1
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Molton O, Bignucolo O, Kellenberger S. Identification of the modulatory Ca 2+-binding sites of acid-sensing ion channel 1a. Open Biol 2024; 14:240028. [PMID: 38896086 DOI: 10.1098/rsob.240028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/28/2024] [Indexed: 06/21/2024] Open
Abstract
Acid-sensing ion channels (ASICs) are neuronal Na+-permeable ion channels activated by extracellular acidification. ASICs are involved in learning, fear sensing, pain sensation and neurodegeneration. Increasing the extracellular Ca2+ concentration decreases the H+ sensitivity of ASIC1a, suggesting a competition for binding sites between H+ and Ca2+ ions. Here, we predicted candidate residues for Ca2+ binding on ASIC1a, based on available structural information and our molecular dynamics simulations. With functional measurements, we identified several residues in cavities previously associated with pH-dependent gating, whose mutation reduced the modulation by extracellular Ca2+ of the ASIC1a pH dependence of activation and desensitization. This occurred likely owing to a disruption of Ca2+ binding. Our results link one of the two predicted Ca2+-binding sites in each ASIC1a acidic pocket to the modulation of channel activation. Mg2+ regulates ASICs in a similar way as does Ca2+. We show that Mg2+ shares some of the binding sites with Ca2+. Finally, we provide evidence that some of the ASIC1a Ca2+-binding sites are functionally conserved in the splice variant ASIC1b. Our identification of divalent cation-binding sites in ASIC1a shows how Ca2+ affects ASIC1a gating, elucidating a regulatory mechanism present in many ion channels.
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Affiliation(s)
- Ophélie Molton
- Department of Biomedical Sciences, University of Lausanne , 1011 Lausanne, Switzerland
| | | | - Stephan Kellenberger
- Department of Biomedical Sciences, University of Lausanne , 1011 Lausanne, Switzerland
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2
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Purohit R, Couch T, MacLean DM. Proline substitutions in the ASIC1 β11-12 linker slow desensitization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593312. [PMID: 38798386 PMCID: PMC11118455 DOI: 10.1101/2024.05.09.593312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Desensitization is a prominent feature of nearly all ligand gated ion channels. Acid-sensing ion channels (ASIC) undergo desensitization within hundreds of milliseconds to seconds upon continual extracellular acidification. The ASIC mechanism of desensitization is primarily due to the isomerization or "flipping" of a short linker joining the 11th and 12th beta sheets in the extracellular domain. In the resting and active states this β11-12 linker adopts an "upward" conformation while in the desensitized conformation the linker assumes a "downward" state. To accommodate this "downward" state, specific peptide bonds within the linker adopt either trans-like or cis-like conformations. Since proline-containing peptide bonds undergo cis-trans isomerization very slowly, we hypothesized that introducing proline residues in the linker may slow or even abolish ASIC desensitization, potentially providing a valuable research tools. Proline substitutions in the chicken ASIC1 β11-12 linker (L414P and Y416P) slowed desensitization decays approximately 100 to 1000-fold as measured in excised patches. Both L414P and Y416P shifted the steady state desensitization curves to more acidic pHs while activation curves and ion selectivity of these slow-desensitizing currents were largely unaffected. To investigate the functional stoichiometry of desensitization in the trimeric ASIC, we created families of L414P and Y416P concatemers with zero, one, two or three proline substitutions in all possible configurations. Introducing one or two L414P or Y416P mutations only slightly attenuated desensitization, suggesting that conformational changes in the remaining faster wild type subunits were sufficient to desensitize the channel. These data highlight the unusual cis-trans isomerization mechanism of ASIC desensitization and support a model where a single subunit is sufficient to desensitize the entire channel.
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Affiliation(s)
- Rutambhara Purohit
- Department of Pharmacology and Physiology, University of Rochester Medical Center
| | - Tyler Couch
- Department of Pharmacology and Physiology, University of Rochester Medical Center
| | - David M MacLean
- Department of Pharmacology and Physiology, University of Rochester Medical Center
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3
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Kalienkova V, Dandamudi M, Paulino C, Lynagh T. Structural basis for excitatory neuropeptide signaling. Nat Struct Mol Biol 2024; 31:717-726. [PMID: 38337033 PMCID: PMC11026163 DOI: 10.1038/s41594-023-01198-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 12/05/2023] [Indexed: 02/12/2024]
Abstract
Rapid signaling between neurons is mediated by ligand-gated ion channels, cell-surface proteins with an extracellular ligand-binding domain and a membrane-spanning ion channel domain. The degenerin/epithelial sodium channel (DEG/ENaC) superfamily is diverse in terms of its gating stimuli, with some DEG/ENaCs gated by neuropeptides, and others gated by pH, mechanical force or enzymatic activity. The mechanism by which ligands bind to and activate DEG/ENaCs is poorly understood. Here we dissected the structural basis for neuropeptide-gated activity of a neuropeptide-gated DEG/ENaC, FMRFamide-gated sodium channel 1 (FaNaC1) from the annelid worm Malacoceros fuliginosus, using cryo-electron microscopy. Structures of FaNaC1 in the ligand-free resting state and in several ligand-bound states reveal the ligand-binding site and capture the ligand-induced conformational changes of channel gating, which we verified with complementary mutagenesis experiments. Our results illuminate channel gating in DEG/ENaCs and offer a structural template for experimental dissection of channel pharmacology and ion conduction.
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Affiliation(s)
- Valeria Kalienkova
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Cristina Paulino
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
- Biochemistry Center, Heidelberg University, Heidelberg, Germany.
| | - Timothy Lynagh
- Michael Sars Centre, University of Bergen, Bergen, Norway.
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4
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Holm CM, Topaktas AB, Dannesboe J, Pless SA, Heusser SA. Dynamic conformational changes of acid-sensing ion channels in different desensitizing conditions. Biophys J 2024:S0006-3495(24)00240-6. [PMID: 38549370 DOI: 10.1016/j.bpj.2024.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/21/2024] [Accepted: 03/26/2024] [Indexed: 04/18/2024] Open
Abstract
Acid-sensing ion channels (ASICs) are proton-gated cation channels that contribute to fast synaptic transmission and have roles in fear conditioning and nociception. Apart from activation at low pH, ASIC1a also undergoes several types of desensitization, including acute desensitization, which terminates activation; steady-state desensitization, which occurs at sub-activating proton concentrations and limits subsequent activation; and tachyphylaxis, which results in a progressive decrease in response during a series of activations. Structural insights from a desensitized state of ASIC1 have provided great spatial detail, but dynamic insights into conformational changes in different desensitizing conditions are largely missing. Here, we use electrophysiology and voltage-clamp fluorometry to follow the functional changes of the pore along with conformational changes at several positions in the extracellular and upper transmembrane domain via cysteine-labeled fluorophores. Acute desensitization terminates activation in wild type, but introducing an N414K mutation in the β11-12 linker of mouse ASIC1a interfered with this process. The mutation also affected steady-state desensitization and led to pronounced tachyphylaxis. Although the extracellular domain of this mutant remained sensitive to pH and underwent pH-dependent conformational changes, these conformational changes did not necessarily lead to desensitization. N414K-containing channels also remained sensitive to a known peptide modulator that increases steady-state desensitization, indicating that the mutation only reduced, but not precluded, desensitization. Together, this study contributes to our understanding of the fundamental properties of ASIC1a desensitization, emphasizing the complex interplay between the conformational changes of the extracellular domain and the pore during channel activation and desensitization.
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Affiliation(s)
- Caroline Marcher Holm
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Asli B Topaktas
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark; Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Johs Dannesboe
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stephan A Pless
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Stephanie A Heusser
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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5
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Brown C, Ghosh S, McAllister R, Kumar M, Walker G, Sun E, Aman T, Panda A, Kumar S, Li W, Coleman J, Liu Y, Rothman JE, Bhattacharyya M, Gupta K. A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579775. [PMID: 38405833 PMCID: PMC10888908 DOI: 10.1101/2024.02.10.579775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The intricate molecular environment of the native membrane profoundly influences every aspect of membrane protein (MP) biology. Despite this, the most prevalent method of studying MPs uses detergent-like molecules that disrupt and remove this vital local membrane context. This severely impedes our ability to quantitatively decipher the local molecular context and comprehend its regulatory role in the structure, function, and biogenesis of MPs. Using a library of membrane-active polymers we have developed a platform for the high-throughput analysis of the membrane proteome. The platform enables near-complete spatially resolved extraction of target MPs directly from their endogenous membranes into native nanodiscs that maintain the local membrane context. We accompany this advancement with an open-access quantitative database that provides the most efficient extraction conditions of 2065 unique mammalian MPs. Our method enables rapid and near-complete extraction and purification of target MPs directly from their endogenous organellar membranes at physiological expression levels while maintaining the nanoscale local membrane environment. Going beyond the plasma membrane proteome, our platform enables extraction from any target organellar membrane including the endoplasmic reticulum, mitochondria, lysosome, Golgi, and even transient organelles such as the autophagosome. To further validate this platform we took several independent MPs and demonstrated how our resource can enable rapid extraction and purification of target MPs from different organellar membranes with high efficiency and purity. Further, taking two synaptic vesicle MPs, we show how the database can be extended to capture multiprotein complexes between overexpressed MPs. We expect these publicly available resources to empower researchers across disciplines to capture membrane 'nano-scoops' containing a target MP efficiently and interface with structural, functional, and other bioanalytical approaches. We demonstrate an example of this by combining our extraction platform with single-molecule TIRF imaging to demonstrate how it can enable rapid determination of homo-oligomeric states of target MPs in native cell membranes.
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Affiliation(s)
- Caroline Brown
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Snehasish Ghosh
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Rachel McAllister
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Mukesh Kumar
- F.M. Kirby Neurobiology Center, Department of Neurobiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gerard Walker
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Eric Sun
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Talat Aman
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Shailesh Kumar
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Wenxue Li
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Jeff Coleman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Yansheng Liu
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - James E Rothman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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6
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Glukhov G, Karlova M, Kravchuk E, Glukhova A, Trifonova E, Sokolova OS. Purification of Potassium Ion Channels Using Styrene-Maleic Acid Copolymers. Methods Mol Biol 2024; 2796:73-86. [PMID: 38856895 DOI: 10.1007/978-1-0716-3818-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Structural studies require the production of target proteins in large quantities and with a high degree of purity. For membrane proteins, the bottleneck in determining their structure is the extraction of the target protein from the cell membranes. A detergent that improperly mimics the hydrophobic environment of the protein of interest can also significantly alter its structure. Recently, using lipodiscs with styrene-maleic acid (SMA), copolymers became a promising strategy for the purification of membrane proteins. Here, we describe in detail the one-step affinity purification of potassium ion channels solubilized in SMA and sample preparation for future structural studies.
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Affiliation(s)
- Grigory Glukhov
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Maria Karlova
- Faculty of Biology, Moscow Lomonosov University, Moscow, Russia
| | | | - Anna Glukhova
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | | | - Olga S Sokolova
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China.
- Faculty of Biology, Moscow Lomonosov University, Moscow, Russia.
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7
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Cullinan MM, Klipp RC, Camenisch A, Bankston JR. Dynamic landscape of the intracellular termini of acid-sensing ion channel 1a. eLife 2023; 12:RP90755. [PMID: 38054969 PMCID: PMC10699805 DOI: 10.7554/elife.90755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Abstract
Acid-sensing ion channels (ASICs) are trimeric proton-gated sodium channels. Recent work has shown that these channels play a role in necroptosis following prolonged acidic exposure like occurs in stroke. The C-terminus of ASIC1a is thought to mediate necroptotic cell death through interaction with receptor interacting serine threonine kinase 1 (RIPK1). This interaction is hypothesized to be inhibited at rest via an interaction between the C- and N-termini which blocks the RIPK1 binding site. Here, we use two transition metal ion FRET methods to investigate the conformational dynamics of the termini at neutral and acidic pH. We do not find evidence that the termini are close enough to be bound while the channel is at rest and find that the termini may modestly move closer together during acidification. At rest, the N-terminus adopts a conformation parallel to the membrane about 10 Å away. The distal end of the C-terminus may also spend time close to the membrane at rest. After acidification, the proximal portion of the N-terminus moves marginally closer to the membrane whereas the distal portion of the C-terminus swings away from the membrane. Together these data suggest that a new hypothesis for RIPK1 binding during stroke is needed.
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Affiliation(s)
- Megan M Cullinan
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Robert C Klipp
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | | | - John R Bankston
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
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8
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Rook ML, McCullock TW, Couch T, Lueck JD, MacLean DM. Photomodulation of the ASIC1a acidic pocket destabilizes the open state. Protein Sci 2023; 32:e4800. [PMID: 37805833 PMCID: PMC10599103 DOI: 10.1002/pro.4800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023]
Abstract
Acid-sensing ion channels (ASICs) are important players in detecting extracellular acidification throughout the brain and body. ASICs have large extracellular domains containing two regions replete with acidic residues: the acidic pocket, and the palm domain. In the resting state, the acidic pocket is in an expanded conformation but collapses in low pH conditions as the acidic side chains are neutralized. Thus, extracellular acidification has been hypothesized to collapse the acidic pocket that, in turn, ultimately drives channel activation. However, several observations run counter to this idea. To explore how collapse or mobility of the acidic pocket is linked to channel gating, we employed two distinct tools. First, we incorporated the photocrosslinkable noncanonical amino acids (ncAAs) 4-azido-L-phenylalanine (AzF) or 4-benzoyl-L-phenylalanine (BzF) into several positions in the acidic pocket. At both E315 and Y318, AzF incorporation followed by UV irradiation led to right shifts in pH response curves and accelerations of desensitization and deactivation, consistent with restrictions of acidic pocket mobility destabilizing the open state. Second, we reasoned that because Cl- ions are found in the open and desensitized structures but absent in the resting state structures, Cl- substitution would provide insight into how stability of the pocket is linked to gating. Anion substitution resulted in faster deactivation and desensitization, consistent with the acidic pocket regulating the stability of the open state. Taken together, our data support a model where acidic pocket collapse is not essential for channel activation. Rather, collapse of the acidic pocket influences the stability of the open state of the pore.
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Affiliation(s)
- Matthew L. Rook
- Department of Pharmacology and Physiology, School of Medicine and DentistryUniversity of RochesterRochesterNew YorkUSA
| | - Tyler W. McCullock
- Department of Pharmacology and Physiology, School of Medicine and DentistryUniversity of RochesterRochesterNew YorkUSA
| | - Tyler Couch
- Department of Pharmacology and Physiology, School of Medicine and DentistryUniversity of RochesterRochesterNew YorkUSA
| | - John D. Lueck
- Department of Pharmacology and Physiology, School of Medicine and DentistryUniversity of RochesterRochesterNew YorkUSA
- Deparment of Neurology, School of Medicine and DentistryUniversity of RochesterRochesterNew YorkUSA
- Center for RNA BiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - David M. MacLean
- Department of Pharmacology and Physiology, School of Medicine and DentistryUniversity of RochesterRochesterNew YorkUSA
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9
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Liu F, Dang Y, Li L, Feng H, Li J, Wang H, Zhang X, Zhang Z, Ye S, Tian Y, Chen Q. Structure and mechanism of a neuropeptide-activated channel in the ENaC/DEG superfamily. Nat Chem Biol 2023; 19:1276-1285. [PMID: 37550431 DOI: 10.1038/s41589-023-01401-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
Phe-Met-Arg-Phe-amide (FMRFamide)-activated sodium channels (FaNaCs) are a family of channels activated by the neuropeptide FMRFamide, and, to date, the underlying ligand gating mechanism remains unknown. Here we present the high-resolution cryo-electron microscopy structures of Aplysia californica FaNaC in both apo and FMRFamide-bound states. AcFaNaC forms a chalice-shaped trimer and possesses several notable features, including two FaNaC-specific insertion regions, a distinct finger domain and non-domain-swapped transmembrane helix 2 in the transmembrane domain (TMD). One FMRFamide binds to each subunit in a cleft located in the top-most region of the extracellular domain, with participation of residues from the neighboring subunit. Bound FMRFamide adopts an extended conformation. FMRFamide binds tightly to A. californica FaNaC in an N terminus-in manner, which causes collapse of the binding cleft and induces large local conformational rearrangements. Such conformational changes are propagated downward toward the TMD via the palm domain, possibly resulting in outward movement of the TMD and dilation of the ion conduction pore.
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Affiliation(s)
- Fenglian Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Yu Dang
- State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lu Li
- Academy of Medical Engineering and Translational Medicine (AMT) and Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, Tianjin, China
| | - Hao Feng
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Jianlin Li
- Academy of Medical Engineering and Translational Medicine (AMT) and Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, Tianjin, China
| | - Haowei Wang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Xu Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Zhe Zhang
- State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China.
| | - Yutao Tian
- Academy of Medical Engineering and Translational Medicine (AMT) and Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, Tianjin, China.
| | - Qingfeng Chen
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China.
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10
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Cullinan MM, Klipp RC, Camenisch A, Bankston JR. Dynamic landscape of the intracellular termini of acid-sensing ion channel 1a. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547693. [PMID: 37461628 PMCID: PMC10350031 DOI: 10.1101/2023.07.05.547693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Acid-sensing ion channels (ASICs) are trimeric proton-gated sodium channels. Recently it has been shown that these channels play a role in necroptosis following prolonged acidic exposure like occurs in stroke. The C-terminus of the channel is thought to mediate necroptotic cell death through interaction with receptor interacting serine threonine kinase 1 (RIPK1). This interaction is hypothesized to be inhibited at rest via an interaction between the C-terminus and the N-terminus which blocks the RIPK1 binding site. Here, we use a combination of two transition metal ion FRET methods to investigate the conformational dynamics of the termini while the channel is closed and desensitized. We do not find evidence that the termini are close enough to be bound while the channel is at rest and find that the termini may modestly move closer together when desensitized. At rest, the N-terminus adopts a conformation parallel to the membrane about 10 Å away. The distal end of the C-terminus may also spend time close to the membrane at rest. After acidification, the proximal portion of the N-terminus moves marginally closer to the membrane whereas the distal portion of the C-terminus swings away from the membrane. Together these data suggest that a new hypothesis for RIPK1 binding during stroke is needed.
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Affiliation(s)
- Megan M Cullinan
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Robert C Klipp
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Abigail Camenisch
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - John R Bankston
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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11
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Kaulich E, McCubbin PTN, Schafer WR, Walker DS. Physiological insight into the conserved properties of Caenorhabditis elegans acid-sensing degenerin/epithelial sodium channels. J Physiol 2023; 601:1625-1653. [PMID: 36200489 PMCID: PMC10424705 DOI: 10.1113/jp283238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022] Open
Abstract
Acid-sensing ion channels (ASICs) are members of the diverse family of degenerin/epithelial sodium channels (DEG/ENaCs). They perform a wide range of physiological roles in healthy organisms, including in gut function and synaptic transmission, but also play important roles in disease, as acidosis is a hallmark of painful inflammatory and ischaemic conditions. We performed a screen for acid sensitivity on all 30 subunits of the Caenorhabditis elegans DEG/ENaC family using two-electrode voltage clamp in Xenopus oocytes. We found two groups of acid-sensitive DEG/ENaCs characterised by being either inhibited or activated by increasing proton concentrations. Three of these acid-sensitive C. elegans DEG/ENaCs were activated by acidic pH, making them functionally similar to the vertebrate ASICs. We also identified three new members of the acid-inhibited DEG/ENaC group, giving a total of seven additional acid-sensitive channels. We observed sensitivity to the anti-hypertensive drug amiloride as well as modulation by the trace element zinc. Acid-sensitive DEG/ENaCs were found to be expressed in both neurons and non-neuronal tissue, highlighting the likely functional diversity of these channels. Our findings provide a framework to exploit the C. elegans channels as models to study the function of these acid-sensing channels in vivo, as well as to study them as potential targets for anti-helminthic drugs. KEY POINTS: Acidosis plays many roles in healthy physiology, including synaptic transmission and gut function, but is also a key feature of inflammatory pain, ischaemia and many other conditions. Cells monitor acidosis of their surroundings via pH-sensing channels, including the acid-sensing ion channels (ASICs). These are members of the degenerin/epithelial sodium channel (DEG/ENaC) family, along with, as the name suggests, vertebrate ENaCs and degenerins of the roundworm Caenorhabditis elegans. By screening all 30 C. elegans DEG/ENaCs for pH dependence, we describe, for the first time, three acid-activated members, as well as three additional acid-inhibited channels. We surveyed both groups for sensitivity to amiloride and zinc; like their mammalian counterparts, their currents can be blocked, enhanced or unaffected by these modulators. Likewise, they exhibit diverse ion selectivity. Our findings underline the diversity of acid-sensitive DEG/ENaCs across species and provide a comparative resource for better understanding the molecular basis of their function.
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Affiliation(s)
- Eva Kaulich
- Neurobiology DivisionMRC Laboratory of Molecular BiologyCambridgeUK
| | | | - William R. Schafer
- Neurobiology DivisionMRC Laboratory of Molecular BiologyCambridgeUK
- Department of BiologyKU LeuvenLeuvenBelgium
| | - Denise S. Walker
- Neurobiology DivisionMRC Laboratory of Molecular BiologyCambridgeUK
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12
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Lemmens-Gruber R, Tzotzos S. The Epithelial Sodium Channel-An Underestimated Drug Target. Int J Mol Sci 2023; 24:ijms24097775. [PMID: 37175488 PMCID: PMC10178586 DOI: 10.3390/ijms24097775] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/15/2023] Open
Abstract
Epithelial sodium channels (ENaC) are part of a complex network of interacting biochemical pathways and as such are involved in several disease states. Dependent on site and type of mutation, gain- or loss-of-function generated symptoms occur which span from asymptomatic to life-threatening disorders such as Liddle syndrome, cystic fibrosis or generalized pseudohypoaldosteronism type 1. Variants of ENaC which are implicated in disease assist further understanding of their molecular mechanisms in order to create models for specific pharmacological targeting. Identification and characterization of ENaC modifiers not only furthers our basic understanding of how these regulatory processes interact, but also enables discovery of new therapeutic targets for the disease conditions caused by ENaC dysfunction. Numerous test compounds have revealed encouraging results in vitro and in animal models but less in clinical settings. The EMA- and FDA-designated orphan drug solnatide is currently being tested in phase 2 clinical trials in the setting of acute respiratory distress syndrome, and the NOX1/ NOX4 inhibitor setanaxib is undergoing clinical phase 2 and 3 trials for therapy of primary biliary cholangitis, liver stiffness, and carcinoma. The established ENaC blocker amiloride is mainly used as an add-on drug in the therapy of resistant hypertension and is being studied in ongoing clinical phase 3 and 4 trials for special applications. This review focuses on discussing some recent developments in the search for novel therapeutic agents.
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Affiliation(s)
- Rosa Lemmens-Gruber
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, A-1090 Vienna, Austria
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13
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Tam SW, Huffer K, Li M, Swartz KJ. Ion permeation pathway within the internal pore of P2X receptor channels. eLife 2023; 12:84796. [PMID: 36940138 PMCID: PMC10027316 DOI: 10.7554/elife.84796] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/07/2023] [Indexed: 03/21/2023] Open
Abstract
P2X receptor channels are trimeric ATP-activated ion channels expressed in neuronal and non-neuronal cells that are attractive therapeutic targets for human disorders. Seven subtypes of P2X receptor channels have been identified in mammals that can form both homomeric and heteromeric channels. P2X1-4 and P2X7 receptor channels are cation-selective, whereas P2X5 has been reported to have both cation and anion permeability. P2X receptor channel structures reveal that each subunit is comprised of two transmembrane helices, with both N-and C-termini on the intracellular side of the membrane and a large extracellular domain that contains the ATP binding sites at subunit interfaces. Recent structures of ATP-bound P2X receptors with the activation gate open reveal the unanticipated presence of a cytoplasmic cap over the central ion permeation pathway, leaving lateral fenestrations that may be largely buried within the membrane as potential pathways for ions to permeate the intracellular end of the pore. In the present study, we identify a critical residue within the intracellular lateral fenestrations that is readily accessible to thiol-reactive compounds from both sides of the membrane and where substitutions influence the relative permeability of the channel to cations and anions. Taken together, our results demonstrate that ions can enter or exit the internal pore through lateral fenestrations that play a critical role in determining the ion selectivity of P2X receptor channels.
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Affiliation(s)
- Stephanie W Tam
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Kate Huffer
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Mufeng Li
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
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14
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Korkosh VS, Tikhonov DB. Analysis of residue-residue interactions in the structures of ASIC1a suggests possible gating mechanisms. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:111-119. [PMID: 36690863 DOI: 10.1007/s00249-023-01628-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/25/2023]
Abstract
The gating mechanism of acid-sensitive ion channels (ASICs) remains unclear, despite the availability of atomic-scale structures in various functional states. The collapse of the acidic pocket and structural changes in the low-palm region are assumed to trigger activation. For the acidic pocket, protonation of some residues can minimize repulsion in the collapsed conformation. The relationship between low-palm rearrangements and gating is unknown. In this work, we performed a Monte Carlo energy optimization of known ASIC1a structures and determined the residue-residue interactions in different functional states. For rearrangements in the acidic pocket, our results are consistent with previously proposed mechanisms, although significant complexity was revealed for the residue-residue interactions. The data support the proposal of a gating mechanism in the low-palm region, in which residues E80 and E417 share a proton to activate the channel.
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Affiliation(s)
- Vyacheslav S Korkosh
- Sechenov Institute of Evolutionary Physiology and Biochemistry, St. Petersburg, Russia
| | - Denis B Tikhonov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, St. Petersburg, Russia.
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15
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Ananchenko A, Musgaard M. Multiscale molecular dynamics simulations predict arachidonic acid binding sites in human ASIC1a and ASIC3 transmembrane domains. J Gen Physiol 2023; 155:213797. [PMID: 36625864 PMCID: PMC9836442 DOI: 10.1085/jgp.202213259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/20/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
Acid-sensing ion channels (ASICs) play important roles in inflammatory pathways by conducting ions across the neuronal membrane in response to proton binding under acidic conditions. Recent studies have shown that ASICs can be modulated by arachidonic acid (AA), and, in the case of the ASIC3 subtype, even activated by AA at physiological pH. However, the mechanism by which these fatty acids act on the channel is still unknown. Here, we have used multiscale molecular dynamics simulations to predict a putative, general binding region of AA to models of the human ASIC protein. We have identified, in agreement with recent studies, residues in the outer leaflet transmembrane region which interact with AA. In addition, despite their similar modulation, we observe subtle differences in the AA interaction pattern between human ASIC1a and human ASIC3, which can be reversed by mutating three key residues at the outer leaflet portion of TM1. We further probed interactions with these residues in hASIC3 using atomistic simulations and identified possible AA coordinating interactions; salt bridge interactions of AA with R65hASIC3 and R68hASIC3 and AA tail interactions with the Y58hASIC3 aromatic ring. We have shown that longer fatty acid tails with more double bonds have increased relative occupancy in this region of the channel, a finding supported by recent functional studies. We further proposed that the modulatory effect of AA on ASIC does not result from changes in local membrane curvature. Rather, we speculate that it may occur through structural changes to the ion channel upon AA binding.
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Affiliation(s)
- Anna Ananchenko
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Maria Musgaard
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
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16
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Bondar AN. Interplay between local protein interactions and water bridging of a proton antenna carboxylate cluster. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184052. [PMID: 36116514 DOI: 10.1016/j.bbamem.2022.184052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 08/17/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Proteins that bind protons at cell membrane interfaces often expose to the bulk clusters of carboxylate and histidine sidechains that capture protons transiently and, in proton transporters, deliver protons to an internal site. The protonation-coupled dynamics of bulk-exposed carboxylate clusters, also known as proton antennas, is poorly described. An essential open question is how water-mediated bridges between sidechains of the cluster respond to protonation change and facilitate transient proton storage. To address this question, here I studied the protonation-coupled dynamics at the proton-binding antenna of PsbO, a small extrinsinc subunit of the photosystem II complex, with atomistic molecular dynamics simulations and systematic graph-based analyses of dynamic protein and protein-water hydrogen-bond networks. The protonation of specific carboxylate groups is found to impact the dynamics of their local protein-water hydrogen-bond clusters. Regardless of the protonation state considered for PsbO, carboxylate pairs that can sample direct hydrogen bonding, or bridge via short hydrogen-bonded water chains, anchor to nearby basic or polar protein sidechains. As a result, carboxylic sidechains of the hypothesized antenna cluster are part of dynamic hydrogen bond networks that may rearrange rapidly when the protonation changes.
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Affiliation(s)
- Ana-Nicoleta Bondar
- University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, Bucharest-Măgurele 077125, Romania; Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, 52425 Jülich, Germany; Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, D-14195 Berlin, Germany.
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17
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Kaulich E, Grundy LJ, Schafer WR, Walker DS. The diverse functions of the DEG/ENaC family: linking genetic and physiological insights. J Physiol 2022; 601:1521-1542. [PMID: 36314992 PMCID: PMC10148893 DOI: 10.1113/jp283335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
The DEG/ENaC family of ion channels was defined based on the sequence similarity between degenerins (DEG) from the nematode Caenorhabditis elegans and subunits of the mammalian epithelial sodium channel (ENaC), and also includes a diverse array of non-voltage-gated cation channels from across animal phyla, including the mammalian acid-sensing ion channels (ASICs) and Drosophila pickpockets. ENaCs and ASICs have wide ranging medical importance; for example, ENaCs play an important role in respiratory and renal function, and ASICs in ischaemia and inflammatory pain, as well as being implicated in memory and learning. Electrophysiological approaches, both in vitro and in vivo, have played an essential role in establishing the physiological properties of this diverse family, identifying an array of modulators and implicating them in an extensive range of cellular functions, including mechanosensation, acid sensation and synaptic modulation. Likewise, genetic studies in both invertebrates and vertebrates have played an important role in linking our understanding of channel properties to function at the cellular and whole animal/behavioural level. Drawing together genetic and physiological evidence is essential to furthering our understanding of the precise cellular roles of DEG/ENaC channels, with the diversity among family members allowing comparative physiological studies to dissect the molecular basis of these diverse functions.
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Affiliation(s)
- Eva Kaulich
- Neurobiology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Laura J Grundy
- Neurobiology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - William R Schafer
- Neurobiology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK.,Department of Biology, KU Leuven, Leuven, Belgium
| | - Denise S Walker
- Neurobiology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
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18
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Verkest C, Salinas M, Diochot S, Deval E, Lingueglia E, Baron A. Mechanisms of Action of the Peptide Toxins Targeting Human and Rodent Acid-Sensing Ion Channels and Relevance to Their In Vivo Analgesic Effects. Toxins (Basel) 2022; 14:toxins14100709. [PMID: 36287977 PMCID: PMC9612379 DOI: 10.3390/toxins14100709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Acid-sensing ion channels (ASICs) are voltage-independent H+-gated cation channels largely expressed in the nervous system of rodents and humans. At least six isoforms (ASIC1a, 1b, 2a, 2b, 3 and 4) associate into homotrimers or heterotrimers to form functional channels with highly pH-dependent gating properties. This review provides an update on the pharmacological profiles of animal peptide toxins targeting ASICs, including PcTx1 from tarantula and related spider toxins, APETx2 and APETx-like peptides from sea anemone, and mambalgin from snake, as well as the dimeric protein snake toxin MitTx that have all been instrumental to understanding the structure and the pH-dependent gating of rodent and human cloned ASICs and to study the physiological and pathological roles of native ASICs in vitro and in vivo. ASICs are expressed all along the pain pathways and the pharmacological data clearly support a role for these channels in pain. ASIC-targeting peptide toxins interfere with ASIC gating by complex and pH-dependent mechanisms sometimes leading to opposite effects. However, these dual pH-dependent effects of ASIC-inhibiting toxins (PcTx1, mambalgin and APETx2) are fully compatible with, and even support, their analgesic effects in vivo, both in the central and the peripheral nervous system, as well as potential effects in humans.
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Affiliation(s)
- Clément Verkest
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
- Department of Anesthesiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Miguel Salinas
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
| | - Sylvie Diochot
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
| | - Emmanuel Deval
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
| | - Eric Lingueglia
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
| | - Anne Baron
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
- Correspondence:
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19
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Krishnarjuna B, Ramamoorthy A. Detergent-Free Isolation of Membrane Proteins and Strategies to Study Them in a Near-Native Membrane Environment. Biomolecules 2022; 12:1076. [PMID: 36008970 PMCID: PMC9406181 DOI: 10.3390/biom12081076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Atomic-resolution structural studies of membrane-associated proteins and peptides in a membrane environment are important to fully understand their biological function and the roles played by them in the pathology of many diseases. However, the complexity of the cell membrane has severely limited the application of commonly used biophysical and biochemical techniques. Recent advancements in NMR spectroscopy and cryoEM approaches and the development of novel membrane mimetics have overcome some of the major challenges in this area. For example, the development of a variety of lipid-nanodiscs has enabled stable reconstitution and structural and functional studies of membrane proteins. In particular, the ability of synthetic amphipathic polymers to isolate membrane proteins directly from the cell membrane, along with the associated membrane components such as lipids, without the use of a detergent, has opened new avenues to study the structure and function of membrane proteins using a variety of biophysical and biological approaches. This review article is focused on covering the various polymers and approaches developed and their applications for the functional reconstitution and structural investigation of membrane proteins. The unique advantages and limitations of the use of synthetic polymers are also discussed.
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Affiliation(s)
- Bankala Krishnarjuna
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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20
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Piper SJ, Johnson RM, Wootten D, Sexton PM. Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM. Chem Rev 2022; 122:13989-14017. [PMID: 35849490 DOI: 10.1021/acs.chemrev.1c00837] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.
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Affiliation(s)
- Sarah J Piper
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Rachel M Johnson
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Denise Wootten
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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21
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Liin SI. ASIC3, a proton-gated ion channel with preference for polyunsaturated lipids with specific headgroup and tail properties. J Gen Physiol 2022; 154:e202213171. [PMID: 35583814 PMCID: PMC9121178 DOI: 10.1085/jgp.202213171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Commentary highlighting valuable mechanistic insights provided by Klipp and Bankston on ASIC3 regulation by lipids.
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Affiliation(s)
- Sara I. Liin
- Department of Biomedical and Clinical Sciences, Division of Neurobiology, Linköping University, Linköping, Sweden
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22
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Klipp RC, Bankston JR. Structural determinants of acid-sensing ion channel potentiation by single chain lipids. J Gen Physiol 2022; 154:e202213156. [PMID: 35583813 PMCID: PMC9120901 DOI: 10.1085/jgp.202213156] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/02/2022] [Indexed: 01/07/2023] Open
Abstract
Acid-sensing ion channels (ASICs) are sensitized to activation by inflammatory mediators such as the polyunsaturated fatty acid (PUFA) arachidonic acid (AA). Previous work has shown that AA can potentiate ASIC currents at subsaturating proton concentrations, but the structural mechanisms of this change in gating are not understood. Here we show that PUFAs cause multiple gating changes in ASIC3, including shifting the pH dependence of activation, slowing the rate of desensitization, and increasing the current even at a saturating pH. The impact on gating depends on the nature of both the head and tail of the lipid, with the head group structure primarily determining the magnitude of the effect on the channel. An N-acyl amino acid (NAAA), arachidonyl glycine (AG), is such a strong regulator that it can act as a ligand at neutral pH. Mutation of an arginine in the outer segment of TM1 (R64) eliminated the effect of docosahexaenoic acid (DHA) even at high concentrations, suggesting a potential interaction site for the lipid on the channel. Our results suggest a model in which PUFAs bind to ASICs via both their tail group and an electrostatic interaction between the negatively charged PUFA head group and the positively charged arginine side chain. These data provide the first look at the structural features of lipids that are important for modulating ASICs and suggest a potential binding site for PUFAs on the channel.
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Affiliation(s)
- Robert C. Klipp
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - John R. Bankston
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO
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23
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On the quest of small molecules that can mimic Psalmotoxin-1, the most powerful peptidic modulator of the acid sensing channel ASIC1a. Struct Chem 2022. [DOI: 10.1007/s11224-021-01826-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Vallée C, Howlin BJ, Lewis R. Single ion free energy calculation in ASIC1: the importance of the HG loop. Phys Chem Chem Phys 2022; 24:13824-13830. [PMID: 35616206 DOI: 10.1039/d2cp01563c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acid Sensing Ion Channels (ASICs) are one of the most studied channels of the Epithelial Sodium Channel/Degenerin (ENaC/DEG) superfamily. They are responsible for excitatory responses following acidification of the extracellular medium and are involved in several important physiological roles. The ASIC1 subunit can form a functional homotrimeric channel and its structure is currently the most characterised of the whole ENaC/DEG family. Here we computed the free energy profiles for single ion permeation in two different structures of ASIC1 using both Na+ and Cl- as permeating ions. The first structure is the open structure of the channel from the PDB entry 4NTW, and the second structure is the closed structure with the re-entrant loop which contains the highly conserved 'HG' motif form PDB entry 6VTK. Both structures show cation selective free energy profiles, however the profiles of the permeating Na+ differ significantly between the two structures. Indeed, whereas there is only a small energetically favorable (-0.5 kcal mol-1) location for Na+ in the open channel (4NTW) near the end of the pore, we observed a clear ion binding site (-7.8 kcal mol-1) located in between the 'GAS' belt and the 'HG' loop for the channel containing the re-entrant loop (6VTK). Knowing that the 'GAS' motif was determined as the selectivity filter, our results support previous observations while addressing the importance of the 'HG' motif for the interactions between the pore and the permeating cations.
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Affiliation(s)
- Cédric Vallée
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK. .,Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK.,School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - Brendan J Howlin
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK. .,Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Rebecca Lewis
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK. .,School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
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25
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Zhang L, Wang X, Chen J, Kleyman TR, Sheng S. Accessibility of ENaC extracellular domain central core residues. J Biol Chem 2022; 298:101860. [PMID: 35339489 PMCID: PMC9052164 DOI: 10.1016/j.jbc.2022.101860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 11/20/2022] Open
Abstract
The epithelial Na+ channel (ENaC)/degenerin family has a similar extracellular architecture, where specific regulatory factors interact and alter channel gating behavior. The extracellular palm domain serves as a key link to the channel pore. In this study, we used cysteine-scanning mutagenesis to assess the functional effects of Cys-modifying reagents on palm domain β10 strand residues in mouse ENaC. Of the 13 ENaC α subunit mutants with Cys substitutions examined, only mutants at sites in the proximal region of β10 exhibited changes in channel activity in response to methanethiosulfonate reagents. Additionally, Cys substitutions at three proximal sites of β and γ subunit β10 strands also rendered mutant channels methanethiosulfonate-responsive. Moreover, multiple Cys mutants were activated by low concentrations of thiophilic Cd2+. Using the Na+ self-inhibition response to assess ENaC gating behavior, we identified four α, two β, and two γ subunit β10 strand mutations that changed the Na+ self-inhibition response. Our results suggest that the proximal regions of β10 strands in all three subunits are accessible to small aqueous compounds and Cd2+ and have a role in modulating ENaC gating. These results are consistent with a structural model of mouse ENaC that predicts the presence of aqueous tunnels adjacent to the proximal part of β10 and with previously resolved structures of a related family member where palm domain structural transitions were observed with channels in an open or closed state.
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Affiliation(s)
- Lei Zhang
- Departments of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xueqi Wang
- Departments of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jingxin Chen
- Departments of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Thomas R Kleyman
- Departments of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| | - Shaohu Sheng
- Departments of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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26
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Abd El-Aziz TM, Kaur A, Shapiro MS, Stockand JD, Archer CR. Optogenetic Control of PIP2 Interactions Shaping ENaC Activity. Int J Mol Sci 2022; 23:ijms23073884. [PMID: 35409240 PMCID: PMC8998630 DOI: 10.3390/ijms23073884] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
The activity of the epithelial Na+ Channel (ENaC) is strongly dependent on the membrane phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2). PIP2 binds two distinct cationic clusters within the N termini of β- and γ-ENaC subunits (βN1 and γN2). The affinities of these sites were previously determined using short synthetic peptides, yet their role in sensitizing ENaC to changes in PIP2 levels in the cellular system is not well established. We addressed this question by comparing the effects of PIP2 depletion and recovery on ENaC channel activity and intracellular Na+ levels [Na+]i. We tested effects on ENaC activity with mutations to the PIP2 binding sites using the optogenetic system CIBN/CRY2-OCRL to selectively deplete PIP2. We monitored changes of [Na+]i by measuring the fluorescent Na+ indicator, CoroNa Green AM, and changes in channel activity by performing patch clamp electrophysiology. Whole cell patch clamp measurements showed a complete lack of response to PIP2 depletion and recovery in ENaC with mutations to βN1 or γN2 or both sites, compared to wild type ENaC. Whereas mutant βN1 also had no change in CoroNa Green fluorescence in response to PIP2 depletion, γN2 did have reduced [Na+]i, which was explained by having shorter CoroNa Green uptake and half-life. These results suggest that CoroNa Green measurements should be interpreted with caution. Importantly, the electrophysiology results show that the βN1 and γN2 sites on ENaC are each necessary to permit maximal ENaC activity in the presence of PIP2.
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Affiliation(s)
- Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78228, USA; (T.M.A.E.-A.); (M.S.S.); (J.D.S.)
- Faculty of Science, Zoology Department, Minia University, El-Minia 61519, Egypt
| | - Amanpreet Kaur
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA;
| | - Mark S. Shapiro
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78228, USA; (T.M.A.E.-A.); (M.S.S.); (J.D.S.)
| | - James D. Stockand
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78228, USA; (T.M.A.E.-A.); (M.S.S.); (J.D.S.)
| | - Crystal R. Archer
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78228, USA; (T.M.A.E.-A.); (M.S.S.); (J.D.S.)
- Correspondence:
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27
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Orekhov PS, Bozdaganyan ME, Voskoboynikova N, Mulkidjanian AY, Karlova MG, Yudenko A, Remeeva A, Ryzhykau YL, Gushchin I, Gordeliy VI, Sokolova OS, Steinhoff HJ, Kirpichnikov MP, Shaitan KV. Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review. NANOMATERIALS 2022; 12:nano12030361. [PMID: 35159706 PMCID: PMC8838559 DOI: 10.3390/nano12030361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene–maleic acid (SMA), diisobutylene–maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.
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Affiliation(s)
- Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
- Correspondence: (P.S.O.); (K.V.S.)
| | - Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Natalia Voskoboynikova
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Karlova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Valentin I. Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Correspondence: (P.S.O.); (K.V.S.)
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28
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Acid-Sensing Ion Channels in Glial Cells. MEMBRANES 2022; 12:membranes12020119. [PMID: 35207041 PMCID: PMC8878633 DOI: 10.3390/membranes12020119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/29/2021] [Accepted: 01/17/2022] [Indexed: 12/13/2022]
Abstract
Acid-sensing ion channels (ASICs) are proton-gated cation channels and key mediators of responses to neuronal injury. ASICs exhibit unique patterns of distribution in the brain, with high expression in neurons and low expression in glial cells. While there has been a lot of focus on ASIC in neurons, less is known about the roles of ASICs in glial cells. ASIC1a is expressed in astrocytes and might contribute to synaptic transmission and long-term potentiation. In oligodendrocytes, constitutive activation of ASIC1a participates in demyelinating diseases. ASIC1a, ASIC2a, and ASIC3, found in microglial cells, could mediate the inflammatory response. Under pathological conditions, ASIC dysregulation in glial cells can contribute to disease states. For example, activation of astrocytic ASIC1a may worsen neurodegeneration and glioma staging, activation of microglial ASIC1a and ASIC2a may perpetuate ischemia and inflammation, while oligodendrocytic ASIC1a might be involved in multiple sclerosis. This review concentrates on the unique ASIC components in each of the glial cells and integrates these glial-specific ASICs with their physiological and pathological conditions. Such knowledge provides promising evidence for targeting of ASICs in individual glial cells as a therapeutic strategy for a diverse range of conditions.
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29
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Chen Z, Lin S, Xie T, Lin JM, Canessa CM. A flexible GAS belt responds to pore mutations changing the ion selectivity of proton-gated channels. J Gen Physiol 2022; 154:212811. [PMID: 34766968 PMCID: PMC8594623 DOI: 10.1085/jgp.202112978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/18/2021] [Accepted: 10/18/2021] [Indexed: 11/20/2022] Open
Abstract
Proton-gated ion channels conduct mainly Na+ to induce postsynaptic membrane depolarization. Finding the determinants of ion selectivity requires knowledge of the pore structure in the open conformation, but such information is not yet available. Here, the open conformation of the hASIC1a channel was computationally modeled, and functional effects of pore mutations were analyzed in light of the predicted structures. The open pore structure shows two constrictions of similar diameter formed by the backbone of the GAS belt and, right beneath it, by the side chains of H28 from the reentrant loop. Models of nonselective mutant channels, but not those that maintain ion selectivity, predict enlargement of the GAS belt, suggesting that this motif is quite flexible and that the loss of stabilizing interactions in the central pore leads to changes in size/shape of the belt. Our results are consistent with the "close-fit" mechanism governing selectivity of hASIC1a, wherein the backbone of the GAS substitutes at least part of the hydration shell of a permeant ion to enable crossing the pore constriction.
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Affiliation(s)
- Zhuyuan Chen
- Department of Basic Sciences, Tsinghua University School of Medicine, Beijing, China
| | - Sheng Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
| | - Tianze Xie
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
| | - Cecilia M Canessa
- Department of Basic Sciences, Tsinghua University School of Medicine, Beijing, China.,Cellular and Molecular Physiology, Yale University, New Haven, CT
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30
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Broadbent L, Depping P, Lodé A, Vaitsopoulou A, Hardy D, Ayub H, Mitchell-White J, Kerr ID, Goddard AD, Bill RM, Rothnie AJ. Detergent-Free Membrane Protein Purification Using SMA Polymer. Methods Mol Biol 2022; 2507:389-404. [PMID: 35773594 DOI: 10.1007/978-1-0716-2368-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
One of the big challenges for the study of structure and function of membrane proteins is the need to extract them from the membrane. Traditionally this was achieved using detergents which disrupt the membrane and form a micelle around the protein, but this can cause issues with protein function and/or stability. In 2009 an alternative approach was reported, using styrene maleic acid (SMA) copolymer to extract small discs of lipid bilayer encapsulated by the polymer and termed SMALPs (SMA lipid particles). Since then this approach has been shown to work for a range of different proteins from many different expression systems. It allows the extraction and purification of a target protein while maintaining a lipid bilayer environment. Recently this has led to several new high-resolution structures and novel insights to function. As with any method there are some limitations and issues to be aware of. Here we describe a standard protocol for preparation of the polymer and its use for membrane protein purification, and also include details of typical challenges that may be encountered and possible ways to address those.
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Affiliation(s)
- Luke Broadbent
- College of Health & Life Sciences, Aston University, Birmingham, UK
| | - Peer Depping
- College of Health & Life Sciences, Aston University, Birmingham, UK
| | - Alexis Lodé
- College of Health & Life Sciences, Aston University, Birmingham, UK
| | | | - David Hardy
- College of Health & Life Sciences, Aston University, Birmingham, UK
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Hoor Ayub
- College of Health & Life Sciences, Aston University, Birmingham, UK
- Faculty of Health & Life Sciences, Coventry University, Coventry, UK
| | - James Mitchell-White
- School of Life Sciences, University of Nottingham Medical School, Queen's Medical Centre, Nottingham, UK
| | - Ian D Kerr
- School of Life Sciences, University of Nottingham Medical School, Queen's Medical Centre, Nottingham, UK
| | - Alan D Goddard
- College of Health & Life Sciences, Aston University, Birmingham, UK
| | - Roslyn M Bill
- College of Health & Life Sciences, Aston University, Birmingham, UK
| | - Alice J Rothnie
- College of Health & Life Sciences, Aston University, Birmingham, UK.
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31
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Dimitrova VS, Song S, Karagiaridi A, Marand A, Pinkett HW. Detergent Alternatives: Membrane Protein Purification Using Synthetic Nanodisc Polymers. Methods Mol Biol 2022; 2507:375-387. [PMID: 35773593 PMCID: PMC9361707 DOI: 10.1007/978-1-0716-2368-8_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of styrene maleic acid (SMA) and diisobutylene maleic acid (DIBMA) copolymers provides an alternative to traditional detergent extraction of integral membrane proteins. By inserting into the membrane, these polymers can extract membrane proteins along with lipids in the form of native nanodiscs made by poly(styrene co-maleic anhydride) derivatives. Unlike detergent solubilization, where membrane proteins may lose annular lipids necessary for proper folding and stability, native nanodiscs allow for proteins to reside in the natural lipid environment. In addition, polymer-based nanodiscs can be purified using common chromatography methods similar to protocols established with detergent solubilization purification. Here we describe the solubilization screening and purification of an integral membrane protein using several commercial copolymers.
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Affiliation(s)
| | - Saemee Song
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Department of Infectious Diseases Research, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | | | - Anika Marand
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Heather W Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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32
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Hawkins OP, Jahromi CPT, Gulamhussein AA, Nestorow S, Bahra T, Shelton C, Owusu-Mensah QK, Mohiddin N, O'Rourke H, Ajmal M, Byrnes K, Khan M, Nahar NN, Lim A, Harris C, Healy H, Hasan SW, Ahmed A, Evans L, Vaitsopoulou A, Akram A, Williams C, Binding J, Thandi RK, Joby A, Guest A, Tariq MZ, Rasool F, Cavanagh L, Kang S, Asparuhov B, Jestin A, Dafforn TR, Simms J, Bill RM, Goddard AD, Rothnie AJ. Membrane protein extraction and purification using partially-esterified SMA polymers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183758. [PMID: 34480878 PMCID: PMC8484863 DOI: 10.1016/j.bbamem.2021.183758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/16/2021] [Accepted: 08/24/2021] [Indexed: 12/15/2022]
Abstract
Styrene maleic acid (SMA) polymers have proven to be very successful for the extraction of membrane proteins, forming SMA lipid particles (SMALPs), which maintain a lipid bilayer around the membrane protein. SMALP-encapsulated membrane proteins can be used for functional and structural studies. The SMALP approach allows retention of important protein-annular lipid interactions, exerts lateral pressure, and offers greater stability than traditional detergent solubilisation. However, SMA polymer does have some limitations, including a sensitivity to divalent cations and low pH, an absorbance spectrum that overlaps with many proteins, and possible restrictions on protein conformational change. Various modified polymers have been developed to try to overcome these challenges, but no clear solution has been found. A series of partially-esterified variants of SMA (SMA 2625, SMA 1440 and SMA 17352) has previously been shown to be highly effective for solubilisation of plant and cyanobacterial thylakoid membranes. It was hypothesised that the partial esterification of maleic acid groups would increase tolerance to divalent cations. Therefore, these partially-esterified polymers were tested for the solubilisation of lipids and membrane proteins, and their tolerance to magnesium ions. It was found that all partially esterified polymers were capable of solubilising and purifying a range of membrane proteins, but the yield of protein was lower with SMA 1440, and the degree of purity was lower for both SMA 1440 and SMA 17352. SMA 2625 performed comparably to SMA 2000. SMA 1440 also showed an increased sensitivity to divalent cations. Thus, it appears the interactions between SMA and divalent cations are more complex than proposed and require further investigation.
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Affiliation(s)
- Olivia P Hawkins
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | | | - Aiman A Gulamhussein
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Stephanie Nestorow
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Taranpreet Bahra
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Christian Shelton
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Quincy K Owusu-Mensah
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Naadiya Mohiddin
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Hannah O'Rourke
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Mariam Ajmal
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Kara Byrnes
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Madiha Khan
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Nila N Nahar
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Arcella Lim
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Cassandra Harris
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Hannah Healy
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Syeda W Hasan
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Asma Ahmed
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Lora Evans
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Afroditi Vaitsopoulou
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Aneel Akram
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Chris Williams
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Johanna Binding
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Rumandeep K Thandi
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Aswathy Joby
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Ashley Guest
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Mohammad Z Tariq
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Farah Rasool
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Luke Cavanagh
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Simran Kang
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Biser Asparuhov
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Aleksandr Jestin
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - John Simms
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Roslyn M Bill
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alan D Goddard
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alice J Rothnie
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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33
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Rook ML, Ananchenko A, Musgaard M, MacLean DM. Molecular Investigation of Chicken Acid-Sensing Ion Channel 1 β11-12 Linker Isomerization and Channel Kinetics. Front Cell Neurosci 2021; 15:761813. [PMID: 34924957 PMCID: PMC8675884 DOI: 10.3389/fncel.2021.761813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Structures of the trimeric acid-sensing ion channel have been solved in the resting, toxin-bound open and desensitized states. Within the extracellular domain, there is little difference between the toxin-bound open state and the desensitized state. The main exception is that a loop connecting the 11th and 12th β-strand, just two amino acid residues long, undergoes a significant and functionally critical re-orientation or flipping between the open and desensitized conformations. Here we investigate how specific interactions within the surrounding area influence linker stability in the "flipped" desensitized state using all-atom molecular dynamics simulations. An inherent challenge is bringing the relatively slow channel desensitization and recovery processes (in the milliseconds to seconds) within the time window of all-atom simulations (hundreds of nanoseconds). To accelerate channel behavior, we first identified the channel mutations at either the Leu414 or Asn415 position with the fastest recovery kinetics followed by molecular dynamics simulations of these mutants in a deprotonated state, accelerating recovery. By mutating one residue in the loop and examining the evolution of interactions in the neighbor, we identified a novel electrostatic interaction and validated prior important interactions. Subsequent functional analysis corroborates these findings, shedding light on the molecular factors controlling proton-mediated transitions between functional states of the channel. Together, these data suggest that the flipped loop in the desensitized state is stabilized by interactions from surrounding regions keeping both L414 and N415 in place. Interestingly, very few mutations in the loop allow for equivalent channel kinetics and desensitized state stability. The high degree of sequence conservation in this region therefore indicates that the stability of the ASIC desensitized state is under strong selective pressure and underlines the physiological importance of desensitization.
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Affiliation(s)
- Matthew L. Rook
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, United States
| | - Anna Ananchenko
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Maria Musgaard
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - David M. MacLean
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, United States
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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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35
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Vallée C, Howlin B, Lewis R. Ion Selectivity in the ENaC/DEG Family: A Systematic Review with Supporting Analysis. Int J Mol Sci 2021; 22:ijms222010998. [PMID: 34681656 PMCID: PMC8536179 DOI: 10.3390/ijms222010998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/16/2022] Open
Abstract
The Epithelial Sodium Channel/Degenerin (ENaC/DEG) family is a superfamily of sodium-selective channels that play diverse and important physiological roles in a wide variety of animal species. Despite their differences, they share a high homology in the pore region in which the ion discrimination takes place. Although ion selectivity has been studied for decades, the mechanisms underlying this selectivity for trimeric channels, and particularly for the ENaC/DEG family, are still poorly understood. This systematic review follows PRISMA guidelines and aims to determine the main components that govern ion selectivity in the ENaC/DEG family. In total, 27 papers from three online databases were included according to specific exclusion and inclusion criteria. It was found that the G/SxS selectivity filter (glycine/serine, non-conserved residue, serine) and other well conserved residues play a crucial role in ion selectivity. Depending on the ion type, residues with different properties are involved in ion permeability. For lithium against sodium, aromatic residues upstream of the selectivity filter seem to be important, whereas for sodium against potassium, negatively charged residues downstream of the selectivity filter seem to be important. This review provides new perspectives for further studies to unravel the mechanisms of ion selectivity.
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Affiliation(s)
- Cédric Vallée
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK; (C.V.); (B.H.)
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - Brendan Howlin
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK; (C.V.); (B.H.)
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Rebecca Lewis
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK; (C.V.); (B.H.)
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
- Correspondence:
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Sheikh ZP, Wulf M, Friis S, Althaus M, Lynagh T, Pless SA. The M1 and pre-M1 segments contribute differently to ion selectivity in ASICs and ENaCs. J Gen Physiol 2021; 153:212604. [PMID: 34436511 PMCID: PMC8404453 DOI: 10.1085/jgp.202112899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/26/2021] [Indexed: 11/20/2022] Open
Abstract
The ability to discriminate between different ionic species, termed ion selectivity, is a key feature of ion channels and forms the basis for their physiological function. Members of the degenerin/epithelial sodium channel (DEG/ENaC) superfamily of trimeric ion channels are typically sodium selective, but to a surprisingly variable degree. While acid-sensing ion channels (ASICs) are weakly sodium selective (sodium:potassium ratio ∼10:1), ENaCs show a remarkably high preference for sodium over potassium (>500:1). This discrepancy may be expected to originate from differences in the pore-lining second transmembrane segment (M2). However, these show a relatively high degree of sequence conservation between ASICs and ENaCs, and previous functional and structural studies could not unequivocally establish that differences in M2 alone can account for the disparate degrees of ion selectivity. By contrast, surprisingly little is known about the contributions of the first transmembrane segment (M1) and the preceding pre-M1 region. In this study, we used conventional and noncanonical amino acid-based mutagenesis in combination with a variety of electrophysiological approaches to show that the pre-M1 and M1 regions of mASIC1a channels are major determinants of ion selectivity. Mutational investigations of the corresponding regions in hENaC show that these regions contribute less to ion selectivity, despite affecting ion conductance. In conclusion, our work suggests that the remarkably different degrees of sodium selectivity in ASICs and ENaCs are achieved through different mechanisms. These results further highlight how M1 and pre-M1 are likely to differentially affect pore structure in these related channels.
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Affiliation(s)
- Zeshan P Sheikh
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Wulf
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | | | - Mike Althaus
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Timothy Lynagh
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Stephan A Pless
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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Methods for the solubilisation of membrane proteins: the micelle-aneous world of membrane protein solubilisation. Biochem Soc Trans 2021; 49:1763-1777. [PMID: 34415288 PMCID: PMC8421053 DOI: 10.1042/bst20210181] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
The solubilisation of membrane proteins (MPs) necessitates the overlap of two contradictory events; the extraction of MPs from their native lipid membranes and their subsequent stabilisation in aqueous environments. Whilst the current myriad of membrane mimetic systems provide a range of modus operandi, there are no golden rules for selecting the optimal pipeline for solubilisation of a specific MP hence a miscellaneous approach must be employed balancing both solubilisation efficiency and protein stability. In recent years, numerous diverse lipid membrane mimetic systems have been developed, expanding the pool of available solubilisation strategies. This review provides an overview of recent developments in the membrane mimetic field, with particular emphasis placed upon detergents, polymer-based nanodiscs and amphipols, highlighting the latest reagents to enter the toolbox of MP research.
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39
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Wu Y, Chen Z, Sigworth FJ, Canessa CM. Structure and analysis of nanobody binding to the human ASIC1a ion channel. eLife 2021; 10:67115. [PMID: 34319232 PMCID: PMC8318589 DOI: 10.7554/elife.67115] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
ASIC1a is a proton-gated sodium channel involved in modulation of pain, fear, addiction, and ischemia-induced neuronal injury. We report isolation and characterization of alpaca-derived nanobodies (Nbs) that specifically target human ASIC1a. Cryo-electron microscopy of the human ASIC1a channel at pH 7.4 in complex with one of these, Nb.C1, yielded a structure at 2.9 Å resolution. It is revealed that Nb.C1 binds to a site overlapping with that of the Texas coral snake toxin (MitTx1) and the black mamba venom Mambalgin-1; however, the Nb.C1-binding site does not overlap with that of the inhibitory tarantula toxin psalmotoxin-1 (PcTx1). Fusion of Nb.C1 with PcTx1 in a single polypeptide markedly enhances the potency of PcTx1, whereas competition of Nb.C1 and MitTx1 for binding reduces channel activation by the toxin. Thus, Nb.C1 is a molecular tool for biochemical and structural studies of hASIC1a; a potential antidote to the pain-inducing component of coral snake bite; and a candidate to potentiate PcTx1-mediated inhibition of hASIC1a in vivo for therapeutic applications.
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Affiliation(s)
- Yangyu Wu
- Basic Sciences Department, Tsinghua University School of Medicine, Beijing, China
| | - Zhuyuan Chen
- Basic Sciences Department, Tsinghua University School of Medicine, Beijing, China
| | - Fred J Sigworth
- Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, United States
| | - Cecilia M Canessa
- Basic Sciences Department, Tsinghua University School of Medicine, Beijing, China.,Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, United States
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40
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Couch T, Berger K, Kneisley DL, McCullock TW, Kammermeier P, Maclean DM. Topography and motion of acid-sensing ion channel intracellular domains. eLife 2021; 10:68955. [PMID: 34292153 PMCID: PMC8341984 DOI: 10.7554/elife.68955] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/21/2021] [Indexed: 01/12/2023] Open
Abstract
Acid-sensing ion channels (ASICs) are trimeric cation-selective channels activated by decreases in extracellular pH. The intracellular N and C terminal tails of ASIC1 influence channel gating, trafficking, and signaling in ischemic cell death. Despite several X-ray and cryo-EM structures of the extracellular and transmembrane segments of ASIC1, these important intracellular tails remain unresolved. Here, we describe the coarse topography of the chicken ASIC1 intracellular domains determined by fluorescence resonance energy transfer (FRET), measured using either fluorescent lifetime imaging or patch clamp fluorometry. We find the C terminal tail projects into the cytosol by approximately 35 Å and that the N and C tails from the same subunits are closer than adjacent subunits. Using pH-insensitive fluorescent proteins, we fail to detect any relative movement between the N and C tails upon extracellular acidification but do observe axial motions of the membrane proximal segments toward the plasma membrane. Taken together, our study furnishes a coarse topographic map of the ASIC intracellular domains while providing directionality and context to intracellular conformational changes induced by extracellular acidification.
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Affiliation(s)
- Tyler Couch
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, Reno, United States
| | - Kyle Berger
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
| | - Dana L Kneisley
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
| | - Tyler W McCullock
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, Reno, United States
| | - Paul Kammermeier
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
| | - David M Maclean
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
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41
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Guo Y. Detergent-free systems for structural studies of membrane proteins. Biochem Soc Trans 2021; 49:1361-1374. [PMID: 34110369 PMCID: PMC8276625 DOI: 10.1042/bst20201080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/03/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022]
Abstract
Membrane proteins play vital roles in living organisms, serving as targets for most currently prescribed drugs. Membrane protein structural biology aims to provide accurate structural information to understand their mechanisms of action. The advance of membrane protein structural biology has primarily relied on detergent-based methods over the past several decades. However, detergent-based approaches have significant drawbacks because detergents often damage the native protein-lipid interactions, which are often crucial for maintaining the natural structure and function of membrane proteins. Detergent-free methods recently have emerged as alternatives with a great promise, e.g. for high-resolution structure determinations of membrane proteins in their native cell membrane lipid environments. This minireview critically examines the current status of detergent-free methods by a comparative analysis of five groups of membrane protein structures determined using detergent-free and detergent-based methods. This analysis reveals that current detergent-free systems, such as the styrene-maleic acid lipid particles (SMALP), the diisobutyl maleic acid lipid particles (DIBMALP), and the cycloalkane-modified amphiphile polymer (CyclAPol) technologies are not better than detergent-based approaches in terms of maintenance of native cell membrane lipids on the transmembrane domain and high-resolution structure determination. However, another detergent-free technology, the native cell membrane nanoparticles (NCMN) system, demonstrated improved maintenance of native cell membrane lipids with the studied membrane proteins, and produced particles that were suitable for high-resolution structural analysis. The ongoing development of new membrane-active polymers and their optimization will facilitate the maturation of these new detergent-free systems.
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Affiliation(s)
- Youzhong Guo
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
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42
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Overduin M, Trieber C, Prosser RS, Picard LP, Sheff JG. Structures and Dynamics of Native-State Transmembrane Protein Targets and Bound Lipids. MEMBRANES 2021; 11:451. [PMID: 34204456 PMCID: PMC8235241 DOI: 10.3390/membranes11060451] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023]
Abstract
Membrane proteins work within asymmetric bilayers of lipid molecules that are critical for their biological structures, dynamics and interactions. These properties are lost when detergents dislodge lipids, ligands and subunits, but are maintained in native nanodiscs formed using styrene maleic acid (SMA) and diisobutylene maleic acid (DIBMA) copolymers. These amphipathic polymers allow extraction of multicomponent complexes of post-translationally modified membrane-bound proteins directly from organ homogenates or membranes from diverse types of cells and organelles. Here, we review the structures and mechanisms of transmembrane targets and their interactions with lipids including phosphoinositides (PIs), as resolved using nanodisc systems and methods including cryo-electron microscopy (cryo-EM) and X-ray diffraction (XRD). We focus on therapeutic targets including several G protein-coupled receptors (GPCRs), as well as ion channels and transporters that are driving the development of next-generation native nanodiscs. The design of new synthetic polymers and complementary biophysical tools bodes well for the future of drug discovery and structural biology of native membrane:protein assemblies (memteins).
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada;
| | - Catharine Trieber
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada;
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON L5L 1C6, Canada; (R.S.P.); (L.-P.P.)
| | - Louis-Philippe Picard
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON L5L 1C6, Canada; (R.S.P.); (L.-P.P.)
| | - Joey G. Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON K1A 0R6, Canada;
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43
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Biological insights from SMA-extracted proteins. Biochem Soc Trans 2021; 49:1349-1359. [PMID: 34110372 PMCID: PMC8286838 DOI: 10.1042/bst20201067] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/08/2023]
Abstract
In the twelve years since styrene maleic acid (SMA) was first used to extract and purify a membrane protein within a native lipid bilayer, this technological breakthrough has provided insight into the structural and functional details of protein–lipid interactions. Most recently, advances in cryo-EM have demonstrated that SMA-extracted membrane proteins are a rich-source of structural data. For example, it has been possible to resolve the details of annular lipids and protein–protein interactions within complexes, the nature of lipids within central cavities and binding pockets, regions involved in stabilising multimers, details of terminal residues that would otherwise remain unresolved and the identification of physiologically relevant states. Functionally, SMA extraction has allowed the analysis of membrane proteins that are unstable in detergents, the characterization of an ultrafast component in the kinetics of electron transfer that was not possible in detergent-solubilised samples and quantitative, real-time measurement of binding assays with low concentrations of purified protein. While the use of SMA comes with limitations such as its sensitivity to low pH and divalent cations, its major advantage is maintenance of a protein's lipid bilayer. This has enabled researchers to view and assay proteins in an environment close to their native ones, leading to new structural and mechanistic insights.
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44
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Rook ML, Miaro M, Couch T, Kneisley DL, Musgaard M, MacLean DM. Mutation of a conserved glutamine residue does not abolish desensitization of acid-sensing ion channel 1. THE JOURNAL OF GENERAL PHYSIOLOGY 2021; 153:212203. [PMID: 34061161 PMCID: PMC8167889 DOI: 10.1085/jgp.202012855] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 05/13/2021] [Indexed: 12/14/2022]
Abstract
Desensitization is a common feature of ligand-gated ion channels, although the molecular cause varies widely between channel types. Mutations that greatly reduce or nearly abolish desensitization have been described for many ligand-gated ion channels, including glutamate, GABA, glycine, and nicotinic receptors, but not for acid-sensing ion channels (ASICs) until recently. Mutating Gln276 to a glycine (Q276G) in human ASIC1a was reported to mostly abolish desensitization at both the macroscopic and the single channel levels, potentially providing a valuable tool for subsequent studies. However, we find that in both human and chicken ASIC1, the effect of Q276G is modest. In chicken ASIC1, the equivalent Q277G slightly reduces desensitization when using pH 6.5 as a stimulus but desensitizes, essentially like wild-type, when using more acidic pH values. In addition, steady-state desensitization is intact, albeit right-shifted, and recovery from desensitization is accelerated. Molecular dynamics simulations indicate that the Gln277 side chain participates in a hydrogen bond network that might stabilize the desensitized conformation. Consistent with this, destabilizing this network with the Q277N or Q277L mutations largely mimics the Q277G phenotype. In human ASIC1a, the Q276G mutation also reduces desensitization, but not to the extent reported previously. Interestingly, the kinetic consequences of Q276G depend on the human variant used. In the common G212 variant, Q276G slows desensitization, while in the rare D212 variant desensitization accelerates. Our data reveal that while the Q/G mutation does not abolish or substantially impair desensitization as previously reported, it does point to unexpected differences between chicken and human ASICs and the need for careful scrutiny before using this mutation in future studies.
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Affiliation(s)
- Matthew L Rook
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
| | - Megan Miaro
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Tyler Couch
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
| | - Dana L Kneisley
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
| | - Maria Musgaard
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - David M MacLean
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
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45
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Abstract
The Epithelial Na+ Channel, ENaC, comprised of 3 subunits (αβγ, or sometimes δβγENaC), plays a critical role in regulating salt and fluid homeostasis in the body. It regulates fluid reabsorption into the blood stream from the kidney to control blood volume and pressure, fluid absorption in the lung to control alveolar fluid clearance at birth and maintenance of normal airway surface liquid throughout life, and fluid absorption in the distal colon and other epithelial tissues. Moreover, recent studies have also revealed a role for sodium movement via ENaC in nonepithelial cells/tissues, such as endothelial cells in blood vessels and neurons. Over the past 25 years, major advances have been made in our understanding of ENaC structure, function, regulation, and role in human disease. These include the recently solved three-dimensional structure of ENaC, ENaC function in various tissues, and mutations in ENaC that cause a hereditary form of hypertension (Liddle syndrome), salt-wasting hypotension (PHA1), or polymorphism in ENaC that contributes to other diseases (such as cystic fibrosis). Moreover, great strides have been made in deciphering the regulation of ENaC by hormones (e.g., the mineralocorticoid aldosterone, glucocorticoids, vasopressin), ions (e.g., Na+ ), proteins (e.g., the ubiquitin-protein ligase NEDD4-2, the kinases SGK1, AKT, AMPK, WNKs & mTORC2, and proteases), and posttranslational modifications [e.g., (de)ubiquitylation, glycosylation, phosphorylation, acetylation, palmitoylation]. Characterization of ENaC structure, function, regulation, and role in human disease, including using animal models, are described in this article, with a special emphasis on recent advances in the field. © 2021 American Physiological Society. Compr Physiol 11:1-29, 2021.
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Affiliation(s)
- Daniela Rotin
- The Hospital for Sick Children, and The University of Toronto, Toronto, Canada
| | - Olivier Staub
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
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46
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Brown CJ, Trieber C, Overduin M. Structural biology of endogenous membrane protein assemblies in native nanodiscs. Curr Opin Struct Biol 2021; 69:70-77. [PMID: 33915422 DOI: 10.1016/j.sbi.2021.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/11/2021] [Accepted: 03/21/2021] [Indexed: 01/17/2023]
Abstract
The advent of amphiphilic copolymers enables integral membrane proteins to be solubilized into stable 10-30 nm native nanodiscs to resolve their multisubunit structures, post-translational modifications, endogenous lipid bilayers, and small molecule ligands. This breakthrough has positioned biological membrane:protein assemblies (memteins) as fundamental functional units of cellular membranes. Herein, we review copolymer design strategies and methods for the characterization of transmembrane proteins within native nanodiscs by cryo-electron microscopy (cryo-EM), transmission electron microscopy, nuclear magnetic resonance spectroscopy, electron paramagnetic resonance, X-ray diffraction, surface plasmon resonance, and mass spectrometry.
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Affiliation(s)
- Chanelle J Brown
- Department of Chemistry and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, USA
| | - Catharine Trieber
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.
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47
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Chen Z, Kuenze G, Meiler J, Canessa CM. An arginine residue in the outer segment of hASIC1a TM1 affects both proton affinity and channel desensitization. J Gen Physiol 2021; 153:211986. [PMID: 33851970 PMCID: PMC8050794 DOI: 10.1085/jgp.202012802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/14/2020] [Accepted: 03/11/2021] [Indexed: 12/25/2022] Open
Abstract
Acid-sensing ion channels (ASICs) respond to changes in pH in the central and peripheral nervous systems and participate in synaptic plasticity and pain perception. Understanding the proton-mediated gating mechanism remains elusive despite the of their structures in various conformational states. We report here that R64, an arginine located in the outer segment of the first transmembrane domain of all three isoforms of mammalian ASICs, markedly impacts the apparent proton affinity of activation and the degree of desensitization from the open and preopen states. Rosetta calculations of free energy changes predict that substitutions of R64 in hASIC1a by aromatic residues destabilize the closed conformation while stabilizing the open conformation. Accordingly, F64 enhances the efficacy of proton-mediated gating of hASIC1a, which increases the apparent pH50 and facilitates channel opening when only one or two subunits are activated. F64 also lengthens the duration of opening events, thus keeping channels open for extended periods of time and diminishing low pH-induced desensitization. Our results indicate that activation of a proton sensor(s) with pH50 equal to or greater than pH 7.2–7.1 opens F64hASIC1a, whereas it induces steady-state desensitization in wildtype channels due to the high energy of activation imposed by R64, which prevents opening of the pore. Together, these findings suggest that activation of a high-affinity proton-sensor(s) and a common gating mechanism may mediate the processes of activation and steady-state desensitization of hASIC1a.
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Affiliation(s)
- Zhuyuan Chen
- Department of Basic Sciences, Tsinghua University School of Medicine, Beijing, China
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN.,Center for Structural Biology, Vanderbilt University, Nashville, TN.,Institute for Drug Discovery, Leipzig University, Leipzig, Germany
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN.,Center for Structural Biology, Vanderbilt University, Nashville, TN.,Department of Pharmacology, Vanderbilt University, Nashville, TN.,Institute for Drug Discovery, Leipzig University, Leipzig, Germany
| | - Cecilia M Canessa
- Department of Basic Sciences, Tsinghua University School of Medicine, Beijing, China.,Cellular and Molecular Physiology, Yale University, New Haven, CT
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48
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Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy. Q Rev Biophys 2021; 54:e6. [PMID: 33785082 DOI: 10.1017/s0033583521000044] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based nanodiscs, lauryl maltoside-neopentyl glycol, glyco-diosgenin, and amphipols (APols) are the most popular surfactants at the vitrification step. Surfactant exchange is frequently used between MP purification and grid preparation, requiring extensive optimization each time the study of a new MP is undertaken. The variety of both the surfactants and experimental approaches used over the past few years bears witness to the need to continue developing innovative surfactants and optimizing conditions for sample preparation. The possibilities offered by novel APols for EM applications are discussed.
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49
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Vullo S, Ambrosio N, Kucera JP, Bignucolo O, Kellenberger S. Kinetic analysis of ASIC1a delineates conformational signaling from proton-sensing domains to the channel gate. eLife 2021; 10:66488. [PMID: 33729158 PMCID: PMC8009679 DOI: 10.7554/elife.66488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/16/2021] [Indexed: 11/13/2022] Open
Abstract
Acid-sensing ion channels (ASICs) are neuronal Na+ channels that are activated by a drop in pH. Their established physiological and pathological roles, involving fear behaviors, learning, pain sensation, and neurodegeneration after stroke, make them promising targets for future drugs. Currently, the ASIC activation mechanism is not understood. Here, we used voltage-clamp fluorometry (VCF) combined with fluorophore-quencher pairing to determine the kinetics and direction of movements. We show that conformational changes with the speed of channel activation occur close to the gate and in more distant extracellular sites, where they may be driven by local protonation events. Further, we provide evidence for fast conformational changes in a pathway linking protonation sites to the channel pore, in which an extracellular interdomain loop interacts via aromatic residue interactions with the upper end of a transmembrane helix and would thereby open the gate.
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Affiliation(s)
- Sabrina Vullo
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Ambrosio
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Jan P Kucera
- Department of Physiology, University of Bern, Bern, Switzerland
| | - Olivier Bignucolo
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland.,SIB, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stephan Kellenberger
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
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50
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Sarkar D, Harms H, Galleano I, Sheikh ZP, Pless SA. Ion channel engineering using protein trans-splicing. Methods Enzymol 2021; 654:19-48. [PMID: 34120713 DOI: 10.1016/bs.mie.2021.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Conventional site-directed mutagenesis and genetic code expansion approaches have been instrumental in providing detailed functional and pharmacological insight into membrane proteins such as ion channels. Recently, this has increasingly been complemented by semi-synthetic strategies, in which part of the protein is generated synthetically. This means a vast range of chemical modifications, including non-canonical amino acids (ncAA), backbone modifications, chemical handles, fluorescent or spectroscopic labels and any combination of these can be incorporated. Among these approaches, protein trans-splicing (PTS) is particularly promising for protein reconstitution in live cells. It relies on one or more split inteins, which can spontaneously and covalently link flanking peptide or protein sequences. Here, we describe the use of PTS and its variant tandem PTS (tPTS) in semi-synthesis of ion channels in Xenopus laevis oocytes to incorporate ncAAs, post-translational modifications or metabolically stable mimics thereof. This strategy has the potential to expand the type and number of modifications in ion channel research.
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Affiliation(s)
- Debayan Sarkar
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Hendrik Harms
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Iacopo Galleano
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Zeshan Pervez Sheikh
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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