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Kallure GS, Pal K, Zhou Y, Lingle CJ, Chowdhury S. High-resolution structures illuminate key principles underlying voltage and LRRC26 regulation of Slo1 channels. bioRxiv 2023:2023.12.20.572542. [PMID: 38187713 PMCID: PMC10769243 DOI: 10.1101/2023.12.20.572542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Multi-modal regulation of Slo1 channels by membrane voltage, intracellular calcium, and auxiliary subunits enables its pleiotropic physiological functions. Our understanding of how voltage impacts Slo1 conformational dynamics and the mechanisms by which auxiliary subunits, particularly of the LRRC (Leucine Rich Repeat containing) family of proteins, modulate its voltage gating remain unresolved. Here, we used single particle cryo-electron microscopy to determine structures of human Slo1 mutants which functionally stabilize the closed pore (F315A) or the activated voltage-sensor (R207A). Our structures, obtained under calcium-free conditions, reveal that a key step in voltage-sensing by Slo1 involves a rotameric flip of the voltage-sensing charges (R210 and R213) moving them by ∼6 Å across a hydrophobic gasket. Next we obtained reconstructions of a complex of human Slo1 with the human LRRC26 (γ1) subunit in absence of calcium. Together with extensive biochemical tests, we show that the extracellular domains of γ1 form a ring of interlocked dominos that stabilizes the quaternary assembly of the complex and biases Slo1:γ1 assembly towards high stoichiometric complexes. The transmembrane helix of γ1 is kinked and tightly packed against the Slo1 voltage-sensor. We hypothesize that γ1 subunits exert relatively small effects on early steps in voltage-gating but structurally stabilize non-S4 helices of Slo1 voltage-sensor which energetically facilitate conformational rearrangements that occur late in voltage stimulated transitions.
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2
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Lu J, Dreyer I, Dickinson MS, Panzer S, Jaślan D, Navarro-Retamal C, Geiger D, Terpitz U, Becker D, Stroud RM, Marten I, Hedrich R. Vicia faba SV channel VfTPC1 is a hyperexcitable variant of plant vacuole Two Pore Channels. eLife 2023; 12:e86384. [PMID: 37991833 PMCID: PMC10665017 DOI: 10.7554/elife.86384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 10/12/2023] [Indexed: 11/23/2023] Open
Abstract
To fire action-potential-like electrical signals, the vacuole membrane requires the two-pore channel TPC1, formerly called SV channel. The TPC1/SV channel functions as a depolarization-stimulated, non-selective cation channel that is inhibited by luminal Ca2+. In our search for species-dependent functional TPC1 channel variants with different luminal Ca2+ sensitivity, we found in total three acidic residues present in Ca2+ sensor sites 2 and 3 of the Ca2+-sensitive AtTPC1 channel from Arabidopsis thaliana that were neutral in its Vicia faba ortholog and also in those of many other Fabaceae. When expressed in the Arabidopsis AtTPC1-loss-of-function background, wild-type VfTPC1 was hypersensitive to vacuole depolarization and only weakly sensitive to blocking luminal Ca2+. When AtTPC1 was mutated for these VfTPC1-homologous polymorphic residues, two neutral substitutions in Ca2+ sensor site 3 alone were already sufficient for the Arabidopsis At-VfTPC1 channel mutant to gain VfTPC1-like voltage and luminal Ca2+ sensitivity that together rendered vacuoles hyperexcitable. Thus, natural TPC1 channel variants exist in plant families which may fine-tune vacuole excitability and adapt it to environmental settings of the particular ecological niche.
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Affiliation(s)
- Jinping Lu
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
- School of Life Sciences, Zhengzhou UniversityZhengzhouChina
| | - Ingo Dreyer
- Universidad de Talca, Faculty of Engineering, Center of Bioinformatics, Simulation and ModelingTalcaChile
| | - Miles Sasha Dickinson
- University of California San Francisco, Department of Biochemistry and BiophysicsSan FranciscoUnited States
| | - Sabine Panzer
- Julius-Maximilians-Universität (JMU), Biocenter, Theodor-Boveri-Institute, Department of Biotechnology and BiophysicsWürzburgGermany
| | - Dawid Jaślan
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
- Ludwig Maximilians-Universität, Faculty of Medicine, Walther Straub Institute of Pharmacology and ToxicologyMunichGermany
| | - Carlos Navarro-Retamal
- Universidad de Talca, Faculty of Engineering, Center of Bioinformatics, Simulation and ModelingTalcaChile
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege ParkUnited States
| | - Dietmar Geiger
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
| | - Ulrich Terpitz
- Julius-Maximilians-Universität (JMU), Biocenter, Theodor-Boveri-Institute, Department of Biotechnology and BiophysicsWürzburgGermany
| | - Dirk Becker
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
| | - Robert M Stroud
- University of California San Francisco, Department of Biochemistry and BiophysicsSan FranciscoUnited States
| | - Irene Marten
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
| | - Rainer Hedrich
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
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3
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Hedrich R, Müller TD, Marten I, Becker D. TPC1 vacuole SV channel gains further shape - voltage priming of calcium-dependent gating. Trends Plant Sci 2023; 28:673-684. [PMID: 36740491 DOI: 10.1016/j.tplants.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/20/2022] [Accepted: 01/11/2023] [Indexed: 05/13/2023]
Abstract
Across phyla, voltage-gated ion channels (VGICs) allow excitability. The vacuolar two-pore channel AtTPC1 from the tiny mustard plant Arabidopsis thaliana has emerged as a paradigm for deciphering the role of voltage and calcium signals in membrane excitation. Among the numerous experimentally determined structures of VGICs, AtTPC1 was the first to be revealed in a closed and resting state, fueling speculation about structural rearrangements during channel activation. Two independent reports on the structure of a partially opened AtTPC1 channel protein have led to working models that offer promising insights into the molecular switches associated with the gating process. We review new structure-function models and also discuss the evolutionary impact of two-pore channels (TPCs) on K+ homeostasis and vacuolar excitability.
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Affiliation(s)
- Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, 97082 Würzburg, Germany.
| | - Thomas D Müller
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, 97082 Würzburg, Germany
| | - Irene Marten
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, 97082 Würzburg, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, 97082 Würzburg, Germany
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4
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Dutta D. Interplay between membrane proteins and membrane protein-lipid pertaining to plant salinity stress. Cell Biochem Funct 2023. [PMID: 37158622 DOI: 10.1002/cbf.3798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 04/03/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
High salinity in agricultural lands is one of the predominant issues limiting agricultural yields. Plants have developed several mechanisms to withstand salinity stress, but the mechanisms are not effective enough for most crops to prevent and persist the salinity stress. Plant salt tolerance pathways involve membrane proteins that have a crucial role in sensing and mitigating salinity stress. Due to a strategic location interfacing two distinct cellular environments, membrane proteins can be considered checkpoints to the salt tolerance pathways in plants. Related membrane proteins functions include ion homeostasis, osmosensing or ion sensing, signal transduction, redox homeostasis, and small molecule transport. Therefore, modulating plant membrane proteins' function, expression, and distribution can improve plant salt tolerance. This review discusses the membrane protein-protein and protein-lipid interactions related to plant salinity stress. It will also highlight the finding of membrane protein-lipid interactions from the context of recent structural evidence. Finally, the importance of membrane protein-protein and protein-lipid interaction is discussed, and a future perspective on studying the membrane protein-protein and protein-lipid interactions to develop strategies for improving salinity tolerance is proposed.
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Affiliation(s)
- Debajyoti Dutta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
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5
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Mérida-Quesada F, Vergara-Valladares F, Rubio-Meléndez ME, Hernández-Rojas N, González-González A, Michard E, Navarro-Retamal C, Dreyer I. TPC1-Type Channels in Physcomitrium patens: Interaction between EF-Hands and Ca 2. Plants (Basel) 2022; 11:plants11243527. [PMID: 36559639 PMCID: PMC9783492 DOI: 10.3390/plants11243527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 05/26/2023]
Abstract
Two-pore channels (TPCs) are members of the superfamily of ligand-gated and voltage-sensitive ion channels in the membranes of intracellular organelles of eukaryotic cells. The evolution of ordinary plant TPC1 essentially followed a very conservative pattern, with no changes in the characteristic structural footprints of these channels, such as the cytosolic and luminal regions involved in Ca2+ sensing. In contrast, the genomes of mosses and liverworts encode also TPC1-like channels with larger variations at these sites (TPC1b channels). In the genome of the model plant Physcomitrium patens we identified nine non-redundant sequences belonging to the TPC1 channel family, two ordinary TPC1-type, and seven TPC1b-type channels. The latter show variations in critical amino acids in their EF-hands essential for Ca2+ sensing. To investigate the impact of these differences between TPC1 and TPC1b channels, we generated structural models of the EF-hands of PpTPC1 and PpTPC1b channels. These models were used in molecular dynamics simulations to determine the frequency with which calcium ions were present in a coordination site and also to estimate the average distance of the ions from the center of this site. Our analyses indicate that the EF-hand domains of PpTPC1b-type channels have a lower capacity to coordinate calcium ions compared with those of common TPC1-like channels.
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Affiliation(s)
- Franko Mérida-Quesada
- Programa de Doctorado en Ciencias mención Modelado de Sistemas Químicos y Biológicos, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
| | - Fernando Vergara-Valladares
- Programa de Doctorado en Ciencias mención Modelado de Sistemas Químicos y Biológicos, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
| | - María Eugenia Rubio-Meléndez
- Electrical Signaling in Plants (ESP) Laboratory–Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
| | - Naomí Hernández-Rojas
- Electrical Signaling in Plants (ESP) Laboratory–Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
| | - Angélica González-González
- Programa de Doctorado en Ciencias mención Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay, Talca CL-3460000, Chile
| | - Erwan Michard
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay, Talca CL-3460000, Chile
| | - Carlos Navarro-Retamal
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay, Talca CL-3460000, Chile
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742-5815, USA
| | - Ingo Dreyer
- Electrical Signaling in Plants (ESP) Laboratory–Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
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6
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Suda H, Toyota M. Integration of long-range signals in plants: A model for wound-induced Ca 2+, electrical, ROS, and glutamate waves. Curr Opin Plant Biol 2022; 69:102270. [PMID: 35926395 DOI: 10.1016/j.pbi.2022.102270] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/13/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Plants show long-range cytosolic Ca2+ signal transduction in response to wounding. Recent advances in in vivo imaging techniques have helped visualize spatiotemporal dynamics of the systemic Ca2+ signals and provided new insights into underlying molecular mechanisms, in which ion channels of the GLUTAMATE RECEPTOR-LIKE (GLR) family are critical for the sensory system. These, along with MECHANOSENSITIVE CHANNEL OF SMALL CONDUCTANCE-LIKE 10 (MSL10) and Arabidopsis H+-ATPase (AHA1) regulate the propagation system. In addition, membrane potential, reactive oxygen species (ROS), and glutamate waves operate in parallel to long-range signal transduction. We summarize these findings and introduce a model that integrates long-range Ca2+, electrical, ROS, and glutamate signals in systemic wound responses.
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Affiliation(s)
- Hiraku Suda
- Department of Biochemistry and Molecular Biology, Saitama University, Saitama, Japan
| | - Masatsugu Toyota
- Department of Biochemistry and Molecular Biology, Saitama University, Saitama, Japan; Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE), Kyoto, Japan; Department of Botany, University of Wisconsin-Madison, WI, USA.
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7
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Yudovich S, Marzouqe A, Kantorovitsch J, Teblum E, Chen T, Enderlein J, Miller EW, Weiss S. Electrically Controlling and Optically Observing the Membrane Potential of Supported Lipid Bilayers. Biophys J 2022; 121:2624-2637. [PMID: 35619563 DOI: 10.1016/j.bpj.2022.05.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 04/26/2022] [Accepted: 05/23/2022] [Indexed: 11/02/2022] Open
Abstract
Supported lipid bilayers are a well-developed model system for the study of membranes and their associated proteins, such as membrane channels, enzymes, and receptors. These versatile model membranes can be made from various components, ranging from simple synthetic phospholipids to complex mixtures of constituents, mimicking the cell membrane with its relevant physiochemical and molecular phenomena. In addition, the high stability of supported lipid bilayers allows for their study via a wide array of experimental probes. In this work, we describe a platform for supported lipid bilayers that is accessible both electrically and optically, and demonstrate direct optical observation of the transmembrane potential of supported lipid bilayers. We show that the polarization of the supported membrane can be electrically controlled and optically probed using voltage-sensitive dyes. Membrane polarization dynamics is understood through electrochemical impedance spectroscopy and the analysis of an equivalent electrical circuit model. In addition, we describe the effect of the conducting electrode layer on the fluorescence of the optical probe through metal-induced energy transfer, and show that while this energy transfer has an adverse effect on the voltage sensitivity of the fluorescent probe, its strong distance dependency allows for axial localization of fluorescent emitters with ultrahigh accuracy. We conclude with a discussion on possible applications of this platform for the study of voltage-dependent membrane proteins and other processes in membrane biology and surface science.
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Affiliation(s)
- Shimon Yudovich
- Department of Physics, Bar-Ilan University, Ramat-Gan, 52900, Israel; Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 52900, Israel.
| | - Adan Marzouqe
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 52900, Israel; Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Joseph Kantorovitsch
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Eti Teblum
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Tao Chen
- Third Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Jörg Enderlein
- Third Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, Germany
| | - Evan W Miller
- Departments of Chemistry, Molecular & Cell Biology, and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, United States
| | - Shimon Weiss
- Department of Physics, Bar-Ilan University, Ramat-Gan, 52900, Israel; Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 52900, Israel; Departments of Chemistry and Biochemistry, Physiology, and California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA 90095.
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8
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Kehlenbeck DM, Traore DAK, Josts I, Sander S, Moulin M, Haertlein M, Prevost S, Forsyth VT, Tidow H. Cryo-EM structure of MsbA in saposin-lipid nanoparticles (Salipro) provides insights into nucleotide coordination. FEBS J 2022; 289:2959-2970. [PMID: 34921499 DOI: 10.1111/febs.16327] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/05/2021] [Accepted: 12/16/2021] [Indexed: 01/28/2023]
Abstract
The ATP-binding cassette transporter MsbA is a lipid flippase, translocating lipid A, glycolipids, and lipopolysaccharides from the inner to the outer leaflet of the inner membrane of Gram-negative bacteria. It has been used as a model system for time-resolved structural studies as several MsbA structures in different states and reconstitution systems (detergent/nanodiscs/peptidiscs) are available. However, due to the limited resolution of the available structures, detailed structural information on the bound nucleotides has remained elusive. Here, we have reconstituted MsbA in saposin A-lipoprotein nanoparticles (Salipro) and determined the structure of ADP-vanadate-bound MsbA by single-particle cryo-electron microscopy to 3.5 Å resolution. This procedure has resulted in significantly improved resolution and enabled us to model all side chains and visualise detailed ADP-vanadate interactions in the nucleotide-binding domains. The approach may be applicable to other dynamic membrane proteins.
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Affiliation(s)
- Dominique-Maurice Kehlenbeck
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany.,Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France
| | - Daouda A K Traore
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France.,Faculty of Natural Sciences, Keele University, UK.,Faculté des Sciences et Techniques, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Inokentijs Josts
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | - Simon Sander
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | - Martine Moulin
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France
| | - Sylvain Prevost
- Large Scale Structures Group, Institut Laue-Langevin, Grenoble, France
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France.,Faculty of Natural Sciences, Keele University, UK
| | - Henning Tidow
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany
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9
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Dickinson MS, Lu J, Gupta M, Marten I, Hedrich R, Stroud RM. Molecular basis of multistep voltage activation in plant two-pore channel 1. Proc Natl Acad Sci U S A 2022; 119:e2110936119. [PMID: 35210362 DOI: 10.1073/pnas.2110936119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
Despite decades of biophysical and structural research, little is understood about how voltage-gated ion channels (VGICs) activate during membrane depolarization, and less is known about how VGICs can be modulated by lipids and other ligands. We identify multiple functional states of the voltage- and Ca2+-gated ion channel TPC1 from Arabidopsis thaliana (AtTPC1), which confers electrical excitability to the plant vacuole. Here, we show how a voltage-sensing domain (VSD) functions during electrical activation and the mechanism of inhibition by vacuolar Ca2+. We show that the VSD undergoes large-scale, domain-wide structural changes during activation that involves Ca2+-dependent in-membrane plane rotation, subsequent charge transfer, and a Ca2+-dependent gate in the pore mouth that is allosterically coupled to the VSD. Voltage-gated ion channels confer excitability to biological membranes, initiating and propagating electrical signals across large distances on short timescales. Membrane excitation requires channels that respond to changes in electric field and couple the transmembrane voltage to gating of a central pore. To address the mechanism of this process in a voltage-gated ion channel, we determined structures of the plant two-pore channel 1 at different stages along its activation coordinate. These high-resolution structures of activation intermediates, when compared with the resting-state structure, portray a mechanism in which the voltage-sensing domain undergoes dilation and in-membrane plane rotation about the gating charge–bearing helix, followed by charge translocation across the charge transfer seal. These structures, in concert with patch-clamp electrophysiology, show that residues in the pore mouth sense inhibitory Ca2+ and are allosterically coupled to the voltage sensor. These conformational changes provide insight into the mechanism of voltage-sensor domain activation in which activation occurs vectorially over a series of elementary steps.
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10
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Ye F, Xu L, Li X, Zeng W, Gan N, Zhao C, Yang W, Jiang Y, Guo J. Voltage-gating and cytosolic Ca 2+ activation mechanisms of Arabidopsis two-pore channel AtTPC1. Proc Natl Acad Sci U S A 2021; 118:e2113946118. [PMID: 34845029 DOI: 10.1073/pnas.2113946118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 11/18/2022] Open
Abstract
Arabidopsis thaliana two-pore channel AtTPC1 is a voltage-gated, Ca2+-modulated, nonselective cation channel that is localized in the vacuolar membrane and responsible for generating slow vacuolar (SV) current. Under depolarizing membrane potential, cytosolic Ca2+ activates AtTPC1 by binding at the EF-hand domain, whereas luminal Ca2+ inhibits the channel by stabilizing the voltage-sensing domain II (VSDII) in the resting state. Here, we present 2.8 to 3.3 Å cryoelectron microscopy (cryo-EM) structures of AtTPC1 in two conformations, one in closed conformation with unbound EF-hand domain and resting VSDII and the other in a partially open conformation with Ca2+-bound EF-hand domain and activated VSDII. Structural comparison between the two different conformations allows us to elucidate the structural mechanisms of voltage gating, cytosolic Ca2+ activation, and their coupling in AtTPC1. This study also provides structural insight into the general voltage-gating mechanism among voltage-gated ion channels.
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11
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Hirazawa K, Tateyama M, Kubo Y, Shimomura T. Phosphoinositide regulates dynamic movement of the S4 voltage sensor in the second repeat in two-pore channel 3. J Biol Chem 2021; 297:101425. [PMID: 34800436 PMCID: PMC8665364 DOI: 10.1016/j.jbc.2021.101425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/24/2022] Open
Abstract
The two-pore channels (TPCs) are voltage-gated cation channels consisting of single polypeptides with two repeats of a canonical 6-transmembrane unit. TPCs are known to be regulated by various physiological signals such as membrane voltage and phosphoinositide (PI). The fourth helix in the second repeat (second S4) plays a major role in detecting membrane voltage, whereas the first repeat contains a PI binding site. Therefore, each of these stimuli is detected by a unique repeat to regulate the gating of the TPC central pore. How these various stimuli regulate the dynamic structural rearrangement of the TPC molecule remain unknown. Here, we found that PI binding to the first repeat in TPC3 regulates the movement of the distally located second S4 helix, showing that the PI-binding signal is not confined to the pore gate but also transmitted to the voltage sensor. Using voltage clamp fluorometry, measurement of gating charges, and Cys-accessibility analysis, we observed that PI binding significantly potentiates the voltage dependence of the movement of the second S4 helix. Notably, voltage clamp fluorometry analysis revealed that the voltage-dependent movement of the second S4 helix occurred in two phases, of which the second phase corresponds to the transfer of the gating charges. This movement was observed in the voltage range where gate-opening occurs and was potentiated by PI. In conclusion, this regulation of the second S4 helix by PI indicates a tight inter-repeat coupling within TPC3, a feature which might be conserved among TPC family members to integrate various physiological signals.
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Affiliation(s)
- Kiichi Hirazawa
- Division of Biophysics and Neurobiology, National Institute for Physiological Sciences, Okazaki, Japan; Department of Physiological Sciences, The Graduate University for Advanced Studies, Hayama, Japan
| | - Michihiro Tateyama
- Division of Biophysics and Neurobiology, National Institute for Physiological Sciences, Okazaki, Japan; Department of Physiological Sciences, The Graduate University for Advanced Studies, Hayama, Japan
| | - Yoshihiro Kubo
- Division of Biophysics and Neurobiology, National Institute for Physiological Sciences, Okazaki, Japan; Department of Physiological Sciences, The Graduate University for Advanced Studies, Hayama, Japan
| | - Takushi Shimomura
- Division of Biophysics and Neurobiology, National Institute for Physiological Sciences, Okazaki, Japan; Department of Physiological Sciences, The Graduate University for Advanced Studies, Hayama, Japan.
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12
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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13
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Kacher YG, Karlova MG, Glukhov GS, Zhang H, Zaklyazminskaya EV, Loussouarn G, Sokolova OS. The Integrative Approach to Study of the Structure and Functions of Cardiac Voltage-Dependent Ion Channels. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Konečná V, Bray S, Vlček J, Bohutínská M, Požárová D, Choudhury RR, Bollmann-Giolai A, Flis P, Salt DE, Parisod C, Yant L, Kolář F. Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles. Nat Commun 2021; 12:4979. [PMID: 34404804 DOI: 10.1038/s41467-021-25256-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/21/2021] [Indexed: 01/26/2023] Open
Abstract
Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms. Relative contributions of pre-existing versus de novo genomic variation to adaptation remain unclear. Here, the authors address this problem by examining the adaptation of autotetraploid Arabidopsis arenosa to serpentine soils and find that both types of variations contribute to rapid adaptation.
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15
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Jodaitis L, van Oene T, Martens C. Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins. Int J Mol Sci 2021; 22:7267. [PMID: 34298884 PMCID: PMC8306737 DOI: 10.3390/ijms22147267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid-protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid-protein interactions in the mechanism of membrane proteins.
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Affiliation(s)
| | | | - Chloé Martens
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (L.J.); (T.v.O.)
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16
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D'Amore A, Gradogna A, Palombi F, Minicozzi V, Ceccarelli M, Carpaneto A, Filippini A. The Discovery of Naringenin as Endolysosomal Two-Pore Channel Inhibitor and Its Emerging Role in SARS-CoV-2 Infection. Cells 2021; 10:1130. [PMID: 34067054 DOI: 10.3390/cells10051130] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 12/23/2022] Open
Abstract
The flavonoid naringenin (Nar), present in citrus fruits and tomatoes, has been identified as a blocker of an emerging class of human intracellular channels, namely the two-pore channel (TPC) family, whose role has been established in several diseases. Indeed, Nar was shown to be effective against neoangiogenesis, a process essential for solid tumor progression, by specifically impairing TPC activity. The goal of the present review is to illustrate the rationale that links TPC channels to the mechanism of coronavirus infection, and how their inhibition by Nar could be an efficient pharmacological strategy to fight the current pandemic plague COVID-19.
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17
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Kurgan KW, Chen B, Brown KA, Falco Cobra P, Ye X, Ge Y, Gellman SH. Stable Picodisc Assemblies from Saposin Proteins and Branched Detergents. Biochemistry 2021; 60:1108-1119. [PMID: 33755420 DOI: 10.1021/acs.biochem.0c00924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methods for maintaining membrane proteins in their native state after removal from the lipid bilayer are essential for the study of this important class of biomacromolecules. Common solubilization strategies range from the use of detergents to more complex systems that involve a polypeptide working in concert with lipids or detergents, such as nanodiscs, picodiscs, and peptidiscs, in which an engineered protein or synthetic peptide surrounds the membrane protein along with a lipid sheath. Picodiscs employ the protein saposin A, which naturally functions to facilitate lipid degradation in the lysozome. Saposin A-amphiphile complexes therefore tend to be most stable at acidic pH, which is not optimal for most membrane protein applications. In search of new picodisc assemblies, we have explored pairings of saposin A or other saposin proteins with a range of detergents, and we have identified a number of combinations that spontaneously co-assemble at neutral pH. The resulting picodiscs are stable for weeks and have been characterized by size-exclusion chromatography, native mass spectrometry, and small angle X-ray scattering. The new assemblies are formed by double-tail detergents rather than more traditional single-tail detergents; the double-tail detergents can be seen as structurally intermediate between single-tail detergents and common lipids. In addition to saposin A, an engineered variant of saposin B (designated saposin BW) forms picodisc assemblies. These findings provide a framework for future efforts to solubilize membrane proteins with multiple picodisc systems that were previously unknown.
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18
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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19
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Fletcher-Taylor S, Thapa P, Sepela RJ, Kaakati R, Yarov-Yarovoy V, Sack JT, Cohen BE. Distinguishing Potassium Channel Resting State Conformations in Live Cells with Environment-Sensitive Fluorescence. ACS Chem Neurosci 2020; 11:2316-2326. [PMID: 32579336 DOI: 10.1021/acschemneuro.0c00276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Ion channels are polymorphic membrane proteins whose high-resolution structures offer images of individual conformations, giving us starting points for identifying the complex and transient allosteric changes that give rise to channel physiology. Here, we report live-cell imaging of voltage-dependent structural changes of voltage-gated Kv2.1 channels using peptidyl tarantula toxins labeled with an environment-sensitive fluorophore, whose spectral shifts enable identification of voltage-dependent conformation changes in the resting voltage sensing domain (VSD) of the channel. We synthesize a new environment-sensitive, far-red fluorophore, julolidine phenoxazone (JP) azide, and conjugate it to tarantula toxin GxTX to characterize Kv2.1 VSD allostery during membrane depolarization. JP has an inherent response to the polarity of its immediate surroundings, offering site-specific structural insight into each channel conformation. Using voltage-clamp spectroscopy to collect emission spectra as a function of membrane potential, we find that they vary with toxin labeling site, the presence of Kv2 channels, and changes in membrane potential. With a high-affinity conjugate in which the fluorophore itself interacts closely with the channel, the emission shift midpoint is 50 mV more negative than the Kv2.1 gating current midpoint. This suggests that substantial conformational changes at the toxin-channel interface are associated with early gating charge transitions and these are not concerted with VSD motions at more depolarized potentials. These fluorescent probes enable study of conformational changes that can be correlated with electrophysiology, putting channel structures and models into a context of live-cell membranes and physiological states.
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20
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Dodd R, Schofield DJ, Wilkinson T, Britton ZT. Generating therapeutic monoclonal antibodies to complex multi-spanning membrane targets: Overcoming the antigen challenge and enabling discovery strategies. Methods 2020; 180:111-26. [PMID: 32422249 DOI: 10.1016/j.ymeth.2020.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/21/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
Complex integral membrane proteins, which are embedded in the cell surface lipid bilayer by multiple transmembrane spanning helices, encompass families of proteins which are important target classes for drug discovery. These protein families include G protein-coupled receptors, ion channels and transporters. Although these proteins have typically been targeted by small molecule drugs and peptides, the high specificity of monoclonal antibodies offers a significant opportunity to selectively modulate these target proteins. However, it remains the case that isolation of antibodies with desired pharmacological function(s) has proven difficult due to technical challenges in preparing membrane protein antigens suitable to support antibody drug discovery. In this review recent progress in defining strategies for generation of membrane protein antigens is outlined. We also highlight antibody isolation strategies which have generated antibodies which bind the membrane protein and modulate the protein function.
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21
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Lloris-Garcerá P, Klinter S, Chen L, Skynner MJ, Löving R, Frauenfeld J. DirectMX - One-Step Reconstitution of Membrane Proteins From Crude Cell Membranes Into Salipro Nanoparticles. Front Bioeng Biotechnol 2020; 8:215. [PMID: 32266242 PMCID: PMC7096351 DOI: 10.3389/fbioe.2020.00215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/03/2020] [Indexed: 01/14/2023] Open
Abstract
Integral membrane proteins (IMPs) are central to many physiological processes and represent ∼60% of current drug targets. An intricate interplay with the lipid molecules in the cell membrane is known to influence the stability, structure and function of IMPs. Detergents are commonly used to solubilize and extract IMPs from cell membranes. However, due to the loss of the lipid environment, IMPs usually tend to be unstable and lose function in the continuous presence of detergent. To overcome this problem, various technologies have been developed, including protein engineering by mutagenesis to improve IMP stability, as well as methods to reconstitute IMPs into detergent-free entities, such as nanodiscs based on apolipoprotein A or its membrane scaffold protein (MSP) derivatives, amphipols, and styrene-maleic acid copolymer-lipid particles (SMALPs). Although significant progress has been made in this field, working with inherently unstable human IMP targets (e.g., GPCRs, ion channels and transporters) remains a challenging task. Here, we present a novel methodology, termed DirectMX (for direct membrane extraction), taking advantage of the saposin-lipoprotein (Salipro) nanoparticle technology to reconstitute fragile IMPs directly from human crude cell membranes. We demonstrate the applicability of the DirectMX methodology by the reconstitution of a human solute carrier transporter and a wild-type GPCR belonging to the human chemokine receptor (CKR) family. We envision that DirectMX bears the potential to enable studies of IMPs that so far remained inaccessible to other solubilization, stabilization or reconstitution methods.
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22
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Taylor KC, Kang PW, Hou P, Yang ND, Kuenze G, Smith JA, Shi J, Huang H, White KM, Peng D, George AL, Meiler J, McFeeters RL, Cui J, Sanders CR. Structure and physiological function of the human KCNQ1 channel voltage sensor intermediate state. eLife 2020; 9:e53901. [PMID: 32096762 PMCID: PMC7069725 DOI: 10.7554/elife.53901] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Voltage-gated ion channels feature voltage sensor domains (VSDs) that exist in three distinct conformations during activation: resting, intermediate, and activated. Experimental determination of the structure of a potassium channel VSD in the intermediate state has previously proven elusive. Here, we report and validate the experimental three-dimensional structure of the human KCNQ1 voltage-gated potassium channel VSD in the intermediate state. We also used mutagenesis and electrophysiology in Xenopus laevisoocytes to functionally map the determinants of S4 helix motion during voltage-dependent transition from the intermediate to the activated state. Finally, the physiological relevance of the intermediate state KCNQ1 conductance is demonstrated using voltage-clamp fluorometry. This work illuminates the structure of the VSD intermediate state and demonstrates that intermediate state conductivity contributes to the unusual versatility of KCNQ1, which can function either as the slow delayed rectifier current (IKs) of the cardiac action potential or as a constitutively active epithelial leak current.
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Affiliation(s)
- Keenan C Taylor
- Department of Biochemistry, Vanderbilt UniversityNashvilleUnited States
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
| | - Po Wei Kang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Panpan Hou
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Nien-Du Yang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
- Departments of Chemistry and Pharmacology, Vanderbilt UniversityNashvilleUnited States
| | - Jarrod A Smith
- Department of Biochemistry, Vanderbilt UniversityNashvilleUnited States
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Hui Huang
- Department of Biochemistry, Vanderbilt UniversityNashvilleUnited States
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
| | - Kelli McFarland White
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Dungeng Peng
- Department of Biochemistry, Vanderbilt UniversityNashvilleUnited States
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical CenterNashvilleUnited States
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of MedicineChicagoUnited States
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
- Departments of Chemistry and Pharmacology, Vanderbilt UniversityNashvilleUnited States
- Department of Bioinformatics, Vanderbilt University Medical CenterNashvilleUnited States
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama in HuntsvilleHuntsvilleUnited States
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt UniversityNashvilleUnited States
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
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23
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Dickinson MS, Myasnikov A, Eriksen J, Poweleit N, Stroud RM. Resting state structure of the hyperdepolarization activated two-pore channel 3. Proc Natl Acad Sci U S A 2020; 117:1988-93. [PMID: 31924746 DOI: 10.1073/pnas.1915144117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Voltage-gated ion channels endow membranes with excitability and the means to propagate action potentials that form the basis of all neuronal signaling. We determined the structure of a voltage-gated sodium channel, two-pore channel 3 (TPC3), which generates ultralong action potentials. TPC3 is distinguished by activation only at extreme membrane depolarization (V50 ∼ +75 mV), in contrast to other TPCs and NaV channels that activate between -20 and 0 mV. We present electrophysiological evidence that TPC3 voltage activation depends only on voltage sensing domain 2 (VSD2) and that each of the three gating arginines in VSD2 reduces the activation threshold. The structure presents a chemical basis for sodium selectivity, and a constricted gate suggests a closed pore consistent with extreme voltage dependence. The structure, confirmed by our electrophysiology, illustrates the configuration of a bona fide resting state voltage sensor, observed without the need for any inhibitory ligand, and independent of any chemical or mutagenic alteration.
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24
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Kasimova MA, Tewari D, Cowgill JB, Ursuleaz WC, Lin JL, Delemotte L, Chanda B. Helix breaking transition in the S4 of HCN channel is critical for hyperpolarization-dependent gating. eLife 2019; 8:e53400. [PMID: 31774399 PMCID: PMC6904216 DOI: 10.7554/elife.53400] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/19/2019] [Indexed: 12/19/2022] Open
Abstract
In contrast to most voltage-gated ion channels, hyperpolarization- and cAMP gated (HCN) ion channels open on hyperpolarization. Structure-function studies show that the voltage-sensor of HCN channels are unique but the mechanisms that determine gating polarity remain poorly understood. All-atom molecular dynamics simulations (~20 μs) of HCN1 channel under hyperpolarization reveals an initial downward movement of the S4 voltage-sensor but following the transfer of last gating charge, the S4 breaks into two sub-helices with the lower sub-helix becoming parallel to the membrane. Functional studies on bipolar channels show that the gating polarity strongly correlates with helical turn propensity of the substituents at the breakpoint. Remarkably, in a proto-HCN background, the replacement of breakpoint serine with a bulky hydrophobic amino acid is sufficient to completely flip the gating polarity from inward to outward-rectifying. Our studies reveal an unexpected mechanism of inward rectification involving a linker sub-helix emerging from HCN S4 during hyperpolarization.
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Affiliation(s)
- Marina A Kasimova
- Science for Life Laboratory, Department of Applied PhysicsKTH Royal Institute of TechnologyStockholmSweden
| | - Debanjan Tewari
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
| | - John B Cowgill
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
- Graduate program in BiophysicsUniversity of WisconsinMadisonUnited States
| | | | - Jenna L Lin
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
- Graduate program in BiophysicsUniversity of WisconsinMadisonUnited States
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied PhysicsKTH Royal Institute of TechnologyStockholmSweden
| | - Baron Chanda
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
- Department of Biomolecular ChemistryUniversity of Wisconsin-MadisonMadisonUnited States
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25
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Kostelic MM, Ryan AM, Reid DJ, Noun JM, Marty MT. Expanding the Types of Lipids Amenable to Native Mass Spectrometry of Lipoprotein Complexes. J Am Soc Mass Spectrom 2019; 30:1416-1425. [PMID: 30972726 PMCID: PMC6675625 DOI: 10.1007/s13361-019-02174-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 05/12/2023]
Abstract
Native mass spectrometry (MS) has become an important tool for the analysis of membrane proteins. Although detergent micelles are the most commonly used method for solubilizing membrane proteins for native MS, nanoscale lipoprotein complexes such as nanodiscs are emerging as a promising complementary approach because they solubilize membrane proteins in a lipid bilayer environment. However, prior native MS studies of intact nanodiscs have employed only a limited set of phospholipids that are similar in mass. Here, we extend the range of lipids that are amenable to native MS of nanodiscs by combining lipids with masses that are simple integer multiples of each other. Although these lipid combinations create complex distributions, overlap between resonant peak series allows interpretation of nanodisc spectra containing glycolipids, sterols, and cardiolipin. We also investigate the gas-phase stability of nanodiscs with these new lipids towards collisional activation. We observe that negative ionization mode or charge reduction stabilizes nanodiscs and is essential to preserving labile lipids such as sterols. These new approaches to native MS of nanodiscs will enable future studies of membrane proteins embedded in model membranes that more accurately mimic natural bilayers. Graphical Abstract.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Alex M Ryan
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Jibriel M Noun
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA.
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26
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Kostelic MM, Ryan AM, Reid DJ, Noun JM, Marty MT. Expanding the Types of Lipids Amenable to Native Mass Spectrometry of Lipoprotein Complexes. J Am Soc Mass Spectrom 2019; 30:1416-1425. [PMID: 30972726 DOI: 10.1007/s13361-13019-02174-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 05/26/2023]
Abstract
Native mass spectrometry (MS) has become an important tool for the analysis of membrane proteins. Although detergent micelles are the most commonly used method for solubilizing membrane proteins for native MS, nanoscale lipoprotein complexes such as nanodiscs are emerging as a promising complementary approach because they solubilize membrane proteins in a lipid bilayer environment. However, prior native MS studies of intact nanodiscs have employed only a limited set of phospholipids that are similar in mass. Here, we extend the range of lipids that are amenable to native MS of nanodiscs by combining lipids with masses that are simple integer multiples of each other. Although these lipid combinations create complex distributions, overlap between resonant peak series allows interpretation of nanodisc spectra containing glycolipids, sterols, and cardiolipin. We also investigate the gas-phase stability of nanodiscs with these new lipids towards collisional activation. We observe that negative ionization mode or charge reduction stabilizes nanodiscs and is essential to preserving labile lipids such as sterols. These new approaches to native MS of nanodiscs will enable future studies of membrane proteins embedded in model membranes that more accurately mimic natural bilayers. Graphical Abstract.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Alex M Ryan
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Jibriel M Noun
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA.
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27
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Dai G, Aman TK, DiMaio F, Zagotta WN. The HCN channel voltage sensor undergoes a large downward motion during hyperpolarization. Nat Struct Mol Biol 2019; 26:686-694. [PMID: 31285608 PMCID: PMC6692172 DOI: 10.1038/s41594-019-0259-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022]
Abstract
Voltage-gated ion channels (VGICs) contain positively-charged residues within the S4 helix of the voltage-sensing domain (VSD) that are displaced in response to changes in transmembrane voltage, promoting conformational changes that open the pore. Pacemaker HCN channels are unique among VGICs because their open probability is increased by membrane hyperpolarization rather than depolarization. Here we measured the precise movement of the S4 helix of a sea urchin HCN channel using transition metal ion fluorescence resonance energy transfer (tmFRET). We show that the S4 undergoes a significant (~10 Å) downward movement in response to membrane hyperpolarization. Furthermore, by applying distance constraints determined from tmFRET experiments to Rosetta modeling, we reveal that the C-terminal part of the S4 helix exhibits an unexpected tilting motion during hyperpolarization activation. These data provide a long-sought glimpse of the hyperpolarized state of a functioning VSD and also a framework for understanding the dynamics of reverse gating in HCN channels.
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Affiliation(s)
- Gucan Dai
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Teresa K Aman
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
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28
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Autzen HE, Julius D, Cheng Y. Membrane mimetic systems in CryoEM: keeping membrane proteins in their native environment. Curr Opin Struct Biol 2019; 58:259-268. [PMID: 31279500 DOI: 10.1016/j.sbi.2019.05.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 05/24/2019] [Accepted: 05/27/2019] [Indexed: 01/02/2023]
Abstract
Advances in electron microscopes, detectors and data processing algorithms have greatly facilitated the structural determination of many challenging integral membrane proteins that have been evasive to crystallization. These breakthroughs facilitate the application and development of various membrane protein solubilization approaches for structural studies, including reconstitution into lipid nanoparticles. In this review, we discuss various approaches for preparing transmembrane proteins for structural determination with single-particle electron cryo microscopy (cryoEM).
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Affiliation(s)
- Henriette E Autzen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - David Julius
- Department of Physiology, University of California, San Francisco, CA 94143, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.
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29
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Affiliation(s)
- Sandipan Chowdhury
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Baron Chanda
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA. .,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
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30
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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31
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Basu K, Green EM, Cheng Y, Craik CS. Why recombinant antibodies - benefits and applications. Curr Opin Biotechnol 2019; 60:153-158. [PMID: 30849700 DOI: 10.1016/j.copbio.2019.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/22/2018] [Accepted: 01/21/2019] [Indexed: 01/07/2023]
Abstract
Antibodies (Abs) are ubiquitous reagents for biological and biochemical research and are rapidly expanding into new therapeutic areas. They are one of the most important probes for determining how proteins function under normal and pathophysiological conditions. Abs are required for the quantification of targets, detection of temporal and spatial patterns of protein expression in cells and tissues, and identification of interacting partners and their biological activities. Their remarkable specificity and unique binding properties can facilitate three-dimensional structure determination using X-ray crystallography and electron cryomicroscopy. While hybridoma technology that involves animal immunization is often productive, many antigen targets do not generate useful Abs. This is particularly true if unique states of the target or critical non-immunogenic target sequences need to be recognized by the Abs. By using the methods of recombinant antibody generation, identification, and engineering, these 'hybridoma-refractory' antigens can be readily targeted. Specific, reproducible, and renewable recombinant Abs are proving to be invaluable reagents in applications ranging from biological discovery to structure determination of challenging macromolecules.
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Affiliation(s)
- Koli Basu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, United States
| | - Evan M Green
- Department of Biochemistry and Biophysics, University of California, San Francisco, United States
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, United States; Howard Hughes Medical Institute, University of California, San Francisco, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, United States
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32
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Xu H, Li T, Rohou A, Arthur CP, Tzakoniati F, Wong E, Estevez A, Kugel C, Franke Y, Chen J, Ciferri C, Hackos DH, Koth CM, Payandeh J. Structural Basis of Nav1.7 Inhibition by a Gating-Modifier Spider Toxin. Cell 2019; 176:702-715.e14. [PMID: 30661758 DOI: 10.1016/j.cell.2018.12.018] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/11/2018] [Accepted: 12/11/2018] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium (Nav) channels are targets of disease mutations, toxins, and therapeutic drugs. Despite recent advances, the structural basis of voltage sensing, electromechanical coupling, and toxin modulation remains ill-defined. Protoxin-II (ProTx2) from the Peruvian green velvet tarantula is an inhibitor cystine-knot peptide and selective antagonist of the human Nav1.7 channel. Here, we visualize ProTx2 in complex with voltage-sensor domain II (VSD2) from Nav1.7 using X-ray crystallography and cryoelectron microscopy. Membrane partitioning orients ProTx2 for unfettered access to VSD2, where ProTx2 interrogates distinct features of the Nav1.7 receptor site. ProTx2 positions two basic residues into the extracellular vestibule to antagonize S4 gating-charge movement through an electrostatic mechanism. ProTx2 has trapped activated and deactivated states of VSD2, revealing a remarkable ∼10 Å translation of the S4 helix, providing a structural framework for activation gating in voltage-gated ion channels. Finally, our results deliver key templates to design selective Nav channel antagonists.
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Affiliation(s)
- Hui Xu
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA
| | - Tianbo Li
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA 94080, USA.
| | - Alexis Rohou
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA.
| | | | - Foteini Tzakoniati
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA
| | - Evera Wong
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
| | - Alberto Estevez
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA
| | - Christine Kugel
- Department of Biomolecular Resources, Genentech, South San Francisco, CA 94080, USA
| | - Yvonne Franke
- Department of Biomolecular Resources, Genentech, South San Francisco, CA 94080, USA
| | - Jun Chen
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA 94080, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA
| | - David H Hackos
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA.
| | - Christopher M Koth
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA.
| | - Jian Payandeh
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA.
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