scholarly journals Structural and molecular insight into the pH-induced low-permeability of the voltage-gated potassium channel Kv1.2 through dewetting of the water cavity

2019 ◽  
Author(s):  
Juhwan Lee ◽  
Mooseok Kang ◽  
Sangyeol Kim ◽  
Iksoo Chang
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Potassium Ion ◽  
Low Permeability ◽  
Voltage Gated ◽  
Kv Channels ◽  
Proton Concentration ◽  
Electrical Voltage ◽  
Gating Mechanism ◽  
Ph Dependent

AbstractUnderstanding the gating mechanism of ion channel proteins is key to understanding the regulation of cell signaling through these channels. Channel opening and closing are regulated by diverse environmental factors that include temperature, electrical voltage across the channel, and proton concentration. Low permeability in voltage-gated potassium ion channels (Kv) is intimately correlated with the prolonged action potential duration observed in many acidosis diseases. The Kv channels consist of voltage-sensing domains (S1–S4 helices) and central pore domains (S5–S6 helices) that include a selectivity filter and water-filled cavity. The voltage-sensing domain is responsible for the voltage-gating of Kv channels. While the low permeability of Kv channels to potassium ion is highly correlated with the cellular proton concentration, it is unclear how an intracellular acidic condition drives their closure, which may indicate an additional pH-dependent gating mechanism of the Kv family. Here, we show that two residues E327 and H418 in the proximity of the water cavity of Kv1.2 play crucial roles as a pH switch. In addition, we present a structural and molecular concept of the pH-dependent gating of Kv1.2 in atomic detail, showing that the protonation of E327 and H418 disrupts the electrostatic balance around the S6 helices, which leads to a straightening transition in the shape of their axes and causes dewetting of the water-filled cavity and closure of the channel. Our work offers a conceptual advancement to the regulation of the pH-dependent gating of various voltage-gated ion channels and their related biological functions.Author SummaryThe acid sensing ion channels are a biological machinery for maintaining the cell functional under the acidic or basic cellular environment. Understanding the pH-dependent gating mechanism of such channels provides the structural insight to design the molecular strategy in regulating the acidosis. Here, we studied the voltage-gated potassium ion channel Kv1.2 which senses not only the electrical voltage across the channels but also the cellular acidity. We uncovered that two key residues E327 and H418 in the pore domain of Kv1.2 channel play a role as pH-switch in that their protonation control the gating of the pore in Kv1.2 channel. It offered a molecular insight how the acidity reduces the ion permeability in voltage-gated potassium channels.

Ion Channel Permeation and Selectivity

2019 ◽  
Author(s):  
Juan J. Nogueira ◽  
Ben Corry
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Ion Selectivity ◽  
Ionic Currents ◽  
Biological Processes ◽  
Ion Permeation ◽  
Voltage Gated ◽  
Physical Mechanisms ◽  
Theoretical Approaches ◽  
Mechanistic Insight

Many biological processes essential for life rely on the transport of specific ions at specific times across cell membranes. Such exquisite control of ionic currents, which is regulated by protein ion channels, is fundamental for the proper functioning of the cells. It is not surprising, therefore, that the mechanism of ion permeation and selectivity in ion channels has been extensively investigated by means of experimental and theoretical approaches. These studies have provided great mechanistic insight but have also raised new questions that are still unresolved. This chapter first summarizes the main techniques that have provided significant knowledge about ion permeation and selectivity. It then discusses the physical mechanisms leading to ion permeation and the explanations that have been proposed for ion selectivity in voltage-gated potassium, sodium, and calcium channels.

scholarly journals Crystallization of a potassium ion channel and X-ray and neutron data collection

2019 ◽  
Vol 75 (6) ◽  
pp. 435-438 ◽  
Author(s):  
Patricia S. Langan ◽  
Venu Gopal Vandavasi ◽  
Brendan Sullivan ◽  
Joel Harp ◽  
Kevin Weiss ◽  
...  
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Potassium Ion ◽  
Potassium Ion Channels ◽  
Potassium Ions ◽  
Potassium Ion Channel ◽  
Neutron Data ◽  
Data Set ◽  
X Ray ◽  
Neutron Diffractometer

The mechanism by which potassium ions are transported through ion channels is currently being investigated by several groups using many different techniques. Clarification of the location of water molecules during transport is central to understanding how these integral membrane proteins function. Neutrons have a unique sensitivity to both hydrogen and potassium, rendering neutron crystallography capable of distinguishing waters from K+ ions. Here, the collection of a complete neutron data set from a potassium ion channel to a resolution of 3.55 Å using the Macromolecular Neutron Diffractometer (MaNDi) is reported. A room-temperature X-ray data set was also collected from the same crystal to a resolution of 2.50 Å. Upon further refinement, these results will help to further clarify the ion/water population within the selectivity filter of potassium ion channels.

scholarly journals Application of rate-equilibrium free energy relationship analysis to nonequilibrium ion channel gating mechanisms

2009 ◽  
Vol 134 (2) ◽  
pp. 129-136 ◽  
Author(s):  
László Csanády
Keyword(s):  
Free Energy ◽  
Ion Channels ◽  
Transition State ◽  
Ion Channel ◽  
Conformational Transition ◽  
Limited Information ◽  
Relationship Analysis ◽  
Gating Mechanisms ◽  
Gating Mechanism ◽  
Transition State Structures

Rate-equilibrium free energy relationship (REFER) analysis provides information on transition-state structures and has been applied to reveal the temporal sequence in which the different regions of an ion channel protein move during a closed–open conformational transition. To date, the theory used to interpret REFER relationships has been developed only for equilibrium mechanisms. Gating of most ion channels is an equilibrium process, but recently several ion channels have been identified to have retained nonequilibrium traits in their gating cycles, inherited from transporter-like ancestors. So far it has not been examined to what extent REFER analysis is applicable to such systems. By deriving the REFER relationships for a simple nonequilibrium mechanism, this paper addresses whether an equilibrium mechanism can be distinguished from a nonequilibrium one by the characteristics of their REFER plots, and whether information on the transition-state structures can be obtained from REFER plots for gating mechanisms that are known to be nonequilibrium cycles. The results show that REFER plots do not carry information on the equilibrium nature of the underlying gating mechanism. Both equilibrium and nonequilibrium mechanisms can result in linear or nonlinear REFER plots, and complementarity of REFER slopes for opening and closing transitions is a trivial feature true for any mechanism. Additionally, REFER analysis provides limited information about the transition-state structures for gating schemes that are known to be nonequilibrium cycles.

Voltage-Gated Ion Channels and Hereditary Disease

1999 ◽  
Vol 79 (4) ◽  
pp. 1317-1372 ◽  
Author(s):  
Frank Lehmann-Horn ◽  
Karin Jurkat-Rott
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Recombinant Dna ◽  
Hereditary Disease ◽  
Hereditary Diseases ◽  
Technological Advancement ◽  
Myotonia Congenita ◽  
Voltage Gated ◽  
Voltage Gated Ion Channels ◽  
Gated Ion Channels

By the introduction of technological advancement in methods of structural analysis, electronics, and recombinant DNA techniques, research in physiology has become molecular. Additionally, focus of interest has been moving away from classical physiology to become increasingly centered on mechanisms of disease. A wonderful example for this development, as evident by this review, is the field of ion channel research which would not be nearly as advanced had it not been for human diseases to clarify. It is for this reason that structure-function relationships and ion channel electrophysiology cannot be separated from the genetic and clinical description of ion channelopathies. Unique among reviews of this topic is that all known human hereditary diseases of voltage-gated ion channels are described covering various fields of medicine such as neurology (nocturnal frontal lobe epilepsy, benign neonatal convulsions, episodic ataxia, hemiplegic migraine, deafness, stationary night blindness), nephrology (X-linked recessive nephrolithiasis, Bartter), myology (hypokalemic and hyperkalemic periodic paralysis, myotonia congenita, paramyotonia, malignant hyperthermia), cardiology (LQT syndrome), and interesting parallels in mechanisms of disease emphasized. Likewise, all types of voltage-gated ion channels for cations (sodium, calcium, and potassium channels) and anions (chloride channels) are described together with all knowledge about pharmacology, structure, expression, isoforms, and encoding genes.

Voltage clamp fluorimetry studies of mammalian voltage-gated K+ channel gating

2007 ◽  
Vol 35 (5) ◽  
pp. 1080-1082 ◽  
Author(s):  
T.W. Claydon ◽  
D. Fedida
Keyword(s):  
Ion Channel ◽  
Potassium Channel ◽  
Real Time ◽  
Voltage Clamp ◽  
Conformational Changes ◽  
Channel Gating ◽  
K Channel ◽  
Voltage Gated ◽  
Kv Channels ◽  
Health And Disease

VCF (voltage clamp fluorimetry) provides a powerful technique to observe real-time conformational changes that are associated with ion channel gating. The present review highlights the insights such experiments have provided in understanding Kv (voltage-gated potassium) channel gating, with particular emphasis on the study of mammalian Kv1 channels. Further applications of VCF that would contribute to our understanding of the modulation of Kv channels in health and disease are also discussed.

The conformational analysis of a synthetic S4 peptide corresponding to a voltage-gated potassium ion channel protein

FEBS Letters ◽  
1994 ◽  
Vol 349 (3) ◽  
pp. 371-374 ◽  
Author(s):  
Parvez I. Haris ◽  
Bala Ramesh ◽  
Stephen Brazier ◽  
Dennis Chapman
Keyword(s):  
Conformational Analysis ◽  
Ion Channel ◽  
Potassium Ion ◽  
Potassium Ion Channel ◽  
Voltage Gated ◽  
Channel Protein

scholarly journals Insights into the molecular mechanism for hyperpolarization-dependent activation of HCN channels

2018 ◽  
Vol 115 (34) ◽  
pp. E8086-E8095 ◽  
Author(s):  
Galen E. Flynn ◽  
William N. Zagotta
Keyword(s):  
Ion Channels ◽  
Cyclic Nucleotide ◽  
Electromechanical Coupling ◽  
Canonical Model ◽  
Hcn Channels ◽  
Voltage Gated ◽  
Kv Channels ◽  
Recovery From Inactivation ◽  
Voltage Dependent ◽  
Pore Domain

Hyperpolarization-activated, cyclic nucleotide-gated (HCN) ion channels are both voltage- and ligand-activated membrane proteins that contribute to electrical excitability and pace-making activity in cardiac and neuronal cells. These channels are members of the voltage-gated Kv channel superfamily and cyclic nucleotide-binding domain subfamily of ion channels. HCN channels have a unique feature that distinguishes them from other voltage-gated channels: the HCN channel pore opens in response to hyperpolarizing voltages instead of depolarizing voltages. In the canonical model of electromechanical coupling, based on Kv channels, a change in membrane voltage activates the voltage-sensing domains (VSD) and the activation energy passes to the pore domain (PD) through a covalent linker that connects the VSD to the PD. In this investigation, the covalent linkage between the VSD and PD, the S4-S5 linker, and nearby regions of spHCN channels were mutated to determine the functional role each plays in hyperpolarization-dependent activation. The results show that: (i) the S4-S5 linker is not required for hyperpolarization-dependent activation or ligand-dependent gating; (ii) the S4 C-terminal region (S4C-term) is not necessary for ligand-dependent gating but is required for hyperpolarization-dependent activation and acts like an autoinhibitory domain on the PD; (iii) the S5N-term region is involved in VSD–PD coupling and holding the pore closed; and (iv) spHCN channels have two voltage-dependent processes, a hyperpolarization-dependent activation and a depolarization-dependent recovery from inactivation. These results are inconsistent with the canonical model of VSD–PD coupling in Kv channels and elucidate the mechanism for hyperpolarization-dependent activation of HCN channels.

scholarly journals Approaches for unveiling the kinetic mechanisms of voltage gated ion channels in neurons

2019 ◽  
Author(s):  
◽  
Marco Antonio Navarro
Keyword(s):  
Experimental Data ◽  
Ion Channels ◽  
Ion Channel ◽  
Rate Constants ◽  
Markov Models ◽  
Neuronal Firing ◽  
Voltage Gated ◽  
Voltage Gated Ion Channels ◽  
Parameter Constraints ◽  
Gated Ion Channels

Ionic currents drive cellular function within all living cells to perform highly specific tasks. For excitable cells, such as muscle and neurons, voltage-gated ion channels have finely tuned kinetics that allow the transduction of Action potentials to other cells. Voltage-gated ion channels are molecular machines that open and close depending on electrical potential. Neuronal firing rates are largely determined by the overall availability of voltage-gated Na+ and K+ currents.This work describes new approaches for collecting and analyzing experimental data that can be used to streamline experiments. Ion channels are composed of multimeric complexes regulated by intracellular factors producing complex kinetics. The stochastic behavior of thousands of individual ion hannels coordinates to produce cellular activity. To describe their activity and test hypotheses about the channel, experimenters often fit Markov models to a set of experimental data. Markov models are defined by a set of states, whose transitions described by rate constants. To improve the modeling process, we have developed computational approaches to introduce kinetic constraints that reduces the parameter search space. This work describes the implementation and mathematical transformations required to describe linear and non-linear parameter constraints that govern rate constants. Not all ion channel behaviors can easily be described by rate constants. Therefore, we developed and implemented a penalty-based mechanism that can be used to guide the optimization engine to produce a model with a desired behavior, such as single-channel open probability and use dependent effects. To streamline data collection for experiments in brain slice preparations, we developed a 3D virtual software environment that incorporates data from micro-positioning motors and scientific cameras in real-time. This environment provides positional feedback to the investigator and allows for the creation of data maps including both images and electrical recordings. We have also produced semi-automatic targeting procedures that simplifies the overall experimental experience. Experimentally, this work also examines how the kinetic mechanism of voltage gated Na channels regulates the neuronal firing of brainstem respiratory neurons. These raphe neurons are intrinsic pacemakers that do not rely on synaptic connections to elicit activity. I explored how intracellular calcium regulates the kinetics of TTX-sensitive Na+ currents using whole-cell patch clamp electrophysiology. Established with intracellular Ca2+ buffers, high [Ca2+] levels greater than ~7 [micro]M did not change the voltage dependence of steady-state activation and inactivation, but slightly slowed inactivation time course. However, the recovery from inactivation and use dependence inactivation is slowed by high intracellular [Ca2+]. Overall, these approaches described in this work have improved data acquisition and data analysis to create better ion channel models and enhance the electrophysiology experience.

scholarly journals Panama: A tool for ion channel biophysics simulation

2018 ◽  
Author(s):  
Anuj Guruacharya
Keyword(s):  
Ion Channels ◽  
Potassium Channels ◽  
Calcium Channels ◽  
Ion Channel ◽  
Chloride Channels ◽  
High Threshold ◽  
Spreadsheet Program ◽  
Online Tool ◽  
Voltage Gated ◽  
Web App

I have created an online tool and an R library that simulates biophysics of voltage-gated ion channels. It is made publicly available as an R library called Panama at github.com/anuj2054/panama and as a web app at neuronsimulator.com. A need for such a tool was observed after surveying available software packages. I found that the available packages are either not robust enough to simulate multiple ion channels, too complicated, usable only as desktop software, not optimized for mobile devices, not interactive, lacking intuitive graphical controls, or not appropriate for undergraduate education. My app simulates the physiology of 11 different channels - voltage-gated sodium, potassium, and chloride channels; channels causing A-current, M-current, and After-HyperPolarization (AHP) current; calcium-activated potassium channels; low threshold T type calcium channels and high threshold L type calcium channels; leak sodium and leak potassium channels. It can simulate these channels under both current clamp and voltage clamp conditions. As we change the input values on the app, the output can be instantaneously visualized on the web browser and downloaded as a data table to be further analyzed in a spreadsheet program. The app is a first of its kind, mobile-friendly and touch-screen-friendly online tool that can be used to teach undergraduate neuroscience classes. It can also be used by researchers on their local computers as part of an R library. It has intuitive touch-optimized controls, instantaneous graphical output, and yet is pedagogically robust for education and casual research purposes.Neuroscience education, ion channel biophysics, Hodgkin-Huxley simulation, web app for neuroscience

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