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Miles AJ, Drew ED, Wallace BA. DichroIDP: a method for analyses of intrinsically disordered proteins using circular dichroism spectroscopy. Commun Biol 2023; 6:823. [PMID: 37553525 PMCID: PMC10409736 DOI: 10.1038/s42003-023-05178-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 07/25/2023] [Indexed: 08/10/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are comprised of significant numbers of residues that form neither helix, sheet, nor any other canonical type of secondary structure. They play important roles in a broad range of biological processes, such as molecular recognition and signalling, largely due to their chameleon-like ability to change structure from unordered when free in solution to ordered when bound to partner molecules. Circular dichroism (CD) spectroscopy is a widely-used method for characterising protein secondary structures, but analyses of IDPs using CD spectroscopy have suffered because the methods and reference datasets used for the empirical determination of secondary structures do not contain adequate representations of unordered structures. This work describes the creation, validation and testing of a standalone Windows-based application, DichroIDP, and a new reference dataset, IDP175, which is suitable for analyses of proteins containing significant amounts of disordered structure. DichroIDP enables secondary structure determinations of IDPs and proteins containing intrinsically disordered regions.
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Affiliation(s)
- Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck University of London, London, WC1E 7HX, UK
| | - Elliot D Drew
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Zappi, London, NW1 7JN, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck University of London, London, WC1E 7HX, UK.
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D'Avanzo N, Miles AJ, Powl AM, Nichols CG, Wallace BA, O'Reilly AO. The T1-tetramerisation domain of Kv1.2 rescues expression and preserves function of a truncated NaChBac sodium channel. FEBS Lett 2022; 596:772-783. [PMID: 35015304 PMCID: PMC9303580 DOI: 10.1002/1873-3468.14279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022]
Abstract
Cytoplasmic domains frequently promote functional assembly of multimeric ion channels. To investigate structural determinants of this process, we generated the ‘T1‐chimera’ construct of the NaChBac sodium channel by truncating its C‐terminal domain and splicing the T1‐tetramerisation domain of the Kv1.2 channel to the N terminus. Purified T1‐chimera channels were tetrameric, conducted Na+ when reconstituted into proteoliposomes, and were functionally blocked by the drug mibefradil. Both the T1‐chimera and full‐length NaChBac had comparable expression levels in the membrane, whereas a NaChBac mutant lacking a cytoplasmic domain had greatly reduced membrane expression. Our findings support a model whereby bringing the transmembrane regions into close proximity enables their tetramerisation. This phenomenon is found with other channels, and thus, our findings substantiate this as a common assembly mechanism.
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Affiliation(s)
- Nazzareno D'Avanzo
- Department of Pharmacology and Physiology, Université de Montréal, Canada
| | - Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck, University of London, UK
| | - Andrew M Powl
- Institute of Structural and Molecular Biology, Birkbeck, University of London, UK
| | - Colin G Nichols
- Department of Cell Biology and Physiology, Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, USA
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck, University of London, UK
| | - Andrias O O'Reilly
- School of Biological & Environmental Sciences, Liverpool John Moores University, UK
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Gomes Ramalli S, John Miles A, Janes RW, Wallace BA. The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development. J Mol Biol 2022; 434:167441. [PMID: 34999124 DOI: 10.1016/j.jmb.2022.167441] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/19/2021] [Accepted: 01/01/2022] [Indexed: 12/20/2022]
Abstract
The Protein Circular Dichroism Data Bank (PCDDB) [https://pcddb.cryst.bbk.ac.uk] is an established resource for the biological, biophysical, chemical, bioinformatics, and molecular biology communities. It is a freely-accessible repository of validated protein circular dichroism (CD) spectra and associated sample and other metadata, with entries having links to other bioinformatics resources including, amongst others, structure (PDB) and sequence (UniProt) databases, as well as to published papers which produced the data and cite the database entries. It includes primary (unprocessed) and final (processed) spectral data, which are available in both text and pictorial formats, as well as detailed sample and validation information produced for each of the entries. Recently the metadata content associated with each of the entries, as well as the number and structural breadth of the protein components included, have been expanded. The PCDDB includes data on both wild-type and mutant proteins, and because CD studies primarily examine proteins in solution, it also contains examples of the effects of different environments on their structures, plus thermal unfolding/folding series. Methods for both sequence and spectral comparisons are included. The data included in the PCDDB complement results from crystal, cryo-electron microscopy, NMR spectroscopy, bioinformatics characterisations and classifications, and other structural information available for the proteins via links to other databases. The entries in the PCDDB have been used for the development of new analytical methodologies, for interpreting spectral and other biophysical data, and for providing insight into structures and functions of individual soluble and membrane proteins and protein complexes.
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Affiliation(s)
- Sergio Gomes Ramalli
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Andrew John Miles
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Robert W Janes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK.
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Miles AJ, Ramalli SG, Wallace BA. DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data. Protein Sci 2021; 31:37-46. [PMID: 34216059 PMCID: PMC8740839 DOI: 10.1002/pro.4153] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 11/06/2022]
Abstract
Circular dichroism (CD) spectroscopy is a widely‐used method for characterizing the secondary structures of proteins. The well‐established and highly used analysis website, DichroWeb (located at: http://dichroweb.cryst.bbk.ac.uk/html/home.shtml) enables the facile quantitative determination of helix, sheet, and other secondary structure contents of proteins based on their CD spectra. DichroWeb includes a range of reference datasets and algorithms, plus graphical and quantitative methods for determining the quality of the analyses produced. This article describes the current website content, usage and accessibility, as well as the many upgraded features now present in this highly popular tool that was originally created nearly two decades ago.
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Affiliation(s)
- Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck University of London, London, UK
| | - Sergio G Ramalli
- Institute of Structural and Molecular Biology, Birkbeck University of London, London, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck University of London, London, UK
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Groves K, Ashcroft AE, Cryar A, Sula A, Wallace BA, Stocks BB, Burns C, Cooper-Shepherd D, De Lorenzi E, Rodriguez E, Zhang H, Ault JR, Ferguson J, Phillips JJ, Pacholarz K, Thalassinos K, Luckau L, Ashton L, Durrant O, Barran P, Dalby P, Vicedo P, Colombo R, Davis R, Parakra R, Upton R, Hill S, Wood V, Soloviev Z, Quaglia M. Reference Protocol to Assess Analytical Performance of Higher Order Structural Analysis Measurements: Results from an Interlaboratory Comparison. Anal Chem 2021; 93:9041-9048. [PMID: 34165299 DOI: 10.1021/acs.analchem.0c04625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Measurements of protein higher order structure (HOS) provide important information on stability, potency, efficacy, immunogenicity, and biosimilarity of biopharmaceuticals, with a significant number of techniques and methods available to perform these measurements. The comparison of the analytical performance of HOS methods and the standardization of the results is, however, not a trivial task, due to the lack of reference protocols and reference measurement procedures. Here, we developed a protocol to structurally alter and compare samples of somatropin, a recombinant biotherapeutic, and describe the results obtained by using a number of techniques, methods and in different laboratories. This, with the final aim to provide tools and generate a pool of data to compare and benchmark analytical platforms and define method sensitivity to structural changes. Changes in somatropin HOS, induced by the presence of zinc at increasing concentrations, were observed, both globally and at more localized resolution, across many of the methods utilized in this study and with different sensitivities, suggesting the suitability of the protocol to improve understanding of inter- and cross-platform measurement comparability and assess analytical performance as appropriate.
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Affiliation(s)
- K Groves
- National Measurement Laboratory, LGC Ltd. Queens Road, Teddington, Middlesex TW11 0LY, U.K
| | - A E Ashcroft
- Astbury Centre for Structural Molecular Biology & School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - A Cryar
- National Measurement Laboratory, LGC Ltd. Queens Road, Teddington, Middlesex TW11 0LY, U.K
| | - A Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, U.K
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, U.K
| | - B B Stocks
- National Research Council Canada, 1200 Montreal Road, Ottawa K1A 0R6, Canada
| | - C Burns
- Biotherapeutics Division, National Institute for Biological Standards and Control, Blanche Lane South Mimms, Potters Bar, Hertfordshire EN6 3QG, U.K
| | - D Cooper-Shepherd
- National Measurement Laboratory, LGC Ltd. Queens Road, Teddington, Middlesex TW11 0LY, U.K
| | - E De Lorenzi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - E Rodriguez
- UCB Celltech, 216 Bath Road, Slough, Berkshire SL1 3WE, U.K
| | - H Zhang
- Department of Biochemical Engineering, University College London, London WC1E 6BT, U.K
| | - J R Ault
- Astbury Centre for Structural Molecular Biology & School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - J Ferguson
- Biotherapeutics Division, National Institute for Biological Standards and Control, Blanche Lane South Mimms, Potters Bar, Hertfordshire EN6 3QG, U.K
| | - J J Phillips
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, , U.K
| | - K Pacholarz
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - K Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6AR, U.K
| | - L Luckau
- National Measurement Laboratory, LGC Ltd. Queens Road, Teddington, Middlesex TW11 0LY, U.K
| | - L Ashton
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, U.K
| | - O Durrant
- UCB Celltech, 216 Bath Road, Slough, Berkshire SL1 3WE, U.K
| | - P Barran
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - P Dalby
- Department of Biochemical Engineering, University College London, London WC1E 6BT, U.K
| | - P Vicedo
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - R Colombo
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - R Davis
- UCB Celltech, 216 Bath Road, Slough, Berkshire SL1 3WE, U.K
| | - R Parakra
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, , U.K
| | - R Upton
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - S Hill
- National Measurement Laboratory, LGC Ltd. Queens Road, Teddington, Middlesex TW11 0LY, U.K
| | - V Wood
- Department of Biochemical Engineering, University College London, London WC1E 6BT, U.K
| | - Z Soloviev
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6AR, U.K
| | - M Quaglia
- National Measurement Laboratory, LGC Ltd. Queens Road, Teddington, Middlesex TW11 0LY, U.K
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Sula A, Hollingworth D, Ng LCT, Larmore M, DeCaen PG, Wallace BA. A tamoxifen receptor within a voltage-gated sodium channel. Mol Cell 2021; 81:1160-1169.e5. [PMID: 33503406 PMCID: PMC7980221 DOI: 10.1016/j.molcel.2020.12.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 08/24/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022]
Abstract
Voltage-gated sodium channels are targets for many analgesic and antiepileptic drugs whose therapeutic mechanisms and binding sites have been well characterized. We describe the identification of a previously unidentified receptor site within the NavMs voltage-gated sodium channel. Tamoxifen, an estrogen receptor modulator, and its primary and secondary metabolic products bind at the intracellular exit of the channel, which is a site that is distinct from other previously characterized sodium channel drug sites. These compounds inhibit NavMs and human sodium channels with similar potencies and prevent sodium conductance by delaying channel recovery from the inactivated state. This study therefore not only describes the structure and pharmacology of a site that could be leveraged for the development of new drugs for the treatment of sodium channelopathies but may also have important implications for off-target health effects of this widely used therapeutic drug.
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Affiliation(s)
- Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - David Hollingworth
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Leo C T Ng
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Megan Larmore
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Paul G DeCaen
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK.
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Sait LG, Sula A, Ghovanloo MR, Hollingworth D, Ruben PC, Wallace BA. Cannabidiol interactions with voltage-gated sodium channels. eLife 2020; 9:58593. [PMID: 33089780 PMCID: PMC7641581 DOI: 10.7554/elife.58593] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated sodium channels are targets for a range of pharmaceutical drugs developed for the treatment of neurological diseases. Cannabidiol (CBD), the non-psychoactive compound isolated from cannabis plants, was recently approved for treatment of two types of epilepsy associated with sodium channel mutations. This study used high-resolution X-ray crystallography to demonstrate the detailed nature of the interactions between CBD and the NavMs voltage-gated sodium channel, and electrophysiology to show the functional effects of binding CBD to these channels. CBD binds at a novel site at the interface of the fenestrations and the central hydrophobic cavity of the channel. Binding at this site blocks the transmembrane-spanning sodium ion translocation pathway, providing a molecular mechanism for channel inhibition. Modelling studies suggest why the closely-related psychoactive compound tetrahydrocannabinol may not have the same effects on these channels. Finally, comparisons are made with the TRPV2 channel, also recently proposed as a target site for CBD. In summary, this study provides novel insight into a possible mechanism for CBD interactions with sodium channels.
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Affiliation(s)
- Lily Goodyer Sait
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Mohammad-Reza Ghovanloo
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - David Hollingworth
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Peter C Ruben
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
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Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. An intrinsically disordered proteins community for ELIXIR. F1000Res 2019; 8. [PMID: 31824649 PMCID: PMC6880265 DOI: 10.12688/f1000research.20136.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2019] [Indexed: 01/20/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, Institute of Cancer Research, UK, London, SW3 6JB, UK
| | - M Madan Babu
- MRC Laboratory of Molecular Biology,, Cambridge, CB2 0QH, UK
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, 38000, France
| | - Alan Bridge
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Zsuzsanna Dosztanyi
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | | | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Isabella C Felli
- Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - John M Hancock
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Jen Harrow
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Desmond Higgins
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Philippe Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Balint Mészáros
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Marco Necci
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - Christos A Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas (CERTH), Thessalonica, 57001, Greece
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Roberta Pierattelli
- Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Patrick Ruch
- HES-SO/HEG and SIB Text Mining, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Gabriella Rustici
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Pedro Romero
- University of Wisconsin-Madison, Madison, WI, 53706-1544, USA
| | | | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Malvika Sharan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Denis C Shields
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Joel L Sussman
- Department of Structural Biology and the Israel Structural Proteomics, Center (ISPC), Weizmann Institute of Science, Reḥovot, 7610001, Israel
| | | | - Peter Tompa
- VIB Center for Structural Biology (CSB), VIB Flemish Institute for Biotechnology, Brussels, 1050, Belgium
| | - Michael Turewicz
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, GesundheitsCampus 4, Bochum, 44801, Germany
| | - Jiri Vondrasek
- Institute of Organic Chemistry and Biochemistry, CAS, Prague, Czech Republic
| | - Wim F Vranken
- VUB/ULB Interuniversity Institute of Bioinformatics in Brussels and Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Bonnie Ann Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1H 0HA, UK
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
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Kumagai PS, Sousa VK, Donato M, Itri R, Beltramini LM, Araujo APU, Buerck J, Wallace BA, Lopes JLS. Unveiling the binding and orientation of the antimicrobial peptide Plantaricin 149 in zwitterionic and negatively charged membranes. Eur Biophys J 2019; 48:621-633. [PMID: 31324942 DOI: 10.1007/s00249-019-01387-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/05/2019] [Accepted: 07/01/2019] [Indexed: 12/24/2022]
Abstract
Antimicrobial peptides are a large group of natural compounds which present promising properties for the pharmaceutical and food industries, such as broad-spectrum activity, potential for use as natural preservatives, and reduced propensity for development of bacterial resistance. Plantaricin 149 (Pln149), isolated from Lactobacillus plantarum NRIC 149, is an intrinsically disordered peptide with the ability to inhibit bacteria from the Listeria and Staphylococcus genera, and which is capable of promoting inhibition and disruption of yeast cells. In this study, the interactions of Pln149 with model membranes composed of zwitterionic and/or anionic phospholipids were investigated using a range of biophysical techniques, including isothermal titration calorimetry, surface tension measurements, synchrotron radiation circular dichroism spectroscopy, oriented circular dichroism spectroscopy, and optical microscopy, to elucidate these peptides' mode of interactions and provide insight into their functional roles. In anionic model membranes, the binding of Pln149 to lipid bilayers is an endothermic process and induces a helical secondary structure in the peptide. The helices bind parallel to the surfaces of lipid bilayers and can promote vesicle disruption, depending on peptide concentration. Although Pln149 has relatively low affinity for zwitterionic liposomes, it is able to adsorb at their lipid interfaces, disturbing the lipid packing, assuming a similar parallel helix structure with a surface-bound orientation, and promoting an increase in the membrane surface area. Such findings can explain the intriguing inhibitory action of Pln149 in yeast cells whose cell membranes have a significant zwitterionic lipid composition.
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Affiliation(s)
- Patricia S Kumagai
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, 13563-120, Brazil
| | - Victor K Sousa
- Departamento Física Aplicada, Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, São Paulo, SP, 05508-090, Brazil
| | - Maressa Donato
- Departamento Física Aplicada, Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, São Paulo, SP, 05508-090, Brazil
| | - Rosangela Itri
- Departamento Física Aplicada, Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, São Paulo, SP, 05508-090, Brazil
| | - Leila M Beltramini
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, 13563-120, Brazil
| | - Ana P U Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, 13563-120, Brazil
| | - Jochen Buerck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Jose L S Lopes
- Departamento Física Aplicada, Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, São Paulo, SP, 05508-090, Brazil.
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10
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Ke S, Ulmschneider MB, Wallace BA, Ulmschneider JP. Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel. Biophys J 2018; 115:1920-1930. [PMID: 30366630 DOI: 10.1016/j.bpj.2018.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 01/09/2023] Open
Abstract
Voltage-gated sodium channels undergo transitions between open, closed, and inactivated states, enabling regulation of the translocation of sodium ions across membranes. A recently published crystal structure of the full-length prokaryotic NavMs crystal structure in the activated open conformation has revealed the presence of a novel motif consisting of an extensive network of salt bridges involving residues in the voltage sensor, S4-S5 linker, pore, and C-terminal domains. This motif has been proposed to be responsible for maintaining an open conformation that enables ion translocation through the channel. In this study, we have used long-time molecular dynamics calculations without artificial restraints to demonstrate that the interaction network of full-length NavMs indeed prevents a rapid collapse and closure of the gate, in marked difference to earlier studies of the pore-only construct in which the gate had to be restrained to remain open. Interestingly, a frequently discussed "hydrophobic gating" mechanism at nanoscopic level is also observed in our simulations, in which the discontinuous water wire close to the gate region leads to an energetic barrier for ion conduction. In addition, we demonstrate the effects of in silico mutations of several of the key residues in the motif on the open channel's stability and functioning, correlating them with existing functional studies on this channel and homologous disease-associated mutations in human sodium channels; we also examine the effects of truncating/removing the voltage sensor and C-terminal domains in maintaining an open gate.
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Affiliation(s)
- Song Ke
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | | | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom.
| | - Jakob P Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China.
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11
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Tolchard J, Walpole SJ, Miles AJ, Maytum R, Eaglen LA, Hackstadt T, Wallace BA, Blumenschein TMA. The intrinsically disordered Tarp protein from chlamydia binds actin with a partially preformed helix. Sci Rep 2018; 8:1960. [PMID: 29386631 PMCID: PMC5792643 DOI: 10.1038/s41598-018-20290-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/16/2018] [Indexed: 12/02/2022] Open
Abstract
Tarp (translocated actin recruiting phosphoprotein) is an effector protein common to all chlamydial species that functions to remodel the host-actin cytoskeleton during the initial stage of infection. In C. trachomatis, direct binding to actin monomers has been broadly mapped to a 100-residue region (726-825) which is predicted to be predominantly disordered, with the exception of a ~10-residue α-helical patch homologous to other WH2 actin-binding motifs. Biophysical investigations demonstrate that a Tarp726-825 construct behaves as a typical intrinsically disordered protein; within it, NMR relaxation measurements and chemical shift analysis identify the ten residue WH2-homologous region to exhibit partial α-helix formation. Isothermal titration calorimetry experiments on the same construct in the presence of monomeric G-actin show a well defined binding event with a 1:1 stoichiometry and Kd of 102 nM, whilst synchrotron radiation circular dichroism spectroscopy suggests the binding is concomitant with an increase in helical secondary structure. Furthermore, NMR experiments in the presence of G-actin indicate this interaction affects the proposed WH2-like α-helical region, supporting results from in silico docking calculations which suggest that, when folded, this α-helix binds within the actin hydrophobic cleft as seen for other actin-associated proteins.
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Affiliation(s)
- James Tolchard
- Center for Molecular and Structural Biology, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Samuel J Walpole
- Center for Molecular and Structural Biology, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Robin Maytum
- School of Life Sciences, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK
| | - Lawrence A Eaglen
- Center for Molecular and Structural Biology, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Ted Hackstadt
- Host-parasite Interactions Section, Laboratory of Intracellular Parasites, NIAID, NIH, Rocky Mountain Laboratories, Hamilton, MT, 59840, USA
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Tharin M A Blumenschein
- Center for Molecular and Structural Biology, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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12
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Whitmore L, Mavridis L, Wallace BA, Janes RW. DichroMatch at the protein circular dichroism data bank (DM@PCDDB): A web-based tool for identifying protein nearest neighbors using circular dichroism spectroscopy. Protein Sci 2017; 27:10-13. [PMID: 28580679 PMCID: PMC5734389 DOI: 10.1002/pro.3207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 11/23/2022]
Abstract
Circular dichroism spectroscopy is a well‐used, but simple method in structural biology for providing information on the secondary structure and folds of proteins. DichroMatch (DM@PCDDB) is an online tool that is newly available in the Protein Circular Dichroism Data Bank (PCDDB), which takes advantage of the wealth of spectral and metadata deposited therein, to enable identification of spectral nearest neighbors of a query protein based on four different methods of spectral matching. DM@PCDDB can potentially provide novel information about structural relationships between proteins and can be used in comparison studies of protein homologs and orthologs.
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Affiliation(s)
- Lee Whitmore
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Lazaros Mavridis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Robert W Janes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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13
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Sula A, Wallace BA. Interpreting the functional role of a novel interaction motif in prokaryotic sodium channels. J Gen Physiol 2017; 149:613-622. [PMID: 28522439 PMCID: PMC5460950 DOI: 10.1085/jgp.201611740] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/01/2017] [Indexed: 01/17/2023] Open
Abstract
Sula and Wallace explore evidence supporting a role for a novel interaction motif in the gating of prokaryotic sodium channels. Voltage-gated sodium channels enable the translocation of sodium ions across cell membranes and play crucial roles in electrical signaling by initiating the action potential. In humans, mutations in sodium channels give rise to several neurological and cardiovascular diseases, and hence they are targets for pharmaceutical drug developments. Prokaryotic sodium channel crystal structures have provided detailed views of sodium channels, which by homology have suggested potentially important functionally related structural features in human sodium channels. A new crystal structure of a full-length prokaryotic channel, NavMs, in a conformation we proposed to represent the open, activated state, has revealed a novel interaction motif associated with channel opening. This motif is associated with disease when mutated in human sodium channels and plays an important and dynamic role in our new model for channel activation.
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Affiliation(s)
- Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, England, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, England, UK
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14
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Abstract
Summary Integral membrane proteins that form helical pores and bundles constitute major drug targets, and many of their structures have been defined by crystallography and cryo-electron microscopy. The gating of channels and ligand binding of transporters generally involve changes in orientation of one or more the constituent helices in the structures. At present there is no standard easily accessible means for defining the orientation of a helix in a membrane protein structure. AnglerFish is a web-based tool for parameterising the angles of transmembrane helices based on PDB coordinates, with the helical orientations defined by the angles ‘tilt’ and ‘swing’. AnglerFish is particularly useful for defining changes in structure between different states, including both symmetric and asymmetric transitions, and can be used to quantitate differences between related structures or different subunits within the same structure. Availability and Implementation AnglerFish is freely available at http://anglerfish.cryst.bbk.ac.uk. The website is implemented in Perl-cgi and Apache and operation in all major browsers is supported. The source code is available at GitHub. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew Colledge
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
- To whom correspondence should be addressed.
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15
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Sula A, Booker J, Ng LCT, Naylor CE, DeCaen PG, Wallace BA. The complete structure of an activated open sodium channel. Nat Commun 2017; 8:14205. [PMID: 28205548 PMCID: PMC5316852 DOI: 10.1038/ncomms14205] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/08/2016] [Indexed: 12/11/2022] Open
Abstract
Voltage-gated sodium channels (Navs) play essential roles in excitable tissues, with their activation and opening resulting in the initial phase of the action potential. The cycling of Navs through open, closed and inactivated states, and their closely choreographed relationships with the activities of other ion channels lead to exquisite control of intracellular ion concentrations in both prokaryotes and eukaryotes. Here we present the 2.45 Å resolution crystal structure of the complete NavMs prokaryotic sodium channel in a fully open conformation. A canonical activated conformation of the voltage sensor S4 helix, an open selectivity filter leading to an open activation gate at the intracellular membrane surface and the intracellular C-terminal domain are visible in the structure. It includes a heretofore unseen interaction motif between W77 of S3, the S4–S5 interdomain linker, and the C-terminus, which is associated with regulation of opening and closing of the intracellular gate. Voltage-gated sodium (Nav) channels are crucial for action potential initiation in excitable cells. Here the authors present the complete structure of prokaryotic NavMs in a fully open state, providing structural insight into the opening and closure of the channel's intracellular gate.
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Affiliation(s)
- Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
| | - Jennifer Booker
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
| | - Leo C T Ng
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 E Superior, Chicago, Illinois 60611, USA
| | - Claire E Naylor
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
| | - Paul G DeCaen
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 E Superior, Chicago, Illinois 60611, USA
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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16
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Yoneda JS, Miles AJ, Araujo APU, Wallace BA. Differential dehydration effects on globular proteins and intrinsically disordered proteins during film formation. Protein Sci 2017; 26:718-726. [PMID: 28097742 PMCID: PMC5368061 DOI: 10.1002/pro.3118] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 12/22/2022]
Abstract
Globular proteins composed of different secondary structures and fold types were examined by synchrotron radiation circular dichroism spectroscopy to determine the effects of dehydration on their secondary structures. They exhibited only minor changes upon removal of bulk water during film formation, contrary to previously reported studies of proteins dehydrated by lyophilization (where substantial loss of helical structure and gain in sheet structure was detected). This near lack of conformational change observed for globular proteins contrasts with intrinsically disordered proteins (IDPs) dried in the same manner: the IDPs, which have almost completely unordered structures in solution, exhibited increased amounts of regular (mostly helical) secondary structures when dehydrated, suggesting formation of new intra-protein hydrogen bonds replacing solvent-protein hydrogen bonds, in a process which may mimic interactions that occur when IDPs bind to partner molecules. This study has thus shown that the secondary structures of globular and intrinsically disordered proteins behave very differently upon dehydration, and that films are a potentially useful format for examining dehydrated soluble proteins and assessing IDPs structures.
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Affiliation(s)
- Juliana Sakamoto Yoneda
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK.,Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Andew J Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | | | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
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17
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Field LM, Emyr Davies TG, O'Reilly AO, Williamson MS, Wallace BA. Voltage-gated sodium channels as targets for pyrethroid insecticides. Eur Biophys J 2017; 46:675-679. [PMID: 28070661 PMCID: PMC5599462 DOI: 10.1007/s00249-016-1195-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/13/2016] [Accepted: 12/18/2016] [Indexed: 11/02/2022]
Abstract
The pyrethroid insecticides are a very successful group of compounds that have been used extensively for the control of arthropod pests of agricultural crops and vectors of animal and human disease. Unfortunately, this has led to the development of resistance to the compounds in many species. The mode of action of pyrethroids is known to be via interactions with the voltage-gated sodium channel. Understanding how binding to the channel is affected by amino acid substitutions that give rise to resistance has helped to elucidate the mode of action of the compounds and the molecular basis of their selectivity for insects vs mammals and between insects and other arthropods. Modelling of the channel/pyrethroid interactions, coupled with the ability to express mutant channels in oocytes and study function, has led to knowledge of both how the channels function and potentially how to design novel insecticides with greater species selectivity.
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Affiliation(s)
| | | | | | | | - B A Wallace
- Birkbeck College, University of London, London, WC1E 7HX, UK
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18
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Chin S, Yang D, Miles AJ, Eckford PDW, Molinski S, Wallace BA, Bear CE. Attenuation of Phosphorylation-dependent Activation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Disease-causing Mutations at the Transmission Interface. J Biol Chem 2016; 292:1988-1999. [PMID: 28003367 PMCID: PMC5290968 DOI: 10.1074/jbc.m116.762633] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/07/2016] [Indexed: 12/21/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a multidomain membrane protein that functions as a phosphorylation-regulated anion channel. The interface between its two cytosolic nucleotide binding domains and coupling helices conferred by intracellular loops extending from the channel pore domains has been referred to as a transmission interface and is thought to be critical for the regulated channel activity of CFTR. Phosphorylation of the regulatory domain of CFTR by protein kinase A (PKA) is required for its channel activity. However, it was unclear if phosphorylation modifies the transmission interface. Here, we studied purified full-length CFTR protein using spectroscopic techniques to determine the consequences of PKA-mediated phosphorylation. Synchrotron radiation circular dichroism spectroscopy confirmed that purified full-length wild-type CFTR is folded and structurally responsive to phosphorylation. Intrinsic tryptophan fluorescence studies of CFTR showed that phosphorylation reduced iodide-mediated quenching, consistent with an effect of phosphorylation in burying tryptophans at the transmission interface. Importantly, the rate of phosphorylation-dependent channel activation was compromised by the introduction of disease-causing mutations in either of the two coupling helices predicted to interact with nucleotide binding domain 1 at the interface. Together, these results suggest that phosphorylation modifies the interface between the catalytic and pore domains of CFTR and that this modification facilitates CFTR channel activation.
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Affiliation(s)
- Stephanie Chin
- From the Programme of Molecular Structure and Function, Hospital for Sick Children, Toronto M5G 0A4, Canada; the Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Donghe Yang
- From the Programme of Molecular Structure and Function, Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Andrew J Miles
- the Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Paul D W Eckford
- From the Programme of Molecular Structure and Function, Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Steven Molinski
- From the Programme of Molecular Structure and Function, Hospital for Sick Children, Toronto M5G 0A4, Canada; the Department of Biochemistry, University of Toronto, Toronto, Canada
| | - B A Wallace
- the Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Christine E Bear
- From the Programme of Molecular Structure and Function, Hospital for Sick Children, Toronto M5G 0A4, Canada; the Department of Biochemistry, University of Toronto, Toronto, Canada; the Department of Physiology, University of Toronto, Toronto, Canada.
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19
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Penny CJ, Rahman T, Sula A, Miles AJ, Wallace BA, Patel S. Isolated pores dissected from human two-pore channel 2 are functional. Sci Rep 2016; 6:38426. [PMID: 27941820 PMCID: PMC5150636 DOI: 10.1038/srep38426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/08/2016] [Indexed: 01/30/2023] Open
Abstract
Multi-domain voltage-gated ion channels appear to have evolved through sequential rounds of intragenic duplication from a primordial one-domain precursor. Whereas modularity within one-domain symmetrical channels is established, little is known about the roles of individual regions within more complex asymmetrical channels where the domains have undergone substantial divergence. Here we isolated and characterised both of the divergent pore regions from human TPC2, a two-domain channel that holds a key intermediate position in the evolution of voltage-gated ion channels. In HeLa cells, each pore localised to the ER and caused Ca2+ depletion, whereas an ER-targeted pore mutated at a residue that inactivates full-length TPC2 did not. Additionally, one of the pores expressed at high levels in E. coli. When purified, it formed a stable, folded tetramer. Liposomes reconstituted with the pore supported Ca2+ and Na+ uptake that was inhibited by known blockers of full-length channels. Computational modelling of the pore corroborated cationic permeability and drug interaction. Therefore, despite divergence, both pores are constitutively active in the absence of their partners and retain several properties of the wild-type pore. Such symmetrical ‘pore-only’ proteins derived from divergent channel domains may therefore provide tractable tools for probing the functional architecture of complex ion channels.
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Affiliation(s)
- Christopher J Penny
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK
| | - Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Sandip Patel
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
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20
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Whitmore L, Miles AJ, Mavridis L, Janes RW, Wallace BA. PCDDB: new developments at the Protein Circular Dichroism Data Bank. Nucleic Acids Res 2016; 45:D303-D307. [PMID: 27613420 PMCID: PMC5210608 DOI: 10.1093/nar/gkw796] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/19/2016] [Indexed: 01/08/2023] Open
Abstract
The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, searching algorithms, data formats, data content, auxillary information, and validation techniques, as well as, of course, an increase in the number of holdings. It provides a site (http://pcddb.cryst.bbk.ac.uk) for authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. It also includes links for each entry to bioinformatics databases. The data are freely available to accessors either as single files or as complete data bank downloads. The PCDDB has found broad usage by the structural biology, bioinformatics, analytical and pharmaceutical communities, and has formed the basis for new software and methods developments.
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Affiliation(s)
- Lee Whitmore
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Andrew John Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Lazaros Mavridis
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Robert W Janes
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
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21
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Miller WC, Miles AJ, Wallace BA. Structure of the C-terminal domain of the prokaryotic sodium channel orthologue NsvBa. Eur Biophys J 2016; 45:807-814. [PMID: 27106836 DOI: 10.1007/s00249-016-1125-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 01/13/2023]
Abstract
Crystallographic and electrophysiological studies have recently provided insight into the structure, function, and drug binding of prokaryotic sodium channels. These channels exhibit significant sequence identities, especially in their transmembrane regions, with human voltage-gated sodium channels. However, rather than being single polypeptides with four homologous domains, they are tetramers of single domain polypeptides, with a C-terminal domain (CTD) composed of an inter-subunit four helix coiled coil. The structures of the CTDs differ between orthologues. In NavBh and NavMs, the C-termini form a disordered region adjacent to the final transmembrane helix, followed by a coiled-coil region, as demonstrated by synchrotron radiation circular dichroism (SRCD) and double electron-electron resonance electron paramagnetic resonance spectroscopic measurements. In contrast, in the crystal structure of the NavAe orthologue, the entire C-terminus is comprised of a helical region followed by a coiled coil. In this study, we have examined the CTD of the NsvBa from Bacillus alcalophilus, which unlike other orthologues is predicted by different methods to have different types of structures: either a disordered region adjacent to the transmembrane region, followed by a helical coiled coil, or a fully helical CTD. To discriminate between the two possible structures, we have used SRCD spectroscopy to experimentally determine the secondary structure of the C-terminus of this orthologue and used the results as the basis for modeling the open and closed conformations of the channel.
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Affiliation(s)
- W C Miller
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
- School of Biological Sciences, University of Kent, Canterbury, UK
| | - A J Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK.
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22
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Naylor CE, Bagnéris C, DeCaen PG, Sula A, Scaglione A, Clapham DE, Wallace BA. Molecular basis of ion permeability in a voltage-gated sodium channel. EMBO J 2016; 35:820-30. [PMID: 26873592 PMCID: PMC4972137 DOI: 10.15252/embj.201593285] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/18/2016] [Indexed: 12/20/2022] Open
Abstract
Voltage‐gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na+ ≈ Li+ ≫ K+, Ca2+, Mg2+) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones.
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Affiliation(s)
- Claire E Naylor
- Institute of Structural and Molecular Biology, Birkbeck College University of London, London, UK
| | - Claire Bagnéris
- Institute of Structural and Molecular Biology, Birkbeck College University of London, London, UK
| | - Paul G DeCaen
- Department of Cardiology, Howard Hughes Medical Institute Boston Children's Hospital, Boston, MA, USA Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College University of London, London, UK
| | - Antonella Scaglione
- Department of Cardiology, Howard Hughes Medical Institute Boston Children's Hospital, Boston, MA, USA Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - David E Clapham
- Department of Cardiology, Howard Hughes Medical Institute Boston Children's Hospital, Boston, MA, USA Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College University of London, London, UK
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23
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Erskine PT, Fokas A, Muriithi C, Rehman H, Yates LA, Bowyer A, Findlow IS, Hagan R, Werner JM, Miles AJ, Wallace BA, Wells SA, Wood SP, Cooper JB. X-ray, spectroscopic and normal-mode dynamics of calexcitin: structure-function studies of a neuronal calcium-signalling protein. ACTA ACUST UNITED AC 2015; 71:615-31. [PMID: 25760610 DOI: 10.1107/s1399004714026704] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 12/04/2014] [Indexed: 01/28/2023]
Abstract
The protein calexcitin was originally identified in molluscan photoreceptor neurons as a 20 kDa molecule which was up-regulated and phosphorylated following a Pavlovian conditioning protocol. Subsequent studies showed that calexcitin regulates the voltage-dependent potassium channel and the calcium-dependent potassium channel as well as causing the release of calcium ions from the endoplasmic reticulum (ER) by binding to the ryanodine receptor. A crystal structure of calexcitin from the squid Loligo pealei showed that the fold is similar to that of another signalling protein, calmodulin, the N- and C-terminal domains of which are known to separate upon calcium binding, allowing interactions with the target protein. Phosphorylation of calexcitin causes it to translocate to the cell membrane, where its effects on membrane excitability are exerted and, accordingly, L. pealei calexcitin contains two protein kinase C phosphorylation sites (Thr61 and Thr188). Thr-to-Asp mutations which mimic phosphorylation of the protein were introduced and crystal structures of the corresponding single and double mutants were determined, which suggest that the C-terminal phosphorylation site (Thr188) exerts the greatest effects on the protein structure. Extensive NMR studies were also conducted, which demonstrate that the wild-type protein predominantly adopts a more open conformation in solution than the crystallographic studies have indicated and, accordingly, normal-mode dynamic simulations suggest that it has considerably greater capacity for flexible motion than the X-ray studies had suggested. Like calmodulin, calexcitin consists of four EF-hand motifs, although only the first three EF-hands of calexcitin are involved in binding calcium ions; the C-terminal EF-hand lacks the appropriate amino acids. Hence, calexcitin possesses two functional EF-hands in close proximity in its N-terminal domain and one functional calcium site in its C-terminal domain. There is evidence that the protein has two markedly different affinities for calcium ions, the weaker of which is most likely to be associated with binding of calcium ions to the protein during neuronal excitation. In the current study, site-directed mutagenesis has been used to abolish each of the three calcium-binding sites of calexcitin, and these experiments suggest that it is the single calcium-binding site in the C-terminal domain of the protein which is likely to have a sensory role in the neuron.
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Affiliation(s)
- P T Erskine
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - A Fokas
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - C Muriithi
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - H Rehman
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - L A Yates
- Centre of Biological Sciences, University of Southampton, Southampton SO17 1BJ, England
| | - A Bowyer
- Centre of Biological Sciences, University of Southampton, Southampton SO17 1BJ, England
| | - I S Findlow
- Centre of Biological Sciences, University of Southampton, Southampton SO17 1BJ, England
| | - R Hagan
- Centre of Biological Sciences, University of Southampton, Southampton SO17 1BJ, England
| | - J M Werner
- Centre of Biological Sciences, University of Southampton, Southampton SO17 1BJ, England
| | - A J Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England
| | - S A Wells
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - S P Wood
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - J B Cooper
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
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24
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Amey JS, O'Reilly AO, Burton MJ, Puinean AM, Mellor IR, Duce IR, Field LM, Wallace BA, Williamson MS, Davies TGE. An evolutionarily-unique heterodimeric voltage-gated cation channel found in aphids. FEBS Lett 2015; 589:598-607. [PMID: 25637326 PMCID: PMC4332693 DOI: 10.1016/j.febslet.2015.01.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/31/2014] [Accepted: 01/05/2015] [Indexed: 01/05/2023]
Abstract
Aphids have a unique heterodimeric voltage-gated sodium channel. The aphid channel has an atypical ion-selectivity filter (DENS rather than DEKA). The channel’s novel selectivity filter may result in a loss of sodium selectivity. This is the only identifiable voltage-gated sodium channel in aphid genome(s). This channel has most likely arisen by gene fission or gene duplication.
We describe the identification in aphids of a unique heterodimeric voltage-gated sodium channel which has an atypical ion selectivity filter and, unusually for insect channels, is highly insensitive to tetrodotoxin. We demonstrate that this channel has most likely arisen by adaptation (gene fission or duplication) of an invertebrate ancestral mono(hetero)meric channel. This is the only identifiable voltage-gated sodium channel homologue in the aphid genome(s), and the channel’s novel selectivity filter motif (DENS instead of the usual DEKA found in other eukaryotes) may result in a loss of sodium selectivity, as indicated experimentally in mutagenised Drosophila channels.
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Affiliation(s)
- Joanna S Amey
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Andrias O O'Reilly
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom; School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Mark J Burton
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, United Kingdom; Department of Cell Physiology and Pharmacology, College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom
| | - Alin M Puinean
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Ian R Mellor
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, United Kingdom
| | - Ian R Duce
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, United Kingdom
| | - Linda M Field
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Martin S Williamson
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - T G Emyr Davies
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom.
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25
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Saha SC, Powl AM, Wallace BA, de Planque MRR, Morgan H. Screening ion-channel ligand interactions with passive pumping in a microfluidic bilayer lipid membrane chip. Biomicrofluidics 2015; 9:014103. [PMID: 25610515 PMCID: PMC4288537 DOI: 10.1063/1.4905313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 12/19/2014] [Indexed: 05/16/2023]
Abstract
We describe a scalable artificial bilayer lipid membrane platform for rapid electrophysiological screening of ion channels and transporters. A passive pumping method is used to flow microliter volumes of ligand solution across a suspended bilayer within a microfluidic chip. Bilayers are stable at flow rates up to ∼0.5 μl/min. Phospholipid bilayers are formed across a photolithographically defined aperture made in a dry film resist within the microfluidic chip. Bilayers are stable for many days and the low shunt capacitance of the thin film support gives low-noise high-quality single ion channel recording. Dose-dependent transient blocking of α-hemolysin with β-cyclodextrin (β-CD) and polyethylene glycol is demonstrated and dose-dependent blocking studies of the KcsA potassium channel with tetraethylammonium show the potential for determining IC50 values. The assays are fast (30 min for a complete IC50 curve) and simple and require very small amounts of compounds (100 μg in 15 μl). The technology can be scaled so that multiple bilayers can be addressed, providing a screening platform for ion channels, transporters, and nanopores.
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Affiliation(s)
- Shimul C Saha
- Electronics and Computer Science and Institute for Life Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Andrew M Powl
- Institute of Structural and Molecular Biology, Birkbeck College, University of London , London WC1E 7HX, United Kingdom
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London , London WC1E 7HX, United Kingdom
| | - Maurits R R de Planque
- Electronics and Computer Science and Institute for Life Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Hywel Morgan
- Electronics and Computer Science and Institute for Life Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
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26
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Bagnéris C, Naylor CE, McCusker EC, Wallace BA. Structural model of the open-closed-inactivated cycle of prokaryotic voltage-gated sodium channels. ACTA ACUST UNITED AC 2014; 145:5-16. [PMID: 25512599 PMCID: PMC4278185 DOI: 10.1085/jgp.201411242] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In excitable cells, the initiation of the action potential results from the opening of voltage-gated sodium channels. These channels undergo a series of conformational changes between open, closed, and inactivated states. Many models have been proposed for the structural transitions that result in these different functional states. Here, we compare the crystal structures of prokaryotic sodium channels captured in the different conformational forms and use them as the basis for examining molecular models for the activation, slow inactivation, and recovery processes. We compare structural similarities and differences in the pore domains, specifically in the transmembrane helices, the constrictions within the pore cavity, the activation gate at the cytoplasmic end of the last transmembrane helix, the C-terminal domain, and the selectivity filter. We discuss the observed differences in the context of previous models for opening, closing, and inactivation, and present a new structure-based model for the functional transitions. Our proposed prokaryotic channel activation mechanism is then compared with the activation transition in eukaryotic sodium channels.
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Affiliation(s)
- Claire Bagnéris
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England, UK
| | - Claire E Naylor
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England, UK
| | - Emily C McCusker
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England, UK
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27
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Lopes JLS, Miles AJ, Whitmore L, Wallace BA. Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: applications in secondary structure analyses. Protein Sci 2014; 23:1765-72. [PMID: 25262612 DOI: 10.1002/pro.2558] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/23/2014] [Indexed: 11/10/2022]
Abstract
Circular dichroism (CD) spectroscopy is a valuable method for defining canonical secondary structure contents of proteins based on empirically-defined spectroscopic signatures derived from proteins with known three-dimensional structures. Many proteins identified as being "Intrinsically Disordered Proteins" have a significant amount of their structure that is neither sheet, helix, nor turn; this type of structure is often classified by CD as "other", "random coil", "unordered", or "disordered". However the "other" category can also include polyproline II (PPII)-type structures, whose spectral properties have not been well-distinguished from those of unordered structures. In this study, synchrotron radiation circular dichroism spectroscopy was used to investigate the spectral properties of collagen and polyproline, which both contain PPII-type structures. Their native spectra were compared as representatives of PPII structures. In addition, their spectra before and after treatment with various conditions to produce unfolded or denatured structures were also compared, with the aim of defining the differences between CD spectra of PPII and disordered structures. We conclude that the spectral features of collagen are more appropriate than those of polyproline for use as the representative spectrum for PPII structures present in typical amino acid-containing proteins, and that the single most characteristic spectroscopic feature distinguishing a PPII structure from a disordered structure is the presence of a positive peak around 220nm in the former but not in the latter. These spectra are now available for inclusion in new reference data sets used for CD analyses of the secondary structures of soluble proteins.
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Affiliation(s)
- Jose L S Lopes
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
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28
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Kalsi S, Powl AM, Wallace BA, Morgan H, de Planque MRR. Shaped apertures in photoresist films enhance the lifetime and mechanical stability of suspended lipid bilayers. Biophys J 2014; 106:1650-9. [PMID: 24739164 PMCID: PMC4008792 DOI: 10.1016/j.bpj.2014.02.033] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 02/12/2014] [Accepted: 02/26/2014] [Indexed: 11/22/2022] Open
Abstract
Planar lipid bilayers suspended in apertures provide a controlled environment for ion channel studies. However, short lifetimes and poor mechanical stability of suspended bilayers limit the experimental throughput of bilayer electrophysiology experiments. Although bilayers are more stable in smaller apertures, ion channel incorporation through vesicle fusion with the suspended bilayer becomes increasingly difficult. In an alternative bilayer stabilization approach, we have developed shaped apertures in SU8 photoresist that have tapered sidewalls and a minimum diameter between 60 and 100 μm. Bilayers formed at the thin tip of these shaped apertures, either with the painting or the folding method, display drastically increased lifetimes, typically >20 h, and mechanical stability, being able to withstand extensive perturbation of the buffer solution. Single-channel electrical recordings of the peptide alamethicin and of the proteoliposome-delivered potassium channel KcsA demonstrate channel conductance with low noise, made possible by the small capacitance of the 50 μm thick SU8 septum, which is only thinned around the aperture, and unimpeded proteoliposome fusion, enabled by the large aperture diameter. We anticipate that these shaped apertures with micrometer edge thickness can substantially enhance the throughput of channel characterization by bilayer lipid membrane electrophysiology, especially in combination with automated parallel bilayer platforms.
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Affiliation(s)
- Sumit Kalsi
- Electronics and Computer Science, University of Southampton, Southampton, United Kingdom; Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.
| | - Andrew M Powl
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Hywel Morgan
- Electronics and Computer Science, University of Southampton, Southampton, United Kingdom; Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Maurits R R de Planque
- Electronics and Computer Science, University of Southampton, Southampton, United Kingdom; Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.
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29
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O'Reilly AO, Williamson MS, González-Cabrera J, Turberg A, Field LM, Wallace BA, Davies TGE. Predictive 3D modelling of the interactions of pyrethroids with the voltage-gated sodium channels of ticks and mites. Pest Manag Sci 2014; 70:369-77. [PMID: 23589444 DOI: 10.1002/ps.3561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/04/2013] [Accepted: 04/15/2013] [Indexed: 05/27/2023]
Abstract
BACKGROUND The pyrethroid insecticides are a very successful group of compounds that target invertebrate voltage-gated sodium channels and are widely used in the control of insects, ticks and mites. It is well established that some pyrethroids are good insecticides whereas others are more effective as acaricides. This species specificity is advantageous for controlling particular pest(s) in the presence of another non-target invertebrate, for example controlling the Varroa mite in honeybee colonies. RESULTS We applied in silico techniques to compare the voltage-gated sodium channels of insects versus ticks and mites and their interactions with a range of pyrethroids and DDT analogues. We identified a single amino acid difference within the pyrethroid binding pocket of ticks/mites that may have significant impact on the effectiveness of pyrethroids as acaricides. Other individual amino acid differences within the binding pocket in distinct tick and mite species may provide a basis for future acaricidal selectivity. CONCLUSIONS Three-dimensional modelling of the pyrethroid/DDT receptor site has led to a new hypothesis to explain the preferential binding of acaricidal pyrethroids to the sodium channels of ticks/mites. This is important for understanding pyrethroid selectivity and the potential effects of mutations that can give rise to resistance to pyrethroids in commercially-important pest species.
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Affiliation(s)
- Andrias O O'Reilly
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Bavaria, Germany
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30
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Lopes JLS, Orcia D, Araujo APU, DeMarco R, Wallace BA. Folding factors and partners for the intrinsically disordered protein micro-exon gene 14 (MEG-14). Biophys J 2014; 104:2512-20. [PMID: 23746524 DOI: 10.1016/j.bpj.2013.03.063] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/27/2013] [Accepted: 03/12/2013] [Indexed: 01/09/2023] Open
Abstract
The micro-exon genes (MEG) of Schistosoma mansoni, a parasite responsible for the second most widely spread tropical disease, code for small secreted proteins with sequences unique to the Schistosoma genera. Bioinformatics analyses suggest the soluble domain of the MEG-14 protein will be largely disordered, and using synchrotron radiation circular dichroism spectroscopy, its secondary structure was shown to be essentially completely unfolded in aqueous solution. It does, however, show a strong propensity to fold into more ordered structures under a wide range of conditions. Partial folding was produced by increasing temperature (in a reversible process), contrary to the behavior of most soluble proteins. Furthermore, significant folding was observed in the presence of negatively charged lipids and detergents, but not in zwitterionic or neutral lipids or detergents. Absorption onto a surface followed by dehydration stimulated it to fold into a helical structure, as it did when the aqueous solution was replaced by nonaqueous solvents. Hydration of the dehydrated folded protein was accompanied by complete unfolding. These results support the identification of MEG-14 as a classic intrinsically disordered protein, and open the possibility of its interaction/folding with different partners and factors being related to multifunctional roles and states within the host.
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Affiliation(s)
- Jose Luiz S Lopes
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
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31
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McCusker EC, Bagnéris C, Naylor CE, Cole AR, D'Avanzo N, Nichols CG, Wallace BA. Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing. Nat Commun 2013; 3:1102. [PMID: 23033078 PMCID: PMC3493636 DOI: 10.1038/ncomms2077] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/20/2012] [Indexed: 02/03/2023] Open
Abstract
Sodium-gated ion channels open and close in response to the flow of ions. Here, McCusker et al. report the open structure of a sodium-gated ion channel pore from a bacterial homologue, and show, by comparison with the closed structure, that the movement of a C-terminal helix is sufficient to open the channel. Voltage-gated sodium channels are vital membrane proteins essential for electrical signalling; in humans, they are key targets for the development of pharmaceutical drugs. Here we report the crystal structure of an open-channel conformation of NavMs, the bacterial channel pore from the marine bacterium Magnetococcus sp. (strain MC-1). It differs from the recently published crystal structure of a closed form of a related bacterial sodium channel (NavAb) by having its internal cavity accessible to the cytoplasmic surface as a result of a bend/rotation about a central residue in the carboxy-terminal transmembrane segment. This produces an open activation gate of sufficient diameter to allow hydrated sodium ions to pass through. Comparison of the open and closed structures provides new insight into the features of the functional states present in the activation cycles of sodium channels and the mechanism of channel opening and closing.
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Affiliation(s)
- Emily C McCusker
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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32
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Janes RW, Miles AJ, Woollett B, Whitmore L, Klose D, Wallace BA. Circular dichroism spectral data and metadata in the Protein Circular Dichroism Data Bank (PCDDB): a tutorial guide to accession and deposition. Chirality 2012; 24:751-63. [PMID: 22674824 DOI: 10.1002/chir.22050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 03/14/2012] [Indexed: 11/11/2022]
Abstract
The Protein Circular Dichroism Data Bank (PCDDB) is a web-based resource containing circular dichroism (CD) and synchrotron radiation circular dichroism spectral and associated metadata located at http://pcddb.cryst.bbk.ac.uk. This resource provides a freely available, user-friendly means of accessing validated CD spectra and their associated experimental details and metadata, thereby enabling broad usage of this material and new developments across the structural biology, chemistry, and bioinformatics communities. The resource also enables researchers utilizing CD as an experimental technique to have a means of storing their data at a secure site from which it is easily retrievable, thereby making their results publicly accessible, a current requirement of many grant-funding agencies world-wide, as well as meeting the data-sharing requirements for journal publications. This tutorial provides extensive information on searching, accessing, and downloading procedures for those who wish to utilize the data available in the data bank, and detailed information on deposition procedures for creating and validating entries, including comprehensive explanations of their contents and formats, for those who wish to include their data in the data bank.
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Affiliation(s)
- Robert W Janes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
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33
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Abstract
Circular dichroism (CD) spectroscopy is a widely used method for examining the structure, folding and conformational changes of proteins. A new online CD analysis server (DichroMatch) has been developed for identifying proteins with similar spectral characteristics by detecting possible structurally and functionally related proteins and homologues. DichroMatch includes six different methods for determining the spectral nearest neighbours to a query protein spectrum and provides metrics of how similar these spectra are and, if corresponding crystal structures are available for the closest matched proteins, information on their secondary structures and fold classifications. By default, DichroMatch uses all the entries in the Protein Circular Dichroism Data Bank (PCDDB) for its comparison set, providing the broadest range of publicly available protein spectra to match with the unknown protein. Alternatively, users can download or create their own specialized data sets, thereby enabling comparisons between the structures of related proteins such as wild-type versus mutants or homologues or a series of spectra of the same protein under different conditions. The DichroMatch server is freely available at http://dichromatch.cryst.bbk.ac.uk.
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Affiliation(s)
- D P Klose
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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Powl AM, Miles AJ, Wallace BA. Transmembrane and extramembrane contributions to membrane protein thermal stability: studies with the NaChBac sodium channel. Biochim Biophys Acta 2011; 1818:889-95. [PMID: 22226848 DOI: 10.1016/j.bbamem.2011.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 11/30/2011] [Accepted: 12/20/2011] [Indexed: 11/16/2022]
Abstract
The thermal stabilities of the extramembranous and transmembranous regions of the bacterial voltage-gated sodium channel NaChBac have been characterised using thermal-melt synchrotron radiation circular dichroism (SRCD) spectroscopy. A series of constructs, ranging from the full-length protein containing both the C-terminal cytoplasmic and the transmembranous domains, to proteins with decreasing amounts of the cytoplasmic domain, were examined in order to separately define the roles of these two types of domains in the stability and processes of unfolding of a membrane protein. The sensitivity of the SRCD measurements over a wide range of wavelengths and temperatures has meant that subtle but reproducible conformational changes could be detected with accuracy. The residues in the C-terminal extramembranous domain were highly susceptible to thermal denaturation, but for the most part the transmembrane residues were not thermally-labile and retained their helical character even at very elevated temperatures. The process of thermal unfolding involved an initial irreversible unfolding of the highly labile distal extramembranous C-terminal helical region, which was accompanied by a reversible unfolding of a small number of helical residues in the transmembrane domain. This was then followed by the irreversible unfolding of a limited number of additional transmembrane helical residues at greatly elevated temperatures. Hence this study has been able to determine the different contributions and roles of the transmembrane and extramembrane residues in the processes of thermal denaturation of this multipass integral membrane protein.
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Affiliation(s)
- Andrew M Powl
- Department of Crystallography, University of London, London, UK
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35
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Wilson MA, Wei C, Bjelkmar P, Wallace BA, Pohorille A. Molecular dynamics simulation of the antiamoebin ion channel: linking structure and conductance. Biophys J 2011; 100:2394-402. [PMID: 21575573 DOI: 10.1016/j.bpj.2011.03.054] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 03/21/2011] [Accepted: 03/24/2011] [Indexed: 11/19/2022] Open
Abstract
Molecular-dynamics simulations were carried out to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistent with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive. The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be nonconducting. The conductance of the hexamer was estimated to be 115 ± 34 pS and 74 ± 20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis, we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K⁺ and Cl⁻ with their first solvation shells intact. The free energy barrier encountered by K⁺ is only 2.2 kcal/mol whereas Cl⁻ encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics.
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Affiliation(s)
- Michael A Wilson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
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Abstract
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In excitable cells, the main mediators of sodium conductance
across
membranes are voltage-gated sodium channels (NaVs). Eukaryotic
NaVs are essential elements in neuronal signaling and muscular
contraction and in humans have been causally related to a variety
of neurological and cardiovascular channelopathies. They are complex
heavily glycosylated intrinsic membrane proteins present in only trace
quantities that have proven to be challenging objects of study. However,
in recent years, a number of simpler prokaryotic sodium channels have
been identified, with NaChBac from Bacillus halodurans being the most well-characterized to date. The availability of a
bacterial NaV that is amenable to heterologous expression
and functional characterization in both bacterial and mammalian systems
has provided new opportunities for structure–function studies.
This review describes features of NaChBac as an exemplar of this class
of bacterial channels, compares prokaryotic and eukaryotic NaVs with respect to their structural organization, pharmacological
profiling, and functional kinetics, and discusses how voltage-gated
ion channels may have evolved to deal with the complex functional
demands of higher organisms.
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Affiliation(s)
- Kalypso Charalambous
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
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Miles AJ, Wallace BA, Esmann M. Correlation of structural and functional thermal stability of the integral membrane protein Na,K-ATPase. Biochim Biophys Acta 2011; 1808:2573-80. [PMID: 21712026 DOI: 10.1016/j.bbamem.2011.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Revised: 06/03/2011] [Accepted: 06/14/2011] [Indexed: 10/18/2022]
Abstract
The membrane-bound cation-transporting P-type Na,K-ATPase isolated from pig kidney membranes is much more resistant towards thermal inactivation than the almost identical membrane-bound Na,K-ATPase isolated from shark rectal gland membranes. The loss of enzymatic activity is correlated well with changes in protein structure as determined using synchrotron radiation circular dichroism (SRCD) spectroscopy. The enzymatic activity is lost at a 12°C higher temperature for pig enzyme than for shark enzyme, and the major changes in protein secondary structure also occur at T(m)'s that are ~10-15°C higher for the pig than for the shark enzyme. The temperature optimum for the rate of hydrolysis of ATP is about 42°C for shark and about 57°C for pig, both of which are close to the temperatures for onset of thermal unfolding. These results suggest that the active site region may be amongst the earliest parts of the structure to unfold. Detergent-solubilized Na,K-ATPases from the two sources show the similar differences in thermal stability as the membrane-bound species, but inactivation occurs at a lower temperature for both, and may reflect the stabilizing effect of a bilayer versus a micellar environment.
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Affiliation(s)
- Andrew J Miles
- Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK
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Platzer G, Schedlbauer A, Chemelli A, Ozdowy P, Coudevylle N, Auer R, Kontaxis G, Hartl M, Miles AJ, Wallace BA, Glatter O, Bister K, Konrat R. The metastasis-associated extracellular matrix protein osteopontin forms transient structure in ligand interaction sites. Biochemistry 2011; 50:6113-24. [PMID: 21609000 DOI: 10.1021/bi200291e] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Osteopontin (OPN) is an acidic hydrophilic glycophosphoprotein that was first identified as a major sialoprotein in bones. It functions as a cell attachment protein displaying a RGD cell adhesion sequence and as a cytokine that signals through integrin and CD44 cell adhesion molecules. OPN is also implicated in human tumor progression and cell invasion. OPN has intrinsic transforming activity, and elevated OPN levels promote metastasis. OPN gene expression is also strongly activated in avian fibroblasts simultaneously transformed by the v-myc and v-mil(raf) oncogenes. Here we have investigated the solution structure of a 220-amino acid recombinant OPN protein by an integrated structural biology approach employing bioinformatic sequence analysis, multidimensional nuclear magnetic resonance spectroscopy, synchrotron radiation circular dichroism spectroscopy, and small-angle X-ray scattering. These studies suggest that OPN is an intrinsically unstructured protein in solution. Although OPN does not fold into a single defined structure, its conformational flexibility significantly deviates from random coil-like behavior. OPN comprises distinct local secondary structure elements with reduced conformational flexibility and substantially populates a compact subspace displaying distinct tertiary contacts. These compacted regions of OPN encompass the binding sites for α(V)β(III) integrin and heparin. The conformational flexibility combined with the modular architecture of OPN may represent an important structural prerequisite for its functional diversity.
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Affiliation(s)
- Gerald Platzer
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria
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Abdul-Gader A, Miles AJ, Wallace BA. A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy. Bioinformatics 2011; 27:1630-6. [PMID: 21505036 DOI: 10.1093/bioinformatics/btr234] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
MOTIVATION Empirical analyses of protein secondary structures based on circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectroscopic data rely on the availability of reference datasets comprised of spectra of relevant proteins, whose crystal structures have been determined. Datasets comprised of only soluble proteins have not proven suitable for analysing the spectra of membrane proteins. RESULTS A new reference dataset, MP180, has been created containing the spectra of 30 membrane proteins encompassing the secondary structure and fold space covered by all known membrane protein structures. In addition a mixed soluble and membrane protein dataset, SMP180, has been created, which includes 98 soluble protein spectra (SP) plus the MP180 spectra. Calculations of both membrane and soluble protein secondary structures using SMP180 are significantly improved with respect to those produced, using soluble protein-only datasets. The SMP180 dataset also enables determination of the percentage of transmembrane residues, thus enhancing the information previously obtainable from CD spectroscopy. AVAILABILITY AND IMPLEMENTATION Reference dataset online at the DichroWeb analysis server (http://dichroweb.cryst.bbk.ac.uk); individual protein spectra in the Protein Circular Dichroism Data Bank (http://pcddb.cryst.bbk.ac.uk).
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Affiliation(s)
- Ali Abdul-Gader
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
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McCusker EC, D'Avanzo N, Nichols CG, Wallace BA. Simplified bacterial "pore" channel provides insight into the assembly, stability, and structure of sodium channels. J Biol Chem 2011; 286:16386-91. [PMID: 21454659 PMCID: PMC3091244 DOI: 10.1074/jbc.c111.228122] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Eukaryotic sodium channels are important membrane proteins involved in ion
permeation, homeostasis, and electrical signaling. They are long, multidomain
proteins that do not express well in heterologous systems, and hence,
structure/function and biochemical studies on purified sodium channel proteins
have been limited. Bacteria produce smaller, homologous tetrameric single domain
channels specific for the conductance of sodium ions. They consist of N-terminal
voltage sensor and C-terminal pore subdomains. We designed a functional
pore-only channel consisting of the final two transmembrane helices, the
intervening P-region, and the C-terminal extramembranous region of the sodium
channel from the marine bacterium Silicibacter pomeroyi. This
sodium “pore” channel forms a tetrameric, folded structure that is
capable of supporting sodium flux in phospholipid vesicles. The pore-only
channel is more thermally stable than its full-length counterpart, suggesting
that the voltage sensor subdomain may destabilize the full-length channel. The
pore subdomains can assemble, fold, and function independently from the voltage
sensor and exhibit similar ligand-blocking characteristics as the intact
channel. The availability of this simple pore-only construct should enable
high-level expression for the testing of potential new ligands and enhance our
understanding of the structural features that govern sodium selectivity and
permeability.
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Affiliation(s)
- Emily C McCusker
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
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Whitmore L, Woollett B, Miles AJ, Janes RW, Wallace BA. The protein circular dichroism data bank, a Web-based site for access to circular dichroism spectroscopic data. Structure 2011; 18:1267-9. [PMID: 20947015 DOI: 10.1016/j.str.2010.08.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 08/02/2010] [Accepted: 08/13/2010] [Indexed: 11/29/2022]
Abstract
The Protein Circular Dichroism Data Bank (PCDDB) is a newly released resource for structural biology. It is a web-accessible (http://pcddb.cryst.bbk.ac.uk) data bank for circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectra and their associated experimental and secondary metadata, with links to protein sequence and structure data banks. It is designed to provide a public repository for CD spectroscopic data on macromolecules, to parallel the Protein Data Bank (PDB) for crystallographic, electron microscopic, and nuclear magnetic resonance spectroscopic data. Similarly to the PDB, it includes validation checking procedures to ensure good practice and the integrity of the deposited data. This paper reports on the first public release of the PCDDB, which provides access to spectral data that comprise standard reference datasets.
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Affiliation(s)
- Lee Whitmore
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
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Beich-Frandsen M, Vecerek B, Konarev PV, Sjöblom B, Kloiber K, Hämmerle H, Rajkowitsch L, Miles AJ, Kontaxis G, Wallace BA, Svergun DI, Konrat R, Bläsi U, Djinovic-Carugo K. Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq. Nucleic Acids Res 2011; 39:4900-15. [PMID: 21330354 PMCID: PMC3113564 DOI: 10.1093/nar/gkq1346] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The hexameric Escherichia coli RNA chaperone Hfq (Hfq(Ec)) is involved in riboregulation of target mRNAs by small trans-encoded RNAs. Hfq proteins of different bacteria comprise an evolutionarily conserved core, whereas the C-terminus is variable in length. Although the structure of the conserved core has been elucidated for several Hfq proteins, no structural information has yet been obtained for the C-terminus. Using bioinformatics, nuclear magnetic resonance spectroscopy, synchrotron radiation circular dichroism (SRCD) spectroscopy and small angle X-ray scattering we provide for the first time insights into the conformation and dynamic properties of the C-terminal extension of Hfq(Ec). These studies indicate that the C-termini are flexible and extend laterally away from the hexameric core, displaying in this way features typical of intrinsically disordered proteins that facilitate intermolecular interactions. We identified a minimal, intrinsically disordered region of the C-terminus supporting the interactions with longer RNA fragments. This minimal region together with rest of the C-terminal extension provides a flexible moiety capable of tethering long and structurally diverse RNA molecules. Furthermore, SRCD spectroscopy supported the hypothesis that RNA fragments exceeding a certain length interact with the C-termini of Hfq(Ec).
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Affiliation(s)
- Mads Beich-Frandsen
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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Meersman F, Atilgan C, Miles AJ, Bader R, Shang W, Matagne A, Wallace BA, Koch MHJ. Consistent picture of the reversible thermal unfolding of hen egg-white lysozyme from experiment and molecular dynamics. Biophys J 2011; 99:2255-63. [PMID: 20923660 DOI: 10.1016/j.bpj.2010.07.060] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 07/15/2010] [Accepted: 07/23/2010] [Indexed: 11/19/2022] Open
Abstract
Synchrotron radiation circular dichroism, Fourier transform infrared, and nuclear magnetic resonance spectroscopies, and small-angle x-ray scattering were used to monitor the reversible thermal unfolding of hen egg white lysozyme. The results were compared with crystal structures and high- and low-temperature structures derived from molecular-dynamics calculations. The results of both experimental and computational methods indicate that the unfolding process starts with the loss of β-structures followed by the reversible loss of helix content from ∼40% at 20°C to 27% at 70°C and ∼20% at 77°C, beyond which unfolding becomes irreversible. Concomitantly there is a reversible increase in the radius of gyration of the protein from 15 Å to 18 Å. The reversible decrease in forward x-ray scattering demonstrates a lack of aggregation upon unfolding, suggesting the change is due to a larger dilation of hydration water than of bulk water. Molecular-dynamics simulations suggest a similar sequence of events and are in good agreement with the (1)H(N) chemical shift differences in nuclear magnetic resonance. This study demonstrates the power of complementary methods for elucidating unfolding/refolding processes and the nature of both the unfolded structure, for which there is no crystallographic data, and the partially unfolded forms of the protein that can lead to fibril formation and disease.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium.
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Zhai J, Miles AJ, Pattenden LK, Lee TH, Augustin MA, Wallace BA, Aguilar MI, Wooster TJ. Changes in beta-lactoglobulin conformation at the oil/water interface of emulsions studied by synchrotron radiation circular dichroism spectroscopy. Biomacromolecules 2010; 11:2136-42. [PMID: 20690721 DOI: 10.1021/bm100510j] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure of proteins at interfaces is a key factor determining the stability as well as organoleptic properties of food emulsions. While it is widely believed that proteins undergo conformational changes at interfaces, the measurement of these structural changes remains a significant challenge. In this study, the conformational changes of beta-lactoglobulin (beta-Lg) upon adsorption to the interface of hexadecane oil-in-water emulsions were investigated using synchrotron radiation circular dichroism (SRCD) spectroscopy. Far-UV SRCD spectra showed that adsorption of beta-Lg to the O/W interface caused a significant increase in non-native alpha-helix structure, accompanied by a concomitant loss of beta-sheet structure. Near-UV SRCD spectra revealed that a considerable disruption of beta-Lg tertiary structure occurred upon adsorption. Moreover, heat-induced changes to the non-native beta-Lg conformation at the oil/water interface were very small compared to the dramatic loss of beta-Lg secondary structure that occurred during heating in solution, suggesting that the interface has a stabilizing effect on the structure of non-native beta-Lg. Overall, our findings provide insight into the conformational behavior of proteins at oil/water interfaces and demonstrate the applicability of SRCD spectroscopy for measuring the conformation of adsorbed proteins in optically turbid emulsions.
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Affiliation(s)
- Jiali Zhai
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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Moore B, Miles AJ, Guerra-Giraldez C, Simpson P, Iwata M, Wallace BA, Matthews SJ, Smith DF, Brown KA. Structural basis of molecular recognition of the Leishmania small hydrophilic endoplasmic reticulum-associated protein (SHERP) at membrane surfaces. J Biol Chem 2010; 286:9246-56. [PMID: 21106528 PMCID: PMC3059043 DOI: 10.1074/jbc.m110.130427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The 57-residue small hydrophilic endoplasmic reticulum-associated protein (SHERP) shows highly specific, stage-regulated expression in the non-replicative vector-transmitted stages of the kinetoplastid parasite, Leishmania major, the causative agent of human cutaneous leishmaniasis. Previous studies have demonstrated that SHERP localizes as a peripheral membrane protein on the cytosolic face of the endoplasmic reticulum and on outer mitochondrial membranes, whereas its high copy number suggests a critical function in vivo. However, the absence of defined domains or identifiable orthologues, together with lack of a clear phenotype in transgenic parasites lacking SHERP, has limited functional understanding of this protein. Here, we use a combination of biophysical and biochemical methods to demonstrate that SHERP can be induced to adopt a globular fold in the presence of anionic lipids or SDS. Cross-linking and binding studies suggest that SHERP has the potential to form a complex with the vacuolar type H(+)-ATPase. Taken together, these results suggest that SHERP may function in modulating cellular processes related to membrane organization and/or acidification during vector transmission of infective Leishmania.
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Affiliation(s)
- Benjamin Moore
- Division of Cell and Molecular Biology, Centre for Molecular Microbiology and Infection, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
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Whitmore L, Woollett B, Miles AJ, Klose DP, Janes RW, Wallace BA. PCDDB: the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata. Nucleic Acids Res 2010; 39:D480-6. [PMID: 21071417 PMCID: PMC3013654 DOI: 10.1093/nar/gkq1026] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Protein Circular Dichroism Data Bank (PCDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their associated experimental metadata. All entries undergo validation and curation procedures to ensure completeness, consistency and quality of the data included. A web-based interface enables users to browse and query sample types, sample conditions, experimental parameters and provides spectra in both graphical display format and as downloadable text files. The entries are linked, when appropriate, to primary sequence (UniProt) and structural (PDB) databases, as well as to secondary databases such as the Enzyme Commission functional classification database and the CATH fold classification database, as well as to literature citations. The PCDDB is available at: http://pcddb.cryst.bbk.ac.uk.
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Affiliation(s)
- Lee Whitmore
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
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Abstract
Summary: The defined secondary structure of proteins method is often considered the gold standard for assignment of secondary structure from three-dimensional coordinates. However, there are alternative methods. ‘2Struc: The Secondary Structure Server’ has been created as a single point of access for eight different secondary structure assignment methods. It has been designed to enable comparisons between methods for analyzing the secondary structure content for a single protein. It also includes a second functionality, ‘Compare-the-Protein’ to enable comparisons of the secondary structure features from any one method to be made within a collection of nuclear magnetic resonance models, or between the crystal structures of two different proteins. Availability:http://2struc.cryst.bbk.ac.uk Contact:r.w.janes@qmul.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- D P Klose
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
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Wallace BA, Kohl N, Teeter MM. Crambin in phospholipid vesicles: Circular dichroism analysis of crystal structure relevance. Proc Natl Acad Sci U S A 2010; 81:1406-10. [PMID: 16593429 PMCID: PMC344844 DOI: 10.1073/pnas.81.5.1406] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Crambin, a hydrophobic plant seed protein that exhibits sequence homology to membrane-active plant toxins, was incorporated into phospholipid vesicles. Circular dichroism spectroscopy indicates that its structure in vesicles is nearly identical to its structure in 60% ethanol solution, the solvent from which the protein was crystallized. The secondary structure predicted from the circular dichroism data of the ethanol solution closely resembles that determined by x-ray diffraction of the crystals. This agreement suggests that the x-ray structure may form a useful basis for modeling the structure and behavior of lipophilic plant toxins. Finally, because the structure of crambin has been determined in an organic solvent medium, it provides a protein standard for examination of the effect of solvent dipole moment on the circular dichroism spectra of proteins, which may be important for interpretation of data for membrane proteins.
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Affiliation(s)
- B A Wallace
- Department of Biochemistry, Columbia University, New York, NY 10032
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Wallace BA, Veatch WR, Blout ER. The effects of lipid environment, ion-binding and chemical modifications on the structure of the gramicidin transmembrane channel. Biophys J 2010; 37:197-9. [PMID: 19431476 DOI: 10.1016/s0006-3495(82)84667-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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