1
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Liu Y, Li C, Freites JA, Tobias DJ, Voth GA. Quantitative insights into the mechanism of proton conduction and selectivity for the human voltage-gated proton channel Hv1. Proc Natl Acad Sci U S A 2024; 121:e2407479121. [PMID: 39259593 DOI: 10.1073/pnas.2407479121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 08/09/2024] [Indexed: 09/13/2024] Open
Abstract
Human voltage-gated proton (hHv1) channels are crucial for regulating essential biological processes such as immune cell respiratory burst, sperm capacitation, and cancer cell migration. Despite the significant concentration difference between protons and other ions in physiological conditions, hHv1 demonstrates remarkable proton selectivity. Our calculations of single-proton, cation, and anion permeation free energy profiles quantitatively demonstrate that the proton selectivity of the wild-type channel originates from its strong proton affinity via the titration of the key residues D112 and D174, although the channel imposes similar kinetic blocking effects for protons compared to other ions. A two-proton knock-on model is proposed to mathematically explain the electrophysiological measurements of the pH-dependent proton conductance in the conductive state. Moreover, it is shown that the anion selectivity of the D112N mutant channel is tied to impaired proton transport and substantial anion leakage.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL 60637
| | - Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL 60637
| | | | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL 60637
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2
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Lazaridis T. Proton Paths in Models of the Hv1 Proton Channel. J Phys Chem B 2023; 127:7937-7945. [PMID: 37695850 DOI: 10.1021/acs.jpcb.3c03960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
The voltage-gated proton channel (Hv1) plays an essential role in numerous biological processes, but a detailed molecular understanding of its function is lacking. The lack of reliable structures for the open and resting states is a major handicap. Several models have been built based on homologous voltage sensors and the structure of a chimera between the mouse homologue and a phosphatase voltage sensor, but their validity is uncertain. In addition, differing views exist regarding the mode of proton translocation, the role of specific residues, and the mechanism of pH effects on voltage gating. Here we use classical proton hopping simulations under a voltage biasing force to evaluate some of the proposed structural models and explore the mechanism of proton conduction. Paradoxically, some models proposed for the closed state allow for proton permeation more easily than models for the open state. An open state model with a D112-R211 salt bridge (R3D) allows proton transport more easily than models with a D112-R208 salt bridge (R2D). However, its permeation rate seems too high, considering experimental conductances. In all cases, the proton permeates through a water wire, bypassing the salt-bridged D112 rather than being shuttled by D112. Attempts to protonate D112 are rejected due to its strong interaction with an arginine. Consistent with proton selectivity, no Na+ permeation was observed in the R2D models. As a negative control, simulations with the Kv1.2-Kv2.1 paddle-chimera voltage sensor, which is not expected to conduct protons, did not show proton permeation under the same conditions. Hydrogen bond connectivity graphs show a constriction at D112, but cannot discriminate between open and closed states.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY, 160 Convent Avenue, New York, New York 10031, United States
- Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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3
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Chaves G, Jardin C, Derst C, Musset B. Voltage-Gated Proton Channels in the Tree of Life. Biomolecules 2023; 13:1035. [PMID: 37509071 PMCID: PMC10377628 DOI: 10.3390/biom13071035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
With a single gene encoding HV1 channel, proton channel diversity is particularly low in mammals compared to other members of the superfamily of voltage-gated ion channels. Nonetheless, mammalian HV1 channels are expressed in many different tissues and cell types where they exert various functions. In the first part of this review, we regard novel aspects of the functional expression of HV1 channels in mammals by differentially comparing their involvement in (1) close conjunction with the NADPH oxidase complex responsible for the respiratory burst of phagocytes, and (2) in respiratory burst independent functions such as pH homeostasis or acid extrusion. In the second part, we dissect expression of HV channels within the eukaryotic tree of life, revealing the immense diversity of the channel in other phylae, such as mollusks or dinoflagellates, where several genes encoding HV channels can be found within a single species. In the last part, a comprehensive overview of the biophysical properties of a set of twenty different HV channels characterized electrophysiologically, from Mammalia to unicellular protists, is given.
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Affiliation(s)
- Gustavo Chaves
- Center of Physiology, Pathophysiology and Biophysics, The Nuremberg Location, Paracelsus Medical University, 90419 Nuremberg, Germany
| | - Christophe Jardin
- Center of Physiology, Pathophysiology and Biophysics, The Nuremberg Location, Paracelsus Medical University, 90419 Nuremberg, Germany
| | - Christian Derst
- Center of Physiology, Pathophysiology and Biophysics, The Nuremberg Location, Paracelsus Medical University, 90419 Nuremberg, Germany
| | - Boris Musset
- Center of Physiology, Pathophysiology and Biophysics, The Nuremberg Location, Paracelsus Medical University, 90419 Nuremberg, Germany
- Center of Physiology, Pathophysiology and Biophysics, The Salzburg Location, Paracelsus Medical University, 5020 Salzburg, Austria
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4
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Boytsov D, Brescia S, Chaves G, Koefler S, Hannesschlaeger C, Siligan C, Goessweiner-Mohr N, Musset B, Pohl P. Trapped Pore Waters in the Open Proton Channel H V 1. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205968. [PMID: 36683221 DOI: 10.1002/smll.202205968] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The voltage-gated proton channel, HV 1, is crucial for innate immune responses. According to alternative hypotheses, protons either hop on top of an uninterrupted water wire or bypass titratable amino acids, interrupting the water wire halfway across the membrane. To distinguish between both hypotheses, the water mobility for the putative case of an uninterrupted wire is estimated. The predicted single-channel water permeability 2.3 × 10-12 cm3 s-1 reflects the permeability-governing number of hydrogen bonds between water molecules in single-file configuration and pore residues. However, the measured unitary water permeability does not confirm the predicted value. Osmotic deflation of reconstituted lipid vesicles reveals negligible water permeability of the HV 1 wild-type channel and the D174A mutant open at 0 mV. The conductance of 1400 H+ s-1 per wild-type channel agrees with the calculated diffusion limit for a ≈2 Å capture radius for protons. Removal of a charged amino acid (D174) at the pore mouth decreases H+ conductance by reducing the capture radius. At least one intervening amino acid contributes to H+ conductance while interrupting the water wire across the membrane.
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Affiliation(s)
- Danila Boytsov
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, 40, Gruberstr, Austria
| | - Stefania Brescia
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, 40, Gruberstr, Austria
| | - Gustavo Chaves
- Institute of Physiology, Pathophysiology and Biophysics, CPPB, Paracelsus Medical University, 90419, Nuremberg, Germany
| | - Sabina Koefler
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, 40, Gruberstr, Austria
| | | | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, 40, Gruberstr, Austria
| | | | - Boris Musset
- Institute of Physiology, Pathophysiology and Biophysics, CPPB, Paracelsus Medical University, 90419, Nuremberg, Germany
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, 40, Gruberstr, Austria
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5
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Gating Mechanism of the Voltage-Gated Proton Channel Studied by Molecular Dynamics Simulations. Molecules 2022; 27:molecules27072277. [PMID: 35408673 PMCID: PMC9000549 DOI: 10.3390/molecules27072277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/20/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
The voltage-gated proton channel Hv1 has important roles in proton extrusion, pH homeostasis, sperm motility, and cancer progression. The Hv1 channel has also been found to be highly expressed in cell lines and tissue samples from patients with breast cancer. A high-resolution closed-state structure has been reported for the mouse Hv1 chimera channel (mHv1cc), solved by X-ray crystallography, but the open-state structure of Hv1 has not been solved. Since Hv1 is a promising drug target, various groups have proposed open conformations by molecular modeling and simulation studies. However, the gating mechanism and the open-state conformation under the membrane potential are still debate. Here, we present a molecular dynamics study considering membrane potential and pH conditions. The closed-state structure of mHv1cc was used to run molecular dynamics (MD) simulations with respect to electric field and pH conditions in order to investigate the mechanism of proton transfer. We observed a continuous hydrogen bond chain of water molecules called a water-wire to be formed through the channel pore in the channel opening, triggered by downward displacement of the S2 helix and upward movement of the S4 helix relative to other helices. Due to the movement of the S2 and S4 helices, the internal salt bridge network was rearranged, and the hydrophobic gating layers were destroyed. In line with previous experimental and simulation observations, our simulation results led us to propose a new gating mechanism for the Hv1 proton channel, and may provide valuable information for novel drug discovery.
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6
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Inhibiting Hv1 channel in peripheral sensory neurons attenuates chronic inflammatory pain and opioid side effects. Cell Res 2022; 32:461-476. [PMID: 35115667 PMCID: PMC9061814 DOI: 10.1038/s41422-022-00616-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 01/04/2022] [Indexed: 02/05/2023] Open
Abstract
Both opioids and nonsteroidal anti-inflammatory drugs (NSAIDS) produce deleterious side effects and fail to provide sustained relief in patients with chronic inflammatory pain. Peripheral neuroinflammation (PN) is critical for initiation and development of inflammatory pain. A better understanding of molecular mechanisms underlying PN would facilitate the discovery of new analgesic targets and the development of new therapeutics. Emerging evidence suggests that peripheral sensory neurons are not only responders to painful stimuli, but are also actively engaged in inflammation and immunity, whereas the intrinsic regulatory mechanism is poorly understood. Here we report the expression of proton-selective ion channel Hv1 in peripheral sensory neurons in rodents and humans, which was previously shown as selectively expressed in microglia in mammalian central nervous system. Neuronal Hv1 was up-regulated by PN or depolarizing stimulation, which in turn aggravates inflammation and nociception. Inhibiting neuronal Hv1 genetically or by a newly discovered selective inhibitor YHV98-4 reduced intracellular alkalization and ROS production in inflammatory pain, mitigated the imbalance in downstream SHP-1-pAKT signaling, and also diminished pro-inflammatory chemokine release to alleviate nociception and morphine-induced hyperalgesia and tolerance. Thus, our data reveal neuronal Hv1 as a novel target in analgesia strategy and managing opioids-related side effects.
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7
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A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces. Proc Natl Acad Sci U S A 2021; 118:2113141118. [PMID: 34857630 DOI: 10.1073/pnas.2113141118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 11/18/2022] Open
Abstract
Water-assisted proton transport through confined spaces influences many phenomena in biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in the confined pathways provide the environment and the medium for the hydrated excess proton migration via Grotthuss shuttling. However, a definitive collective variable (CV) that accurately couples the hydration and the connectivity of the proton wire with the proton translocation has remained elusive. To address this important challenge-and thus to define a quantitative paradigm for facile proton transport in confined spaces-a CV is derived in this work from graph theory, which is verified to accurately describe water wire formation and breakage coupled to the proton translocation in carbon nanotubes and the Cl-/H+ antiporter protein, ClC-ec1. Significant alterations in the conformations and thermodynamics of water wires are uncovered after introducing an excess proton into them. Large barriers in the proton translocation free-energy profiles are found when water wires are defined to be disconnected according to the new CV, even though the pertinent confined space is still reasonably well hydrated and-by the simple measure of the mere existence of a water structure-the proton transport would have been predicted to be facile via that oversimplified measure. In this paradigm, however, the simple presence of water is not sufficient for inferring proton translocation, since an excess proton itself is able to drive hydration, and additionally, the water molecules themselves must be adequately connected to facilitate any successful proton transport.
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8
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Sokolov VS, Cherny VV, Ayuyan AG, DeCoursey TE. Analysis of an electrostatic mechanism for ΔpH dependent gating of the voltage-gated proton channel, H V1, supports a contribution of protons to gating charge. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148480. [PMID: 34363792 PMCID: PMC8432343 DOI: 10.1016/j.bbabio.2021.148480] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/23/2021] [Accepted: 08/02/2021] [Indexed: 11/23/2022]
Abstract
Voltage-gated proton channels (HV1) resemble the voltage-sensing domain of other voltage-gated ion channels, but differ in containing the conduction pathway. Essential to the functions of HV1 channels in many cells and species is a unique feature called ΔpH dependent gating. The pH on both sides of the membrane strictly regulates the voltage range of channel opening, generally resulting in exclusively outward proton current. Two types of mechanisms could produce ΔpH dependent gating. The "countercharge" mechanism proposes that protons destabilize salt bridges between amino acids in the protein that stabilize specific gating configurations (closed or open). An "electrostatic" mechanism proposes that protons bound to the channel alter the electrical field sensed by the protein. Obligatory proton binding within the membrane electrical field would contribute to measured gating charge. Estimations on the basis of the electrostatic model explain ΔpH dependent gating, but quantitative modeling requires calculations of the electric field inside the protein which, in turn, requires knowledge of its structure. We conclude that both mechanisms operate and contribute to ΔpH dependent gating of HV1.
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Affiliation(s)
- Valerij S Sokolov
- Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences, Moscow 119071, Russia
| | - Vladimir V Cherny
- Department of Physiology & Biophysics, Rush University, Chicago, IL 60612, USA
| | - Artem G Ayuyan
- Department of Physiology & Biophysics, Rush University, Chicago, IL 60612, USA
| | - Thomas E DeCoursey
- Department of Physiology & Biophysics, Rush University, Chicago, IL 60612, USA.
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9
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Cherny VV, Musset B, Morgan D, Thomas S, Smith SME, DeCoursey TE. Engineered high-affinity zinc binding site reveals gating configurations of a human proton channel. J Gen Physiol 2021; 152:152076. [PMID: 32902579 PMCID: PMC7537347 DOI: 10.1085/jgp.202012664] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/10/2020] [Indexed: 11/23/2022] Open
Abstract
The voltage-gated proton channel (HV1) is a voltage sensor that also conducts protons. The singular ability of protons to penetrate proteins complicates distinguishing closed and open channels. When we replaced valine with histidine at position 116 in the external vestibule of hHV1, current was potently inhibited by externally applied Zn2+ in a construct lacking the two His that bind Zn2+ in WT channels. High-affinity binding with profound effects at 10 nM Zn2+ at pHo 7 suggests additional groups contribute. We hypothesized that Asp185, which faces position 116 in our closed-state model, contributes to Zn2+ chelation. Confirming this prediction, V116H/D185N abolished Zn2+ binding. Studied in a C-terminal truncated monomeric construct, V116H channels activated rapidly. Anomalously, Zn2+ slowed activation, producing a time constant independent of both voltage and Zn2+ concentration. We hypothesized that slow turn-on of H+ current in the presence of Zn2+ reflects the rate of Zn2+ unbinding from the channel, analogous to drug-receptor dissociation reactions. This behavior in turn suggests that the affinity for Zn2+ is greater in the closed state of hHV1. Supporting this hypothesis, pulse pairs revealed a rapid component of activation whose amplitude decreased after longer intervals at negative voltages as closed channels bound Zn2+. The lower affinity of Zn2+ in open channels is consistent with the idea that structural rearrangements within the transmembrane region bring Arg205 near position 116, electrostatically expelling Zn2+. This phenomenon provides direct evidence that Asp185 opposes position 116 in closed channels and that Arg205 moves between them when the channel opens.
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Affiliation(s)
| | - Boris Musset
- Institut für Physiologie und Pathophysiologie, Paracelsus Medizinische Privatuniversität, Nürnberg, Germany
| | - Deri Morgan
- Department of Physiology & Biophysics, Rush University, Chicago IL
| | - Sarah Thomas
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA
| | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA
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10
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Alberini G, Benfenati F, Maragliano L. Structural Mechanism of ω-Currents in a Mutated Kv7.2 Voltage Sensor Domain from Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:1354-1367. [PMID: 33570938 PMCID: PMC8023575 DOI: 10.1021/acs.jcim.0c01407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Activation of voltage-gated
ion channels is regulated by conformational
changes of the voltage sensor domains (VSDs), four water- and ion-impermeable
modules peripheral to the central, permeable pore domain. Anomalous
currents, defined as ω-currents, have been recorded in response
to mutations of residues on the VSD S4 helix and associated with ion
fluxes through the VSDs. In humans, gene defects in the potassium
channel Kv7.2 result in a broad range of epileptic disorders, from
benign neonatal seizures to severe epileptic encephalopathies. Experimental
evidence suggests that the R207Q mutation in S4, associated with peripheral
nerve hyperexcitability, induces ω-currents at depolarized potentials,
but the fine structural details are still elusive. In this work, we
use atom-detailed molecular dynamics simulations and a refined model
structure of the Kv7.2 VSD in the active conformation in a membrane/water
environment to study the effect of R207Q and four additional mutations
of proven clinical importance. Our results demonstrate that the R207Q
mutant shows the most pronounced increase of hydration in the internal
VSD cavity, a feature favoring the occurrence of ω-currents.
Free energy and kinetics calculations of sodium permeation through
the native and mutated VSD indicate as more favorable the formation
of a cationic current in the latter. Overall, our simulations establish
a mechanistic linkage between genetic variations and their physiological
outcome, by providing a computational description that includes both
thermodynamic and kinetic features of ion permeation associated with
ω-currents.
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Affiliation(s)
- Giulio Alberini
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,Department of Experimental Medicine, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132 Genova, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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11
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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12
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Lim VT, Geragotelis AD, Lim NM, Freites JA, Tombola F, Mobley DL, Tobias DJ. Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations. Sci Rep 2020; 10:13587. [PMID: 32788614 PMCID: PMC7423955 DOI: 10.1038/s41598-020-70369-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Hv1 is a voltage-gated proton channel whose main function is to facilitate extrusion of protons from the cell. The development of effective channel blockers for Hv1 can lead to new therapeutics for the treatment of maladies related to Hv1 dysfunction. Although the mechanism of proton permeation in Hv1 remains to be elucidated, a series of small molecules have been discovered to inhibit Hv1. Here, we computed relative binding free energies of a prototypical Hv1 blocker on a model of human Hv1 in an open state. We used alchemical free energy perturbation techniques based on atomistic molecular dynamics simulations. The results support our proposed open state model and shed light on the preferred tautomeric state of the channel blocker. This work lays the groundwork for future studies on adapting the blocker molecule for more effective inhibition of Hv1.
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Affiliation(s)
- Victoria T Lim
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | | | - Nathan M Lim
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - J Alfredo Freites
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Francesco Tombola
- Department of Physiology and Biophysics, University of California, Irvine, CA, 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, 92697, USA
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, 92697, USA.
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13
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Voltage-dependent structural models of the human Hv1 proton channel from long-timescale molecular dynamics simulations. Proc Natl Acad Sci U S A 2020; 117:13490-13498. [PMID: 32461356 DOI: 10.1073/pnas.1920943117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The voltage-gated Hv1 proton channel is a ubiquitous membrane protein that has roles in a variety of cellular processes, including proton extrusion, pH regulation, production of reactive oxygen species, proliferation of cancer cells, and increased brain damage during ischemic stroke. A crystal structure of an Hv1 construct in a putative closed state has been reported, and structural models for the channel open state have been proposed, but a complete characterization of the Hv1 conformational dynamics under an applied membrane potential has been elusive. We report structural models of the Hv1 voltage-sensing domain (VSD), both in a hyperpolarized state and a depolarized state resulting from voltage-dependent conformational changes during a 10-μs-timescale atomistic molecular dynamics simulation in an explicit membrane environment. In response to a depolarizing membrane potential, the S4 helix undergoes an outward displacement, leading to changes in the VSD internal salt-bridge network, resulting in a reshaping of the permeation pathway and a significant increase in hydrogen bond connectivity throughout the channel. The total gating charge displacement associated with this transition is consistent with experimental estimates. Molecular docking calculations confirm the proposed mechanism for the inhibitory action of 2-guanidinobenzimidazole (2GBI) derived from electrophysiological measurements and mutagenesis. The depolarized structural model is also consistent with the formation of a metal bridge between residues located in the core of the VSD. Taken together, our results suggest that these structural models are representative of the closed and open states of the Hv1 channel.
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14
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Cummins PL, Gready JE. Kohn-Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco. J Phys Chem B 2020; 124:3015-3026. [PMID: 32208706 DOI: 10.1021/acs.jpcb.0c01169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ribulose 1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) plays a fundamental role in the carbon cycle by fixing the atmospheric CO2 used in photosynthesis. Rubisco is all the more remarkable because it must catalyze some difficult multistep reaction chemistry involving proton transfers within the one active site. In the present study, we have used Kohn-Sham density functional theory at the B3LYP/6-31G* level with basis set superposition error and dispersion corrections (B3LYP-gCP-D3) to examine the possibility that the proton transfers can take place through molecular wires (including active-site water molecules) via the classical Grotthuss proton-shuttle mechanism. The results support an essential role for water molecules found in the crystal structures of Rubisco complexes as facilitators of proton transport in all the rate-limiting (catalytic) reaction steps through a network of short proton wires within the Rubisco active site. We suggest that completion of the initial product turnover (cycle) requires two excess protons produced in the initial carbamylation that is required for Rubisco activation. By use of proton wires, a large number of reaction steps may be accommodated within a single active site without necessitating the input of excessive conformational strain energy arising from the movement of residue side chains into positions where direct protonation of substrates can occur. The involvement of the identified types of proton wires in the kinetic mechanism is capable of providing a unique explanation for various experimental observations, including deuterium isotope effects and the results of site-directed mutagenesis experiments, and may thus provide a realistic solution to the problem of Rubisco's challenging chemistry.
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Affiliation(s)
- Peter L Cummins
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
| | - Jill E Gready
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
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15
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Groome JR, Bayless-Edwards L. Roles for Countercharge in the Voltage Sensor Domain of Ion Channels. Front Pharmacol 2020; 11:160. [PMID: 32180723 PMCID: PMC7059764 DOI: 10.3389/fphar.2020.00160] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated ion channels share a common structure typified by peripheral, voltage sensor domains. Their S4 segments respond to alteration in membrane potential with translocation coupled to ion permeation through a central pore domain. The mechanisms of gating in these channels have been intensely studied using pioneering methods such as measurement of charge displacement across a membrane, sequencing of genes coding for voltage-gated ion channels, and the development of all-atom molecular dynamics simulations using structural information from prokaryotic and eukaryotic channel proteins. One aspect of this work has been the description of the role of conserved negative countercharges in S1, S2, and S3 transmembrane segments to promote sequential salt-bridge formation with positively charged residues in S4 segments. These interactions facilitate S4 translocation through the lipid bilayer. In this review, we describe functional and computational work investigating the role of these countercharges in S4 translocation, voltage sensor domain hydration, and in diseases resulting from countercharge mutations.
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Affiliation(s)
- James R. Groome
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
| | - Landon Bayless-Edwards
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
- Oregon Health and Sciences University School of Medicine, Portland, OR, United States
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16
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De La Rosa V, Ramsey IS. Gating Currents in the Hv1 Proton Channel. Biophys J 2019; 114:2844-2854. [PMID: 29925021 DOI: 10.1016/j.bpj.2018.04.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 04/19/2018] [Accepted: 04/30/2018] [Indexed: 11/25/2022] Open
Abstract
The Hv1 proton channel shares striking structural homology with fourth transmembrane helical segment-type voltage-sensor (VS) domains but manifests distinctive functional properties, including a proton-selective "aqueous" conductance and allosteric control of voltage-dependent gating by changes in the transmembrane pH gradient. The mechanisms responsible for Hv1's functional properties remain poorly understood, in part because methods for measuring gating currents that directly report VS activation have not yet been described. Here, we describe an approach that allows robust and reproducible measurement of gating-associated charge movements in Hv1. Gating currents reveal that VS activation and proton-selective aqueous conductance opening are thermodynamically distinct steps in the Hv1 activation pathway and show that pH changes directly alter VS activation. The availability of an assay for gating currents in Hv1 may aid future efforts to elucidate the molecular mechanisms of gating cooperativity, pH-dependent modulation, and H+ selectivity in a model VS domain protein.
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Affiliation(s)
- Victor De La Rosa
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia
| | - Ian Scott Ramsey
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia.
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17
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Hydrophobic gasket mutation produces gating pore currents in closed human voltage-gated proton channels. Proc Natl Acad Sci U S A 2019; 116:18951-18961. [PMID: 31462498 PMCID: PMC6754559 DOI: 10.1073/pnas.1905462116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A large family of membrane proteins, voltage-gated ion channels, regulate a vast array of physiological functions in essentially all life forms. How these molecules sense membrane potential and respond by creating ionic conduction is incompletely understood. The voltage sensors of these channels contain a “hydrophobic gasket,” a ring of hydrophobic amino acids near the center of the membrane, separating internal and external aqueous solutions. Although voltage-gated proton channels, HV1, resemble voltage-sensing domains of other channels, they differ fundamentally. On depolarization, HV1 conducts protons, whereas other voltage sensors open a physically distinct pore. We identify Val109, Phe150, Val177, and Val178 as the hHV1 hydrophobic gasket. Replacement with less hydrophobic amino acids accelerated channel opening and caused proton-selective leak through closed channels. The hydrophobic gasket (HG), a ring of hydrophobic amino acids in the voltage-sensing domain of most voltage-gated ion channels, forms a constriction between internal and external aqueous vestibules. Cationic Arg or Lys side chains lining the S4 helix move through this “gating pore” when the channel opens. S4 movement may occur during gating of the human voltage-gated proton channel, hHV1, but proton current flows through the same pore in open channels. Here, we replaced putative HG residues with less hydrophobic residues or acidic Asp. Substitution of individuals, pairs, or all 3 HG positions did not impair proton selectivity. Evidently, the HG does not act as a secondary selectivity filter. However, 2 unexpected functions of the HG in HV1 were discovered. Mutating HG residues independently accelerated channel opening and compromised the closed state. Mutants exhibited open–closed gating, but strikingly, at negative voltages where “normal” gating produces a nonconducting closed state, the channel leaked protons. Closed-channel proton current was smaller than open-channel current and was inhibited by 10 μM Zn2+. Extreme hyperpolarization produced a deeper closed state through a weakly voltage-dependent transition. We functionally identify the HG as Val109, Phe150, Val177, and Val178, which play a critical and exclusive role in preventing H+ influx through closed channels. Molecular dynamics simulations revealed enhanced mobility of Arg208 in mutants exhibiting H+ leak. Mutation of HG residues produces gating pore currents reminiscent of several channelopathies.
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18
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On the control of the proton current in the voltage-gated proton channel Hv1. Proc Natl Acad Sci U S A 2018; 115:10321-10326. [PMID: 30254162 DOI: 10.1073/pnas.1809766115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The nature of the action of voltage-activated proton transport proteins is a conundrum of great current interest. Here we approach this issue by exploring the action of Hv1, a voltage-gated proton channel found in different cells in humans and other organisms. Our study focuses on evaluating the free energy of transporting a proton through the channel, as well as the effect of the proton transfer through D112, in both the closed and open channel conformations. It is found that D112 allows a transported proton to bypass the electrostatic barrier of the open channel, while not being able to help in passing the barrier in the closed form. This reflects the change in position of the gating arginine residues relative to D112, upon voltage activation. Significantly, the effect of D112 accounts for the observed trend in selectivity by overcoming the electrostatic barrier at its highest point. Thus, the calculations provide a structure/function correlation for the Hv1 system. The present work also clarifies that the action of Hv1 is not controlled by a Grotthuss mechanism but, as is always the case, by the protein electrostatic potential at the rate-limiting barriers.
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19
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Bayless-Edwards L, Winston V, Lehmann-Horn F, Arinze P, Groome JR, Jurkat-Rott K. Na V1.4 DI-S4 periodic paralysis mutation R222W enhances inactivation and promotes leak current to attenuate action potentials and depolarize muscle fibers. Sci Rep 2018; 8:10372. [PMID: 29991727 PMCID: PMC6039468 DOI: 10.1038/s41598-018-28594-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/20/2018] [Indexed: 01/24/2023] Open
Abstract
Hypokalemic periodic paralysis is a skeletal muscle disease characterized by episodic weakness associated with low serum potassium. We compared clinical and biophysical effects of R222W, the first hNaV1.4 domain I mutation linked to this disease. R222W patients exhibited a higher density of fibers with depolarized resting membrane potentials and produced action potentials that were attenuated compared to controls. Functional characterization of the R222W mutation in heterologous expression included the inactivation deficient IFM/QQQ background to isolate activation. R222W decreased sodium current and slowed activation without affecting probability. Consistent with the phenotype of muscle weakness, R222W shifted fast inactivation to hyperpolarized potentials, promoted more rapid entry, and slowed recovery. R222W increased the extent of slow inactivation and slowed its recovery. A two-compartment skeletal muscle fiber model revealed that defects in fast inactivation sufficiently explain action potential attenuation in patients. Molecular dynamics simulations showed that R222W disrupted electrostatic interactions within the gating pore, supporting the observation that R222W promotes omega current at hyperpolarized potentials. Sodium channel inactivation defects produced by R222W are the primary driver of skeletal muscle fiber action potential attenuation, while hyperpolarization-induced omega current produced by that mutation promotes muscle fiber depolarization.
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Affiliation(s)
| | - Vern Winston
- Department of Biological Sciences, Idaho State University, 83209, Pocatello, ID, USA
| | | | - Paula Arinze
- Department of Biological Sciences, Idaho State University, 83209, Pocatello, ID, USA
| | - James R Groome
- Department of Biological Sciences, Idaho State University, 83209, Pocatello, ID, USA.
| | - Karin Jurkat-Rott
- Department of Neuroanesthesiology, Clinic for Neurosurgery, Ulm University, Guenzburg, Germany
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20
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DeCoursey TE. Voltage and pH sensing by the voltage-gated proton channel, H V1. J R Soc Interface 2018; 15:20180108. [PMID: 29643227 PMCID: PMC5938591 DOI: 10.1098/rsif.2018.0108] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/19/2018] [Indexed: 12/15/2022] Open
Abstract
Voltage-gated proton channels are unique ion channels, membrane proteins that allow protons but no other ions to cross cell membranes. They are found in diverse species, from unicellular marine life to humans. In all cells, their function requires that they open and conduct current only under certain conditions, typically when the electrochemical gradient for protons is outwards. Consequently, these proteins behave like rectifiers, conducting protons out of cells. Their activity has electrical consequences and also changes the pH on both sides of the membrane. Here we summarize what is known about the way these proteins sense the membrane potential and the pH inside and outside the cell. Currently, it is hypothesized that membrane potential is sensed by permanently charged arginines (with very high pKa) within the protein, which results in parts of the protein moving to produce a conduction pathway. The mechanism of pH sensing appears to involve titratable side chains of particular amino acids. For this purpose their pKa needs to be within the operational pH range. We propose a 'counter-charge' model for pH sensing in which electrostatic interactions within the protein are selectively disrupted by protonation of internally or externally accessible groups.
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Affiliation(s)
- Thomas E DeCoursey
- Department of Physiology & Biophysics, Rush University, 1750 West Harrison, Chicago, IL 60612, USA
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21
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Monteleone S, Lieb A, Pinggera A, Negro G, Fuchs JE, Hofer F, Striessnig J, Tuluc P, Liedl KR. Mechanisms Responsible for ω-Pore Currents in Ca v Calcium Channel Voltage-Sensing Domains. Biophys J 2017; 113:1485-1495. [PMID: 28978442 PMCID: PMC5627182 DOI: 10.1016/j.bpj.2017.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/28/2017] [Accepted: 08/07/2017] [Indexed: 12/27/2022] Open
Abstract
Mutations of positively charged amino acids in the S4 transmembrane segment of a voltage-gated ion channel form ion-conducting pathways through the voltage-sensing domain, named ω-current. Here, we used structure modeling and MD simulations to predict pathogenic ω-currents in CaV1.1 and CaV1.3 Ca2+ channels bearing several S4 charge mutations. Our modeling predicts that mutations of CaV1.1-R1 (R528H/G, R897S) or CaV1.1-R2 (R900S, R1239H) linked to hypokalemic periodic paralysis type 1 and of CaV1.3-R3 (R990H) identified in aldosterone-producing adenomas conducts ω-currents in resting state, but not during voltage-sensing domain activation. The mechanism responsible for the ω-current and its amplitude depend on the number of charges in S4, the position of the mutated S4 charge and countercharges, and the nature of the replacing amino acid. Functional characterization validates the modeling prediction showing that CaV1.3-R990H channels conduct ω-currents at hyperpolarizing potentials, but not upon membrane depolarization compared with wild-type channels.
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Affiliation(s)
- Stefania Monteleone
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Andreas Lieb
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria; Institute of Neurology, University College London, London, United Kingdom
| | - Alexandra Pinggera
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria; Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Giulia Negro
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Florian Hofer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Jörg Striessnig
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Petronel Tuluc
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria.
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria.
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22
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DeCoursey TE, Morgan D, Musset B, Cherny VV. Insights into the structure and function of HV1 from a meta-analysis of mutation studies. J Gen Physiol 2017; 148:97-118. [PMID: 27481712 PMCID: PMC4969798 DOI: 10.1085/jgp.201611619] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/30/2016] [Indexed: 01/26/2023] Open
Abstract
The voltage-gated proton channel (HV1) is a widely distributed, proton-specific ion channel with unique properties. Since 2006, when genes for HV1 were identified, a vast array of mutations have been generated and characterized. Accessing this potentially useful resource is hindered, however, by the sheer number of mutations and interspecies differences in amino acid numbering. This review organizes all existing information in a logical manner to allow swift identification of studies that have characterized any particular mutation. Although much can be gained from this meta-analysis, important questions about the inner workings of HV1 await future revelation.
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Affiliation(s)
- Thomas E DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
| | - Deri Morgan
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
| | - Boris Musset
- Institut für Physiologie, PMU Klinikum Nürnberg, 90419 Nürnberg, Germany
| | - Vladimir V Cherny
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
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23
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DeCoursey TE. CrossTalk proposal: Proton permeation through H V 1 requires transient protonation of a conserved aspartate in the S1 transmembrane helix. J Physiol 2017; 595:6793-6795. [PMID: 29023793 DOI: 10.1113/jp274495] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Thomas E DeCoursey
- Department of Physiology and Biophysics, Rush University, Chicago, IL, 60612, USA
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24
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Bennett AL, Ramsey IS. Rebuttal from Ashley L. Bennett and Ian Scott Ramsey. J Physiol 2017; 595:6803. [PMID: 29023729 DOI: 10.1113/jp274984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Ashley L Bennett
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Ian Scott Ramsey
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
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25
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Wilson RH, Zamfir S, Sumner I. Molecular dynamics simulations reveal a new role for a conserved active site asparagine in a ubiquitin-conjugating enzyme. J Mol Graph Model 2017; 76:403-411. [DOI: 10.1016/j.jmgm.2017.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 11/28/2022]
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26
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DeCoursey TE. The intimate and controversial relationship between voltage-gated proton channels and the phagocyte NADPH oxidase. Immunol Rev 2017; 273:194-218. [PMID: 27558336 DOI: 10.1111/imr.12437] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
One of the most fascinating and exciting periods in my scientific career entailed dissecting the symbiotic relationship between two membrane transporters, the Nicotinamide adenine dinucleotide phosphate reduced form (NADPH) oxidase complex and voltage-gated proton channels (HV 1). By the time I entered this field, there had already been substantial progress toward understanding NADPH oxidase, but HV 1 were known only to a tiny handful of cognoscenti around the world. Having identified the first proton currents in mammalian cells in 1991, I needed to find a clear function for these molecules if the work was to become fundable. The then-recent discoveries of Henderson, Chappell, and colleagues in 1987-1988 that led them to hypothesize interactions of both molecules during the respiratory burst of phagocytes provided an excellent opportunity. In a nutshell, both transporters function by moving electrical charge across the membrane: NADPH oxidase moves electrons and HV 1 moves protons. The consequences of electrogenic NADPH oxidase activity on both membrane potential and pH strongly self-limit this enzyme. Fortunately, both consequences specifically activate HV 1, and HV 1 activity counteracts both consequences, a kind of yin-yang relationship. Notwithstanding a decade starting in 1995 when many believed the opposite, these are two separate molecules that function independently despite their being functionally interdependent in phagocytes. The relationship between NADPH oxidase and HV 1 has become a paradigm that somewhat surprisingly has now extended well beyond the phagocyte NADPH oxidase - an industrial strength producer of reactive oxygen species (ROS) - to myriad other cells that produce orders of magnitude less ROS for signaling purposes. These cells with their seven NADPH oxidase (NOX) isoforms provide a vast realm of mechanistic obscurity that will occupy future studies for years to come.
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Affiliation(s)
- Thomas E DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL, USA
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27
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van Keulen SC, Gianti E, Carnevale V, Klein ML, Rothlisberger U, Delemotte L. Does Proton Conduction in the Voltage-Gated H + Channel hHv1 Involve Grotthuss-Like Hopping via Acidic Residues? J Phys Chem B 2017; 121:3340-3351. [PMID: 27801578 PMCID: PMC6310143 DOI: 10.1021/acs.jpcb.6b08339] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hv1s are ubiquitous highly selective voltage-gated proton channels involved in male fertility, immunology, and the invasiveness of certain forms of breast cancer. The mechanism of proton extrusion in Hv1 is not yet understood, while it constitutes the first step toward the design of high-affinity drugs aimed at this important pharmacological target. In this contribution, we explore the details of the mechanism via an integrative approach, using classical and QM/MM molecular dynamics simulations of a monomeric hHv1 model. We propose that protons localize in three binding sites along the channel lumen, formed by three pairs of conserved negatively charged residues lining the pore: D174/E153, D112/D185, and E119/D123. Local rearrangements, involving notably a dihedral transition of F150, a conserved phenylalanine lining the permeation pathway, appear to allow protons to hop from one acidic residue to the next through a bridging water molecule. These results constitute a first attempt at rationalizing hHv1 selectivity for H+ and the role played by D112 in this process. They pave the way for further quantitative characterization of H+ transport in hHv1.
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Affiliation(s)
- Siri C. van Keulen
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Eleonora Gianti
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Michael L. Klein
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Lucie Delemotte
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Present address: Science for Life Laboratory, Department of Theoretical Physics, KTH, Box 1031, SE-171 21 Solna, Stockholm, Sweden
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28
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Gianti E, Delemotte L, Klein ML, Carnevale V. On the role of water density fluctuations in the inhibition of a proton channel. Proc Natl Acad Sci U S A 2016; 113:E8359-E8368. [PMID: 27956641 PMCID: PMC5206518 DOI: 10.1073/pnas.1609964114] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently solved crystal structure of Hv1, we used structural modeling and molecular dynamics simulations to characterize the channel's most relevant conformations along the activation cycle. We then performed computational docking of known Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI) and analogs. Although salt-bridge patterns and electrostatic potential profiles are well-defined and distinctive features of activated versus nonactivated states, the water distribution along the channel lumen is dynamic and reflects a conformational heterogeneity inherent to each state. In fact, pore waters assemble into intermittent hydrogen-bonded clusters that are replaced by the inhibitor moieties upon ligand binding. The entropic gain resulting from releasing these conformationally restrained waters to the bulk solvent is likely a major contributor to the binding free energy. Accordingly, we mapped the water density fluctuations inside the pore of the channel and identified the regions of maximum fluctuation within putative binding sites. Two sites appear as outstanding: One is the already known binding pocket of 2GBI, which is accessible to ligands from the intracellular side; the other is a site located at the exit of the proton permeation pathway. Our analysis of the waters confined in the hydrophobic cavities of Hv1 suggests a general strategy for drug discovery that can be applied to any ion channel.
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Affiliation(s)
- Eleonora Gianti
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Lucie Delemotte
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Michael L Klein
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122;
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122;
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29
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Pathak MM, Tran T, Hong L, Joós B, Morris CE, Tombola F. The Hv1 proton channel responds to mechanical stimuli. J Gen Physiol 2016; 148:405-418. [PMID: 27799320 PMCID: PMC5089936 DOI: 10.1085/jgp.201611672] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/22/2016] [Indexed: 12/21/2022] Open
Abstract
The voltage-gated proton channel, Hv1, is expressed in tissues throughout the body and plays important roles in pH homeostasis and regulation of NADPH oxidase. Hv1 operates in membrane compartments that experience strong mechanical forces under physiological or pathological conditions. In microglia, for example, Hv1 activity is potentiated by cell swelling and causes an increase in brain damage after stroke. The channel complex consists of two proton-permeable voltage-sensing domains (VSDs) linked by a cytoplasmic coiled-coil domain. Here, we report that these VSDs directly respond to mechanical stimuli. We find that membrane stretch facilitates Hv1 channel opening by increasing the rate of activation and shifting the steady-state activation curve to less depolarized potentials. In the presence of a transmembrane pH gradient, membrane stretch alone opens the channel without the need for strong depolarizations. The effect of membrane stretch persists for several minutes after the mechanical stimulus is turned off, suggesting that the channel switches to a "facilitated" mode in which opening occurs more readily and then slowly reverts to the normal mode observed in the absence of membrane stretch. Conductance simulations with a six-state model recapitulate all the features of the channel's response to mechanical stimulation. Hv1 mechanosensitivity thus provides a mechanistic link between channel activation in microglia and brain damage after stroke.
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Affiliation(s)
- Medha M Pathak
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Truc Tran
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Liang Hong
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Béla Joós
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | | | - Francesco Tombola
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
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30
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Randolph AL, Mokrab Y, Bennett AL, Sansom MS, Ramsey IS. Proton currents constrain structural models of voltage sensor activation. eLife 2016; 5. [PMID: 27572256 PMCID: PMC5065317 DOI: 10.7554/elife.18017] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/29/2016] [Indexed: 11/13/2022] Open
Abstract
The Hv1 proton channel is evidently unique among voltage sensor domain proteins in mediating an intrinsic 'aqueous' H+ conductance (GAQ). Mutation of a highly conserved 'gating charge' residue in the S4 helix (R1H) confers a resting-state H+ 'shuttle' conductance (GSH) in VGCs and Ci VSP, and we now report that R1H is sufficient to reconstitute GSH in Hv1 without abrogating GAQ. Second-site mutations in S3 (D185A/H) and S4 (N4R) experimentally separate GSH and GAQ gating, which report thermodynamically distinct initial and final steps, respectively, in the Hv1 activation pathway. The effects of Hv1 mutations on GSH and GAQ are used to constrain the positions of key side chains in resting- and activated-state VS model structures, providing new insights into the structural basis of VS activation and H+ transfer mechanisms in Hv1.
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Affiliation(s)
- Aaron L Randolph
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, United States.,Medical College of Virginia Campus, Virginia Commonwealth University School of Medicine, Richmond, United States
| | - Younes Mokrab
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ashley L Bennett
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, United States.,Medical College of Virginia Campus, Virginia Commonwealth University School of Medicine, Richmond, United States
| | - Mark Sp Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ian Scott Ramsey
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, United States.,Medical College of Virginia Campus, Virginia Commonwealth University School of Medicine, Richmond, United States
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31
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Chaves G, Derst C, Franzen A, Mashimo Y, Machida R, Musset B. Identification of an HV
1 voltage-gated proton channel in insects. FEBS J 2016; 283:1453-64. [DOI: 10.1111/febs.13680] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/05/2016] [Accepted: 02/09/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Gustavo Chaves
- Institute of Complex Systems; Zelluläre Biophysik (ICS-4) Forschungszentrum Jülich; Germany
| | - Christian Derst
- Zoologisches Institut; Biozentrum Universität zu Köln; Germany
| | - Arne Franzen
- Institute of Complex Systems; Zelluläre Biophysik (ICS-4) Forschungszentrum Jülich; Germany
| | - Yuta Mashimo
- Sugadaira Montane Research Center; University of Tsukuba; Ueda Japan
| | - Ryuichiro Machida
- Sugadaira Montane Research Center; University of Tsukuba; Ueda Japan
| | - Boris Musset
- Institute of Complex Systems; Zelluläre Biophysik (ICS-4) Forschungszentrum Jülich; Germany
- Institut für Physiologie und Pathophysiologie; Paracelsus Universität Salzburg Standort Nürnberg; Nuremberg Germany
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32
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Moreau A, Gosselin-Badaroudine P, Boutjdir M, Chahine M. Mutations in the Voltage Sensors of Domains I and II of Nav1.5 that are Associated with Arrhythmias and Dilated Cardiomyopathy Generate Gating Pore Currents. Front Pharmacol 2015; 6:301. [PMID: 26733869 PMCID: PMC4689871 DOI: 10.3389/fphar.2015.00301] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/09/2015] [Indexed: 12/19/2022] Open
Abstract
Voltage gated sodium channels (Nav) are transmembrane proteins responsible for action potential initiation. Mutations mainly located in the voltage sensor domain (VSD) of Nav1.5, the cardiac sodium channel, have been associated with the development of arrhythmias combined with dilated cardiomyopathy. Gating pore currents have been observed with three unrelated mutations associated with similar clinical phenotypes. However, gating pores have never been associated with mutations outside the first domain of Nav1.5. The aim of this study was to explore the possibility that gating pore currents might be caused by the Nav1.5 R225P and R814W mutations (R3, S4 in DI and DII, respectively), which are associated with rhythm disturbances and dilated cardiomyopathy. Nav1.5 WT and mutant channels were transiently expressed in tsA201 cells. The biophysical properties of the alpha pore currents and the presence of gating pore currents were investigated using the patch-clamp technique. We confirmed the previously reported gain of function of the alpha pores of the mutant channels, which mainly consisted of increased window currents mostly caused by shifts in the voltage dependence of activation. We also observed gating pore currents associated with the R225P and R814W mutations. This novel permeation pathway was open under depolarized conditions and remained temporarily open at hyperpolarized potentials after depolarization periods. Gating pore currents could represent a molecular basis for the development of uncommon electrical abnormalities and changes in cardiac morphology. We propose that this biophysical defect be routinely evaluated in the case of Nav1.5 mutations on the VSD.
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Affiliation(s)
- Adrien Moreau
- Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Quebec City QC, Canada
| | | | - Mohamed Boutjdir
- Cardiovascular Research Program, VA New York Harbor Healthcare System, Brooklyn NY, USA
| | - Mohamed Chahine
- Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Quebec CityQC, Canada; Department of Medicine, Université Laval, Quebec CityQC, Canada
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33
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Abstract
Hv1 is a voltage-gated proton-selective channel that plays critical parts in host defense, sperm motility, and cancer progression. Hv1 contains a conserved voltage-sensor domain (VSD) that is shared by a large family of voltage-gated ion channels, but it lacks a pore domain. Voltage sensitivity and proton conductivity are conferred by a unitary VSD that consists of four transmembrane helices. The architecture of Hv1 differs from that of cation channels that form a pore in the center among multiple subunits (as in most cation channels) or homologous repeats (as in voltage-gated sodium and calcium channels). Hv1 forms a dimer in which a cytoplasmic coiled coil underpins the two protomers and forms a single, long helix that is contiguous with S4, the transmembrane voltage-sensing segment. The closed-state structure of Hv1 was recently solved using X-ray crystallography. In this article, we discuss the gating mechanism of Hv1 and focus on cooperativity within dimers and their sensitivity to metal ions.
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Affiliation(s)
- Yasushi Okamura
- Department of Integrative Physiology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan; , ,
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34
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Li Q, Shen R, Treger JS, Wanderling SS, Milewski W, Siwowska K, Bezanilla F, Perozo E. Resting state of the human proton channel dimer in a lipid bilayer. Proc Natl Acad Sci U S A 2015; 112:E5926-35. [PMID: 26443860 PMCID: PMC4640771 DOI: 10.1073/pnas.1515043112] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The voltage-gated proton channel Hv1 plays a critical role in the fast proton translocation that underlies a wide range of physiological functions, including the phagocytic respiratory burst, sperm motility, apoptosis, and metastatic cancer. Both voltage activation and proton conduction are carried out by a voltage-sensing domain (VSD) with strong similarity to canonical VSDs in voltage-dependent cation channels and enzymes. We set out to determine the structural properties of membrane-reconstituted human proton channel (hHv1) in its resting conformation using electron paramagnetic resonance spectroscopy together with biochemical and computational methods. We evaluated existing structural templates and generated a spectroscopically constrained model of the hHv1 dimer based on the Ci-VSD structure at resting state. Mapped accessibility data revealed deep water penetration through hHv1, suggesting a highly focused electric field, comprising two turns of helix along the fourth transmembrane segment. This region likely contains the H(+) selectivity filter and the conduction pore. Our 3D model offers plausible explanations for existing electrophysiological and biochemical data, offering an explicit mechanism for voltage activation based on a one-click sliding helix conformational rearrangement.
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Affiliation(s)
- Qufei Li
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Rong Shen
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Jeremy S Treger
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Sherry S Wanderling
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Wieslawa Milewski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Klaudia Siwowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
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Cherny VV, Morgan D, Musset B, Chaves G, Smith SME, DeCoursey TE. Tryptophan 207 is crucial to the unique properties of the human voltage-gated proton channel, hHV1. ACTA ACUST UNITED AC 2015; 146:343-56. [PMID: 26458876 PMCID: PMC4621752 DOI: 10.1085/jgp.201511456] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/18/2015] [Indexed: 01/19/2023]
Abstract
Part of the "signature sequence" that defines the voltage-gated proton channel (H(V1)) is a tryptophan residue adjacent to the second Arg in the S4 transmembrane helix: RxWRxxR, which is perfectly conserved in all high confidence H(V1) genes. Replacing Trp207 in human HV1 (hH(V1)) with Ala, Ser, or Phe facilitated gating, accelerating channel opening by 100-fold, and closing by 30-fold. Mutant channels opened at more negative voltages than wild-type (WT) channels, indicating that in WT channels, Trp favors a closed state. The Arrhenius activation energy, Ea, for channel opening decreased to 22 kcal/mol from 30-38 kcal/mol for WT, confirming that Trp207 establishes the major energy barrier between closed and open hH(V1). Cation-π interaction between Trp207 and Arg211 evidently latches the channel closed. Trp207 mutants lost proton selectivity at pHo >8.0. Finally, gating that depends on the transmembrane pH gradient (ΔpH-dependent gating), a universal feature of H(V1) that is essential to its biological functions, was compromised. In the WT hH(V1), ΔpH-dependent gating is shown to saturate above pHi or pHo 8, consistent with a single pH sensor with alternating access to internal and external solutions. However, saturation occurred independently of ΔpH, indicating the existence of distinct internal and external pH sensors. In Trp207 mutants, ΔpH-dependent gating saturated at lower pHo but not at lower pHi. That Trp207 mutation selectively alters pHo sensing further supports the existence of distinct internal and external pH sensors. Analogous mutations in H(V1) from the unicellular species Karlodinium veneficum and Emiliania huxleyi produced generally similar consequences. Saturation of ΔpH-dependent gating occurred at the same pHo and pHi in H(V1) of all three species, suggesting that the same or similar group(s) is involved in pH sensing. Therefore, Trp enables four characteristic properties: slow channel opening, highly temperature-dependent gating kinetics, proton selectivity, and ΔpH-dependent gating.
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Affiliation(s)
- Vladimir V Cherny
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
| | - Deri Morgan
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
| | - Boris Musset
- Institute of Complex Systems 4 Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gustavo Chaves
- Institute of Complex Systems 4 Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144
| | - Thomas E DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
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36
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Moreau A, Gosselin-Badaroudine P, Delemotte L, Klein ML, Chahine M. Gating pore currents are defects in common with two Nav1.5 mutations in patients with mixed arrhythmias and dilated cardiomyopathy. ACTA ACUST UNITED AC 2015; 145:93-106. [PMID: 25624448 PMCID: PMC4306709 DOI: 10.1085/jgp.201411304] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nav1.5 channels bearing voltage-sensor domain mutations associated with atypical cardiac arrhythmias and dilated cardiomyopathy generate gating pore currents. The gating pore current, also called omega current, consists of a cation leak through the typically nonconductive voltage-sensor domain (VSD) of voltage-gated ion channels. Although the study of gating pore currents has refined our knowledge of the structure and the function of voltage-gated ion channels, their implication in cardiac disorders has not been established. Two Nav1.5 mutations (R222Q and R225W) located in the VSD are associated with atypical clinical phenotypes involving complex arrhythmias and dilated cardiomyopathy. Using the patch-clamp technique, in silico mutagenesis, and molecular dynamic simulations, we tested the hypothesis that these two mutations may generate gating pore currents, potentially accounting for their clinical phenotypes. Our findings suggest that the gating pore current generated by the R222Q and R225W mutations could constitute the underlying pathological mechanism that links Nav1.5 VSD mutations with human cardiac arrhythmias and dilatation of cardiac chambers.
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Affiliation(s)
- Adrien Moreau
- Centre de Recherche de L'Institut Universitaire en Santé Mentale de Québec, Québec City, Québec G1J 2G3, Canada
| | - Pascal Gosselin-Badaroudine
- Centre de Recherche de L'Institut Universitaire en Santé Mentale de Québec, Québec City, Québec G1J 2G3, Canada
| | - Lucie Delemotte
- Institute of Computational Molecular Science, Temple University, Philadelphia, PA 19122
| | - Michael L Klein
- Institute of Computational Molecular Science, Temple University, Philadelphia, PA 19122
| | - Mohamed Chahine
- Centre de Recherche de L'Institut Universitaire en Santé Mentale de Québec, Québec City, Québec G1J 2G3, Canada Department of Medicine, Université Laval, Québec City, Québec G1K 7P4, Canada
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37
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Interrogation of the intersubunit interface of the open Hv1 proton channel with a probe of allosteric coupling. Sci Rep 2015; 5:14077. [PMID: 26365828 PMCID: PMC4568520 DOI: 10.1038/srep14077] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/14/2015] [Indexed: 12/15/2022] Open
Abstract
The Hv1 voltage-gated proton channel is a dimeric complex consisting of two voltage-sensing domains (VSDs), each containing a gated proton permeation pathway. Dimerization is controlled by a cytoplasmic coiled-coil domain. The transitions from the closed to the open state in the two VSDs are known to occur cooperatively; however, the underlying mechanism is poorly understood. Intersubunit interfaces play a critical role in allosteric processes; but, such interfaces have not been determined in the open Hv1 channel. Here we show that 2-guanidinothiazole derivatives block the two Hv1 VSDs in a cooperative way, and use one of the compounds as a probe of allosteric coupling between open subunits. We find that the extracellular ends of the first transmembrane segments of the VSDs form the intersubunit interface that mediates coupling between binding sites, while the coiled-coil domain does not directly participate in the process. We also find strong evidence that the channel’s proton selectivity filter controls blocker binding cooperativity.
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38
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Pupo A, Baez-Nieto D, Martínez A, Latorre R, González C. Proton channel models filling the gap between experimental data and the structural rationale. Channels (Austin) 2015; 8:180-92. [PMID: 24755912 PMCID: PMC4203746 DOI: 10.4161/chan.28665] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Voltage-gated proton channels are integral membrane proteins with the capacity to permeate elementary particles in a voltage and pH dependent manner. These proteins have been found in several species and are involved in various physiological processes. Although their primary topology is known, lack of details regarding their structures in the open conformation has limited analyses toward a deeper understanding of the molecular determinants of their function and regulation. Consequently, the function-structure relationships have been inferred based on homology models. In the present work, we review the existing proton channel models, their assumptions, predictions and the experimental facts that support them. Modeling proton channels is not a trivial task due to the lack of a close homolog template. Hence, there are important differences between published models. This work attempts to critically review existing proton channel models toward the aim of contributing to a better understanding of the structural features of these proteins.
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39
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Abstract
The main properties of the voltage-gated proton channel (HV1) are described in this review, along with what is known about how the channel protein structure accomplishes its functions. Just as protons are unique among ions, proton channels are unique among ion channels. Their four transmembrane helices sense voltage and the pH gradient and conduct protons exclusively. Selectivity is achieved by the unique ability of H3O(+) to protonate an Asp-Arg salt bridge. Pathognomonic sensitivity of gating to the pH gradient ensures HV1 channel opening only when acid extrusion will result, which is crucial to most of its biological functions. An exception occurs in dinoflagellates in which influx of H(+) through HV1 triggers the bioluminescent flash. Pharmacological interventions that promise to ameliorate cancer, asthma, brain damage in ischemic stroke, Alzheimer's disease, autoimmune diseases, and numerous other conditions await future progress.
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Affiliation(s)
- Thomas E. DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, 1750 West Harrison, Chicago IL, 60612 USA
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40
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Selectivity Mechanism of the Voltage-gated Proton Channel, HV1. Sci Rep 2015; 5:10320. [PMID: 25955978 PMCID: PMC4429351 DOI: 10.1038/srep10320] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/08/2015] [Indexed: 01/04/2023] Open
Abstract
Voltage-gated proton channels, HV1, trigger bioluminescence in dinoflagellates, enable calcification in coccolithophores, and play multifarious roles in human health. Because the proton concentration is minuscule, exquisite selectivity for protons over other ions is critical to HV1 function. The selectivity of the open HV1 channel requires an aspartate near an arginine in the selectivity filter (SF), a narrow region that dictates proton selectivity, but the mechanism of proton selectivity is unknown. Here we use a reduced quantum model to elucidate how the Asp-Arg SF selects protons but excludes other ions. Attached to a ring scaffold, the Asp and Arg side chains formed bidentate hydrogen bonds that occlude the pore. Introducing H3O(+) protonated the SF, breaking the Asp-Arg linkage and opening the conduction pathway, whereas Na(+) or Cl(-) was trapped by the SF residue of opposite charge, leaving the linkage intact, thus preventing permeation. An Asp-Lys SF behaved like the Asp-Arg one and was experimentally verified to be proton-selective, as predicted. Hence, interacting acidic and basic residues form favorable AspH(0)-H2O(0)-Arg(+) interactions with hydronium but unfavorable Asp(-)-X(-)/X(+)-Arg(+) interactions with anions/cations. This proposed mechanism may apply to other proton-selective molecules engaged in bioenergetics, homeostasis, and signaling.
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41
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Abstract
Voltage sensor domains (VSDs) are membrane-bound protein modules that confer voltage sensitivity to membrane proteins. VSDs sense changes in the transmembrane voltage and convert the electrical signal into a conformational change called activation. Activation involves a reorganization of the membrane protein charges that is detected experimentally as transient currents. These so-called gating currents have been investigated extensively within the theoretical framework of so-called discrete-state Markov models (DMMs), whereby activation is conceptualized as a series of transitions across a discrete set of states. Historically, the interpretation of DMM transition rates in terms of transition state theory has been instrumental in shaping our view of the activation process, whose free-energy profile is currently envisioned as composed of a few local minima separated by steep barriers. Here we use atomistic level modeling and well-tempered metadynamics to calculate the configurational free energy along a single transition from first principles. We show that this transition is intrinsically multidimensional and described by a rough free-energy landscape. Remarkably, a coarse-grained description of the system, based on the use of the gating charge as reaction coordinate, reveals a smooth profile with a single barrier, consistent with phenomenological models. Our results bridge the gap between microscopic and macroscopic descriptions of activation dynamics and show that choosing the gating charge as reaction coordinate masks the topological complexity of the network of microstates participating in the transition. Importantly, full characterization of the latter is a prerequisite to rationalize modulation of this process by lipids, toxins, drugs, and genetic mutations.
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42
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Mapping the gating and permeation pathways in the voltage-gated proton channel Hv1. J Mol Biol 2014; 427:131-45. [PMID: 25481746 DOI: 10.1016/j.jmb.2014.11.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 09/10/2014] [Accepted: 11/20/2014] [Indexed: 11/24/2022]
Abstract
Voltage-gated proton channels (Hv1) are ubiquitous throughout nature and are implicated in numerous physiological processes. The gene encoding for Hv1, however, was only identified in 2006. The lack of sufficient structural information of this channel has hampered the understanding of the molecular mechanism of channel activation and proton permeation. This study uses both simulation and experimental approaches to further develop existing models of the Hv1 channel. Our study provides insights into features of channel gating and proton permeation pathway. We compare open- and closed-state structures developed previously with a recent crystal structure that traps the channel in a presumably closed state. Insights into gating pathways were provided using a combination of all-atom molecular dynamics simulations with a swarm of trajectories with the string method for extensive transition path sampling and evolution. A detailed residue-residue interaction profile and a hydration profile were studied to map the gating pathway in this channel. In particular, it allows us to identify potential intermediate states and compare them to the experimentally observed crystal structure of Takeshita et al. (Takeshita K, Sakata S, Yamashita E, Fujiwara Y, Kawanabe A, Kurokawa T, et al. X-ray crystal structure of voltage-gated proton channel. Nature 2014). The mechanisms governing ion transport in the wild-type and mutant Hv1 channels were studied by a combination of electrophysiological recordings and free energy simulations. With these results, we were able to further refine ideas about the location and function of the selectivity filter. The refined structural models will be essential for future investigations of this channel and the development of new drugs targeting cellular proton transport.
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43
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Velez-Vega C, McKay DJJ, Aravamuthan V, Pearlstein R, Duca JS. Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH. J Chem Inf Model 2014; 54:3344-61. [PMID: 25405925 DOI: 10.1021/ci500571h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proton translocation pathways of selected variants of the green fluorescent protein (GFP) and Pseudomonas fluorescens mannitol 2-dehydrogenase (PfM2DH) were investigated via an explicit solvent molecular dynamics-based analysis protocol that allows for direct quantitative relationship between a crystal structure and its time-averaged solute-solvent structure obtained from simulation. Our study of GFP is in good agreement with previous research suggesting that the proton released from the chromophore upon photoexcitation can diffuse through an extended internal hydrogen bonding network that allows for the proton to exit to bulk or be recaptured by the anionic chromophore. Conversely for PfM2DH, we identified the most probable ionization states of key residues along the proton escape channel from the catalytic site to bulk solvent, wherein the solute and high-density solvent crystal structures of binary and ternary complexes were properly reproduced. Furthermore, we proposed a plausible mechanism for this proton translocation process that is consistent with the state-dependent structural shifts observed in our analysis. The time-averaged structures generated from our analyses facilitate validation of MD simulation results and provide a comprehensive profile of the dynamic all-occupancy solvation network within and around a flexible solute, from which detailed hydrogen-bonding networks can be inferred. In this way, potential drawbacks arising from the elucidation of these networks by examination of static crystal structures or via alternate rigid-protein solvation analysis procedures can be overcome. Complementary studies aimed at the effective use of our methodology for alternate implementations (e.g., ligand design) are currently underway.
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Affiliation(s)
- Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
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44
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Palovcak E, Delemotte L, Klein ML, Carnevale V. Evolutionary imprint of activation: the design principles of VSDs. ACTA ACUST UNITED AC 2014; 143:145-56. [PMID: 24470486 PMCID: PMC4001776 DOI: 10.1085/jgp.201311103] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Voltage-sensor domains (VSDs) are modular biomolecular machines that transduce electrical signals in cells through a highly conserved activation mechanism. Here, we investigate sequence-function relationships in VSDs with approaches from information theory and probabilistic modeling. Specifically, we collect over 6,600 unique VSD sequences from diverse, long-diverged phylogenetic lineages and relate the statistical properties of this ensemble to functional constraints imposed by evolution. The VSD is a helical bundle with helices labeled S1-S4. Surrounding conserved VSD residues such as the countercharges and the S2 phenylalanine, we discover sparse networks of coevolving residues. Additional networks are found lining the VSD lumen, tuning the local hydrophilicity. Notably, state-dependent contacts and the absence of coevolution between S4 and the rest of the bundle are imprints of the activation mechanism on the VSD sequence ensemble. These design principles rationalize existing experimental results and generate testable hypotheses.
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Affiliation(s)
- Eugene Palovcak
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122
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45
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Grizel AV, Glukhov GS, Sokolova OS. Mechanisms of activation of voltage-gated potassium channels. Acta Naturae 2014; 6:10-26. [PMID: 25558391 PMCID: PMC4273088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Voltage-gated potassium ion channels (Kv) play an important role in a variety of cellular processes, including the functioning of excitable cells, regulation of apoptosis, cell growth and differentiation, the release of neurotransmitters and hormones, maintenance of cardiac activity, etc. Failure in the functioning of Kv channels leads to severe genetic disorders and the development of tumors, including malignant ones. Understanding the mechanisms underlying Kv channels functioning is a key factor in determining the cause of the diseases associated with mutations in the channels, and in the search for new drugs. The mechanism of activation of the channels is a topic of ongoing debate, and a consensus on the issue has not yet been reached. This review discusses the key stages in studying the mechanisms of functioning of Kv channels and describes the basic models of their activation known to date.
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Affiliation(s)
- A. V. Grizel
- Saint Petersburg State University, 7-9, Universitetskaya nab., 199034, St. Petersburg, Russia
| | - G. S. Glukhov
- Biological Faculty of Moscow State MV Lomonosov University, 1, Leninskie Gory, Bld. 12, 119991, Moscow, Russia
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46
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47
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Molecular determinants of Hv1 proton channel inhibition by guanidine derivatives. Proc Natl Acad Sci U S A 2014; 111:9971-6. [PMID: 24912149 DOI: 10.1073/pnas.1324012111] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The voltage-gated proton channel Hv1 plays important roles in proton extrusion, pH homeostasis, and production of reactive oxygen species in a variety of cell types. Excessive Hv1 activity increases proliferation and invasiveness in cancer cells and worsens brain damage in ischemic stroke. The channel is composed of two subunits, each containing a proton-permeable voltage-sensing domain (VSD) and lacking the pore domain typical of other voltage-gated ion channels. We have previously shown that the compound 2-guanidinobenzimidazole (2GBI) inhibits Hv1 proton conduction by binding to the VSD from its intracellular side. Here, we examine the binding affinities of a series of 2GBI derivatives on human Hv1 channels mutated at positions located in the core of the VSD and apply mutant cycle analysis to determine how the inhibitor interacts with the channel. We identify four Hv1 residues involved in the binding: aspartate 112, phenylalanine 150, serine 181, and arginine 211. 2GBI appears to be oriented in the binding site with its benzo ring pointing to F150, its imidazole ring inserted between residue D112 and residues S181 and R211, and the guanidine group positioned in the proximity of R211. We also identify a modified version of 2GBI that is able to reach the binding site on Hv1 from the extracellular side of the membrane. Understanding how compounds like 2GBI interact with the Hv1 channel is an important step to the development of pharmacological treatments for diseases caused by Hv1 hyperactivity.
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DeCoursey TE, Hosler J. Philosophy of voltage-gated proton channels. J R Soc Interface 2014; 11:20130799. [PMID: 24352668 PMCID: PMC3899857 DOI: 10.1098/rsif.2013.0799] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/22/2013] [Indexed: 02/02/2023] Open
Abstract
In this review, voltage-gated proton channels are considered from a mainly teleological perspective. Why do proton channels exist? What good are they? Why did they go to such lengths to develop several unique hallmark properties such as extreme selectivity and ΔpH-dependent gating? Why is their current so minuscule? How do they manage to be so selective? What is the basis for our belief that they conduct H(+) and not OH(-)? Why do they exist in many species as dimers when the monomeric form seems to work quite well? It is hoped that pondering these questions will provide an introduction to these channels and a way to logically organize their peculiar properties as well as to understand how they are able to carry out some of their better-established biological functions.
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Affiliation(s)
- Thomas E. DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, 1750 West Harrison, Chicago, IL 60612, USA
| | - Jonathan Hosler
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA
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Takeshita K, Sakata S, Yamashita E, Fujiwara Y, Kawanabe A, Kurokawa T, Okochi Y, Matsuda M, Narita H, Okamura Y, Nakagawa A. X-ray crystal structure of voltage-gated proton channel. Nat Struct Mol Biol 2014; 21:352-7. [DOI: 10.1038/nsmb.2783] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 02/03/2014] [Indexed: 12/12/2022]
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Abstract
Voltage-gated proton (Hv1) channels play important roles in the respiratory burst, in pH regulation, in spermatozoa, in apoptosis, and in cancer metastasis. Unlike other voltage-gated cation channels, the Hv1 channel lacks a centrally located pore formed by the assembly of subunits. Instead, the proton permeation pathway in the Hv1 channel is within the voltage-sensing domain of each subunit. The gating mechanism of this pathway is still unclear. Mutagenic and fluorescence studies suggest that the fourth transmembrane (TM) segment (S4) functions as a voltage sensor and that there is an outward movement of S4 during channel activation. Using thermodynamic mutant cycle analysis, we find that the conserved positively charged residues in S4 are stabilized by countercharges in the other TM segments both in the closed and open states. We constructed models of both the closed and open states of Hv1 channels that are consistent with the mutant cycle analysis. These structural models suggest that electrostatic interactions between TM segments in the closed state pull hydrophobic residues together to form a hydrophobic plug in the center of the voltage-sensing domain. Outward S4 movement during channel activation induces conformational changes that remove this hydrophobic plug and instead insert protonatable residues in the center of the channel that, together with water molecules, can form a hydrogen bond chain across the channel for proton permeation. This suggests that salt bridge networks and the hydrophobic plug function as the gate in Hv1 channels and that outward movement of S4 leads to the opening of this gate.
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