1
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DeCoursey TE. Transcendent Aspects of Proton Channels. Annu Rev Physiol 2024; 86:357-377. [PMID: 37931166 PMCID: PMC10938948 DOI: 10.1146/annurev-physiol-042222-023242] [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] [Indexed: 11/08/2023]
Abstract
A handful of biological proton-selective ion channels exist. Some open at positive or negative membrane potentials, others open at low or high pH, and some are light activated. This review focuses on common features that result from the unique properties of protons. Proton conduction through water or proteins differs qualitatively from that of all other ions. Extraordinary proton selectivity is needed to ensure that protons permeate and other ions do not. Proton selectivity arises from a proton pathway comprising a hydrogen-bonded chain that typically includes at least one titratable amino acid side chain. The enormously diverse functions of proton channels in disparate regions of the phylogenetic tree can be summarized by considering the chemical and electrical consequences of proton flux across membranes. This review discusses examples of cells in which proton efflux serves to increase pHi, decrease pHo, control the membrane potential, generate action potentials, or compensate transmembrane movement of electrical charge.
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Affiliation(s)
- Thomas E DeCoursey
- Department of Physiology & Biophysics, Rush University, Chicago, Illinois, USA;
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2
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Kariev AM, Green ME. Water, Protons, and the Gating of Voltage-Gated Potassium Channels. MEMBRANES 2024; 14:37. [PMID: 38392664 PMCID: PMC10890431 DOI: 10.3390/membranes14020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Ion channels are ubiquitous throughout all forms of life. Potassium channels are even found in viruses. Every cell must communicate with its surroundings, so all cells have them, and excitable cells, in particular, especially nerve cells, depend on the behavior of these channels. Every channel must be open at the appropriate time, and only then, so that each channel opens in response to the stimulus that tells that channel to open. One set of channels, including those in nerve cells, responds to voltage. There is a standard model for the gating of these channels that has a section of the protein moving in response to the voltage. However, there is evidence that protons are moving, rather than protein. Water is critical as part of the gating process, although it is hard to see how this works in the standard model. Here, we review the extensive evidence of the importance of the role of water and protons in gating these channels. Our principal example, but by no means the only example, will be the Kv1.2 channel. Evidence comes from the effects of D2O, from mutations in the voltage sensing domain, as well as in the linker between that domain and the gate, and at the gate itself. There is additional evidence from computations, especially quantum calculations. Structural evidence comes from X-ray studies. The hydration of ions is critical in the transfer of ions in constricted spaces, such as the gate region and the pore of a channel; we will see how the structure of the hydrated ion fits with the structure of the channel. In addition, there is macroscopic evidence from osmotic experiments and streaming current measurements. The combined evidence is discussed in the context of a model that emphasizes the role of protons and water in gating these channels.
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Affiliation(s)
- Alisher M Kariev
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Michael E Green
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
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3
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Fernández M, Alvear-Arias JJ, Carmona EM, Carrillo C, Pena-Pichicoi A, Hernandez-Ochoa EO, Neely A, Alvarez O, Latorre R, Garate JA, Gonzalez C. Trapping Charge Mechanism in Hv1 Channels ( CiHv1). Int J Mol Sci 2023; 25:426. [PMID: 38203601 PMCID: PMC10779229 DOI: 10.3390/ijms25010426] [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: 11/21/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
The majority of voltage-gated ion channels contain a defined voltage-sensing domain and a pore domain composed of highly conserved amino acid residues that confer electrical excitability via electromechanical coupling. In this sense, the voltage-gated proton channel (Hv1) is a unique protein in that voltage-sensing, proton permeation and pH-dependent modulation involve the same structural region. In fact, these processes synergistically work in concert, and it is difficult to separate them. To investigate the process of Hv1 voltage sensor trapping, we follow voltage-sensor movements directly by leveraging mutations that enable the measurement of Hv1 channel gating currents. We uncover that the process of voltage sensor displacement is due to two driving forces. The first reveals that mutations in the selectivity filter (D160) located in the S1 transmembrane interact with the voltage sensor. More hydrophobic amino acids increase the energy barrier for voltage sensor activation. On the other hand, the effect of positive charges near position 264 promotes the formation of salt bridges between the arginines of the voltage sensor domain, achieving a stable conformation over time. Our results suggest that the activation of the Hv1 voltage sensor is governed by electrostatic-hydrophobic interactions, and S4 arginines, N264 and selectivity filter (D160) are essential in the Ciona-Hv1 to understand the trapping of the voltage sensor.
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Affiliation(s)
- Miguel Fernández
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso 2351319, Chile; (M.F.); (J.J.A.-A.); (C.C.); (A.P.-P.); (A.N.); (O.A.); (R.L.)
- Millennium Nucleus in NanoBioPhysics, Universidad de Valparaíso, Valparaíso 2351319, Chile
| | - Juan J. Alvear-Arias
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso 2351319, Chile; (M.F.); (J.J.A.-A.); (C.C.); (A.P.-P.); (A.N.); (O.A.); (R.L.)
- Millennium Nucleus in NanoBioPhysics, Universidad de Valparaíso, Valparaíso 2351319, Chile
| | - Emerson M. Carmona
- Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
| | - Christian Carrillo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso 2351319, Chile; (M.F.); (J.J.A.-A.); (C.C.); (A.P.-P.); (A.N.); (O.A.); (R.L.)
- Millennium Nucleus in NanoBioPhysics, Universidad de Valparaíso, Valparaíso 2351319, Chile
| | - Antonio Pena-Pichicoi
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso 2351319, Chile; (M.F.); (J.J.A.-A.); (C.C.); (A.P.-P.); (A.N.); (O.A.); (R.L.)
- Millennium Nucleus in NanoBioPhysics, Universidad de Valparaíso, Valparaíso 2351319, Chile
| | - Erick O. Hernandez-Ochoa
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Alan Neely
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso 2351319, Chile; (M.F.); (J.J.A.-A.); (C.C.); (A.P.-P.); (A.N.); (O.A.); (R.L.)
- Millennium Nucleus in NanoBioPhysics, Universidad de Valparaíso, Valparaíso 2351319, Chile
| | - Osvaldo Alvarez
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso 2351319, Chile; (M.F.); (J.J.A.-A.); (C.C.); (A.P.-P.); (A.N.); (O.A.); (R.L.)
| | - Ramon Latorre
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso 2351319, Chile; (M.F.); (J.J.A.-A.); (C.C.); (A.P.-P.); (A.N.); (O.A.); (R.L.)
| | - Jose A. Garate
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastian, Santiago 7780272, Chile
| | - Carlos Gonzalez
- Millennium Nucleus in NanoBioPhysics, Universidad de Valparaíso, Valparaíso 2351319, Chile
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
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4
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Zhao C, Webster PD, De Angeli A, Tombola F. Mechanically-primed voltage-gated proton channels from angiosperm plants. Nat Commun 2023; 14:7515. [PMID: 37980353 PMCID: PMC10657467 DOI: 10.1038/s41467-023-43280-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/06/2023] [Indexed: 11/20/2023] Open
Abstract
Voltage-gated and mechanically-gated ion channels are distinct classes of membrane proteins that conduct ions across gated pores and are turned on by electrical or mechanical stimuli, respectively. Here, we describe an Hv channel (a.k.a voltage-dependent H+ channel) from the angiosperm plant A. thaliana that gates with a unique modality as it is turned on by an electrical stimulus only after exposure to a mechanical stimulus, a process that we call priming. The channel localizes in the vascular tissue and has homologs in vascular plants. We find that mechanical priming is not required for activation of non-angiosperm Hvs. Guided by AI-generated structural models of plant Hv homologs, we identify a set of residues playing a crucial role in mechanical priming. We propose that Hvs from angiosperm plants require priming because of a network of hydrophilic/charged residues that locks the channels in a silent resting conformation. Mechanical stimuli destabilize the network allowing the conduction pathway to turn on. In contrast to many other channels and receptors, Hv proteins are not thought to possess mechanisms such as inactivation or desensitization. Our findings demonstrate that angiosperm Hv channels are electrically silent until a mechanical stimulation turns on their voltage-dependent activity.
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Affiliation(s)
- Chang Zhao
- Department of Physiology and Biophysics, University of California, Irvine, CA, 92697, USA
| | - Parker D Webster
- Department of Physiology and Biophysics, University of California, Irvine, CA, 92697, USA
| | - Alexis De Angeli
- IPSiM, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France.
| | - Francesco Tombola
- Department of Physiology and Biophysics, University of California, Irvine, CA, 92697, USA.
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5
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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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6
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Kratochvil HT, Watkins LC, Mravic M, Thomaston JL, Nicoludis JM, Somberg NH, Liu L, Hong M, Voth GA, DeGrado WF. Transient water wires mediate selective proton transport in designed channel proteins. Nat Chem 2023; 15:1012-1021. [PMID: 37308712 PMCID: PMC10475958 DOI: 10.1038/s41557-023-01210-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/19/2023] [Indexed: 06/14/2023]
Abstract
Selective proton transport through proteins is essential for forming and using proton gradients in cells. Protons are conducted along hydrogen-bonded 'wires' of water molecules and polar side chains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways, inferred from static protein structures. Here we hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess protons in the water wire. To test this hypothesis, we performed molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 106-fold more selective for H+ over Na+. These studies inform the mechanisms of biological proton conduction and the principles for engineering proton-conductive materials.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA.
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Laura C Watkins
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, IL, USA
- Kemper Insurance, Chicago, IL, USA
| | - Marco Mravic
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
- Department of Integrative Structural and Computational Biology Scripps Research Institute, La Jolla, CA, USA
| | - Jessica L Thomaston
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - John M Nicoludis
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
- Genentech, San Francisco, CA, USA
| | - Noah H Somberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, IL, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA.
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7
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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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8
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Wu X, Zhang L, Hong L. The role of Phe150 in human voltage-gated proton channel. iScience 2022; 25:105420. [PMID: 36388967 PMCID: PMC9646954 DOI: 10.1016/j.isci.2022.105420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/15/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
The voltage-gated proton channel Hv1 is a member of voltage-gated ion channels containing voltage-sensing domains (VSDs). The VSDs are made of four membrane-spanning segments (S1 through S4), and their function is to detect changes in membrane potential in the cells. A highly conserved phenylalanine 150 (F150) is located in the S2 segment of human voltage-gated proton channels. We previously discovered that the F150 is a binding site for the open channel blocker 2GBI. Here, we show that the Hv1 VSD voltage-dependent activation requires a hydrophobic group at position F150. We perform double-mutant cycle analysis to probe interactions between F150 and positively charged arginines in the S4 segment of the channel. Our results indicate that F150 interacts with two arginines (R2 and R3) in the S4 segment and catalyzes the transfer of the S4 arginines in the process of voltage-dependent activation. Hydrophobicity of F150 is crucial for human Hv1 channel voltage-dependent activation F150 interacts with R2 to stabilize the closed state of the Hv1 channel When depolarized, R3 moves upward to interact with F150 stabilizing the open state of Hv1 F150 is essential for the transfer of the Hv1 arginines in the process of voltage sensing
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Affiliation(s)
- Xin Wu
- Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Lu Zhang
- Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Liang Hong
- Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
- Corresponding author
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9
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Llanos MA, Ventura C, Martín P, Enrique N, Felice JI, Gavernet L, Milesi V. Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect. J Chem Inf Model 2022; 62:3200-3212. [PMID: 35758884 DOI: 10.1021/acs.jcim.1c01396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The human voltage-gated proton channel (hHv1) is a highly selective ion channel codified by the HVCN1 gene. It plays a fundamental role in several physiological processes such as innate and adaptive immunity, insulin secretion, and sperm capacitation. Moreover, in humans, a higher hHv1 expression/function has been reported in several types of cancer cells. Here we report a multitemplate homology model of the hHv1 channel, built and refined as a dimer in Rosetta. The model was then subjected to extensive Gaussian accelerated molecular dynamics (GaMD) for enhanced conformational sampling, and representative snapshots were extracted by clustering analysis. Combining different structure- and sequence-based methodologies, we predicted a putative ATP-binding site located on the intracellular portion of the channel. Furthermore, GaMD simulations of the ATP-bound dimeric hHv1 model showed that ATP interacts with a cluster of positively charged residues from the cytoplasmic N and C terminal segments. According to the in silico predictions, we found that 3 mM intracellular ATP significantly increases the H+ current mediated by the hHv1 channel expressed in HEK293 cells and measured by the patch-clamp technique in an inside-out configuration (2.86 ± 0.63 fold over control at +40 mV). When ATP was added on the extracellular side, it was not able to activate the channel supporting the idea that the ATP-binding site resides in the intracellular face of the hHV1 channel. In a physiological and pathophysiological context, this ATP-mediated modulation could integrate the cell metabolic state with the H+ efflux, especially in cells where hHv1 channels are relevant for pH regulation, such as pancreatic β-cells, immune cells, and cancer cells.
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Affiliation(s)
- Manuel A Llanos
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Fac. de Ciencias Exactas, Universidad Nacional de La Plata. La Plata B1900ADU, Buenos Aires, Argentina
| | - Clara Ventura
- Facultad de Ciencias Exactas, Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), UNLP, CONICET, asociado CIC PBA, La Plata B1900BJW, Buenos Aires, Argentina
| | - Pedro Martín
- Facultad de Ciencias Exactas, Departamento de Ciencias Biológicas, Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), UNLP, CONICET, asociado CIC PBA, La Plata B1900BJW, Buenos Aires, Argentina
| | - Nicolás Enrique
- Facultad de Ciencias Exactas, Departamento de Ciencias Biológicas, Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), UNLP, CONICET, asociado CIC PBA, La Plata B1900BJW, Buenos Aires, Argentina
| | - Juan I Felice
- Facultad de Ciencias Exactas, Departamento de Ciencias Biológicas, Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), UNLP, CONICET, asociado CIC PBA, La Plata B1900BJW, Buenos Aires, Argentina
| | - Luciana Gavernet
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Fac. de Ciencias Exactas, Universidad Nacional de La Plata. La Plata B1900ADU, Buenos Aires, Argentina
| | - Verónica Milesi
- Facultad de Ciencias Exactas, Departamento de Ciencias Biológicas, Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), UNLP, CONICET, asociado CIC PBA, La Plata B1900BJW, Buenos Aires, Argentina
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10
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Delgado-Bermúdez A, Yeste M, Bonet S, Pinart E. A Review on the Role of Bicarbonate and Proton Transporters during Sperm Capacitation in Mammals. Int J Mol Sci 2022; 23:ijms23116333. [PMID: 35683013 PMCID: PMC9180951 DOI: 10.3390/ijms23116333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/01/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022] Open
Abstract
Alkalinization of sperm cytosol is essential for plasma membrane hyperpolarization, hyperactivation of motility, and acrosomal exocytosis during sperm capacitation in mammals. The plasma membrane of sperm cells contains different ion channels implicated in the increase of internal pH (pHi) by favoring either bicarbonate entrance or proton efflux. Bicarbonate transporters belong to the solute carrier families 4 (SLC4) and 26 (SLC26) and are currently grouped into Na+/HCO3− transporters and Cl−/HCO3− exchangers. Na+/HCO3− transporters are reported to be essential for the initial and fast entrance of HCO3− that triggers sperm capacitation, whereas Cl−/HCO3− exchangers are responsible for the sustained HCO3− entrance which orchestrates the sequence of changes associated with sperm capacitation. Proton efflux is required for the fast alkalinization of capacitated sperm cells and the activation of pH-dependent proteins; according to the species, this transport can be mediated by Na+/H+ exchangers (NHE) belonging to the SLC9 family and/or voltage-gated proton channels (HVCN1). Herein, we discuss the involvement of each of these channels in sperm capacitation and the acrosome reaction.
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Affiliation(s)
- Ariadna Delgado-Bermúdez
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, ES-17003 Girona, Spain; (A.D.-B.); (M.Y.); (S.B.)
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, ES-17003 Girona, Spain
| | - Marc Yeste
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, ES-17003 Girona, Spain; (A.D.-B.); (M.Y.); (S.B.)
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, ES-17003 Girona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), ES-08010 Barcelona, Spain
| | - Sergi Bonet
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, ES-17003 Girona, Spain; (A.D.-B.); (M.Y.); (S.B.)
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, ES-17003 Girona, Spain
| | - Elisabeth Pinart
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, ES-17003 Girona, Spain; (A.D.-B.); (M.Y.); (S.B.)
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, ES-17003 Girona, Spain
- Correspondence: ; Tel.: +34-972-419-514
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11
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Jardin C, Ohlwein N, Franzen A, Chaves G, Musset B. The pH-dependent gating of the human voltage-gated proton channel from computational simulations. Phys Chem Chem Phys 2022; 24:9964-9977. [PMID: 35445675 DOI: 10.1039/d1cp05609c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Gating of the voltage-gated proton channel HV1 is strongly controlled by pH. There is evidence that this involves the sidechains of titratable amino acids that change their protonation state with changes of the pH. Despite experimental investigations to identify the amino acids involved in pH sensing only few progress has been made, including one histidine at the cytoplasmic side of the channel that is involved in sensing cellular pH. We have used constant pH molecular dynamics simulations in symmetrical and asymmetrical pH conditions across the membrane to investigate the pH- and ΔpH-dependent gating of the human HV1 channel. Therefore, the pKa of every titratable amino acids has been assessed in single simulations. Our simulations captured initial conformational changes between a deactivated and an activated state of the channel induced solely by changes of the pH. The pH-dependent gating is accompanied by an outward displacement of the three S4 voltage sensing arginines that moves the second arginine past the hydrophobic gasket (HG) which separates the inner and outer pores of the channel. HV1 activation, when outer pH increases, involves amino acids at the extracellular entrance of the channel that extend the network of interactions from the external solution down to the HG. Whereas, amino acids at the cytoplasmic entrance of the channel are involved in activation, when inner pH decreases, and in a network of interactions that extend from the cytoplasm up to the HG.
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Affiliation(s)
- Christophe Jardin
- Klinikum Nürnberg Medical School, CPPB, Institute of Physiology, Pathophysiology and Biophysics, Nuremberg, Germany.
| | - Niklas Ohlwein
- Klinikum Nürnberg Medical School, CPPB, Institute of Physiology, Pathophysiology and Biophysics, Nuremberg, Germany. .,Klinik für Anästhesiologie und operative Intensivmedizin, Universitätklinik der Paracelsus Medizinischen Privatuniversität, Nuremberg, Germany
| | - Arne Franzen
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Gustavo Chaves
- Klinikum Nürnberg Medical School, CPPB, Institute of Physiology, Pathophysiology and Biophysics, Nuremberg, Germany.
| | - Boris Musset
- Klinikum Nürnberg Medical School, CPPB, Institute of Physiology, Pathophysiology and Biophysics, Nuremberg, Germany.
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12
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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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13
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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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14
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Abdallah Barjas Qaswal. The Role of Quantum Tunneling of Ions in the Pathogenesis of the Cardiac Arrhythmias Due to Channelopathies, Ischemia, and Mechanical Stretch. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921040072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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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: 4] [Impact Index Per Article: 1.3] [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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16
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Zhao C, Hong L, Galpin JD, Riahi S, Lim VT, Webster PD, Tobias DJ, Ahern CA, Tombola F. HIFs: New arginine mimic inhibitors of the Hv1 channel with improved VSD-ligand interactions. J Gen Physiol 2021; 153:212451. [PMID: 34228044 PMCID: PMC8263924 DOI: 10.1085/jgp.202012832] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
The human voltage-gated proton channel Hv1 is a drug target for cancer, ischemic stroke, and neuroinflammation. It resides on the plasma membrane and endocytic compartments of a variety of cell types, where it mediates outward proton movement and regulates the activity of NOX enzymes. Its voltage-sensing domain (VSD) contains a gated and proton-selective conduction pathway, which can be blocked by aromatic guanidine derivatives such as 2-guanidinobenzimidazole (2GBI). Mutation of Hv1 residue F150 to alanine (F150A) was previously found to increase 2GBI apparent binding affinity more than two orders of magnitude. Here, we explore the contribution of aromatic interactions between the inhibitor and the channel in the presence and absence of the F150A mutation, using a combination of electrophysiological recordings, classic mutagenesis, and site-specific incorporation of fluorinated phenylalanines via nonsense suppression methodology. Our data suggest that the increase in apparent binding affinity is due to a rearrangement of the binding site allowed by the smaller residue at position 150. We used this information to design new arginine mimics with improved affinity for the nonrearranged binding site of the wild-type channel. The new compounds, named “Hv1 Inhibitor Flexibles” (HIFs), consist of two “prongs,” an aminoimidazole ring, and an aromatic group connected by extended flexible linkers. Some HIF compounds display inhibitory properties that are superior to those of 2GBI, thus providing a promising scaffold for further development of high-affinity Hv1 inhibitors.
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Affiliation(s)
- Chang Zhao
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA
| | - Liang Hong
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA
| | - Saleh Riahi
- Department of Chemistry, University of California, Irvine, Irvine, CA
| | - Victoria T Lim
- Department of Chemistry, University of California, Irvine, Irvine, CA
| | - Parker D Webster
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
| | - Douglas J Tobias
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA.,Department of Chemistry, University of California, Irvine, Irvine, CA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA
| | - Francesco Tombola
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA
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17
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Zhao C, Hong L, Riahi S, Lim VT, Tobias DJ, Tombola F. A novel Hv1 inhibitor reveals a new mechanism of inhibition of a voltage-sensing domain. J Gen Physiol 2021; 153:212452. [PMID: 34228045 PMCID: PMC8263925 DOI: 10.1085/jgp.202012833] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Voltage-gated sodium, potassium, and calcium channels consist of four voltage-sensing domains (VSDs) that surround a central pore domain and transition from a down state to an up state in response to membrane depolarization. While many types of drugs bind pore domains, the number of organic molecules known to bind VSDs is limited. The Hv1 voltage-gated proton channel is made of two VSDs and does not contain a pore domain, providing a simplified model for studying how small ligands interact with VSDs. Here, we describe a ligand, named HIF, that interacts with the Hv1 VSD in the up and down states. We find that HIF rapidly inhibits proton conduction in the up state by blocking the open channel, as previously described for 2-guanidinobenzimidazole and its derivatives. HIF, however, interacts with a site slowly accessible in the down state. Functional studies and MD simulations suggest that this interaction traps the compound in a narrow pocket lined with charged residues within the VSD intracellular vestibule, which results in slow recovery from inhibition. Our findings point to a “wrench in gears” mechanism whereby side chains within the binding pocket trap the compound as the teeth of interlocking gears. We propose that the use of screening strategies designed to target binding sites with slow accessibility, similar to the one identified here, could lead to the discovery of new ligands capable of interacting with VSDs of other voltage-gated ion channels in the down state.
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Affiliation(s)
- Chang Zhao
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA
| | - Liang Hong
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
| | - Saleh Riahi
- Department of Chemistry, University of California, Irvine, Irvine, CA
| | - Victoria T Lim
- Department of Chemistry, University of California, Irvine, Irvine, CA
| | - Douglas J Tobias
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA.,Department of Chemistry, University of California, Irvine, Irvine, CA
| | - Francesco Tombola
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA
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18
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Yazdani M, Jia Z, Chen J. Hydrophobic dewetting in gating and regulation of transmembrane protein ion channels. J Chem Phys 2021; 153:110901. [PMID: 32962356 DOI: 10.1063/5.0017537] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water is at the heart of almost all biological phenomena, without which no life that we know of would have been possible. It is a misleadingly complex liquid that exists in near coexistence with the vapor phase under ambient conditions. Confinement within a hydrophobic cavity can tip this balance enough to drive a cooperative dewetting transition. For a nanometer-scale pore, the dewetting transition leads to a stable dry state that is physically open but impermeable to ions. This phenomenon is often referred to as hydrophobic gating. Numerous transmembrane protein ion channels have now been observed to utilize hydrophobic gating in their activation and regulation. Here, we review recent theoretical, simulation, and experimental studies that together have started to establish the principles of hydrophobic gating and discuss how channels of various sizes, topologies, and biological functions can utilize these principles to control the thermodynamic properties of water within their interior pores for gating and regulation. Exciting opportunities remain in multiple areas, particularly on direct experimental detection of hydrophobic dewetting in biological channels and on understanding how the cell may control the hydrophobic gating in regulation of ion channels.
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Affiliation(s)
- Mahdieh Yazdani
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Zhiguang Jia
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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19
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Xenakis MN, Kapetis D, Yang Y, Gerrits MM, Heijman J, Waxman SG, Lauria G, Faber CG, Westra RL, Lindsey PJ, Smeets HJ. Hydropathicity-based prediction of pain-causing NaV1.7 variants. BMC Bioinformatics 2021; 22:212. [PMID: 33892629 PMCID: PMC8063372 DOI: 10.1186/s12859-021-04119-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Mutation-induced variations in the functional architecture of the NaV1.7 channel protein are causally related to a broad spectrum of human pain disorders. Predicting in silico the phenotype of NaV1.7 variant is of major clinical importance; it can aid in reducing costs of in vitro pathophysiological characterization of NaV1.7 variants, as well as, in the design of drug agents for counteracting pain-disease symptoms. Results In this work, we utilize spatial complexity of hydropathic effects toward predicting which NaV1.7 variants cause pain (and which are neutral) based on the location of corresponding mutation sites within the NaV1.7 structure. For that, we analyze topological and scaling hydropathic characteristics of the atomic environment around NaV1.7’s pore and probe their spatial correlation with mutation sites. We show that pain-related mutation sites occupy structural locations in proximity to a hydrophobic patch lining the pore while clustering at a critical hydropathic-interactions distance from the selectivity filter (SF). Taken together, these observations can differentiate pain-related NaV1.7 variants from neutral ones, i.e., NaV1.7 variants not causing pain disease, with 80.5\documentclass[12pt]{minimal}
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\begin{document}$$\%$$\end{document}% specificity [area under the receiver operating characteristics curve = 0.872]. Conclusions Our findings suggest that maintaining hydrophobic NaV1.7 interior intact, as well as, a finely-tuned (dictated by hydropathic interactions) distance from the SF might be necessary molecular conditions for physiological NaV1.7 functioning. The main advantage for using the presented predictive scheme is its negligible computational cost, as well as, hydropathicity-based biophysical rationalization. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04119-2.
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Affiliation(s)
- Makros N Xenakis
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands. .,Research School for Mental Health and Neuroscience (MHeNS), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.
| | - Dimos Kapetis
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Via Celoria 11, 20133, Milan, Italy
| | - Yang Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN, 47907, USA.,Purdue Institute for Integrative Neuroscience, West Lafayette, IN, 47907, USA
| | - Monique M Gerrits
- Department of Clinical Genetics, Maastricht University Medical Center, PO box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Jordi Heijman
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Stephen G Waxman
- Department of Neurology and Center for Neuroscience and Regeneration Research, Yale University School of Medicine, New Haven, CT, 06510, USA.,Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Giuseppe Lauria
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Via Celoria 11, 20133, Milan, Italy.,Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Via G.B. Grassi 74, 20157, Milan, Italy
| | - Catharina G Faber
- Department of Neurology, Maastricht University Medical Center, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Ronald L Westra
- Department of Data Science and Knowledge Engineering, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Patrick J Lindsey
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.,Research School for Oncology and Developmental Biology (GROW), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Hubert J Smeets
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.,Research School for Mental Health and Neuroscience (MHeNS), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
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20
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Qaswal AB, Ababneh O, Khreesha L, Al-Ani A, Suleihat A, Abbad M. Mathematical Modeling of Ion Quantum Tunneling Reveals Novel Properties of Voltage-Gated Channels and Quantum Aspects of Their Pathophysiology in Excitability-Related Disorders. PATHOPHYSIOLOGY 2021; 28:116-154. [PMID: 35366274 PMCID: PMC8830480 DOI: 10.3390/pathophysiology28010010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/08/2023] Open
Abstract
Voltage-gated channels are crucial in action potential initiation and propagation and there are many diseases and disorders related to them. Additionally, the classical mechanics are the main mechanics used to describe the function of the voltage-gated channels and their related abnormalities. However, the quantum mechanics should be considered to unravel new aspects in the voltage-gated channels and resolve the problems and challenges that classical mechanics cannot solve. In the present study, the aim is to mathematically show that quantum mechanics can exhibit a powerful tendency to unveil novel electrical features in voltage-gated channels and be used as a promising tool to solve the problems and challenges in the pathophysiology of excitability-related diseases. The model of quantum tunneling of ions through the intracellular hydrophobic gate is used to evaluate the influence of membrane potential and gating free energy on the tunneling probability, single channel conductance, and quantum membrane conductance. This evaluation is mainly based on graphing the mathematical relationships between these variables. The obtained mathematical graphs showed that ions can achieve significant quantum membrane conductance, which can affect the resting membrane potential and the excitability of cells. In the present work, quantum mechanics reveals original electrical properties associated with voltage-gated channels and introduces new insights and implications into the pathophysiology of excitability- related disorders. In addition, the present work sets a mathematical and theoretical framework that can be utilized to conduct experimental studies in order to explore the quantum aspects of voltage-gated channels and the quantum bioelectrical property of biological membranes.
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Affiliation(s)
- Abdallah Barjas Qaswal
- Department of Internship Program, Jordan University Hospital, The University of Jordan, Amman 11942, Jordan
- Correspondence:
| | - Omar Ababneh
- Department of Anesthesia and Intensive Care, School of Medicine, The University of Jordan, Amman 11942, Jordan;
| | - Lubna Khreesha
- Department of Special Surgery, School of Medicine, The University of Jordan, Amman 11942, Jordan;
| | - Abdallah Al-Ani
- School of Medicine, The University of Jordan, Amman 11942, Jordan;
| | - Ahmad Suleihat
- Department of General Surgery, School of Medicine, The University of Jordan, Amman 11942, Jordan; (A.S.); (M.A.)
| | - Mutaz Abbad
- Department of General Surgery, School of Medicine, The University of Jordan, Amman 11942, Jordan; (A.S.); (M.A.)
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21
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Zhang Y, Haider K, Kaur D, Ngo VA, Cai X, Mao J, Khaniya U, Zhu X, Noskov S, Lazaridis T, Gunner MR. Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.
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Affiliation(s)
- Yingying Zhang
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Kamran Haider
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
| | - Divya Kaur
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Van A. Ngo
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Xiuhong Cai
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Junjun Mao
- Levich Institute, School of Engineering, City College of New York, City University of New York, New York, NY 10031, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Xuyu Zhu
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Sergei Noskov
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, Calgary, AB, Canada
| | - Themis Lazaridis
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
- Department of Chemistry, City College of New York, City University of New York, New York, NY 10031, USA
| | - M. R. Gunner
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
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22
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Zhao C, Tombola F. Voltage-gated proton channels from fungi highlight role of peripheral regions in channel activation. Commun Biol 2021; 4:261. [PMID: 33637875 PMCID: PMC7910559 DOI: 10.1038/s42003-021-01792-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
Here, we report the identification and characterization of the first proton channels from fungi. The fungal proteins are related to animal voltage-gated Hv channels and are conserved in both higher and lower fungi. Channels from Basidiomycota and Ascomycota appear to be evolutionally and functionally distinct. Representatives from the two phyla share several features with their animal counterparts, including structural organization and strong proton selectivity, but they differ from each other and from animal Hvs in terms of voltage range of activation, pharmacology, and pH sensitivity. The activation gate of Hv channels is believed to be contained within the transmembrane core of the protein and little is known about contributions of peripheral regions to the activation mechanism. Using a chimeragenesis approach, we find that intra- and extracellular peripheral regions are main determinants of the voltage range of activation in fungal channels, highlighting the role of these overlooked components in channel gating.
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Affiliation(s)
- Chang Zhao
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
| | - Francesco Tombola
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA.
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA.
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23
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Rao S, Klesse G, Lynch CI, Tucker SJ, Sansom MSP. Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions. J Phys Chem B 2021; 125:981-994. [PMID: 33439645 PMCID: PMC7869105 DOI: 10.1021/acs.jpcb.0c09285] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/13/2020] [Indexed: 12/30/2022]
Abstract
Ion channels are proteins which form gated nanopores in biological membranes. Many channels exhibit hydrophobic gating, whereby functional closure of a pore occurs by local dewetting. The pentameric ligand gated ion channels (pLGICs) provide a biologically important example of hydrophobic gating. Molecular simulation studies comparing additive vs polarizable models indicate predictions of hydrophobic gating are robust to the model employed. However, polarizable models suggest favorable interactions of hydrophobic pore-lining regions with chloride ions, of relevance to both synthetic carriers and channel proteins. Electrowetting of a closed pLGIC hydrophobic gate requires too high a voltage to occur physiologically but may inform designs for switchable nanopores. Global analysis of ∼200 channels yields a simple heuristic for structure-based prediction of (closed) hydrophobic gates. Simulation-based analysis is shown to provide an aid to interpretation of functional states of new channel structures. These studies indicate the importance of understanding the behavior of water and ions within the nanoconfined environment presented by ion channels.
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Affiliation(s)
- Shanlin Rao
- Department
of Biochemistry, University of Oxford, Oxford, U.K.
| | - Gianni Klesse
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford, U.K.
| | | | - Stephen J. Tucker
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford, U.K.
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24
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Refinement of a cryo-EM structure of hERG: Bridging structure and function. Biophys J 2021; 120:738-748. [PMID: 33476597 DOI: 10.1016/j.bpj.2021.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/22/2020] [Accepted: 01/11/2021] [Indexed: 01/16/2023] Open
Abstract
The human-ether-a-go-go-related gene (hERG) encodes the voltage-gated potassium channel (KCNH2 or Kv11.1, commonly known as hERG). This channel plays a pivotal role in the stability of phase 3 repolarization of the cardiac action potential. Although a high-resolution cryo-EM structure is available for its depolarized (open) state, the structure surprisingly did not feature many functionally important interactions established by previous biochemical and electrophysiology experiments. Using molecular dynamics flexible fitting (MDFF), we refined the structure and recovered the missing functionally relevant salt bridges in hERG in its depolarized state. We also performed electrophysiology experiments to confirm the functional relevance of a novel salt bridge predicted by our refinement protocol. Our work shows how refinement of a high-resolution cryo-EM structure helps to bridge the existing gap between the structure and function in the voltage-sensing domain (VSD) of hERG.
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25
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Abstract
Cherny and coworkers use zinc ion as a probe to identify different conformational states of voltage-gated proton (Hv1) channels.
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Affiliation(s)
- H Peter Larsson
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL
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26
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Abstract
The voltage-gated proton channel Hv1 is a member of the voltage-gated ion channel superfamily, which stands out in design: It is a dimer of two voltage-sensing domains (VSDs), each containing a pore pathway, a voltage sensor (S4), and a gate (S1) and forming its own ion channel. Opening of the two channels in the dimer is cooperative. Part of the cooperativity is due to association between coiled-coil domains that extend intracellularly from the S4s. Interactions between the transmembrane portions of the subunits may also contribute, but the nature of transmembrane packing is unclear. Using functional analysis of a mutagenesis scan, biochemistry, and modeling, we find that the subunits form a dimer interface along the entire length of S1, and also have intersubunit contacts between S1 and S4. These interactions exert a strong effect on gating, in particular on the stability of the open state. Our results suggest that gating in Hv1 is tuned by extensive VSD-VSD interactions between the gates and voltage sensors of the dimeric channel.
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Affiliation(s)
- Laetitia Mony
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - David Stroebel
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Ehud Y Isacoff
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720;
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720
- Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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27
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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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28
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A family of hyperpolarization-activated channels selective for protons. Proc Natl Acad Sci U S A 2020; 117:13783-13791. [PMID: 32467169 PMCID: PMC7306766 DOI: 10.1073/pnas.2001214117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Proton (H+) channels are special: They select protons against other ions that are up to a millionfold more abundant. Only a few proton channels have been identified so far. Here, we identify a family of voltage-gated "pacemaker" channels, HCNL1, that are exquisitely selective for protons. HCNL1 activates during hyperpolarization and conducts protons into the cytosol. Surprisingly, protons permeate through the channel's voltage-sensing domain, whereas the pore domain is nonfunctional. Key to proton permeation is a methionine residue that interrupts the series of regularly spaced arginine residues in the S4 voltage sensor. HCNL1 forms a tetramer and thus contains four proton pores. Unlike classic HCN channels, HCNL1 is not gated by cyclic nucleotides. The channel is present in zebrafish sperm and carries a proton inward current that acidifies the cytosol. Our results suggest that protons rather than cyclic nucleotides serve as cellular messengers in zebrafish sperm. Through small modifications in two key functional domains, HCNL1 evolutionarily adapted to a low-Na+ freshwater environment to conserve sperm's ability to depolarize.
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29
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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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30
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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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31
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Jardin C, Chaves G, Musset B. Assessing Structural Determinants of Zn 2+ Binding to Human H V1 via Multiple MD Simulations. Biophys J 2020; 118:1221-1233. [PMID: 31972155 DOI: 10.1016/j.bpj.2019.12.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/20/2019] [Accepted: 12/27/2019] [Indexed: 01/02/2023] Open
Abstract
Voltage-gated proton channels (HV1) are essential for various physiological tasks but are strongly inhibited by Zn2+ cations. Some determinants of Zn2+ binding have been elucidated experimentally and in computational studies. However, the results have always been interpreted under the assumption that Zn2+ binds to monomeric HV1 despite evidence that HV1 expresses as a dimer and that the dimer has a higher affinity for zinc than the monomer and experimental data that suggest coordination in the dimer interface. The results of former studies are also controversial, e.g., supporting either one single or two binding sites. Some structural determinants of the binding are still elusive. We performed a series of molecular dynamics simulations to address different structures of the human proton channel, the monomer and two plausible dimer conformations, to compare their respective potential to interact with and bind Zn2+ via the essential histidines. The series consisted of several copies of the system to generate independent trajectories and increase the significance compared to a single simulation. The amount of time simulated totals 29.9 μs for 126 simulations of systems comprising ∼59,000 to ∼187,000 atoms. Our approach confirms the existence of two binding sites in monomeric and dimeric human HV1. The dimer interface is more efficient for attracting and binding Zn2+ via the essential histidines than the monomer or a dimer with the histidines in the periphery. The higher affinity is due to the residues in the dimer interface that create an attractive electrostatic potential funneling the zinc cations toward the binding sites.
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Affiliation(s)
- Christophe Jardin
- Institute of Physiology and Pathophysiology, Klinikum Nuremberg Medical School, Paracelsus Medical University, Nuremberg, Germany
| | - Gustavo Chaves
- Institute of Physiology and Pathophysiology, Klinikum Nuremberg Medical School, Paracelsus Medical University, Nuremberg, Germany
| | - Boris Musset
- Institute of Physiology and Pathophysiology, Klinikum Nuremberg Medical School, Paracelsus Medical University, Nuremberg, Germany.
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32
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Bayrhuber M, Maslennikov I, Kwiatkowski W, Sobol A, Wierschem C, Eichmann C, Frey L, Riek R. Nuclear Magnetic Resonance Solution Structure and Functional Behavior of the Human Proton Channel. Biochemistry 2019; 58:4017-4027. [PMID: 31365236 DOI: 10.1021/acs.biochem.9b00471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human voltage-gated proton channel [Hv1(1) or VSDO(2)] plays an important role in the human innate immune system. Its structure differs considerably from those of other cation channels. It is built solely of a voltage-sensing domain and thus lacks the central pore domain, which is essential for other cation channels. Here, we determined the solution structure of an N- and C-terminally truncated human Hv1 (Δ-Hv1) in the resting state by nuclear magnetic resonance (NMR) spectroscopy. Δ-Hv1 comprises the typical voltage-sensing antiparallel four-helix bundle (S1-S4) preceded by an amphipathic helix (S0). The solution structure corresponds to an intermediate state between resting and activated forms of voltage-sensing domains. Furthermore, Zn2+-induced closing of proton channel Δ-Hv1 was studied with two-dimensional NMR spectroscopy, which showed that characteristic large scale dynamics of open Δ-Hv1 are absent in the closed state of the channel. Additionally, pH titration studies demonstrated that a higher H+ concentration is required for the protonation of side chains in the Zn2+-induced closed state than in the open state. These observations demonstrate both structural and dynamical changes involved in the process of voltage gating of the Hv1 channel and, in the future, may help to explain the unique properties of unidirectional conductance and the exceptional ion selectivity of the channel.
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Affiliation(s)
- Monika Bayrhuber
- Laboratory of Physical Chemistry , ETH Zürich , Wolfgang-Pauli-Strasse 10 , 8093 Zürich , Switzerland.,Structural Biology Laboratory , Salk Institute , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Innokentiy Maslennikov
- Structural Biology Laboratory , Salk Institute , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States.,School of Pharmacy , Chapman University , 9401 Jeronimo Road , Irvine , California 92618 , United States
| | - Witek Kwiatkowski
- Laboratory of Physical Chemistry , ETH Zürich , Wolfgang-Pauli-Strasse 10 , 8093 Zürich , Switzerland.,Structural Biology Laboratory , Salk Institute , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Alexander Sobol
- Laboratory of Physical Chemistry , ETH Zürich , Wolfgang-Pauli-Strasse 10 , 8093 Zürich , Switzerland
| | - Christoph Wierschem
- Laboratory of Physical Chemistry , ETH Zürich , Wolfgang-Pauli-Strasse 10 , 8093 Zürich , Switzerland
| | - Cédric Eichmann
- Laboratory of Physical Chemistry , ETH Zürich , Wolfgang-Pauli-Strasse 10 , 8093 Zürich , Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry , ETH Zürich , Wolfgang-Pauli-Strasse 10 , 8093 Zürich , Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry , ETH Zürich , Wolfgang-Pauli-Strasse 10 , 8093 Zürich , Switzerland.,Structural Biology Laboratory , Salk Institute , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
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33
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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: 20] [Impact Index Per Article: 4.0] [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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34
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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: 28] [Impact Index Per Article: 5.6] [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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35
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Saotome K, Teng B, Tsui CCA, Lee WH, Tu YH, Kaplan JP, Sansom MSP, Liman ER, Ward AB. Structures of the otopetrin proton channels Otop1 and Otop3. Nat Struct Mol Biol 2019; 26:518-525. [PMID: 31160780 PMCID: PMC6564688 DOI: 10.1038/s41594-019-0235-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/26/2019] [Indexed: 01/08/2023]
Abstract
Otopetrins (Otop1-Otop3) comprise one of two known eukaryotic proton-selective channel families. Otop1 is required for otoconia formation and a candidate mammalian sour taste receptor. Here we report cryo-EM structures of zebrafish Otop1 and chicken Otop3 in lipid nanodiscs. The structures reveal a dimeric architecture, with each subunit forming 12 transmembrane helices divided into structurally similar amino (N) and carboxy (C) domains. Cholesterol-like molecules occupy various sites in Otop1 and Otop3 and occlude a central tunnel. In molecular dynamics simulations, hydrophilic vestibules formed by the N and C domains and in the intrasubunit interface between N and C domains form conduits for water entry into the membrane core, suggesting three potential proton conduction pathways. By mutagenesis, we tested the roles of charged residues in each putative permeation pathway. Our results provide a structural basis for understanding selective proton permeation and gating of this conserved family of proton channels.
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Affiliation(s)
- Kei Saotome
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Bochuan Teng
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Che Chun Alex Tsui
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yu-Hsiang Tu
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Joshua P Kaplan
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emily R Liman
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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36
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Boonamnaj P, Sompornpisut P. Effect of Ionization State on Voltage-Sensor Structure in Resting State of the Hv1 Channel. J Phys Chem B 2019; 123:2864-2873. [DOI: 10.1021/acs.jpcb.9b00634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panisak Boonamnaj
- Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornthep Sompornpisut
- Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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37
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De La Rosa V, Bennett AL, Ramsey IS. Coupling between an electrostatic network and the Zn 2+ binding site modulates Hv1 activation. J Gen Physiol 2018; 150:863-881. [PMID: 29743298 PMCID: PMC5987874 DOI: 10.1085/jgp.201711822] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 02/15/2018] [Accepted: 04/05/2018] [Indexed: 01/20/2023] Open
Abstract
The voltage sensor (VS) domain in Hv1 proton channels mediates a voltage-dependent and H+-selective "aqueous" conductance (GAQ) that is potently modulated by extracellular Zn2+ Although two conserved His residues are required for Zn2+ effects on GAQ gating, the atomic structure of the Zn2+ coordination site and mechanism by which extracellular Zn2+ stabilizes a closed-state conformation remain unknown. Here we use His mutagenesis to identify residues that increase Zn2+ potency and are therefore likely to participate in first solvation shell interactions with Zn2+ Experimental Zn2+-mapping data were then used to constrain the structure of a new resting-state Hv1 model (Hv1 F). Molecular dynamics (MD) simulations show how protein and water atoms directly contribute to octahedral Zn2+ coordination spheres in Zn2+-bound and -unbound Hv1 F models. During MD simulations, we observed correlated movements of Zn2+-interacting side chains and residues in a highly conserved intracellular Coulombic network (ICN) that contains highly conserved Arg "gating charges" in S4 as well as acidic "counter-charges" in S2 and S3 and is known to control VS activation, suggesting that occupancy of the extracellular Zn2+ site is conformationally coupled to reorganization of the ICN. To test this hypothesis, we neutralized an ICN Glu residue (E153) and show that in addition to shifting GAQ activation to more negative voltages, E153A also decreases Zn2+ potency. We speculate that extracellular gating-modifier toxins and other ligands may use a generally similar long-range conformational coupling mechanism to modulate VS activation in related ion channel proteins.
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Affiliation(s)
- Victor De La Rosa
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Medical College of Virginia Campus, Richmond, VA
| | - Ashley L Bennett
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Medical College of Virginia Campus, Richmond, VA
| | - Ian Scott Ramsey
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Medical College of Virginia Campus, Richmond, VA
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38
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Cherny VV, Morgan D, Thomas S, Smith SME, DeCoursey TE. Histidine 168 is crucial for ΔpH-dependent gating of the human voltage-gated proton channel, hH V1. J Gen Physiol 2018; 150:851-862. [PMID: 29743300 PMCID: PMC5987877 DOI: 10.1085/jgp.201711968] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/27/2018] [Indexed: 01/28/2023] Open
Abstract
Voltage-gated proton channels open appropriately in myriad physiological situations because their gating is powerfully modulated by both pHo and pHi. Cherny et al. serendipitously identify a histidine at the inner end of the S3 helix that is required for the response to pHi. We recently identified a voltage-gated proton channel gene in the snail Helisoma trivolvis, HtHV1, and determined its electrophysiological properties. Consistent with early studies of proton currents in snail neurons, HtHV1 opens rapidly, but it unexpectedly exhibits uniquely defective sensitivity to intracellular pH (pHi). The H+ conductance (gH)-V relationship in the voltage-gated proton channel (HV1) from other species shifts 40 mV when either pHi or pHo (extracellular pH) is changed by 1 unit. This property, called ΔpH-dependent gating, is crucial to the functions of HV1 in many species and in numerous human tissues. The HtHV1 channel exhibits normal pHo dependence but anomalously weak pHi dependence. In this study, we show that a single point mutation in human hHV1—changing His168 to Gln168, the corresponding residue in HtHV1—compromises the pHi dependence of gating in the human channel so that it recapitulates the HtHV1 response. This location was previously identified as a contributor to the rapid gating kinetics of HV1 in Strongylocentrotus purpuratus. His168 mutation in human HV1 accelerates activation but accounts for only a fraction of the species difference. H168Q, H168S, or H168T mutants exhibit normal pHo dependence, but changing pHi shifts the gH-V relationship on average by <20 mV/unit. Thus, His168 is critical to pHi sensing in hHV1. His168, located at the inner end of the pore on the S3 transmembrane helix, is the first residue identified in HV1 that significantly impairs pH sensing when mutated. Because pHo dependence remains intact, the selective erosion of pHi dependence supports the idea that there are distinct internal and external pH sensors. Although His168 may itself be a pHi sensor, the converse mutation, Q229H, does not normalize the pHi sensitivity of the HtHV1 channel. We hypothesize that the imidazole group of His168 interacts with nearby Phe165 or other parts of hHV1 to transduce pHi into shifts of voltage-dependent gating.
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Affiliation(s)
| | - 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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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: 47] [Impact Index Per Article: 7.8] [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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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: 26] [Impact Index Per Article: 3.7] [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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41
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Affiliation(s)
- Thomas E DeCoursey
- Department of Physiology and Biophysics, Rush University, Chicago, IL, 60612, USA
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42
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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: 28] [Impact Index Per Article: 3.5] [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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43
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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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44
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Ni G, Wang Y, Cummins S, Walton S, Mounsey K, Liu X, Wei MQ, Wang T. Inhibitory mechanism of peptides with a repeating hydrophobic and hydrophilic residue pattern on interleukin-10. Hum Vaccin Immunother 2016; 13:518-527. [PMID: 27686406 DOI: 10.1080/21645515.2016.1238537] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Interleukin 10 (IL-10) is a cytokine that is able to downregulate inflammation. Its overexpression is directly associated with the difficulty in the clearance of chronic viral infections, such as chronic hepatitis B, hepatitis C and HIV infection, and infection-related cancer. IL-10 signaling blockade has been proposed as a promising way of clearing chronic viral infection and preventing tumor growth in animal models. Recently, we have reported that peptides with a helical repeating pattern of hydrophobic and hydrophilic residues are able to inhibit IL-10 significantly both in vitro and in vivo. 1 In this work, we seek to further study the inhibiting mechanism of these peptides using sequence-modified peptides. As evidenced by both experimental and molecular dynamics simulation in concert the N-terminal hydrophobic peptide constructed with repeating hydrophobic and hydrophilic pattern of residues is more likely to inhibit IL10. In addition, the sequence length and the ability of protonation are also important for inhibition activity.
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Affiliation(s)
- Guoying Ni
- a Genecology Research Centre , University of the Sunshine Coast , Maroochydore , DC , Australia.,b School of Medical Science, Griffith Health Institute , Griffith University , Gold Coast , Australia
| | - Yuejian Wang
- c Cancer Research Institute, Foshan First People's Hospital , Foshan , Guangdong , China
| | - Scott Cummins
- a Genecology Research Centre , University of the Sunshine Coast , Maroochydore , DC , Australia
| | - Shelley Walton
- d Inflammation and Healing Research Cluster, School of Health and Sport Sciences , University of Sunshine Coast , Maroochydore , DC , Australia
| | - Kate Mounsey
- d Inflammation and Healing Research Cluster, School of Health and Sport Sciences , University of Sunshine Coast , Maroochydore , DC , Australia
| | - Xiaosong Liu
- c Cancer Research Institute, Foshan First People's Hospital , Foshan , Guangdong , China.,d Inflammation and Healing Research Cluster, School of Health and Sport Sciences , University of Sunshine Coast , Maroochydore , DC , Australia
| | - Ming Q Wei
- b School of Medical Science, Griffith Health Institute , Griffith University , Gold Coast , Australia
| | - Tianfang Wang
- a Genecology Research Centre , University of the Sunshine Coast , Maroochydore , DC , Australia
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Molecular mechanism of Zn2+ inhibition of a voltage-gated proton channel. Proc Natl Acad Sci U S A 2016; 113:E5962-E5971. [PMID: 27647906 DOI: 10.1073/pnas.1604082113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Voltage-gated proton (Hv1) channels are involved in many physiological processes, such as pH homeostasis and the innate immune response. Zn2+ is an important physiological inhibitor of Hv1. Sperm cells are quiescent in the male reproductive system due to Zn2+ inhibition of Hv1 channels, but become active once introduced into the low-Zn2+-concentration environment of the female reproductive tract. How Zn2+ inhibits Hv1 is not completely understood. In this study, we use the voltage clamp fluorometry technique to identify the molecular mechanism of Zn2+ inhibition of Hv1. We find that Zn2+ binds to both the activated closed and resting closed states of the Hv1 channel, thereby inhibiting both voltage sensor motion and gate opening. Mutations of some Hv1 residues affect only Zn2+ inhibition of the voltage sensor motion, whereas mutations of other residues also affect Zn2+ inhibition of gate opening. These effects are similar in monomeric and dimeric Hv1 channels, suggesting that the Zn2+-binding sites are localized within each subunit of the dimeric Hv1. We propose that Zn2+ binding has two major effects on Hv1: (i) at low concentrations, Zn2+ binds to one site and prevents the opening conformational change of the pore of Hv1, thereby inhibiting proton conduction; and (ii) at high concentrations, Zn2+, in addition, binds to a second site and inhibits the outward movement of the voltage sensor of Hv1. Elucidating the molecular mechanism of how Zn2+ inhibits Hv1 will further our understanding of Hv1 function and might provide valuable information for future drug development for Hv1 channels.
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46
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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: 26] [Impact Index Per Article: 3.3] [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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47
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Okuda H, Yonezawa Y, Takano Y, Okamura Y, Fujiwara Y. Direct Interaction between the Voltage Sensors Produces Cooperative Sustained Deactivation in Voltage-gated H+ Channel Dimers. J Biol Chem 2016; 291:5935-5947. [PMID: 26755722 PMCID: PMC4786727 DOI: 10.1074/jbc.m115.666834] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 12/23/2015] [Indexed: 01/31/2023] Open
Abstract
The voltage-gated H(+) channel (Hv) is a voltage sensor domain-like protein consisting of four transmembrane segments (S1-S4). The native Hv structure is a homodimer, with the two channel subunits functioning cooperatively. Here we show that the two voltage sensor S4 helices within the dimer directly cooperate via a π-stacking interaction between Trp residues at the middle of each segment. Scanning mutagenesis showed that Trp situated around the original position provides the slow gating kinetics characteristic of the dimer's cooperativity. Analyses of the Trp mutation on the dimeric and monomeric channel backgrounds and analyses with tandem channel constructs suggested that the two Trp residues within the dimer are functionally coupled during Hv deactivation but are less so during activation. Molecular dynamics simulation also showed direct π-stacking of the two Trp residues. These results provide new insight into the cooperative function of voltage-gated channels, where adjacent voltage sensor helices make direct physical contact and work as a single unit according to the gating process.
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Affiliation(s)
- Hiroko Okuda
- From Division of Integrative Physiology, Graduate School of Medicine
| | - Yasushige Yonezawa
- the High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University, Kinokawa 649-6493, Wakayama, Japan, and
| | - Yu Takano
- the Institute for Protein Research, and; the Graduate School of Information Sciences, Hiroshima City University, Hiroshima 731-3194, Hiroshima, Japan
| | - Yasushi Okamura
- From Division of Integrative Physiology, Graduate School of Medicine,; the Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Osaka, Japan
| | - Yuichiro Fujiwara
- From Division of Integrative Physiology, Graduate School of Medicine,.
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48
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Allosteric substrate switching in a voltage-sensing lipid phosphatase. Nat Chem Biol 2016; 12:261-7. [PMID: 26878552 PMCID: PMC4798927 DOI: 10.1038/nchembio.2022] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 12/31/2015] [Indexed: 11/29/2022]
Abstract
Allostery provides a critical control over enzyme activity, biasing the catalytic site between inactive and active states. We find the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP), which modifies phosphoinositide signaling lipids (PIPs), to have not one but two sequential active states with distinct substrate specificities, whose occupancy is allosterically controlled by sequential conformations of the voltage sensing domain (VSD). Using fast FRET reporters of PIPs to monitor enzyme activity and voltage clamp fluorometry to monitor conformational changes in the VSD, we find that Ci-VSP switches from inactive to a PIP3-preferring active state when the VSD undergoes an initial voltage sensing motion and then into a second PIP2-preferring active state when the VSD activates fully. This novel 2-step allosteric control over a dual specificity enzyme enables voltage to shape PIP concentrations in time, and provides a mechanism for the complex modulation of PIP-regulated ion channels, transporters, cell motility and endo/exocytosis.
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49
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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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50
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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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