter the porin channels to switch. Thus, this novel method can be a potentially efficient method to study the structural dynamics of the membrane proteins of a living cell.

Plant ion channels: gene families, physiology, and functional genomics analyses

Distinct potassium, anion, and calcium channels in the plasma membrane and vacuolar membrane of plant cells have been identified and characterized by patch clamping. Primarily owing to advances in Arabidopsis genetics and genomics, and yeast functional complementation, many of the corresponding genes have been identified. Recent advances in our understanding of ion channel genes that mediate signal transduction and ion transport are discussed here. Some plant ion channels, for example, ALMT and SLAC anion channel subunits, are unique. The majority of plant ion channel families exhibit homology to animal genes; such families include both hyperpolarization- and depolarization-activated Shaker-type potassium channels, CLC chloride transporters/channels, cyclic nucleotide-gated channels, and ionotropic glutamate receptor homologs. These plant ion channels offer unique opportunities to analyze the structural mechanisms and functions of ion channels. Here we review gene families of selected plant ion channel classes and discuss unique structure-function aspects and their physiological roles in plant cell signaling and transport.

P2X receptors: a third major class of ligand-gated ion channels

Three classes of ligand-gated ion channels are defined by their molecular architecture. The first embraces nicotinic, 5-HT3, glycine and GABA receptors. The second class contains the glutamate receptors-AMPA, kainate and NMDA types. The third class is the P2X receptors for ATP. Current knowledge of the structure of these channels is reviewed, and set beside what is known of their basic functional properties. The aim of this paper is to consider how our more complete understanding of the first two classes of channels might be helpful in forming a molecular picture of P2X receptor function.

The transmembrane segment S6 determines cation versus anion selectivity of TRPM2 and TRPM8

TRPM2 and TRPM8, closely related members of the transient receptor potential (TRP) family, are cation channels activated by quite different mechanisms. Their transmembrane segments S5 and S6 are highly conserved. To identify common structures in S5 and S6 that govern interaction with the pore, we created a chimera in which the S5-pore-S6 region of TRPM8 was inserted into TRPM2, along with a lysine at each transition site. Currents through this chimera were induced by ADP-ribose (ADPR) in cooperation with Ca(2+). In contrast to wild-type TRPM2 channels, currents through the chimera were carried by Cl(-), as demonstrated in ion substitution experiments using the cation N-methyl-D-glucamine (NMDG) and the anion glutamate. Extracellular NMDG had no effects. The substitution of either intracellular or extracellular Cl(-) with glutamate shifted the reversal potential, decreased the current amplitude and induced a voltage-dependent block relieved by depolarization. The lysine in S6 was responsible for the anion selectivity; insertion of a lysine into corresponding sites within S6 of either TRPM2 or TRPM8 created anion channels that were activated by ADPR (TRPM2 I1045K) or by cold temperatures (TRPM8 V976K). The positive charge of the lysine was decisive for the glutamate block because the mutant TRPM2 I1045H displayed cation currents that were blocked at acidic but not alkaline intracellular pH values. We conclude that the distal part of S6 is crucial for the discrimination of charge. Because of the high homology of S6 in the whole TRP family, this new role of S6 may apply to further TRP channels.

A loop network within the anthrax toxin pore positions the phenylalanine clamp in an active conformation

Heptameric pores formed in the endosomal membrane by the protective antigen moiety of anthrax toxin serve as portals for entry of the enzymatic moieties of the toxin into the cytosol. In the aqueous lumen of each pore is a "Phe clamp," a heptad of narrowly apposed Phe residues (Phe-427), that catalyzes the unfolding and translocation of the enzymatic moieties across the membrane. Here, we provide evidence for a "loop swap" between neighboring protective antigen subunits, which is required for efficient translocation and is mediated by a salt bridge formed between the side chains of Lys-397 and Asp-426. We propose that the interaction between residues 397 and 426 creates a structural framework that positions Phe-427 within the pore lumen, forming a functional Phe clamp and, hence, a translocation-competent pore.

A single P-loop glutamate point mutation to either lysine or arginine switches the cation-anion selectivity of the CNGA2 channel

Cyclic nucleotide-gated (CNG) channels play a critical role in olfactory and visual transduction. Site-directed mutagenesis and inside-out patch-clamp recordings were used to investigate ion permeation and selectivity in two mutant homomeric rat olfactory CNGA2 channels expressed in HEK293 cells. A single point mutation of the negatively charged pore loop (P-loop) glutamate (E342) to either a positively charged lysine or arginine resulted in functional channels, which consistently responded to cGMP, although the currents were generally extremely small. The concentration–response curve of the lysine mutant channel was very similar to that of wild-type (WT) channels, suggesting no major structural alteration to the mutant channels. Reversal potential measurements, during cytoplasmic NaCl dilutions, showed that the lysine and the arginine mutations switched the selectivity of the channel from cations (P_Cl/P_Na = 0.07 [WT]) to anions (P_Cl/P_Na = 14 [Lys] or 10 [Arg]). Relative anion permeability sequences for the two mutant channels, measured with bi-ionic substitutions, were NO₃⁻ > I⁻ > Br⁻ > Cl⁻ > F⁻ > acetate⁻, the same as those obtained for anion-selective GABA and glycine channels. The mutant channels also seem to have an extremely small single-channel conductance, measured using noise analysis of about 1–2 pS, compared to a WT value of about 29 pS. The results showed that it is predominantly the charge of the E342 residue in the P-loop, rather than the pore helix dipoles, which controls the cation–anion selectivity of this channel. However, the outward rectification displayed by both mutant channels in symmetrical NaCl solutions suggests that the negative ends of the pore helix dipoles may play a role in reducing the outward movement of Cl⁻ ions through these anion-selective channels. These results have potential implications for the determinants of anion–cation selectivity in the large family of P-loop–containing channels.

Pharmacogenetics and cardiac ion channels

Ion channels control electrical excitability in living cells. In mammalian heart, the opposing actions of Na(+) and Ca(2+) ion influx, and K(+) ion efflux, through cardiac ion channels determine the morphology and duration of action potentials in cardiac myocytes, thus controlling the heartbeat. The last decade has seen a leap in our understanding of the molecular genetic origins of inherited cardiac arrhythmia, largely through identification of mutations in cardiac ion channels and the proteins that regulate them. Further, recent advances have shown that 'acquired arrhythmias', which occur more commonly than inherited arrhythmias, arise due to a variety of environmental factors including side effects of therapeutic drugs and often have a significant genetic component. Here, we review the pharmacogenetics of cardiac ion channels-the interplay between genetic and pharmacological factors that underlie human cardiac arrhythmias.

Permeable ions differentially affect gating kinetics and unitary conductance of L-type calcium channels

Although ion permeation and gating of L-type Ca(2+) channels are generally considered separate processes controlled by distinct components of the channel protein, ion selectivity can vary with the kinetic state. To test this possibility, we studied single-channel currents (cell-attached) of recombinant L-type channels (Ca(V)1.2, beta(2a), and alpha(2)delta) transiently expressed in tsA201 cells in the presence of the channel agonist BayK 8644 which promotes long channel openings (Mode 2 openings). We found that both the brief (Mode 1) and long (Mode 2) mean open times in the presence of Ca(2+) were relatively longer than those with Ba(2+). The unitary slope conductance with Ba(2+) was significantly larger (p<0.05) in Mode 2 openings than for brief Mode 1 openings, whereas the conductance with Ca(2+) did not vary with mode gating. Consequently, the gamma(Ba):gamma(Ca) ratio was greater for Mode 2 than Mode 1 openings. Our findings indicate that both ion permeation and gating kinetics of the L-type channel are differentially modulated by permeable ions. Ca(2+) binding to the L-type channel may stabilize the alteration of channel ion permeability mediated by gating kinetics, and thus, play a role in preventing excessive ion entry when the activation gating of the channel is promoted to the prolonged open state.

Y3+ block demonstrates an intracellular activation gate for the alpha1G T-type Ca2+ channel

Classical electrophysiology and contemporary crystallography suggest that the activation gate of voltage-dependent channels is on the intracellular side, but a more extracellular “pore gate” has also been proposed. We have used the voltage dependence of block by extracellular Y³⁺ as a tool to locate the activation gate of the α1G (Ca_V3.1) T-type calcium channel. Y³⁺ block exhibited no clear voltage dependence from −40 to +40 mV (50% block at 25 nM), but block was relieved rapidly by stronger depolarization. Reblock of the open channel, reflected in accelerated tail currents, was fast and concentration dependent. Closed channels were also blocked by Y³⁺ at a concentration-dependent rate, only eightfold slower than open-channel block. When extracellular Ca²⁺ was replaced with Ba²⁺, the rate of open block by Y³⁺ was unaffected, but closed block was threefold faster than in Ca²⁺, suggesting the slower closed-block rate reflects ion–ion interactions in the pore rather than an extracellularly located gate. Since an extracellular blocker can rapidly enter the closed pore, the primary activation gate must be on the intracellular side of the selectivity filter.

Cloning, immunolocalization, and functional expression of a GABA transporter from the retina of the skate

Termination of GABA signals within the retina occurs through high-affinity reuptake of the released neurotransmitter by GABA transporters (GATs) present in neurons and glia surrounding the release site. In the present work, we have cloned a novel GAT from the retina of the skate (Raja erinacea). The clone codes for a 622 amino acid protein whose sequence has highest similarity to the GABA/β-alanine transporter of the electric ray (Torpedo marmorata) (88% identity) and the GAT-3 isolated from rat brain (75% identity). The protein was expressed inXenopusoocytes and characterized using the two-electrode voltage-clamp technique. Application of GABA induced a dose-dependent inward current, with 8 μM GABA producing a half-maximal response. The current required the presence of extracellular sodium and was unaffected by the GABA receptor blocker picrotoxin or the GAT-1 specific antagonist NO-711. The high homology between the cloned skate GABA transporter and the GAT-3 equivalents of other species, coupled with the strikingly similar pharmacological profile to GAT-3s of other species, lead us to conclude that we had cloned the GAT-3 homologue for the skate. Polyclonal antibodies specific to GAT-3 and the previously cloned skate GAT-1 transporter were used to examine the distribution of GAT-3 and GAT-1 immunoreactivity in the retina and in isolated cells of the skate. Antibodies for both transporters showed labeling in the outer and inner plexiform layers, and staining extended from the outer to inner limiting membranes. Both GAT-1 and GAT-3 antibodies labeled enzymatically isolated Müller cells, while bipolar cells and horizontal cells did not appear to express either transporter. These results imply that GAT-1 and GAT-3 are both present in Müller cells of the skate retina where they are likely involved in regulating extracellular concentrations of GABA.

Dynamic Membrane Topology of the Escherichia coli β-Glucoside Transporter BglF

The Escherichia coli BglF protein, a permease of the phosphoenolpyruvate-dependent phosphotransferase system, catalyzes transport and phosphorylation of beta-glucosides. In addition, BglF regulates bgl operon expression by controlling the activity of the transcriptional regulator BglG via reversible phosphorylation. BglF is composed of three domains; one is hydrophobic, which presumably forms the sugar translocation channel. We studied the topology of this domain by Cys-replacement mutagenesis and chemical modification by thiol reagents. Most Cys substitutions were well tolerated, as demonstrated by the ability of the mutant proteins to catalyze BglF activities. Our results suggest that the membrane domain contains eight transmembrane helices and an alleged cytoplasmic loop that contains two additional helices. The latter region forms a dynamic structure, as evidenced by the alternation of residues near its ends between faced-in and faced-out states. We suggest that this region, together with the two transmembrane helices encompassing it, forms the sugar translocation channel. BglF periplasmic loops are close to the membrane, the first being a reentrant loop. This is the first systematic topological study carried out with an intact phosphotransferase system permease and the first demonstration of a reentrant loop in this group of proteins.

Molecular diversity and regulation of renal potassium channels

K(+) channels are widely distributed in both plant and animal cells where they serve many distinct functions. K(+) channels set the membrane potential, generate electrical signals in excitable cells, and regulate cell volume and cell movement. In renal tubule epithelial cells, K(+) channels are not only involved in basic functions such as the generation of the cell-negative potential and the control of cell volume, but also play a uniquely important role in K(+) secretion. Moreover, K(+) channels participate in the regulation of vascular tone in the glomerular circulation, and they are involved in the mechanisms mediating tubuloglomerular feedback. Significant progress has been made in defining the properties of renal K(+) channels, including their location within tubule cells, their biophysical properties, regulation, and molecular structure. Such progress has been made possible by the application of single-channel analysis and the successful cloning of K(+) channels of renal origin.

Membrane Topology of System Xc- Light Subunit Reveals a Re-entrant Loop with Substrate-restricted Accessibility

Heteromeric amino acid transporters are composed of a heavy and a light subunit linked by a disulfide bridge. 4F2hc/xCT elicits sodium-independent exchange of anionic L-cysteine and L-glutamate (system x(c)(-)). Based on the accessibility of single cysteines to 3-(N-maleimidylpropionyl)biocytin, we propose a topological model for xCT of 12 transmembrane domains with the N and C termini located inside the cell. This location of N and C termini was confirmed by immunofluorescence. Studies of biotinylation and accessibility to sulfhydryl reagents revealed a re-entrant loop within intracellular loops 2 and 3. Residues His(110) and Thr(112), facing outside, are located at the apex of the re-entrant loop. Biotinylation of H110C was blocked by xCT substrates, by the nontransportable inhibitor (S)-4-carboxyphenylglycine, and by the impermeable reagent (2-sulfonatoethyl) methanethiosulfonate, which produced an inactivation of H110C that was protected by L-glutamate and L-cysteine with an IC(50) similar to the K(m). Protection was temperatureindependent. The data indicate that His(110) may lie close to the substrate binding/permeation pathway of xCT. The membrane topology of xCT could serve as a model for other light subunits of heteromeric amino acid transporters.

Topological analysis of glucosyltransferase GtrV of Shigella flexneri by a dual reporter system and identification of a unique reentrant loop

Lipopolysaccharide, particularly the O-antigen component, is one of many virulence determinants necessary for Shigella flexneri pathogenesis. O-Antigen modification is mediated by glucosyltransferase genes (gtr) encoded by temperate serotype-converting bacteriophages. The gtrV gene encodes the GtrV glucosyltransferase, an integral membrane protein that catalyzes the transfer of a glucosyl residue via an alpha1,3 linkage to rhamnose II of the O-antigen unit. This mediates conversion of S. flexneri serotype Y to serotype 5a. Analysis of the GtrV amino acid sequence using computer prediction programs indicated that GtrV had 9-11 transmembrane segments. The computer prediction models were tested by genetically fusing C-terminal deletions of GtrV to a dual reporter system composed of alkaline phosphatase and beta-galactosidase. Sandwiched GtrV-PhoA/LacZ fusions were also constructed at predetermined positions. The enzyme activities of cells with the GtrV-PhoA/LacZ fusions and the particular location of the fusions in the gtrV indicated that GtrV has nine transmembrane segments and one large N-terminal periplasmic loop with the N and C termini located on the cytoplasmic and periplasmic sides of the membrane, respectively. The existence of a unique reentrant loop was discovered after transmembrane segment IV, a feature not documented in other bacterial glycosyltransferases. Its potential role in mediating serotype conversion in S. flexneri is discussed.

Site within N-Methyl-D-aspartate receptor pore modulates channel gating

N-methyl-d-aspartate-type glutamate receptors (NMDARs) are ligand-gated ion channels activated by coagonists glutamate and glycine. NMDARs play a critical role in synaptic plasticity and excitotoxicity, largely because of their high calcium permeability and slow deactivation and desensitization kinetics. NR1 is an obligate subunit in all NMDAR complexes, where it combines with NR2A, 2B, 2C, and/or 2D. NR1 binds glycine, and residue Asn598 in the re-entrant membrane loop M2 largely determines NMDAR calcium permeability. In contrast, NR2 subunits bind glutamate and contain regions that regulate receptor desensitization and deactivation. Here, we report that mutations of NR1(Asn598) in combination with wild-type NR2A, expressed in human embryonic kidney 293 cells, exhibit altered glycine-independent desensitization. In the absence of extracellular calcium, substitution of Arg for Asn598 (NR1R) slowed desensitization by 2- to 3-fold compared with wild-type NR1/NR2A, and glutamate-evoked peak current EC50 and deactivation rate were also affected. Replacement of Asn by Gln (NR1Q) produced two distinct rates of calcium- and glycine-independent desensitization. Moreover, in the presence of extracellular calcium, the voltage-dependent pore block by calcium for the NR1Q mutant mimicked the effects of the positively charged Arg at this site in NR1R on slowing desensitization and deactivation. A kinetic model of the NMDA receptor-channel suggests that these results can be explained by altered gating and not ligand binding. Our data increase understanding of the role that amino acids within the NMDAR pore play in channel gating.