Analysis of Single-Nucleotide Polymorphisms in Human Voltage-Gated Ion Channels.

Voltage-gated ion channels (VGICs) are one of the largest groups of transmembrane proteins. Due to their major role in the generation and propagation of electrical signals, VGICs are considered important from a medical viewpoint, and their dysfunction is often associated with Channelopathies. We identified disease-associated mutations and polymorphisms in these proteins through mapping missense single-nucleotide polymorphisms from the UniProt and ClinVar databases on their amino acid sequence, considering their special topological and functional characteristics. Statistical analysis revealed that disease-associated SNPs are mostly found in the voltage sensor domain and the pore loop. Both of these regions are extremely important for the activation and ion conductivity of VGICs. Moreover, among the most frequently observed mutations are those of arginine to glutamine, to histidine or to cysteine, which can probably be attributed to the extremely important role of arginine residues in the regulation of membrane potential in these proteins. We suggest that topological information in combination with genetic variation data can contribute toward a better evaluation of the effect of currently unclassified mutations in VGICs. It is hoped that potential associations with certain disease phenotypes will be revealed in the future with the use of similar approaches.

Evolution and Structural Characteristics of Plant Voltage-Gated K+ Channels.

Plant voltage-gated K+ channels have been referred to as "plant Shakers" in reference to animal Shaker channels, the first K+ channels identified. Recent advances in our knowledge of K+ channel evolution and structure have significantly deepened the divide between these plant and animal K+ channels, suggesting that it is time to completely retire the "plant Shaker" designation. Evolutionary genomics reveals that plant voltage-gated K+ channels and metazoan Shakers derive from distinct prokaryotic ancestors. The plant channels belong to a lineage that includes cyclic nucleotide-gated channels and metazoan ether-à-go-go and hyperpolarization-activated, cyclic nucleotide-gated channels. We refer to this lineage as the CNBD channel superfamily, because all these channels share a cytoplasmic gating domain homologous to cyclic nucleotide binding domains. The first structures of CNBD superfamily channels reveal marked differences in coupling between the voltage sensor and ion-conducting pore relative to metazoan Shaker channels. Viewing plant voltage-gated K+ channel function through the lens of CNBD superfamily structures should lead to insights into how these channels are regulated.

Short-Term Facilitation at a Detonator Synapse Requires the Distinct Contribution of Multiple Types of Voltage-Gated Calcium Channels.

Neuronal calcium elevations are shaped by several key parameters, including the properties, density, and the spatial location of voltage-gated calcium channels (VGCCs). These features allow presynaptic terminals to translate complex firing frequencies and tune the amount of neurotransmitter released. Although synchronous neurotransmitter release relies on both P/Q- and N-type VGCCs at hippocampal mossy fiber-CA3 synapses, the specific contribution of VGCCs to calcium dynamics, neurotransmitter release, and short-term facilitation remains unknown. Here, we used random-access two-photon calcium imaging together with electrophysiology in acute mouse hippocampal slices to dissect the roles of P/Q- and N-type VGCCs. Our results show that N-type VGCCs control glutamate release at a limited number of release sites through highly localized Ca2+ elevations and support short-term facilitation by enhancing multivesicular release. In contrast, Ca2+ entry via P/Q-type VGCCs promotes the recruitment of additional release sites through spatially homogeneous Ca2+ elevations. Altogether, our results highlight the specialized contribution of P/Q- and N-types VGCCs to neurotransmitter release.SIGNIFICANCE STATEMENT In presynaptic terminals, neurotransmitter release is dynamically regulated by the transient opening of different types of voltage-gated calcium channels. Hippocampal giant mossy fiber terminals display extensive short-term facilitation during repetitive activity, with a large several fold postsynaptic response increase. Though, how giant mossy fiber terminals leverage distinct types of voltage-gated calcium channels to mediate short-term facilitation remains unexplored. Here, we find that P/Q- and N-type VGCCs generate different spatial patterns of calcium elevations in giant mossy fiber terminals and support short-term facilitation through specific participation in two mechanisms. Whereas N-type VGCCs contribute only to the synchronization of multivesicular release, P/Q-type VGCCs act through microdomain signaling to recruit additional release sites.

Oxidative modulation of voltage-gated potassium channels.

SIGNIFICANCE: Voltage-gated K+ channels are a large family of K+-selective ion channel protein complexes that open on membrane depolarization. These K+ channels are expressed in diverse tissues and their function is vital for numerous physiological processes, in particular of neurons and muscle cells. Potentially reversible oxidative regulation of voltage-gated K+ channels by reactive species such as reactive oxygen species (ROS) represents a contributing mechanism of normal cellular plasticity and may play important roles in diverse pathologies including neurodegenerative diseases. RECENT ADVANCES: Studies using various protocols of oxidative modification, site-directed mutagenesis, and structural and kinetic modeling provide a broader phenomenology and emerging mechanistic insights. CRITICAL ISSUES: Physicochemical mechanisms of the functional consequences of oxidative modifications of voltage-gated K+ channels are only beginning to be revealed. In vivo documentation of oxidative modifications of specific amino-acid residues of various voltage-gated K+ channel proteins, including the target specificity issue, is largely absent. FUTURE DIRECTIONS: High-resolution chemical and proteomic analysis of ion channel proteins with respect to oxidative modification combined with ongoing studies on channel structure and function will provide a better understanding of how the function of voltage-gated K+ channels is tuned by ROS and the corresponding reducing enzymes to meet cellular needs.

Characterisation of K+ channels in human fetoplacental vascular smooth muscle cells.

Adequate blood flow through placental chorionic plate resistance arteries (CPAs) is necessary for oxygen and nutrient transfer to the fetus and a successful pregnancy. In non-placental vascular smooth muscle cells (SMCs), K(+) channels regulate contraction, vascular tone and blood flow. Previous studies showed that K(+) channel modulators alter CPA tone, but did not distinguish between effects on K(+) channels in endothelial cells and SMCs. In this study, we developed a preparation of freshly isolated CPASMCs of normal pregnancy and investigated K(+) channel expression and function. CPASMCs were isolated from normal human term placentas using enzymatic digestion. Purity and phenotype was confirmed with immunocytochemistry. Whole-cell patch clamp was used to assess K(+) channel currents, and mRNA and protein expression was determined in intact CPAs and isolated SMCs with RT-PCR and immunostaining. Isolated SMCs expressed α-actin but not CD31, a marker of endothelial cells. CPASMCs and intact CPAs expressed h-caldesmon and non-muscle myosin heavy chain-2; phenotypic markers of contractile and synthetic SMCs respectively. Whole-cell currents were inhibited by 4-AP, TEA, charybdotoxin and iberiotoxin implicating functional K(v) and BK(Ca) channels. 1-EBIO enhanced whole cell currents which were abolished by TRAM-34 and reduced by apamin indicating activation of IK(Ca) and SK(Ca) respectively. BK(Ca), IK(Ca) and SK(Ca)3 mRNA and/or protein were expressed in CPASMCs and intact CPAs. This study provides the first direct evidence for functional K(v), BK(Ca,) IK(Ca) and SK(Ca) channels in CPASMCs. These cells display a mixed phenotype implicating a dual role for CPASMCs in controlling both fetoplacental vascular resistance and vasculogenesis.

Identification of voltage-gated potassium channel subfamilies from sequence information using support vector machine.

Proteins belonging to different subfamilies of Voltage-gated K(+) channels (VKC) are functionally divergent. The traditional method to classify ion channels is more time consuming. Thus, it is highly desirable to develop novel computational methods for VKC subfamily classification. In this study, a support vector machine based method was proposed to predict VKC subfamilies using amino acid and dipeptide compositions. In order to remove redundant information, a novel feature selection technique was employed to single out optimized features. In the jackknife cross-validation, the proposed method (VKCPred) achieved an overall accuracy of 93.09% with 93.22% average sensitivity and 98.34% average specificity, which are superior to that of other two state-of-the-art classifiers. These results indicate that VKCPred can be efficiently used to identify and annotate voltage-gated K(+) channels' subfamilies. The VKCPred software and dataset are freely available at http://cobi.uestc.edu.cn/people/hlin/tools/VKCPred/.

Targeting A-type K(+) channels in primary sensory neurons for bone cancer pain in a rat model.

Cancer pain is one of the most severe types of chronic pain, and the most common cancer pain is bone cancer pain. The treatment of bone cancer pain remains a clinical challenge. Here, we report firstly that A-type K(+) channels in dorsal root ganglion (DRG) are involved in the neuropathy of rat bone cancer pain and are a new target for diclofenac, a nonsteroidal anti-inflammatory drug that can be used for therapy for this distinct pain. There are dynamically functional changes of the A-type K(+) channels in DRG neurons during bone cancer pain. The A-type K(+) currents that mainly express in isolectin B4-positive small DRG neurons are increased on post-tumor day 14 (PTD 14), then faded but still remained at a higher level on PTD 21. Correspondingly, the expression levels of A-type K(+) channel Kv1.4, Kv3.4, and Kv4.3 showed time-dependent changes during bone cancer pain. Diclofenac enhances A-type K(+) currents in the DRG neurons and attenuates bone cancer pain in a dose-dependent manner. The analgesic effect of diclofenac can be reversed or prevented by A-type K(+) channel blocker 4-AP or pandinotoxin-Kα, also by siRNA targeted against rat Kv1.4 or Kv4.3. Repeated diclofenac administration decreased soft tissue swelling adjacent to the tumor and attenuated bone destruction. These results indicate that peripheral A-type K(+) channels were involved in the neuropathy of rat bone cancer pain. Targeting A-type K(+) channels in primary sensory neurons may provide a novel mechanism-based therapeutic strategy for bone cancer pain.

VKCDB: voltage-gated K+ channel database updated and upgraded.

The Voltage-gated K(+) Channel DataBase (VKCDB) (http://vkcdb.biology.ualberta.ca) makes a comprehensive set of sequence data readily available for phylogenetic and comparative analysis. The current update contains 2063 entries for full-length or nearly full-length unique channel sequences from Bacteria (477), Archaea (18) and Eukaryotes (1568), an increase from 346 solely eukaryotic entries in the original release. In addition to protein sequences for channels, corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses. Although the raw database contains a number of fragmentary, duplicated, obsolete and non-channel sequences that were collected in early steps of data collection, the web interface will only return entries that have been validated as likely K(+) channels. The retrieval function of the web interface allows retrieval of entries that contain a substantial fraction of the core structural elements of VKCs, fragmentary entries, or both. The full database can be downloaded as either a MySQL dump or as an XML dump from the web site. We have now implemented automated updates at quarterly intervals.

Classification of voltage-gated K(+) ion channels from 3D pseudo-folding graph representation of protein sequences using genetic algorithm-optimized support vector machines.

Voltage-gated K(+) ion channels (VKCs) are membrane proteins that regulate the passage of potassium ions through membranes. This work reports a classification scheme of VKCs according to the signs of three electrophysiological variables: activation threshold voltage (V(t)), half-activation voltage (V(a50)) and half-inactivation voltage (V(h50)). A novel 3D pseudo-folding graph representation of protein sequences encoded the VKC sequences. Amino acid pseudo-folding 3D distances count (AAp3DC) descriptors, calculated from the Euclidean distances matrices (EDMs) were tested for building the classifiers. Genetic algorithm (GA)-optimized support vector machines (SVMs) with a radial basis function (RBF) kernel well discriminated between VKCs having negative and positive/zero V(t), V(a50) and V(h50) values with overall accuracies about 80, 90 and 86%, respectively, in crossvalidation test. We found contributions of the "pseudo-core" and "pseudo-surface" of the 3D pseudo-folded proteins to the discrimination between VKCs according to the three electrophysiological variables.

Differential distribution of voltage-gated potassium channels Kv 1.1-Kv1.6 in the rat retina during development.

The discharge behavior of neurons depends on a variable expression and sorting pattern of voltage-dependent potassium (Kv) channels that changes during development. The rodent retina represents a neuronal network whose main functions develop after birth. To obtain information about neuronal maturation we analyzed the expression of subunits of the Kv1 subfamily in the rat retina during postnatal development using immunocytochemistry and immunoelectron microscopy. At postnatal day 5 (P5) all the alpha-subunits of Kv1.1-Kv1.6 channels were found to be expressed in the ganglion cell layer (GCL), most of them already at P1 or P3. Their expression upregulates postnatally and the pattern and distribution change in an isoform-specific manner. Additionally Kv1 channels are found in the outer and inner plexiform layer (OPL, IPL) and in the inner nuclear layer (INL) at different postnatal stages. In adult retina the Kv 1.3 channel localizes to the inner and outer segments of cones. In contrast, Kv1.4 is highly expressed in the outer retina at P8. In adult retina Kv1.4 occurs in rod inner segments (RIS) near the connecting cilium where it colocalizes with synapse associated protein SAP 97. By using confocal laser scanning microscopy we showed a differential localization of Kv1.1-1.6 to cholinergic amacrine and rod bipolar cells of the INL of the adult retina.

Local sequence information-based support vector machine to classify voltage-gated potassium channels.

In our previous work, we developed a computational tool, PreK-ClassK-ClassKv, to predict and classify potassium (K+) channels. For K+ channel prediction (PreK) and classification at family level (ClassK), this method performs well. However, it does not perform so well in classifying voltage-gated potassium (Kv) channels (ClassKv). In this paper, a new method based on the local sequence information of Kv channels is introduced to classify Kv channels. Six transmembrane domains of a Kv channel protein are used to define a protein, and the dipeptide composition technique is used to transform an amino acid sequence to a numerical sequence. A Kv channel protein is represented by a vector with 2000 elements, and a support vector machine algorithm is applied to classify Kv channels. This method shows good performance with averages of total accuracy (Acc), sensitivity (SE), specificity (SP), reliability (R) and Matthews correlation coefficient (MCC) of 98.0%, 89.9%, 100%, 0.95 and 0.94 respectively. The results indicate that the local sequence information-based method is better than the global sequence information-based method to classify Kv channels.

VGIchan: prediction and classification of voltage-gated ion channels.

This study describes methods for predicting and classifying voltage-gated ion channels. Firstly, a standard support vector machine (SVM) method was developed for predicting ion channels by using amino acid composition and dipeptide composition, with an accuracy of 82.89% and 85.56%, respectively. The accuracy of this SVM method was improved from 85.56% to 89.11% when combined with PSI-BLAST similarity search. Then we developed an SVM method for classifying ion channels (potassium, sodium, calcium, and chloride) by using dipeptide composition and achieved an overall accuracy of 96.89%. We further achieved a classification accuracy of 97.78% by using a hybrid method that combines dipeptide-based SVM and hidden Markov model methods. A web server VGIchan has been developed for predicting and classifying voltage-gated ion channels using the above approaches.

Cardiac causes of sudden unexpected death in children and their relationship to seizures and syncope: genetic testing for cardiac electropathies.

The sentinel descriptions of congenital long QT syndrome (LQTS) under the eponyms of Jervell and Lange-Nielsen syndrome and Romano-Ward syndrome were provided in 1957 and the early 1960s. In 1995, the discipline of cardiac channelopathies was birthed formally with the landmark discoveries of cardiac channel mutations as the pathogenic basis for LQTS. Over the past decade, the discipline has expanded considerably being comprised of at least a dozen distinct heritable arrhythmia syndromes, several disease-susceptibility genes, and hundreds of implicated mutations. Previously confined to the purview of research testing, diagnostic genetic testing for several channelopathies is now available for routine clinical use.

Complex expression and localization of inactivating Kv channels in cultured hippocampal astrocytes.

Voltage-gated potassium channels are well established as critical for setting action potential frequency, membrane potential, and neurotransmitter release in neurons. However, their role in the "nonexcitable" glial cell type is yet to be fully understood. We used whole cell current kinetics, pharmacology, immunocytochemistry, and RT-PCR to characterize A-type current in hippocampal astrocyte cultures to better understand its function. Pharmacological analysis suggests that approximately 70, 10, and <5% of total A current is associated with Kv4, Kv3, and Kv1 channels, respectively. In addition, pharmacology and kinetics provide evidence for a significant contribution of KChIP accessory proteins to astrocytic A-channel composition. Localization of the Shaw Kv3.4 channel to astrocytic processes and the Shal Kv4.3 channel to soma suggest that these channels serve a specific function. Given this complex A-type channel expression pattern, we assessed the role of A currents in membrane voltage oscillations in response to current injections. Although TEA-sensitive delayed-rectifying currents are involved in the extent of repolarization, 4-AP-sensitive A currents serve to increase the rate. As in neurons, this effect may enable astrocytes to respond rapidly to high-frequency synaptic events. Our results indicate that hippocampal astrocytes in vitro express multiple A-type Kv channel alpha-subunits with accessory, possibly Ca(2+)-sensitive, cytoplasmic subunits that appear to be specifically localized to subcellular membrane compartments. Function of these channels remains to be determined in a physiological setting. However, this study suggests that they enable astrocytes to respond rapidly with membrane voltage oscillations to high-frequency incoming signals, possibly synchronizing astrocyte function to neuronal activity.

Immunohistochemical study on the distribution of the voltage-gated potassium channels in the gerbil cerebellum.

Although there have been many studies on the regional distribution of Kv channels in the rat and mouse cerebellum, there are no reports about Kv channel distribution in the gerbil, which is used as an ischemia animal model. Therefore, we aimed to investigate differences in the spatial patterning of Kv channel alpha-subunit isoforms in the gerbil cerebellum. The greatest concentration of Kv1.2 was found in the basket cell axon plexus and terminal regions around the Purkinje cells. Kv1.1 immunoreactivity was also concentrated in this area although the staining intensity was relatively lower. Both Purkinje cell layer and granular layer were intensely stained with anti-Kv1.3 and Kv1.6 antibodies, whereas immunoreactivities for Kv1.4 and Kv1.5 were detected in the Purkinje cell bodies with much lower intensity in the molecular and granular layers. In the cerebellar nuclei, the cell bodies of cerebellar output neurons showed strong immunoreactivities for Kv1.2, Kv1.4, and Kv1.6 with moderate staining for Kv1.3 and Kv1.5 in the cell bodies. This study on the differential localization patterns of Kv1 channel subunits in the gerbil cerebellum may provide helpful guidelines for correlating current types with particular channels and useful data for the future investigations on the pathological conditions such as ischemia and epilepsy.

Protein-protein interactions of a Kvbeta subunit in the cochlea.

Accessory subunits associated with voltage-gated potassium (Kv) channels can influence the biophysical properties and promote the surface expression of channel-forming alpha-subunits. Previously, we cloned several alpha-subunits and a beta-subunit from a cDNA library of the chicken cochlea. In the present study, we raised an antibody against the N-terminus of chicken Kvbeta1.1 (cKvbeta1.1) and characterized the Kvbeta-related polypeptide in cochlear tissues and heterologous cells. The anti-cKvbeta1.1 antibody recognizes a 45-kDa polypeptide in chick cochlear extracts as well as in Chinese hamster ovary (CHO) cells transfected with cKvbeta1.1. The accessory subunit was localized to the ganglion cells of the chick cochlea using immunohistochemistry and in situ hybridization. Coimmunoprecipitation studies show that Kvbeta1.1 interacts with Shaker channel members Kvalpha1.2 and 1.3, both of which colocalize with beta to the cochlear ganglion cells. Additionally, coimmunoprecipitation studies show that Kvalpha1.2 and 1.3 interact with each other, suggesting that these ion channels are formed by heteromultimers. In comparison, Kvbeta did not coprecipitate with a member of the Shal subfamily. The presence of Kvbeta in the cochlea suggests that this subunit contributes to the modulation of auditory signals in the ganglion cells, presumably by regulating properties of inactivation as well as surface expression of Kvalpha channels.

It's "juxta" potassium channel!

Neuronal excitability depends on the appropriate expression and localization of ion channels. Juxtaparanodal Kv1 channels have been used as a model to study the role of neuroglial interactions in regulating the expression and localization of channels in myelinated axons. Recent advances in our understanding of the composition of juxtaparanodal Kv1 channel protein complexes as well as the cellular and molecular mechanisms underlying their localization at juxtaparanodes are discussed.

Diversity of voltage-dependent K+ channels in human pulmonary artery smooth muscle cells.

Electrical excitability, which plays an important role in excitation-contraction coupling in the pulmonary vasculature, is regulated by transmembrane ion flux in pulmonary artery smooth muscle cells (PASMC). This study examined the heterogeneous nature of native voltage-dependent K(+) channels in human PASMC. Both voltage-gated K(+) (K(V)) currents and Ca(2+)-activated K(+) (K(Ca)) currents were observed and characterized. In cell-attached patches of PASMC bathed in Ca(2+)-containing solutions, depolarization elicited a wide range of K(+) unitary conductances (6-290 pS). When cells were dialyzed with Ca(2+)-free and K(+)-containing solutions, depolarization elicited four components of K(V) currents in PASMC based on the kinetics of current activation and inactivation. Using RT-PCR, we detected transcripts of 1) 22 K(V) channel alpha-subunits (K(V)1.1-1.7, K(V)1.10, K(V)2.1, K(V)3.1, K(V)3.3-3.4, K(V)4.1-4.2, K(V)5.1, K(V) 6.1-6.3, K(V)9.1, K(V)9.3, K(V)10.1, and K(V)11.1), 2) three K(V) channel beta-subunits (K(V)beta 1-3), 3) four K(Ca) channel alpha-subunits (Slo-alpha 1 and SK2-SK4), and 4) four K(Ca) channel beta-subunits (K(Ca)beta 1-4). Our results show that human PASMC exhibit a variety of voltage-dependent K(+) currents with variable kinetics and conductances, which may result from various unique combinations of alpha- and beta-subunits forming the native channels. Functional expression of these channels plays a critical role in the regulation of membrane potential, cytoplasmic Ca(2+), and pulmonary vasomotor tone.

International Union of Pharmacology. XLI. Compendium of voltage-gated ion channels: potassium channels.

This summary article presents an overview of the molecular relationships among the voltage-gated potassium channels and a standard nomenclature for them, which is derived from the IUPHAR Compendium of Voltage-Gated Ion Channels. The complete Compendium, including data tables for each member of the potassium channel family can be found at http://www.iuphar-db.org/iuphar-ic/.