1
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Gabriel TS, Hansen UP, Urban M, Drexler N, Winterstein T, Rauh O, Thiel G, Kast SM, Schroeder I. Asymmetric Interplay Between K + and Blocker and Atomistic Parameters From Physiological Experiments Quantify K + Channel Blocker Release. Front Physiol 2021; 12:737834. [PMID: 34777005 PMCID: PMC8586521 DOI: 10.3389/fphys.2021.737834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022] Open
Abstract
Modulating the activity of ion channels by blockers yields information on both the mode of drug action and on the biophysics of ion transport. Here we investigate the interplay between ions in the selectivity filter (SF) of K+ channels and the release kinetics of the blocker tetrapropylammonium in the model channel KcvNTS. A quantitative expression calculates blocker release rate constants directly from voltage-dependent ion occupation probabilities in the SF. The latter are obtained by a kinetic model of single-channel currents recorded in the absence of the blocker. The resulting model contains only two adjustable parameters of ion-blocker interaction and holds for both symmetric and asymmetric ionic conditions. This data-derived model is corroborated by 3D reference interaction site model (3D RISM) calculations on several model systems, which show that the K+ occupation probability is unaffected by the blocker, a direct consequence of the strength of the ion-carbonyl attraction in the SF, independent of the specific protein background. Hence, KcvNTS channel blocker release kinetics can be reduced to a small number of system-specific parameters. The pore-independent asymmetric interplay between K+ and blocker ions potentially allows for generalizing these results to similar potassium channels.
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Affiliation(s)
- Tobias S Gabriel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Ulf-Peter Hansen
- Department of Structural Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martin Urban
- Physikalische Chemie III, Technische Universita̋t Dortmund, Dortmund, Germany
| | - Nils Drexler
- Institute of Physiology II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Tobias Winterstein
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Oliver Rauh
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universita̋t Dortmund, Dortmund, Germany
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany.,Institute of Physiology II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
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2
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Schmidt M, Schroeder I, Bauer D, Thiel G, Hamacher K. Inferring functional units in ion channel pores via relative entropy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:37-57. [PMID: 33523249 PMCID: PMC7872957 DOI: 10.1007/s00249-020-01480-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 10/11/2020] [Accepted: 11/09/2020] [Indexed: 11/25/2022]
Abstract
Coarse-grained protein models approximate the first-principle physical potentials. Among those modeling approaches, the relative entropy framework yields promising and physically sound results, in which a mapping from the target protein structure and dynamics to a model is defined and subsequently adjusted by an entropy minimization of the model parameters. Minimization of the relative entropy is equivalent to maximization of the likelihood of reproduction of (configurational ensemble) observations by the model. In this study, we extend the relative entropy minimization procedure beyond parameter fitting by a second optimization level, which identifies the optimal mapping to a (dimension-reduced) topology. We consider anisotropic network models of a diverse set of ion channels and assess our findings by comparison to experimental results.
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Affiliation(s)
- Michael Schmidt
- Department of Physics, TU Darmstadt, Karolinenpl. 5, 64289 Darmstadt, Germany
| | - Indra Schroeder
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Daniel Bauer
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Gerhard Thiel
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Kay Hamacher
- Department of Physics, Department of Biology, Department of Computer Science, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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3
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A Functional K + Channel from Tetraselmis Virus 1, a Member of the Mimiviridae. Viruses 2020; 12:v12101107. [PMID: 33003637 PMCID: PMC7650704 DOI: 10.3390/v12101107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/05/2022] Open
Abstract
Potassium ion (K+) channels have been observed in diverse viruses that infect eukaryotic marine and freshwater algae. However, experimental evidence for functional K+ channels among these alga-infecting viruses has thus far been restricted to members of the family Phycodnaviridae, which are large, double-stranded DNA viruses within the phylum Nucleocytoviricota. Recent sequencing projects revealed that alga-infecting members of Mimiviridae, another family within this phylum, may also contain genes encoding K+ channels. Here we examine the structural features and the functional properties of putative K+ channels from four cultivated members of Mimiviridae. While all four proteins contain variations of the conserved selectivity filter sequence of K+ channels, structural prediction algorithms suggest that only two of them have the required number and position of two transmembrane domains that are present in all K+ channels. After in vitro translation and reconstitution of the four proteins in planar lipid bilayers, we confirmed that one of them, a 79 amino acid protein from the virus Tetraselmis virus 1 (TetV-1), forms a functional ion channel with a distinct selectivity for K+ over Na+ and a sensitivity to Ba2+. Thus, virus-encoded K+ channels are not limited to Phycodnaviridae but also occur in the members of Mimiviridae. The large sequence diversity among the viral K+ channels implies multiple events of lateral gene transfer.
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4
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Schönrock M, Thiel G, Laube B. Coupling of a viral K +-channel with a glutamate-binding-domain highlights the modular design of ionotropic glutamate-receptors. Commun Biol 2019; 2:75. [PMID: 30820470 PMCID: PMC6385376 DOI: 10.1038/s42003-019-0320-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/22/2019] [Indexed: 01/12/2023] Open
Abstract
Ionotropic glutamate receptors (iGluRs) mediate excitatory neuronal signaling in the mammalian CNS. These receptors are critically involved in diverse physiological processes; including learning and memory formation, as well as neuronal damage associated with neurological diseases. Based on partial sequence and structural similarities, these complex cation-permeable iGluRs are thought to descend from simple bacterial proteins emerging from a fusion of a substrate binding protein (SBP) and an inverted potassium (K+)-channel. Here, we fuse the pore module of the viral K+-channel KcvATCV-1 to the isolated glutamate-binding domain of the mammalian iGluR subunit GluA1 which is structural homolog to SBPs. The resulting chimera (GluATCV*) is functional and displays the ligand recognition characteristics of GluA1 and the K+-selectivity of KcvATCV-1. These results are consistent with a conserved activation mechanism between a glutamate-binding domain and the pore-module of a K+-channel and support the expected phylogenetic link between the two protein families. Michael Schönrock et al. created a functional chimeric channel composed of the pore domain of the potassium channel, KcvATCV-1, and the glutamate binding domain of the mammalian ionotropic glutamate receptor, GluA1. This chimera recognized glutamate as a ligand while displaying the potassium selectivity of KcvATCV-1; highlighting the modular design of ionotropic glutamate receptors.
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Affiliation(s)
- Michael Schönrock
- Department of Biology, Neurophysiology and Neurosensory Systems, Technische Universität Darmstadt, 64289, Darmstadt, Germany
| | - Gerhard Thiel
- Department of Biology, Plant Membrane Biophysics, Technische Universität Darmstadt, 64289, Darmstadt, Germany
| | - Bodo Laube
- Department of Biology, Neurophysiology and Neurosensory Systems, Technische Universität Darmstadt, 64289, Darmstadt, Germany.
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5
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Hadden JA, Perilla JR. All-atom virus simulations. Curr Opin Virol 2018; 31:82-91. [PMID: 30181049 DOI: 10.1016/j.coviro.2018.08.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/04/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
Abstract
The constant threat of viral disease can be combated by the development of novel vaccines and therapeutics designed to disrupt key features of virus structure or infection cycle processes. Such development relies on high-resolution characterization of viruses and their dynamical behaviors, which are often challenging to obtain solely by experiment. In response, all-atom molecular dynamics simulations are widely leveraged to study the structural components of viruses, leading to some of the largest simulation endeavors undertaken to date. The present work reviews exemplary all-atom simulation work on viruses, as well as progress toward simulating entire virions.
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Affiliation(s)
- Jodi A Hadden
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States.
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
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6
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Andersson AEV, Kasimova MA, Delemotte L. Exploring the Viral Channel Kcv PBCV-1 Function via Computation. J Membr Biol 2018; 251:419-430. [PMID: 29476260 PMCID: PMC6028866 DOI: 10.1007/s00232-018-0022-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/15/2018] [Indexed: 11/30/2022]
Abstract
Viral potassium channels (Kcv) are homologous to the pore module of complex \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {K}^+$$\end{document}K+-selective ion channels of cellular organisms. Due to their relative simplicity, they have attracted interest towards understanding the principles of \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {K}^+$$\end{document}K+ conduction and channel gating. In this work, we construct a homology model of the \documentclass[12pt]{minimal}
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\begin{document}$${\hbox {Kcv}}_{\text{PBCV-1}}$$\end{document}KcvPBCV-1 open state, which we validate by studying the binding of known blockers and by monitoring ion conduction through the channel. Molecular dynamics simulations of this model reveal that the re-orientation of selectivity filter carbonyl groups coincides with the transport of potassium ions, suggesting a possible mechanism for fast gating. In addition, we show that the voltage sensitivity of this mechanism can originate from the relocation of potassium ions inside the selectivity filter. We also explore the interaction of \documentclass[12pt]{minimal}
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\begin{document}$${\hbox {Kcv}}_{\text{PBCV-1}}$$\end{document}KcvPBCV-1 with the surrounding bilayer and observe the binding of lipids in the area between two adjacent subunits. The model is available to the scientific community to further explore the structure/function relationship of Kcv channels.
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Affiliation(s)
- Alma E V Andersson
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden
| | - Marina A Kasimova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden.
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7
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Rauh O, Hansen U, Mach S, Hartel AJ, Shepard KL, Thiel G, Schroeder I. Extended beta distributions open the access to fast gating in bilayer experiments-assigning the voltage-dependent gating to the selectivity filter. FEBS Lett 2017; 591:3850-3860. [PMID: 29106736 PMCID: PMC5747313 DOI: 10.1002/1873-3468.12898] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/17/2017] [Accepted: 10/27/2017] [Indexed: 01/02/2023]
Abstract
Lipid bilayers provide many benefits for ion channel recordings, such as control of membrane composition and transport molecules. However, they suffer from high membrane capacitance limiting the bandwidth and impeding analysis of fast gating. This can be overcome by fitting the deviations of the open-channel noise from the baseline noise by extended beta distributions. We demonstrate this analysis step-by-step by applying it to the example of viral K+ channels (Kcv), from the choice of the gating model through the fitting process, validation of the results, and what kinds of results can be obtained. These voltage sensor-less channels show profoundly voltage-dependent gating with dwell times in the closed state of about 50 μs. Mutations assign it to the selectivity filter.
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Affiliation(s)
- Oliver Rauh
- Plant Membrane BiophysicsTechnische Universität DarmstadtGermany
| | - Ulf‐Peter Hansen
- Department of Structural BiologyChristian‐Albrechts‐University of KielGermany
| | - Sebastian Mach
- Plant Membrane BiophysicsTechnische Universität DarmstadtGermany
| | | | | | - Gerhard Thiel
- Plant Membrane BiophysicsTechnische Universität DarmstadtGermany
| | - Indra Schroeder
- Plant Membrane BiophysicsTechnische Universität DarmstadtGermany
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8
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Güssregen S, Matter H, Hessler G, Lionta E, Heil J, Kast SM. Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series. J Chem Inf Model 2017; 57:1652-1666. [DOI: 10.1021/acs.jcim.6b00765] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan Güssregen
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Hans Matter
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Gerhard Hessler
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Evanthia Lionta
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Jochen Heil
- Physikalische
Chemie III, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Stefan M. Kast
- Physikalische
Chemie III, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
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9
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Rauh O, Urban M, Henkes LM, Winterstein T, Greiner T, Van Etten JL, Moroni A, Kast SM, Thiel G, Schroeder I. Identification of Intrahelical Bifurcated H-Bonds as a New Type of Gate in K + Channels. J Am Chem Soc 2017; 139:7494-7503. [PMID: 28499087 PMCID: PMC6638992 DOI: 10.1021/jacs.7b01158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Gating
of ion channels is based on structural transitions between
open and closed states. To uncover the chemical basis of individual
gates, we performed a comparative experimental and computational analysis
between two K+ channels, KcvS and KcvNTS. These small viral encoded K+ channel proteins, with
a monomer size of only 82 amino acids, resemble the pore module of
all complex K+ channels in terms of structure and function.
Even though both proteins share about 90% amino acid sequence identity,
they exhibit different open probabilities with ca. 90% in KcvNTS and 40% in KcvS. Single channel analysis, mutational
studies and molecular dynamics simulations show that the difference
in open probability is caused by one long closed state in KcvS. This state is structurally created in the tetrameric channel
by a transient, Ser mediated, intrahelical hydrogen bond. The resulting
kink in the inner transmembrane domain swings the aromatic rings from
downstream Phes in the cavity of the channel, which blocks ion flux.
The frequent occurrence of Ser or Thr based helical kinks in membrane
proteins suggests that a similar mechanism could also occur in the
gating of other ion channels.
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Affiliation(s)
- Oliver Rauh
- Plant Membrane Biophysics, Technical University Darmstadt , 64289 Darmstadt, Germany
| | - Martin Urban
- Physikalische Chemie III, Technische Universität Dortmund , 44227 Dortmund, Germany
| | - Leonhard M Henkes
- Physikalische Chemie III, Technische Universität Dortmund , 44227 Dortmund, Germany
| | - Tobias Winterstein
- Plant Membrane Biophysics, Technical University Darmstadt , 64289 Darmstadt, Germany
| | - Timo Greiner
- Plant Membrane Biophysics, Technical University Darmstadt , 64289 Darmstadt, Germany
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska Lincoln , Lincoln, Nebraska 68583-0900, United States
| | - Anna Moroni
- Department of Biosciences and CNR IBF-Mi, Università degli Studi di Milano , 20122 Milano, Italy
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund , 44227 Dortmund, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technical University Darmstadt , 64289 Darmstadt, Germany
| | - Indra Schroeder
- Plant Membrane Biophysics, Technical University Darmstadt , 64289 Darmstadt, Germany
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10
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Ariz-Extreme I, Hub JS. Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM. J Phys Chem B 2017; 121:1506-1519. [PMID: 28128570 DOI: 10.1021/acs.jpcb.6b11279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Membrane channels facilitate the efficient and selective flux of various solutes across biological membranes. A common approach to investigate the selectivity of a channel has been the calculation of potentials of mean force (PMFs) for solute permeation across the pore. PMFs have been frequently computed from molecular dynamics (MD) simulations, yet the three-dimensional reference interaction site model (3D-RISM) has been suggested as a computationally efficient alternative to MD. Whether the two methods yield comparable PMFs for solute permeation has remained unclear. In this study, we calculated potentials of mean force for water, ammonia, urea, molecular oxygen, and methanol across the urea transporter B (UT-B) and aquaporin-1 (AQP1), using 3D-RISM, as well as using MD simulations and umbrella sampling. To allow direct comparison between the PMFs from 3D-RISM and MD, we ensure that all PMFs refer to a well-defined reference area in the bulk or, equivalently, to a well-defined density of channels in the membrane. For PMFs of water permeation, we found reasonable agreement between the two methods, with differences of ≲3 kJ mol-1. In contrast, we found stark discrepancies for the PMFs for all other solutes. Additional calculations confirm that discrepancies between MD and 3D-RISM are not explained by the choice for the closure relation, the definition the reaction coordinate (center of mass-based versus atomic site-based), details of the molecule force field, or fluctuations of the protein. Comparison of the PMFs suggests that 3D-RISM may underestimate effects from hydrophobic solute-channel interactions, thereby, for instance, missing the urea binding sites in UT-B. Furthermore, we speculate that the orientational averages inherent to 3D-RISM might lead to discrepancies in the narrow channel lumen. These findings suggest that current 3D-RISM solvers provide reasonable estimates for the PMF for water permeation, but that they are not suitable to study the selectivity of membrane channels with respect to uncharged nonwater solutes.
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Affiliation(s)
- Igor Ariz-Extreme
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
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11
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Baumeister D, Hertel B, Schroeder I, Gazzarrini S, Kast SM, Van Etten JL, Moroni A, Thiel G. Conversion of an instantaneous activating K + channel into a slow activating inward rectifier. FEBS Lett 2016; 591:295-303. [PMID: 27995608 DOI: 10.1002/1873-3468.12536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 12/27/2022]
Abstract
The miniature channel, Kcv, is a structural equivalent of the pore of all K+ channels. Here, we follow up on a previous observation that a largely voltage-insensitive channel can be converted into a slow activating inward rectifier after extending the outer transmembrane domain by one Ala. This gain of rectification can be rationalized by dynamic salt bridges at the cytosolic entrance to the channel; opening is favored by voltage-sensitive formation of salt bridges and counteracted by their disruption. Such latent voltage sensitivity in the pore could be relevant for the understanding of voltage gating in complex Kv channels.
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Affiliation(s)
- Dirk Baumeister
- Plant Membrane Biophysics, Technical University Darmstadt, Germany
| | - Brigitte Hertel
- Plant Membrane Biophysics, Technical University Darmstadt, Germany
| | - Indra Schroeder
- Plant Membrane Biophysics, Technical University Darmstadt, Germany
| | - Sabrina Gazzarrini
- Department of Biosciences and CNR IBF-Mi, Università degli Studi di Milano, Italy
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Germany
| | - James L Van Etten
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska Lincoln, NE, USA
| | - Anna Moroni
- Department of Biosciences and CNR IBF-Mi, Università degli Studi di Milano, Italy
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technical University Darmstadt, Germany
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12
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Hoffgaard F, Kast S, Moroni A, Thiel G, Hamacher K. Tectonics of a K+ channel: The importance of the N-terminus for channel gating. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:3197-204. [DOI: 10.1016/j.bbamem.2015.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/09/2015] [Accepted: 09/18/2015] [Indexed: 11/16/2022]
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13
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Abstract
The calculation of electrostatic solute-solvent interactions in 3D RISM ("three-dimensional reference interaction site model") integral equation theory is recast in a form that allows for a computational treatment analogous to the "particle-mesh Ewald" formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.
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Affiliation(s)
- Jochen Heil
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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14
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Cosentino C, Alberio L, Gazzarrini S, Aquila M, Romano E, Cermenati S, Zuccolini P, Petersen J, Beltrame M, Van Etten JL, Christie JM, Thiel G, Moroni A. Optogenetics. Engineering of a light-gated potassium channel. Science 2015; 348:707-10. [PMID: 25954011 DOI: 10.1126/science.aaa2787] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/07/2015] [Indexed: 12/18/2022]
Abstract
The present palette of opsin-based optogenetic tools lacks a light-gated potassium (K(+)) channel desirable for silencing of excitable cells. Here, we describe the construction of a blue-light-induced K(+) channel 1 (BLINK1) engineered by fusing the plant LOV2-Jα photosensory module to the small viral K(+) channel Kcv. BLINK1 exhibits biophysical features of Kcv, including K(+) selectivity and high single-channel conductance but reversibly photoactivates in blue light. Opening of BLINK1 channels hyperpolarizes the cell to the K(+) equilibrium potential. Ectopic expression of BLINK1 reversibly inhibits the escape response in light-exposed zebrafish larvae. BLINK1 therefore provides a single-component optogenetic tool that can establish prolonged, physiological hyperpolarization of cells at low light intensities.
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Affiliation(s)
| | - Laura Alberio
- Department of Biosciences, University of Milano, Italy
| | | | - Marco Aquila
- Department of Biosciences, University of Milano, Italy
| | | | | | | | - Jan Petersen
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
| | | | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA
| | - John M Christie
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
| | - Gerhard Thiel
- Membrane Biophysics, Technical University of Darmstadt, Darmstadt, Germany
| | - Anna Moroni
- Department of Biosciences, University of Milano, Italy.
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15
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Chuev GN, Vyalov I, Georgi N. Exact site–site bridge functions for dielectric consistent reference interaction site model: A test for ambient water. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2014.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Siotto F, Martin C, Rauh O, Van Etten JL, Schroeder I, Moroni A, Thiel G. Viruses infecting marine picoplancton encode functional potassium ion channels. Virology 2014; 466-467:103-11. [PMID: 25441713 DOI: 10.1016/j.virol.2014.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/29/2014] [Accepted: 05/03/2014] [Indexed: 01/19/2023]
Abstract
Phycodnaviruses are dsDNA viruses, which infect algae. Their large genomes encode many gene products, like small K(+) channels, with homologs in prokaryotes and eukaryotes. Screening for K(+) channels revealed their abundance in viruses from fresh-water habitats. Recent sequencing of viruses from marine algae or from salt water in Antarctica revealed sequences with the predicted characteristics of K(+) channels but with some unexpected features. Two genes encode either 78 or 79 amino acid proteins, which are the smallest known K(+) channels. Also of interest is an unusual sequence in the canonical α-helixes in K(+) channels. Structural prediction algorithms indicate that the new channels have the conserved α-helix folds but the algorithms failed to identify the expected transmembrane domains flanking the K(+) channel pores. In spite of these unexpected properties electophysiological studies confirmed that the new proteins are functional K(+) channels.
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Affiliation(s)
- Fenja Siotto
- Membrane Biophysics Group, Dept. of Biology, Technical University Darmstadt, Germany
| | - Corinna Martin
- Membrane Biophysics Group, Dept. of Biology, Technical University Darmstadt, Germany
| | - Oliver Rauh
- Membrane Biophysics Group, Dept. of Biology, Technical University Darmstadt, Germany
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, USA
| | - Indra Schroeder
- Membrane Biophysics Group, Dept. of Biology, Technical University Darmstadt, Germany
| | - Anna Moroni
- Dipartimento di Biologia Università degli Studi di Milano e Istituto di Biofisica, CNR, Milano, Italy
| | - Gerhard Thiel
- Membrane Biophysics Group, Dept. of Biology, Technical University Darmstadt, Germany.
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17
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von Charpuis C, Meckel T, Moroni A, Thiel G. The sorting of a small potassium channel in mammalian cells can be shifted between mitochondria and plasma membrane. Cell Calcium 2014; 58:114-21. [PMID: 25449299 DOI: 10.1016/j.ceca.2014.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 09/24/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
Abstract
The two small and similar viral K(+) channels Kcv and Kesv are sorted in mammalian cells and yeast to different destinations. Analysis of the sorting pathways shows that Kcv is trafficking via the secretory pathway to the plasma membrane, while Kesv is inserted via the TIM/TOM complex to the inner membrane of mitochondria. Studies with Kesv mutants show that an N-terminal mitochondrial targeting sequence in this channel is neither necessary nor sufficient for sorting of Kesv the mitochondria. Instead the sorting of Kesv can be redirected from the mitochondria to the plasma membrane by an insertion of ≥2 amino acids in a position sensitive manner into the C-terminal transmembrane domain (TMD2) of this channel. The available data advocate the presence of a C-terminal sorting signal in TMD2 of Kesv channel, which is presumably not determined by the length of this domain.
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Affiliation(s)
- Charlotte von Charpuis
- Plant Membrane Biophysics, TU Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Tobias Meckel
- Plant Membrane Biophysics, TU Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Anna Moroni
- Department of Biology and CNR IBF-Mi, and Istituto Nazionale di Fisica della Materia, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Gerhard Thiel
- Plant Membrane Biophysics, TU Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany.
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18
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Arrigoni C, Schroeder I, Romani G, Van Etten JL, Thiel G, Moroni A. The voltage-sensing domain of a phosphatase gates the pore of a potassium channel. ACTA ACUST UNITED AC 2013; 141:389-95. [PMID: 23440279 PMCID: PMC3581695 DOI: 10.1085/jgp.201210940] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The modular architecture of voltage-gated K(+) (Kv) channels suggests that they resulted from the fusion of a voltage-sensing domain (VSD) to a pore module. Here, we show that the VSD of Ciona intestinalis phosphatase (Ci-VSP) fused to the viral channel Kcv creates Kv(Synth1), a functional voltage-gated, outwardly rectifying K(+) channel. Kv(Synth1) displays the summed features of its individual components: pore properties of Kcv (selectivity and filter gating) and voltage dependence of Ci-VSP (V(1/2) = +56 mV; z of ~1), including the depolarization-induced mode shift. The degree of outward rectification of the channel is critically dependent on the length of the linker more than on its amino acid composition. This highlights a mechanistic role of the linker in transmitting the movement of the sensor to the pore and shows that electromechanical coupling can occur without coevolution of the two domains.
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Affiliation(s)
- Cristina Arrigoni
- Department of Biosciences, Consiglio Nazionale delle Ricerche, Università degli Studi di Milano, 20133 Milano, Italy
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19
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Thiel G, Moroni A, Blanc G, Van Etten JL. Potassium ion channels: could they have evolved from viruses? PLANT PHYSIOLOGY 2013; 162:1215-24. [PMID: 23719891 PMCID: PMC3707557 DOI: 10.1104/pp.113.219360] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 05/23/2013] [Indexed: 06/01/2023]
Abstract
Phylogenetic analyses of small viral K+ channels suggests that they did not originate from their hosts, but instead could be the source of the postulated pore precursor in the evolution of K+ channels.
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Affiliation(s)
- Gerhard Thiel
- Department of Biology, Technische Universität-Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany.
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20
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Braun CJ, Lachnit C, Becker P, Henkes LM, Arrigoni C, Kast SM, Moroni A, Thiel G, Schroeder I. Viral potassium channels as a robust model system for studies of membrane-protein interaction. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1096-103. [PMID: 23791706 DOI: 10.1016/j.bbamem.2013.06.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 05/31/2013] [Accepted: 06/08/2013] [Indexed: 11/15/2022]
Abstract
The viral channel KcvNTS belongs to the smallest K(+) channels known so far. A monomer of a functional homotetramer contains only 82 amino acids. As a consequence of the small size the protein is almost fully submerged into the membrane. This suggests that the channel is presumably sensitive to its lipid environment. Here we perform a comparative analysis for the function of the channel protein embedded in three different membrane environments. 1. Single-channel currents of KcvNTS were recorded with the patch clamp method on the plasma membrane of HEK293 cells. 2. They were also measured after reconstitution of recombinant channel protein into classical planar lipid bilayers and 3. into horizontal bilayers derived from giant unilamellar vesicles (GUVs). The recombinant channel protein was either expressed and purified from Pichia pastoris or from a cell-free expression system; for the latter a new approach with nanolipoprotein particles was used. The data show that single-channel activity can be recorded under all experimental conditions. The main functional features of the channel like a large single-channel conductance (80pS), high open-probability (>50%) and the approximate duration of open and closed dwell times are maintained in all experimental systems. An apparent difference between the approaches was only observed with respect to the unitary conductance, which was ca. 35% lower in HEK293 cells than in the other systems. The reason for this might be explained by the fact that the channel is tagged by GFP when expressed in HEK293 cells. Collectively the data demonstrate that the small viral channel exhibits a robust function in different experimental systems. This justifies an extrapolation of functional data from these systems to the potential performance of the channel in the virus/host interaction. This article is part of a Special Issue entitled: Viral Membrane Proteins-Channels for Cellular Networking.
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Affiliation(s)
- Christian J Braun
- Membrane Biophysics, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Christine Lachnit
- Membrane Biophysics, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Patrick Becker
- Membrane Biophysics, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Leonhard M Henkes
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Cristina Arrigoni
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Anna Moroni
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy; CNR-IBF, Via Celoria 26, 20133 Milano, Italy
| | - Gerhard Thiel
- Membrane Biophysics, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Indra Schroeder
- Membrane Biophysics, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany.
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21
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Schroeder I, Gazzarrini S, Ferrara G, Thiel G, Hansen UP, Moroni A. Creation of a reactive oxygen species-insensitive Kcv channel. Biochemistry 2013; 52:3130-7. [PMID: 23578303 DOI: 10.1021/bi3016197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The current of the minimal viral K(+) channel Kcv(PCBV-1) heterologously expressed in Xenopus oocytes is strongly inhibited by reactive oxygen species (ROS) like H(2)O(2). Possible targets for the ROS effect are two cysteines (C53 and C79) and four methionines (M1, M15, M23, and M26). The C53A/C79A and M23L/M26L double mutations maintained the same ROS sensitivity as the wild type. However, M15L as a single mutant or in combination with C53A/C79A and/or M23L/M26L caused a complete loss of sensitivity to H(2)O(2). These results indicate a prominent role of M15 at the cytosolic end of the outer transmembrane helix for gating of Kcv(PCBV-1). Furthermore, even though the channel lacks a canonical voltage sensor, it exhibits a weak voltage sensitivity, resulting in a slight activation in the millisecond range after a voltage step to negative potentials. The M15L mutation inverts this kinetics into an inactivation, underlining the critical role of this residue for gating. The negative slope of the I-V curves of M15L is the same as in the wild type, indicating that the selectivity filter is not involved.
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Affiliation(s)
- Indra Schroeder
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy.
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22
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Tan Q, Ritzo B, Tian K, Gu LQ. Tuning the tetraethylammonium sensitivity of potassium channel Kcv by subunit combination. ACTA ACUST UNITED AC 2012; 139:295-304. [PMID: 22450486 PMCID: PMC3315146 DOI: 10.1085/jgp.201110725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tetraethylammonium (TEA) is a potassium (K+) channel inhibitor that has been extensively used as a molecular probe to explore the structure of channels’ ion pathway. In this study, we identified that Leu70 of the virus-encoded potassium channel Kcv is a key amino acid that plays an important role in regulating the channel’s TEA sensitivity. Site-directed mutagenesis of Leu70 can change the TEA sensitivity by 1,000-fold from ∼100 µM to ∼100 mM. Because no compelling trends exist to explain this amino acid’s specific interaction with TEA, the role of Leu70 at the binding site is likely to ensure an optimal conformation of the extracellular mouth that confers high TEA affinity. We further assembled the subunits of mutant and wt-Kcv into a series of heterotetramers. The differences in these heterochannels suggest that all of the four subunits in a Kcv channel additively participate in the TEA binding, and each of the four residues at the binding site independently contributes an equal binding energy. We therefore can present a series of mutant/wild-type tetramer combinations that can probe TEA over three orders of magnitude in concentration. This study may give insight into the mechanism for the interaction between the potassium channel and its inhibitor.
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Affiliation(s)
- Qiulin Tan
- Department of Biological Engineering, University of Missouri, Columbia, MO 65211, USA
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23
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Gebhardt M, Henkes LM, Tayefeh S, Hertel B, Greiner T, Van Etten JL, Baumeister D, Cosentino C, Moroni A, Kast SM, Thiel G. Relevance of lysine snorkeling in the outer transmembrane domain of small viral potassium ion channels. Biochemistry 2012; 51:5571-9. [PMID: 22734656 DOI: 10.1021/bi3006016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transmembrane domains (TMDs) are often flanked by Lys or Arg because they keep their aliphatic parts in the bilayer and their charged groups in the polar interface. Here we examine the relevance of this so-called "snorkeling" of a cationic amino acid, which is conserved in the outer TMD of small viral K(+) channels. Experimentally, snorkeling activity is not mandatory for Kcv(PBCV-1) because K29 can be replaced by most of the natural amino acids without any corruption of function. Two similar channels, Kcv(ATCV-1) and Kcv(MT325), lack a cytosolic N-terminus, and neutralization of their equivalent cationic amino acids inhibits their function. To understand the variable importance of the cationic amino acids, we reanalyzed molecular dynamics simulations of Kcv(PBCV-1) and N-terminally truncated mutants; the truncated mutants mimic Kcv(ATCV-1) and Kcv(MT325). Structures were analyzed with respect to membrane positioning in relation to the orientation of K29. The results indicate that the architecture of the protein (including the selectivity filter) is only weakly dependent on TMD length and protonation of K29. The penetration depth of Lys in a given protonation state is independent of the TMD architecture, which leads to a distortion of shorter proteins. The data imply that snorkeling can be important for K(+) channels; however, its significance depends on the architecture of the entire TMD. The observation that the most severe N-terminal truncation causes the outer TMD to move toward the cytosolic side suggests that snorkeling becomes more relevant if TMDs are not stabilized in the membrane by other domains.
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Affiliation(s)
- Manuela Gebhardt
- Botany Institute, Technische Universität Darmstadt, Darmstadt, Germany
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24
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Hamacher K, Greiner T, Ogata H, Van Etten JL, Gebhardt M, Villarreal LP, Cosentino C, Moroni A, Thiel G. Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis. PLoS One 2012; 7:e38826. [PMID: 22685610 PMCID: PMC3369850 DOI: 10.1371/journal.pone.0038826] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 05/11/2012] [Indexed: 11/26/2022] Open
Abstract
Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K(+) channels. To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+) channel pore modules from seven phycodnaviruses to the K(+) channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K(+) channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K(+) channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K(+) channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K(+) channels in algae and perhaps even all cellular organisms.
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Affiliation(s)
- Kay Hamacher
- Computational Biology Group, Technische Universität Darmstadt, Darmstadt, Germany
| | - Timo Greiner
- Membrane Biophysics Group, Technische Universität Darmstadt, Darmstadt, Germany
| | - Hiroyuki Ogata
- Structural and Genomic Information Laboratory, Aix-Marseille University, Marseille, France
| | - James L. Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Manuela Gebhardt
- Membrane Biophysics Group, Technische Universität Darmstadt, Darmstadt, Germany
| | - Luis P. Villarreal
- Center of Virus Research, University of California Irvine, Irvine, California, United States of America
| | | | - Anna Moroni
- Department of Biology, Università degli Studi di Milano, Milan, Italy
| | - Gerhard Thiel
- Membrane Biophysics Group, Technische Universität Darmstadt, Darmstadt, Germany
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25
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Fischer WB, Wang YT, Schindler C, Chen CP. Mechanism of function of viral channel proteins and implications for drug development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 294:259-321. [PMID: 22364876 PMCID: PMC7149447 DOI: 10.1016/b978-0-12-394305-7.00006-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Viral channel-forming proteins comprise a class of viral proteins which, similar to their host companions, are made to alter electrochemical or substrate gradients across lipid membranes. These proteins are active during all stages of the cellular life cycle of viruses. An increasing number of proteins are identified as channel proteins, but the precise role in the viral life cycle is yet unknown for the majority of them. This review presents an overview about these proteins with an emphasis on those with available structural information. A concept is introduced which aligns the transmembrane domains of viral channel proteins with those of host channels and toxins to give insights into the mechanism of function of the viral proteins from potential sequence identities. A summary of to date investigations on drugs targeting these proteins is given and discussed in respect of their mode of action in vivo.
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Affiliation(s)
- Wolfgang B. Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
| | - Yi-Ting Wang
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
| | - Christina Schindler
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
| | - Chin-Pei Chen
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
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26
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Gebhardt M, Hoffgaard F, Hamacher K, Kast SM, Moroni A, Thiel G. Membrane anchoring and interaction between transmembrane domains are crucial for K+ channel function. J Biol Chem 2011; 286:11299-306. [PMID: 21310959 PMCID: PMC3064186 DOI: 10.1074/jbc.m110.211672] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Revised: 01/27/2011] [Indexed: 11/06/2022] Open
Abstract
The small viral channel Kcv is a Kir-like K(+) channel of only 94 amino acids. With this simple structure, the tetramer of Kcv represents the pore module of all complex K(+) channels. To examine the structural contribution of the transmembrane domains (TMDs) to channel function, we performed Ala scanning mutagenesis of the two domains and tested the functionality of the mutants in a yeast complementation assay. The data reveal, in combination with computational models, that the upper halves of both TMDs, which face toward the external medium, are rather rigid, whereas the inner parts are more flexible. The rigidity of the outer TMD is conferred by a number of essential aromatic amino acids that face the membrane and probably anchor this domain in the bilayer. The inner TMD is intimately connected with the rigid part of the outer TMD via π···π interactions between a pair of aromatic amino acids. This structural principle is conserved within the viral K(+) channels and also present in Kir2.2, implying a general importance of this architecture for K(+) channel function.
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Affiliation(s)
| | - Franziska Hoffgaard
- the Computational Biology Group, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Kay Hamacher
- the Computational Biology Group, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Stefan M. Kast
- the Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund, Germany, and
| | - Anna Moroni
- the Department of Biology and Consiglio Nazionale delle Ricerche Istituto di Biofisica-Milano, Università degli Studi di Milano, 20122 Milan, Italy
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27
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Wang K, Xie S, Sun B. Viral proteins function as ion channels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:510-5. [PMID: 20478263 PMCID: PMC7094589 DOI: 10.1016/j.bbamem.2010.05.006] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 04/30/2010] [Accepted: 05/06/2010] [Indexed: 11/26/2022]
Abstract
Viral ion channels are short membrane proteins with 50–120 amino acids and play an important role either in regulating virus replication, such as virus entry, assembly and release or modulating the electrochemical balance in the subcellular compartments of host cells. This review summarizes the recent advances in viral encoded ion channel proteins (or viroporins), including PBCV-1 KcV, influenza M2, HIV-1 Vpu, HCV p7, picornavirus 2B, and coronavirus E and 3a. We focus on their function and mechanisms, and also discuss viral ion channel protein serving as a potential drug target.
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Affiliation(s)
- Kai Wang
- Laboratory of Molecular Virology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 225 South Chongqing Road, Shanghai 200025, China
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28
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Thiel G, Baumeister D, Schroeder I, Kast SM, Van Etten JL, Moroni A. Minimal art: or why small viral K(+) channels are good tools for understanding basic structure and function relations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:580-8. [PMID: 20417613 DOI: 10.1016/j.bbamem.2010.04.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/09/2010] [Accepted: 04/13/2010] [Indexed: 11/17/2022]
Abstract
Some algal viruses contain genes that encode proteins with the hallmarks of K(+) channels. One feature of these proteins is that they are less than 100 amino acids in size, which make them truly minimal for a K(+) channel protein. That is, they consist of only the pore module present in more complex K(+) channels. The combination of miniature size and the functional robustness of the viral K(+) channels make them ideal model systems for studying how K(+) channels work. Here we summarize recent structure/function correlates from these channels, which provide insight into functional properties such as gating, pharmacology and sorting in cells.
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Affiliation(s)
- Gerhard Thiel
- Institute of Botany, Technische Universität Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany.
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29
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Abenavoli A, DiFrancesco ML, Schroeder I, Epimashko S, Gazzarrini S, Hansen UP, Thiel G, Moroni A. Fast and slow gating are inherent properties of the pore module of the K+ channel Kcv. ACTA ACUST UNITED AC 2009; 134:219-29. [PMID: 19720961 PMCID: PMC2737228 DOI: 10.1085/jgp.200910266] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Kcv from the chlorella virus PBCV-1 is a viral protein that forms a tetrameric, functional K+ channel in heterologous systems. Kcv can serve as a model system to study and manipulate basic properties of the K+ channel pore because its minimalistic structure (94 amino acids) produces basic features of ion channels, such as selectivity, gating, and sensitivity to blockers. We present a characterization of Kcv properties at the single-channel level. In symmetric 100 mM K+, single-channel conductance is 114 ± 11 pS. Two different voltage-dependent mechanisms are responsible for the gating of Kcv. “Fast” gating, analyzed by β distributions, is responsible for the negative slope conductance in the single-channel current–voltage curve at extreme potentials, like in MaxiK potassium channels, and can be explained by depletion-aggravated instability of the filter region. The presence of a “slow” gating is revealed by the very low (in the order of 1–4%) mean open probability that is voltage dependent and underlies the time-dependent component of the macroscopic current.
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Affiliation(s)
- Alessandra Abenavoli
- Dipartimento di Biologia and Istituto di Biofisica-Consiglio Nazionale delle Ricerche, Università degli Studi di Milano, 20133 Milan, Italy
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30
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Grunwald I, Rischka K, Kast SM, Scheibel T, Bargel H. Mimicking biopolymers on a molecular scale: nano(bio)technology based on engineered proteins. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2009; 367:1727-1747. [PMID: 19376768 DOI: 10.1098/rsta.2009.0012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proteins are ubiquitous biopolymers that adopt distinct three-dimensional structures and fulfil a multitude of elementary functions in organisms. Recent systematic studies in molecular biology and biotechnology have improved the understanding of basic functional and architectural principles of proteins, making them attractive candidates as concept generators for technological development in material science, particularly in biomedicine and nano(bio)technology. This paper highlights the potential of molecular biomimetics in mimicking high-performance proteins and provides concepts for applications in four case studies, i.e. spider silk, antifreeze proteins, blue mussel adhesive proteins and viral ion channels.
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Affiliation(s)
- Ingo Grunwald
- Department of Adhesive Bonding Technology and Surfaces, Fraunhofer Institute for Manufacturing Technology and Applied Materials Research (IFAM)28359 Bremen, Germany
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Gazzarrini S, Kang M, Abenavoli A, Romani G, Olivari C, Gaslini D, Ferrara G, van Etten JL, Kreim M, Kast SM, Thiel G, Moroni A. Chlorella virus ATCV-1 encodes a functional potassium channel of 82 amino acids. Biochem J 2009; 420:295-303. [PMID: 19267691 PMCID: PMC2903877 DOI: 10.1042/bj20090095] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Chlorella virus PBCV-1 (Paramecium bursaria chlorella virus-1) encodes the smallest protein (94 amino acids, named Kcv) previously known to form a functional K+ channel in heterologous systems. In this paper, we characterize another chlorella virus encoded K+ channel protein (82 amino acids, named ATCV-1 Kcv) that forms a functional channel in Xenopus oocytes and rescues Saccharomyces cerevisiae mutants that lack endogenous K+ uptake systems. Compared with the larger PBCV-1 Kcv, ATCV-1 Kcv lacks a cytoplasmic N-terminus and has a reduced number of charged amino acids in its turret domain. Despite these deficiencies, ATCV-1 Kcv accomplishes all the major features of K+ channels: it assembles into a tetramer, is K+ selective and is inhibited by the canonical K+ channel blockers, barium and caesium. Single channel analyses reveal a stochastic gating behaviour and a voltage-dependent conductance that resembles the macroscopic I/V relationship. One difference between PBCV-1 and ATCV-1 Kcv is that the latter is more permeable to K+ than Rb+. This difference is partially explained by the presence of a tyrosine residue in the selective filter of ATCV-1 Kcv, whereas PBCV-1 Kcv has a phenylalanine. Hence, ATCV-1 Kcv is the smallest protein to form a K+ channel and it will serve as a model for studying structure-function correlations inside the potassium channel pore.
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Affiliation(s)
- Sabrina Gazzarrini
- Department of Biology and CNR - Istituto di Biofisica, Università degli Studi di Milano, Italy
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Salt bridges in the miniature viral channel Kcv are important for function. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:1057-68. [PMID: 19390850 DOI: 10.1007/s00249-009-0451-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 03/14/2009] [Accepted: 03/31/2009] [Indexed: 10/20/2022]
Abstract
The viral potassium channel Kcv comprises only 94 amino acids, which represent the pore module of more complex K(+) channels. As for Kir-type channels, Kcv also has a short N-terminal helix exposed to the cytoplasm, upstream of the first transmembrane domain. Here we show that this helix is relevant for Kcv function. The presence of charged amino acids, which form dynamic inter- and intra-subunit salt bridges is crucial. Electrophysiological measurements, yeast rescue experiments and molecular dynamics simulations show that mutants in which the critical salt bridge formation is impaired have no or reduced channel activity. We conclude that these salt bridges destabilise the complexation of K(+) ions by negative charges on the inner transmembrane domain at the entrance into the cavity. This feature facilitates a continuous and coordinated transfer of ions between the cavity and the cytoplasm for channels without the canonical bundle crossing.
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