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Wei C, Pohorille A. Multi-oligomeric states of alamethicin ion channel: Assemblies and conductance. Biophys J 2023; 122:2531-2543. [PMID: 37161094 PMCID: PMC10323028 DOI: 10.1016/j.bpj.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/03/2023] [Accepted: 05/04/2023] [Indexed: 05/11/2023] Open
Abstract
Transmembrane assemblies of the peptaibol alamethicin (ALM) are among the most extensively studied ion channels not only because of their antimicrobial activity but also as models for channel structure and aggregation. In this study, several oligomeric states of ALM are investigated with molecular dynamics simulations to establish properties of the channel and obtain free energy profiles for ion transport and the corresponding values of conductance. The hexamer, heptamer, and octamer of ALM in phospholipid membrane are found to be stable but highly dynamic in barrel-stave structures, with calculated conductance equal to 18, 195, and 1270 pS, respectively, in 1 M KCl ion solution. The corresponding free energy profiles, reported for the first time, are reconstructed from simulations at applied voltage of 200 mV with the aid of the electrodiffusion model both with and without the knowledge of diffusivity. The calculated free energy barriers are equal to 2.5, 1.5, and 0.5 kcal/mol for K+ and 4.0, 2.2, and 1.5 kcal/mol for Cl-, for hexamer, heptamer, and octamer, respectively. The calculated conductance and the ratio between conductance in consecutive states are in good agreement with those measured experimentally. This suggests that the hexamer is the lowest conducting state, with measured conductance equal to 19 pS. The selectivity of K+ over Cl- is calculated as 1.5 and 2.3 for the octameric and heptameric channels, close to the selectivity measured for high-conductance states. Selectivity increases to 13 in the hexameric channel in which the narrowest Gln7 site has a pore radius of only ∼1.6 Å, again in accord with experiment. A good agreement found between calculated and measured conductance through a hexamer templated on cyclodextrin lands additional support for the results of our simulations, and the comparison with ALM reveals the dependence of conductance on the nature of phospholipid membrane.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Moffett Field, California; SETI Institute, Mountain View, California.
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2
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Sancho-Vaello E, Gil-Carton D, François P, Bonetti EJ, Kreir M, Pothula KR, Kleinekathöfer U, Zeth K. The structure of the antimicrobial human cathelicidin LL-37 shows oligomerization and channel formation in the presence of membrane mimics. Sci Rep 2020; 10:17356. [PMID: 33060695 PMCID: PMC7562864 DOI: 10.1038/s41598-020-74401-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 09/26/2020] [Indexed: 12/22/2022] Open
Abstract
The human cathelicidin LL-37 serves a critical role in the innate immune system defending bacterial infections. LL-37 can interact with molecules of the cell wall and perforate cytoplasmic membranes resulting in bacterial cell death. To test the interactions of LL-37 and bacterial cell wall components we crystallized LL-37 in the presence of detergents and obtained the structure of a narrow tetrameric channel with a strongly charged core. The formation of a tetramer was further studied by cross-linking in the presence of detergents and lipids. Using planar lipid membranes a small but defined conductivity of this channel could be demonstrated. Molecular dynamic simulations underline the stability of this channel in membranes and demonstrate pathways for the passage of water molecules. Time lapse studies of E. coli cells treated with LL-37 show membrane discontinuities in the outer membrane followed by cell wall damage and cell death. Collectively, our results open a venue to the understanding of a novel AMP killing mechanism and allows the rational design of LL-37 derivatives with enhanced bactericidal activity.
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Affiliation(s)
- Enea Sancho-Vaello
- Unidad de Biofisica, Centro Mixto Consejo Superior de Investigaciones Cientificas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, Spain.,Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - David Gil-Carton
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160, Derio, Spain
| | - Patrice François
- Genomic Research Laboratory, Department of Medical Specialities, Geneva University Hospitals, University of Geneva, Genève, Switzerland
| | - Eve-Julie Bonetti
- Genomic Research Laboratory, Department of Medical Specialities, Geneva University Hospitals, University of Geneva, Genève, Switzerland
| | - Mohamed Kreir
- Nanion Technologies GmbH, Gabrielenstraße 9, 80636, Munich, Germany.,Janssen Pharmaceutica NV, Janssen R&D, Nonclinical Safety, Beerse, Belgium
| | - Karunakar Reddy Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Kornelius Zeth
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark.
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3
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Pohorille A, Wilson MA, Wei C. Validity of the Electrodiffusion Model for Calculating Conductance of Simple Ion Channels. J Phys Chem B 2016; 121:3607-3619. [PMID: 27936743 DOI: 10.1021/acs.jpcb.6b09598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We examine the validity and utility of the electrodiffusion (ED) equation, i.e., the generalized Nernst-Planck equation, to characterize, in combination with molecular dynamics, the electrophysiological behavior of simple ion channels. As models, we consider three systems-two naturally occurring channels formed by α-helical bundles of peptaibols, trichotoxin, and alamethicin, and a synthetic, hexameric channel, formed by a peptide that contains only leucine and serine. All these channels mediate transport of potassium and chloride ions. Starting with equilibrium properties, such as the potential of mean force experienced by an ion traversing the channel and diffusivity, obtained from molecular dynamics simulations, the ED equation can be used to determine the full current-voltage dependence with modest or no additional effort. The potential of mean force can be obtained not only from equilibrium simulations, but also, with comparable accuracy, from nonequilibrium simulations at a single voltage. The main assumptions underlying the ED equation appear to hold well for the channels and voltages studied here. To expand the utility of the ED equation, we examine what are the necessary and sufficient conditions for Ohmic and nonrectifying behavior and relate deviations from this behavior to the shape of the ionic potential of mean force.
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Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,Department of Pharmaceutical Chemistry University of California , San Francisco, California 94132, United States
| | - Michael A Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,SETI Institute , 189 N Bernardo Ave #200, Mountain View, California 94043, United States
| | - Chenyu Wei
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,Department of Pharmaceutical Chemistry University of California , San Francisco, California 94132, United States
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Noshiro D, Asami K, Futaki S. Control of leakage activities of alamethicin analogs by metals: Side chain-dependent adverse gating response to Zn2+. Bioorg Med Chem 2012; 20:6870-6. [DOI: 10.1016/j.bmc.2012.09.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 09/16/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
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5
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Alpha-synuclein pore forming activity upon membrane association. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2876-83. [DOI: 10.1016/j.bbamem.2012.07.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 07/09/2012] [Accepted: 07/11/2012] [Indexed: 01/31/2023]
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6
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Hjørringgaard CU, Vad BS, Matchkov VV, Nielsen SB, Vosegaard T, Nielsen NC, Otzen DE, Skrydstrup T. Cyclodextrin-scaffolded alamethicin with remarkably efficient membrane permeabilizing properties and membrane current conductance. J Phys Chem B 2012; 116:7652-9. [PMID: 22676384 DOI: 10.1021/jp2098679] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial resistance to classical antibiotics is a serious medical problem, which continues to grow. Small antimicrobial peptides represent a potential solution and are increasingly being developed as novel therapeutic agents. Many of these peptides owe their antibacterial activity to the formation of trans-membrane ion-channels resulting in cell lysis. However, to further develop the field of peptide antibiotics, a thorough understanding of their mechanism of action is needed. Alamethicin belongs to a class of peptides called peptaibols and represents one of these antimicrobial peptides. To examine the dynamics of assembly and to facilitate a thorough structural evaluation of the alamethicin ion-channels, we have applied click chemistry for the synthesis of templated alamethicin multimers covalently attached to cyclodextrin-scaffolds. Using oriented circular dichroism, calcein release assays, and single-channel current measurements, the α-helices of the templated multimers were demonstrated to insert into lipid bilayers forming highly efficient and remarkably stable ion-channels.
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Affiliation(s)
- Claudia U Hjørringgaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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7
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Noshiro D, Asami K, Futaki S. Metal-assisted channel stabilization: disposition of a single histidine on the N-terminus of alamethicin yields channels with extraordinarily long lifetimes. Biophys J 2010; 98:1801-8. [PMID: 20441743 DOI: 10.1016/j.bpj.2010.01.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 11/08/2009] [Accepted: 01/04/2010] [Indexed: 10/19/2022] Open
Abstract
Alamethicin, a member of the peptaibol family of antibiotics, is a typical channel-forming peptide with a helical structure. The self-assembly of the peptide in the membranes yields voltage-dependent channels. In this study, three alamethicin analogs possessing a charged residue (His, Lys, or Glu) on their N-termini were designed with the expectation of stabilizing the transmembrane structure. A slight elongation of channel lifetime was observed for the Lys and Glu analogs. On the other hand, extensive stabilization of certain channel open states was observed for the His analog. This stabilization was predominantly observed in the presence of metal ions such as Zn(2+), suggesting that metal coordination with His facilitates the formation of a supramolecular assembly in the membranes. Channel stability was greatly diminished by acetylation of the N-terminal amino group, indicating that the N-terminal amino group also plays an important role in metal coordination.
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Affiliation(s)
- Daisuke Noshiro
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
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8
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Strandberg E, Tremouilhac P, Wadhwani P, Ulrich AS. Synergistic transmembrane insertion of the heterodimeric PGLa/magainin 2 complex studied by solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1667-79. [DOI: 10.1016/j.bbamem.2008.12.018] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 11/21/2008] [Accepted: 12/11/2008] [Indexed: 11/16/2022]
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9
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Maddau L, Cabras A, Franceschini A, Linaldeddu BT, Crobu S, Roggio T, Pagnozzi D. Occurrence and characterization of peptaibols from Trichoderma citrinoviride, an endophytic fungus of cork oak, using electrospray ionization quadrupole time-of-flight mass spectrometry. MICROBIOLOGY-SGM 2009; 155:3371-3381. [PMID: 19574303 DOI: 10.1099/mic.0.030916-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A cork oak endophytic strain of Trichoderma citrinoviride, previously selected for its antagonistic potential against various fungal pathogens involved in oak decline, was screened for the production of bioactive secondary metabolites. From liquid culture a mixture of polypeptide antibiotics (peptaibols) belonging to the paracelsin family was isolated and characterized. This peptide mixture was purified by column chromatography and preparative TLC on silica gel, and separated by analytical HPLC. It was analysed by MALDI-TOF MS and nano-ESI-QTOF MS. Tandem mass experiments were performed to determine the amino acid sequences based on the fragmentation pattern of selected parent ions. The mixture comprised 20-residue peptides with C-terminal phenylalaninol and N-terminal acetylation. Twenty-eight amino acid sequences were identified, and amino acid exchanges were located in positions 6, 9, 12 and 17. Among them, seven sequences are new as compared to those reported in the database specifically for peptaibols and in the literature. In addition, we obtained experimental evidence suggesting the existence of non-covalent dimeric forms (homo- and hetero-) of the various peptaibol species. The peptide mixture showed strong antifungal activity toward seven important forest tree pathogens, and it was highly toxic in an Artemia salina (brine shrimp) bioassay. These results emphasize the cryptic role of endophytic fungi as a source of novel bioactive natural products and biocontrol agents.
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Affiliation(s)
- Lucia Maddau
- Dipartimento di Protezione delle Piante, Sezione di Patologia Vegetale, Università di Sassari, Via E. De Nicola 9, 07100 Sassari, Italy
| | - Annalisa Cabras
- Dipartimento di Protezione delle Piante, Sezione di Patologia Vegetale, Università di Sassari, Via E. De Nicola 9, 07100 Sassari, Italy
| | - Antonio Franceschini
- Dipartimento di Protezione delle Piante, Sezione di Patologia Vegetale, Università di Sassari, Via E. De Nicola 9, 07100 Sassari, Italy
| | - Benedetto T Linaldeddu
- Dipartimento di Protezione delle Piante, Sezione di Patologia Vegetale, Università di Sassari, Via E. De Nicola 9, 07100 Sassari, Italy
| | | | - Tonina Roggio
- Porto Conte Ricerche Srl, Tramariglio, Alghero, Italy
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10
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Dittmer J, Thøgersen L, Underhaug J, Bertelsen K, Vosegaard T, Pedersen JM, Schiøtt B, Tajkhorshid E, Skrydstrup T, Nielsen NC. Incorporation of Antimicrobial Peptides into Membranes: A Combined Liquid-State NMR and Molecular Dynamics Study of Alamethicin in DMPC/DHPC Bicelles. J Phys Chem B 2009; 113:6928-37. [DOI: 10.1021/jp811494p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jens Dittmer
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Denmark, Laboratoire de Physique de l’Etat Condensé (LPEC), Université du Maine, Le Mans, France, Bioinformatics Research Center (BiRC), University of Aarhus, Denmark, and Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Lea Thøgersen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Denmark, Laboratoire de Physique de l’Etat Condensé (LPEC), Université du Maine, Le Mans, France, Bioinformatics Research Center (BiRC), University of Aarhus, Denmark, and Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Jarl Underhaug
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Denmark, Laboratoire de Physique de l’Etat Condensé (LPEC), Université du Maine, Le Mans, France, Bioinformatics Research Center (BiRC), University of Aarhus, Denmark, and Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Denmark, Laboratoire de Physique de l’Etat Condensé (LPEC), Université du Maine, Le Mans, France, Bioinformatics Research Center (BiRC), University of Aarhus, Denmark, and Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Denmark, Laboratoire de Physique de l’Etat Condensé (LPEC), Université du Maine, Le Mans, France, Bioinformatics Research Center (BiRC), University of Aarhus, Denmark, and Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Jan M. Pedersen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Denmark, Laboratoire de Physique de l’Etat Condensé (LPEC), Université du Maine, Le Mans, France, Bioinformatics Research Center (BiRC), University of Aarhus, Denmark, and Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Denmark, Laboratoire de Physique de l’Etat Condensé (LPEC), Université du Maine, Le Mans, France, Bioinformatics Research Center (BiRC), University of Aarhus, Denmark, and Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Emad Tajkhorshid
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Denmark, Laboratoire de Physique de l’Etat Condensé (LPEC), Université du Maine, Le Mans, France, Bioinformatics Research Center (BiRC), University of Aarhus, Denmark, and Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Troels Skrydstrup
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Denmark, Laboratoire de Physique de l’Etat Condensé (LPEC), Université du Maine, Le Mans, France, Bioinformatics Research Center (BiRC), University of Aarhus, Denmark, and Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Niels Chr. Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Denmark, Laboratoire de Physique de l’Etat Condensé (LPEC), Université du Maine, Le Mans, France, Bioinformatics Research Center (BiRC), University of Aarhus, Denmark, and Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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11
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Salnikov ES, Zotti MD, Formaggio F, Li X, Toniolo C, OʼNeil JDJ, Raap J, Dzuba SA, Bechinger B. Alamethicin Topology in Phospholipid Membranes by Oriented Solid-state NMR and EPR Spectroscopies: a Comparison. J Phys Chem B 2009; 113:3034-42. [DOI: 10.1021/jp8101805] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evgeniy S. Salnikov
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Marta De Zotti
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Fernando Formaggio
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Xing Li
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Claudio Toniolo
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Joe D. J. OʼNeil
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jan Raap
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Burkhard Bechinger
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
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12
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Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. Biophys J 2008; 95:4337-47. [PMID: 18676652 DOI: 10.1529/biophysj.108.133330] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a simulation study where different resolutions, namely coarse-grained (CG) and all-atom (AA) molecular dynamics simulations, are used sequentially to combine the long timescale reachable by CG simulations with the high resolution of AA simulations, to describe the complete processes of peptide aggregation and pore formation by alamethicin peptides in a hydrated lipid bilayer. In the 1-micros CG simulations the peptides spontaneously aggregate in the lipid bilayer and exhibit occasional transitions between the membrane-spanning and the surface-bound configurations. One of the CG systems at t = 1 micros is reverted to an AA representation and subjected to AA simulation for 50 ns, during which water molecules penetrate the lipid bilayer through interactions with the peptide aggregates, and the membrane starts leaking water. During the AA simulation significant deviations from the alpha-helical structure of the peptides are observed, however, the size and arrangement of the clusters are not affected within the studied time frame. Solid-state NMR experiments designed to match closely the setup used in the molecular dynamics simulations provide strong support for our finding that alamethicin peptides adopt a diverse set of configurations in a lipid bilayer, which is in sharp contrast to the prevailing view of alamethicin oligomers formed by perfectly aligned helical alamethicin peptides in a lipid bilayer.
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13
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Lee JY, Yang ST, Lee SK, Jung HH, Shin SY, Hahm KS, Kim JI. Salt-resistant homodimeric bactenecin, a cathelicidin-derived antimicrobial peptide. FEBS J 2008; 275:3911-20. [DOI: 10.1111/j.1742-4658.2008.06536.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Taira J, Jelokhani-Niaraki M, Osada S, Kato F, Kodama H. Ion-Channel Formation Assisted by Electrostatic Interhelical Interactions in Covalently Dimerized Amphiphilic Helical Peptides. Biochemistry 2008; 47:3705-14. [DOI: 10.1021/bi702371e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Junichi Taira
- Department of Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan, Department of Chemistry, Faculty of Science, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada, and Department of Applied Biological Science, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Masoud Jelokhani-Niaraki
- Department of Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan, Department of Chemistry, Faculty of Science, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada, and Department of Applied Biological Science, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Satoshi Osada
- Department of Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan, Department of Chemistry, Faculty of Science, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada, and Department of Applied Biological Science, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Fumio Kato
- Department of Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan, Department of Chemistry, Faculty of Science, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada, and Department of Applied Biological Science, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Hiroaki Kodama
- Department of Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan, Department of Chemistry, Faculty of Science, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada, and Department of Applied Biological Science, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
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15
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Mayer M, Semetey V, Gitlin I, Yang J, Whitesides GM. Using ion channel-forming peptides to quantify protein-ligand interactions. J Am Chem Soc 2008; 130:1453-65. [PMID: 18179217 DOI: 10.1021/ja077555f] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper proposes a method for sensing affinity interactions by triggering disruption of self-assembly of ion channel-forming peptides in planar lipid bilayers. It shows that the binding of a derivative of alamethicin carrying a covalently attached sulfonamide ligand to carbonic anhydrase II (CA II) resulted in the inhibition of ion channel conductance through the bilayer. We propose that the binding of the bulky CA II protein (MW approximately 30 kD) to the ion channel-forming peptides (MW approximately 2.5 kD) either reduced the tendency of these peptides to self-assemble into a pore or extracted them from the bilayer altogether. In both outcomes, the interactions between the protein and the ligand lead to a disruption of self-assembled pores. Addition of a competitive inhibitor, 4-carboxybenzenesulfonamide, to the solution released CA II from the alamethicin-sulfonamide conjugate and restored the current flow across the bilayer by allowing reassembly of the ion channels in the bilayer. Time-averaged recordings of the current over discrete time intervals made it possible to quantify this monovalent ligand binding interaction. This method gave a dissociation constant of approximately 2 microM for the binding of CA II to alamethicin-sulfonamide in the bilayer recording chamber: this value is consistent with a value obtained independently with CA II and a related sulfonamide derivative by isothermal titration calorimetry.
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Affiliation(s)
- Michael Mayer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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16
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Futaki S, Asami K. Ligand-induced extramembrane conformation switch controlling alamethicin assembly and the channel current. Chem Biodivers 2007; 4:1313-22. [PMID: 17589883 DOI: 10.1002/cbdv.200790112] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this review, we describe our approach to creating artificial receptor-channel proteins or sensor systems, using an extramembrane segment conformationally switchable by external stimuli. Alamethicin is known to self-assemble in membranes to form ion channels with various open states. Employment of an alpha-helical leucine-zipper segment resulted in the effective modulation of the association states of alamethicin to produce a single predominant channel-open state. A decrease in the helical content of the extramembrane segments was found to induce a channel-current increase. Therefore, conformational changes in the extramembrane segments induced by the interaction with ligands can be reflected in the current levels.
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Affiliation(s)
- Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
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17
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Leitgeb B, Szekeres A, Manczinger L, Vágvölgyi C, Kredics L. The history of alamethicin: a review of the most extensively studied peptaibol. Chem Biodivers 2007; 4:1027-51. [PMID: 17589875 DOI: 10.1002/cbdv.200790095] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Balázs Leitgeb
- Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, Hungary
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18
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Abstract
In this short review article, the effects of covalent tethering of alamethicin molecules on channel-forming behavior are described. Broadly speaking, these chemical modifications have provided insight into all three aspects of channel behavior: the structure of the conducting state, the ion-selectivity and ion-permeation properties, and the voltage dependence. Each of these aspects are discussed in turn.
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Affiliation(s)
- G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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19
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Okazaki T, Nagaoka Y, Asami K. Ion channels of N-terminally linked alamethicin dimers: enhancement of cation-selectivity by substitution of Glu for Gln at position 7. Bioelectrochemistry 2006; 70:380-6. [PMID: 16814617 DOI: 10.1016/j.bioelechem.2006.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Revised: 05/08/2006] [Accepted: 05/16/2006] [Indexed: 10/24/2022]
Abstract
Alamethicin forms voltage-gated ion channels that have moderate cation-selectivity. The enhancement of the cation-selectivity by introducing negatively charged residues at positions 7 and 18 has been studied using the tethered homodimers of alamethicin with Q7 and E18 (di-alm-Q7E18) and its analog with E7 and Q18 (di-alm-E7Q18). In the dimeric peptides, monomer peptides are linked at the N-termini by a disulfide bond. Both the peptides formed long lasting ion channels at cis-positive voltages when added to the cis-side membrane. Their long open duration enabled us to obtain current-voltage (I-V(m)) relations and reversal potentials at the single-channel level by applying a voltage ramp during the channel opening. The reversal potentials measured in asymmetric KCl solutions indicated that ionized E7 provided strong cation-selectivity, whereas ionized E18 little influenced the charge selectivity. This was also the case for the macroscopic charge selectivity determined from the reversal potentials obtained by the macroscopic I-V(m) measurements. The results are accounted for by stronger electrostatic interactions between permeant ions and negatively charged residues at the narrowest part of the pore than at the pore mouth.
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Affiliation(s)
- Takashi Okazaki
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
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20
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Peggion C, Coin I, Toniolo C. Total synthesis in solution of alamethicin F50/5 by an easily tunable segment condensation approach. Biopolymers 2005; 76:485-93. [PMID: 15499566 DOI: 10.1002/bip.20161] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A total synthesis in solution of the 19-mer peptide component F50/5 of alamethicin, the most extensively investigated among the channel-former peptaibol antibiotics, is reported. Three peptide segments (A, B, C) were prepared and assembled, followed by incorporation of the acetylated N-terminal amino acid. The synthetic modules B and C are characterized by three Glu(OMe) residues (at positions 7, 18, and 19) that, after completion of the synthesis, were reacted with ammonia to provide alamethicin F50/5. By use of this general strategy, we also prepared the [Gln7, Glu(OMe)18,19] alamethicin F50/5 analogue. The purity and conformation of the final products were assessed by chromatographic, spectrometric, and spectroscopic techniques. This tunable segment condensation approach will pave the way for an easy synthesis of alamethicin analogues bearing amino acid residues with desired side-chain probes even at the N-terminus and in internal positions of the sequence.
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Affiliation(s)
- Cristina Peggion
- Department of Chemistry, University of Padova, 35131 Padova, Italy
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21
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Grotenbreg GM, Witte MD, van Hoof PAV, Spalburg E, Reiss P, Noort D, de Neeling AJ, Koert U, van der Marel GA, Overkleeft HS, Overhand M. Synthesis and biological evaluation of gramicidin S dimers. Org Biomol Chem 2005; 3:233-8. [PMID: 15717418 DOI: 10.1039/b414618b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design and synthesis of analogues of the cyclic beta-sheet gramicidin S (GS), having additional functionalities in their turn regions, is reported. The monomeric GS analogues were transformed into dimers and their activities towards biological membranes, through antimicriobial and hemolytic assays, were evaluated. Finally, conductivity measurements have been performed to elucidate ion channel forming properties.
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Affiliation(s)
- Gijsbert M Grotenbreg
- Leiden Institute of Chemistry, Gorlaeus Laboratories, P. O. Box 9502, 2300, RA Leiden, The Netherlands
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22
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Futaki S, Zhang Y, Kiwada T, Nakase I, Yagami T, Oiki S, Sugiura Y. Gramicidin-based channel systems for the detection of protein-ligand interaction. Bioorg Med Chem 2004; 12:1343-50. [PMID: 15018906 DOI: 10.1016/j.bmc.2003.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2003] [Revised: 06/04/2003] [Accepted: 06/05/2003] [Indexed: 10/26/2022]
Abstract
To detect protein-ligand interaction a gramicidin-based sensor was developed. Biotin was tagged to the C-terminus of gramicidin (Gram-bio 1). The biotin-moiety, which faces the electrolyte, gave little effect on single-channel conductance. Streptavidin added to the electrolyte was detected by Gram-bio 1 through the monitoring channel current using the planar bilayer system. The suppression of macroscopic currents and the acceleration of their decaying time course were observed in a concentration dependent manner. In the single-channel level, however, no significant effect on the single-channel conductance and the open dwell time was observed upon addition of streptavidin. Therefore, streptavidin neither blocked the open channel nor changed the stability of the conducting dimer. Insertion of a linker between gramicidin and biotin did not change the streptavidin-sensitivity of the current reduction. We conclude that the binding of streptavidin to the Gram-bio 1 shifted the distribution of the complex from the membrane to the electrolyte and, thus, reduced the formation of conducting dimer of Gram-bio 1 in the membrane. Interaction of biotin with an anti-biotin antibody was also observed using this system, indicating that this system is applicable for the detection of protein-ligand interaction having a binding constant of approximately 10(8-9) M(-1) or more. Both the adamantane-tagged gramicidin for detection of beta-cyclodextrin and the Strep Tag-II-tagged gramicidin for detection of streptavidin (binding constant: approximately 10(5) M(-1) or less) failed to respond. Thus, high-affinity ligands upon tagging to gramicidin render the gramicidin-based sensor able to execute as a real-time monitoring system for protein-ligand interaction.
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Affiliation(s)
- Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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23
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Jung G, Redemann T, Kroll K, Meder S, Hirsch A, Boheim G. Template-free self-assembling fullerene and lipopeptide conjugates of alamethicin form voltage-dependent ion channels of remarkable stability and activity. J Pept Sci 2004; 9:784-98. [PMID: 14658798 DOI: 10.1002/psc.525] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
N- and C-terminally modified with fullerene or lipopeptide alamethicin molecules were designed for the formation of template-free, self-assembling, voltage-dependent ion conducting channels. The automated solid phase synthesis of the alamethicin-F30 sequence was performed by in situ fluoride activation on 2-chlorotritylchloride-polystyrene resin and the conjugation with fullerenes-C60 and -C70 was carried out in solution. Voltage-dependent bilayer experiments revealed preferred channel sizes for C-terminal alamethicin F30-fullerene-C60 and -C70 conjugates and higher activity compared with native alamethicin, whereas N-terminally linked fullerene balls destabilize pore formation. C-terminal alamethicin F30-fullerene-C70 conjugates show pore states with remarkably long lifetimes of seconds. C-terminal lipopeptide conjugates of alamethicin were prepared by coupling via short peptide spacers with synthetic tripalmitoyl-S-glyceryl-cysteine. which represents the strong membrane anchoring N-terminus of bacterial lipoprotein. Alamethicin-lipopeptide conjugates exhibit high channel forming activities, whereby they self-assemble and adopt preferred pore states with extremely long lifetimes. The novel membrane modifying peptaibol constructs are valuable lead compounds for developments in sensorics related to transmembrane ion conductance.
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Affiliation(s)
- Günther Jung
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany.
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24
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Lougheed T, Zhang Z, Andrew Woolley G, Borisenko V. Engineering charge selectivity in model ion channels. Bioorg Med Chem 2004; 12:1337-42. [PMID: 15018905 DOI: 10.1016/j.bmc.2003.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2003] [Revised: 06/03/2003] [Accepted: 06/08/2003] [Indexed: 11/21/2022]
Abstract
Most ion channel proteins exhibit some degree of charge selectivity, that is, an ability to conduct ions of one charge more efficiently than ions of the opposite charge. The structural origins of charge selectivity remain incompletely understood despite recent advances in the determination of cation-selective and anion-selective channel protein structures. Helix bundle channels formed via self-assembly of the peptide alamethicin provide a tractable model system for exploring the structural basis of charge selectivity. We synthesized covalently-linked alamethicin dimers, with amino acid substitutions at position 18 [lysine (Lys), arginine (Arg), glutamine (Gln), 2,3-diaminopropionic acid (Dpr)] in each helix, to assess the role of this position as a charge-selectivity determinant in alamethicin channels. Of the position 18 substitutions investigated, the Lys derivative exhibited the greatest degree of anion selectivity. Arg-containing channels were slightly less anion-selective than Lys. Interestingly, Dpr channels showed cation selectivity nearly equivalent to that exhibited by the neutral Gln derivative. We suggest that this result is due to a wider pore diameter that permits a greater number of counter-ions leading to enhanced charge screening and a lower effective side-chain positive charge.
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Affiliation(s)
- Tyler Lougheed
- Department of Chemistry, 80 St George St University of Toronto, Toronto, Ontario, Canada M5S 3H6
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25
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Okazaki T, Sakoh M, Nagaoka Y, Asami K. Ion channels of alamethicin dimer N-terminally linked by disulfide bond. Biophys J 2003; 85:267-73. [PMID: 12829482 PMCID: PMC1303083 DOI: 10.1016/s0006-3495(03)74472-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A covalent dimer of alamethicin Rf30 was synthesized by linking the N-termini by a disulfide bond. When the dimer peptides were added to the cis-side of a diphytanoyl PC membrane, macroscopic channel current was induced only at cis positive voltages. The single-channel recordings showed several conductance levels that were alternately stabilized. These results indicate that the dimer peptides form stable channels by N-terminal insertion like alamethicin and that most of the pores are assembled from even numbers of helices. Taking advantages of the long open duration of the dimer peptide channels, the current-voltage (I-V) relations of the single-channels were obtained by applying fast voltage ramps during the open states. The I-V relations showed rectification, such that current from the cis-side toward the trans-side is larger than that in the opposite direction. The intrinsic rectification is mainly attributed to the macro dipoles of parallel peptide helices surrounding a central pore.
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Affiliation(s)
- Takashi Okazaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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26
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Sakoh M, Okazaki T, Nagaoka Y, Asami K. N-terminal insertion of alamethicin in channel formation studied using its covalent dimer N-terminally linked by disulfide bond. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1612:117-21. [PMID: 12729937 DOI: 10.1016/s0005-2736(03)00110-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Alamethicin is supposed to form helix-bundle-type channels by inserting the N terminus into bilayer lipid membranes under sufficient voltages. The N-terminal insertion has been studied with an alamethicin dimer (di-alm) N-terminally linked by a disulfide bond and by the asymmetric addition of dithiothreitol (DTT) and tetrathionate (TT) to the membrane. When di-alm was added to the cis-side membrane, it forms long-lasting channels with the lifetime tau of about 100 ms at cis-positive voltages. The lifetime was reduced to a few milliseconds by addition of DTT to the cis-side membrane, indicating that most of the channels were formed by the monomers (alm-SH) that resulted from the cleavage of the disulfide bond in di-alm. The succeeding addition of TT to the trans-side produced channels of tau=10-20 ms besides the channels of alm-SH. The results suggested that TT reacted with the N-terminal thiol group of alm-SH located at the trans-side of the membrane to alter the lifetime. The N-terminal insertion of alamethicin helices by voltage activation, therefore, was confirmed.
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Affiliation(s)
- Machiko Sakoh
- Institute for Chemical Research, Kyoto University, Uji, 611-0011, Kyoto, Japan
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27
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Tieleman DP, Borisenko V, Sansom MSP, Woolley GA. Understanding pH-dependent selectivity of alamethicin K18 channels by computer simulation. Biophys J 2003; 84:1464-9. [PMID: 12609853 PMCID: PMC1302720 DOI: 10.1016/s0006-3495(03)74959-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Alamethicin K18 is a covalently linked alamethicin dimer in which the glutamine residue at position 18 in each helix has been replaced by a lysine residue. As described in previous work, channels formed by this peptide show pH-dependent selectivity. The maximum anion selectivity of the putative octameric conducting state is obtained at pH 7 or lower. Inasmuch as no change in selectivity is seen between pH 7 and pH 3, and because protons are expected to be in equilibrium with the open state of the channel during a selectivity measurement, the channel is believed to be fully charged (i.e., all eight lysines protonated) at pH 7. In an effort to understand how such a highly charged channel structure is stable in membranes and why it is not more selective for anions, we have performed a number of computer simulations of the system. Molecular dynamics simulations of 10 ns each of the octameric bundle in a lipid bilayer environment are presented, with either zero, four, or eight lysines charged in the absence of salt, and with eight lysines charged in the presence of 0.5 M and 1 M KCl. When no salt is present and all lysines are charged, on average 1.9 Cl(-) ions are inside the channel and the channel significantly deforms. With 0.5 M KCl present, 2.9 Cl(-) ions are inside the channel. With 1 M KCl present, four Cl(-) ions are present and the channel maintains a regular structure. Poisson-Boltzmann calculations on models of the octameric channel also predict an average of 2-4 Cl(-) ions near the lysine residues as a function of ionic strength. These counterions lower the apparent charge of the channel, which may underlie the decrease in selectivity observed experimentally with increasing salt concentrations. We suggest that to increase the selectivity of Alm K18 channels, positive charges could be engineered in a narrower part of the channel.
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Affiliation(s)
- D Peter Tieleman
- Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada.
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28
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Duclohier H, Alder G, Kociolek K, Leplawy MT. Channel properties of template assembled alamethicin tetramers. J Pept Sci 2003; 9:776-83. [PMID: 14658797 DOI: 10.1002/psc.523] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The multiple conductance levels displayed by the antibiotic alamethicin in planar lipid bilayers is explained by a dynamic 'barrel-stave' model, the conducting pore resulting from the aggregation of up to ten helical amphipathic helical monomers. However, the precise assignment of an oligomerization state to a particular single-channel conductance substate is far from being experimentally clear. In addition, it could be useful to tailor a given channel geometry to selectively allow the permeation of solutes with different molecular sizes, whilst retaining a high voltage-dependence. To control the aggregation state of the channel, the TASP (template assembled synthetic proteins) strategy was applied to synthesize structurally defined oligomers, i.e. dimer, trimer, tetramer. The modulation of conductance properties of three alamethicin tetramers with the length and flexibility of the linkers of the 'open' or linear template is described. It is shown that the introduction of an alanine between the contiguous lysines to which are tethered C-terminally modified alamethicin helical monomers stabilizes the open channel states, whereas the alanine substitution by Pro-Gly, a reverse beta-turn promoting motif, increases voltage-dependence and leads to single-channel conductance values more in line with the expected ones from a tetrameric bundle.
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Affiliation(s)
- Hervé Duclohier
- UMR 6026 CNRS-Université de Rennes I, Bâtiment 13, Campus de Beaulieu, 35042 Rennes, France.
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29
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Tieleman DP, Hess B, Sansom MSP. Analysis and evaluation of channel models: simulations of alamethicin. Biophys J 2002; 83:2393-407. [PMID: 12414676 PMCID: PMC1302328 DOI: 10.1016/s0006-3495(02)75253-3] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Alamethicin is an antimicrobial peptide that forms stable channels with well-defined conductance levels. We have used extended molecular dynamics simulations of alamethicin bundles consisting of 4, 5, 6, 7, and 8 helices in a palmitoyl-oleolyl-phosphatidylcholine bilayer to evaluate and analyze channel models and to link the models to the experimentally measured conductance levels. Our results suggest that four helices do not form a stable water-filled channel and might not even form a stable intermediate. The lowest measurable conductance level is likely to correspond to the pentamer. At higher aggregation numbers the bundles become less symmetrical. Water properties inside the different-sized bundles are similar. The hexamer is the most stable model with a stability comparable with simulations based on crystal structures. The simulation was extended from 4 to 20 ns or several times the mean passage time of an ion. Essential dynamics analyses were used to test the hypothesis that correlated motions of the helical bundles account for high-frequency noise observed in open channel measurements. In a 20-ns simulation of a hexameric alamethicin bundle, the main motions are those of individual helices, not of the bundle as a whole. A detailed comparison of simulations using different methods to treat long-range electrostatic interactions (a twin range cutoff, Particle Mesh Ewald, and a twin range cutoff combined with a reaction field correction) shows that water orientation inside the alamethicin channels is sensitive to the algorithms used. In all cases, water ordering due to the protein structure is strong, although the exact profile changes somewhat. Adding an extra 4-nm layer of water only changes the water ordering slightly in the case of particle mesh Ewald, suggesting that periodicity artifacts for this system are not serious.
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Affiliation(s)
- D Peter Tieleman
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
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30
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Mukai Y, Matsushita Y, Niidome T, Hatekeyama T, Aoyag H. Parallel and antiparallel dimers of magainin 2: their interaction with phospholipid membrane and antibacterial activity. J Pept Sci 2002; 8:570-7. [PMID: 12450326 DOI: 10.1002/psc.416] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Magainin 2 (M2) forms pores by associating with several other M2 molecules in lipid membranes and shows antibacterial activity. To examine the effect of M2 dimerization on biological activity and membrane interaction, parallel and antiparallel M2 dimers were prepared from two monomeric precursors. Antibacterial and haemolytic activities were enhanced by dimerization. CD measurements showed that both dimers and monomers have an alpha-helical structure in the presence of lipid vesicles. Tryptophan fluorescence shift and KI quenching studies showed that all the peptides were more deeply embedded in acidic liposomes than in neutral liposomes. Experiments on dye-leakage activity and membrane translocation of peptides suggest that dimers and monomers form pores through lipid membranes, although the pore formation may be accompanied by membrane disturbance. Although dimerization of M2 increased the interaction activity with lipid membranes, no appreciable difference between the activities of parallel and antiparallel M2 dimers was observed.
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Affiliation(s)
- Yasuhiro Mukai
- Department of Applied Chemistry, Faculty of Engineering, Nagasaki University, Nagasaki 852-8521, Japan
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31
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Zhang Y, Futaki S, Kiwada T, Sugiura Y. Detection of protein-ligand interaction on the membranes using C-terminus biotin-tagged alamethicin. Bioorg Med Chem 2002; 10:2635-9. [PMID: 12057652 DOI: 10.1016/s0968-0896(02)00105-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
C-terminal biotin-tagged alamethicin, which has several alpha-aminoisobutyric acid (Aib) residues in its sequence, was synthesized by the preparation of the protected peptide segment using the 2-chlorotrityl resin, followed by conjugation with biotin hydrazide. Suppression of the channel current of the biotin-tagged alamethicin by the addition of streptavidin to the electrolyte was monitorable in real time using the planar lipid-bilayer method. The system was also applicable to the detection of interaction of the biotin-tagged alamethicin with the anti-biotin antibody.
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Affiliation(s)
- Y Zhang
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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32
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Asami K, Okazaki T, Nagai Y, Nagaoka Y. Modifications of alamethicin ion channels by substitution of Glu-7 for Gln-7. Biophys J 2002; 83:219-28. [PMID: 12080114 PMCID: PMC1302141 DOI: 10.1016/s0006-3495(02)75163-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
To evaluate the role of charged residues facing a pore lumen in stability of channel structure and ion permeation, we studied electrical properties of ion channels formed by synthesized native alamethicins (Rf50 (alm-Q7Q18) and Rf30 (alm-Q7E18)) and their analogs with Glu-7 (alm-E7Q18 and alm-E7E18). The single-channel currents were measured over a pH range of 3.5 to 8.7 using planar bilayers of diphytanoyl PC. The peptides all showed multi-level current fluctuations in this pH range. At pH 3.5 the channels formed by the four peptides were similar to each other irrespective of the side chain differences at positions 7 and 18. The ionization of Glu-7 (E7) and Glu-18 (E18) above neutral pH reduced the relative probabilities of low-conductance states (levels 1 and 2) and increased those of high-conductance states (levels 4-6). The channel conductance of the peptides with E7 and/or E18, which was distinct from that of alm-Q7Q18, showed a marked pH-dependence, especially for low-conductance states. The ionization of E7 further reduced the stability of channel structure, altered the current-voltage curve from a superlinear relation to a sublinear one, and enhanced cation selectivity. These results indicate that ionized E7 strongly influences the channel structure and the ion permeation, in contrast to ionized E18.
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Affiliation(s)
- Koji Asami
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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33
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Shenkarev ZO, Balashova TA, Efremov RG, Yakimenko ZA, Ovchinnikova TV, Raap J, Arseniev AS. Spatial structure of zervamicin IIB bound to DPC micelles: implications for voltage-gating. Biophys J 2002; 82:762-71. [PMID: 11806918 PMCID: PMC1301885 DOI: 10.1016/s0006-3495(02)75438-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Zervamicin IIB is a 16-amino acid peptaibol that forms voltage-dependent ion channels with multilevel conductance states in planar lipid bilayers and vesicular systems. The spatial structure of zervamicin IIB bound to dodecylphosphocholine micelles was studied by nuclear magnetic resonance spectroscopy. The set of 20 structures obtained has a bent helical conformation with a mean backbone root mean square deviation value of approximately 0.2 A and resembles the structure in isotropic solvents (Balashova et al., 2000. NMR structure of the channel-former zervamicin IIB in isotropic solvents. FEBS Lett 466:333-336). The N-terminus represents an alpha-helix, whereas the C-terminal part has a mixed 3(10)/alpha(R) hydrogen-bond pattern. In the anisotropic micelle environment, the bending angle on Hyp10 (23 degrees) is smaller than that (47 degrees) in isotropic solvents. In the NOESY (Nuclear Overhauser Effect Spectroscopy) spectra, the characteristic attenuation of the peptide signals by 5- and 16-doxylstearate relaxation probes indicates a peripheral mode of the peptaibol binding to the micelle with the N-terminus immersed slightly deeper into micelle interior. Analysis of the surface hydrophobicity reveals that the zervamicin IIB helix is amphiphilic and well suited to formation of a tetrameric transmembrane bundle, according to the barrel-stave mechanism. The results are discussed in a context of voltage-driven peptaibol insertion into membrane.
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Affiliation(s)
- Z O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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34
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Bak M, Bywater RP, Hohwy M, Thomsen JK, Adelhorst K, Jakobsen HJ, Sørensen OW, Nielsen NC. Conformation of alamethicin in oriented phospholipid bilayers determined by (15)N solid-state nuclear magnetic resonance. Biophys J 2001; 81:1684-98. [PMID: 11509381 PMCID: PMC1301646 DOI: 10.1016/s0006-3495(01)75822-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The conformation of the 20-residue antibiotic ionophore alamethicin in macroscopically oriented phospholipid bilayers has been studied using (15)N solid-state nuclear magnetic resonance (NMR) spectroscopy in combination with molecular modeling and molecular dynamics simulations. Differently (15)N-labeled variants of alamethicin and an analog with three of the alpha-amino-isobutyric acid residues replaced by alanines have been investigated to establish experimental structural constraints and determine the orientation of alamethicin in hydrated phospholipid (dimyristoylphosphatidylcholine) bilayers and to investigate the potential for a major kink in the region of the central Pro(14) residue. From the anisotropic (15)N chemical shifts and (1)H-(15)N dipolar couplings determined for alamethicin with (15)N-labeling on the Ala(6), Val(9), and Val(15) residues and incorporated into phospholipid bilayer with a peptide:lipid molar ratio of 1:8, we deduce that alamethicin has a largely linear alpha-helical structure spanning the membrane with the molecular axis tilted by 10-20 degrees relative to the bilayer normal. In particular, we find compatibility with a straight alpha-helix tilted by 17 degrees and a slightly kinked molecular dynamics structure tilted by 11 degrees relative to the bilayer normal. In contrast, the structural constraints derived by solid-state NMR appear not to be compatible with any of several model structures crossing the membrane with vanishing tilt angle or the earlier reported x-ray diffraction structure (Fox and Richards, Nature. 300:325-330, 1982). The solid-state NMR-compatible structures may support the formation of a left-handed and parallel multimeric ion channel.
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Affiliation(s)
- M Bak
- Laboratory for Biomolecular NMR Spectroscopy, Department of Molecular and Structural Biology, Science Park, University of Aarhus, DK-8000 Aarhus C, Denmark
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35
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Hara T, Kodama H, Kondo M, Wakamatsu K, Takeda A, Tachi T, Matsuzaki K. Effects of peptide dimerization on pore formation: Antiparallel disulfide-dimerized magainin 2 analogue. Biopolymers 2001; 58:437-46. [PMID: 11180056 DOI: 10.1002/1097-0282(20010405)58:4<437::aid-bip1019>3.0.co;2-i] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To elucidate the effects of peptide dimerization on pore formation by magainin 2 (MG2), a covalently linked antiparallel dimer of the MG2 analogue [(F5Y, L6C, F16W, I20C-MG2)(2): II] was synthesized based on the dimer structure revealed by our NMR study. The interactions of the dimer with lipid bilayers were investigated by CD and fluorescence in comparison with a monomer analogue (F5Y, F16W-MG2: I). Similar to I, II was found to form a peptide-lipid supramolecular complex pore accompanied with lipid flip-flop and peptide translocation. The pore formed by II was characterized by a slightly larger pore diameter and a threefold longer lifetime than that of I, although the pore formation rate of the dimer was lower than that of the monomer. The coexistence of the dimer and the monomer exhibited slight but significant synergism in membrane permeabilization, which was maximal at a monomer/dimer ratio of 3. Therefore, we concluded that a pentameric pore composed of one pore-stabilizing dimer and three monomers maximized the overall leakage activity in keeping with our kinetic prediction.
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Affiliation(s)
- T Hara
- Department of Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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36
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Futaki S, Youjun Z, Sugiura Y. Detecting a tag on a channel opening: blockage of the biotinylated channels by streptavidin. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(00)02287-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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37
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Dé E, Chaloin L, Heitz A, Méry J, Molle G, Heitz F. Conformation and ion channel properties of a five-helix Bundle protein. J Pept Sci 2001; 7:41-9. [PMID: 11245204 DOI: 10.1002/psc.293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The primary amphipathic peptide Ac-Met-Gly-Leu-Gly-Leu-Trp-Leu-Leu-Val-Leu10-Ala-Ala-Ala-Leu-Gln-Gly-Ala-Lys-Lys-Lys20-Arg-Lys-Val-NH-CH2-CH2-SH called SPM was able to induce formation of ion channels into planar lipid bilayers with main conductance values of 75 and 950 pS in 1 M KCl. The 75 pS value can be attributed to an aggregate composed of five monomers since the corresponding five-unit bundle (5-SPM) also presented a 70 pS channels under the same conditions. The upper 950 pS level would be generated by a hexameric aggregate. Ion channels induced by both SPM and its pentameric bundle are slightly cation selective but not voltage-dependent. The structural studies showed that the SPM and 5-SPM possess mainly an alpha-helical structure (approximately 40%) and are strongly embedded in the bilayer. This behaviour and the strong hydrophobic interactions occurring between helices in the bundle induce a strong stabilization of 5-SPM in the bilayer and would be responsible for the stepwise current fluctuations observed during the incorporation of 5-SPM into the membrane.
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Affiliation(s)
- E Dé
- UMR 6522 CNRS, IFRMP 23, Faculté des Sciences, Mont-Saint-Aignan, France
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38
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Abstract
Ion-induced interfacial dynamics of phospholipid monolayers were studied by various electrochemical techniques. The lipid monolayers were constructed by using the mercapto derivatives of natural lipids that were self-assembled directly onto gold electrode surfaces in a tails-down fashion. The supported lipid assemblies appeared to act as rather effective electron-tunneling barriers with K3Fe(CN)6 as the redox probe, despite a relatively low surface coverage and/or a disordered surface structure. Upon the stimulation by alkaline-earth ions, the lipid layers appeared to undergo surface reorganization, exposing part of the electrode surface which resulted in the formation of microscopic mass-transfer lipid channels. The dimensions and/or the number of these channels increased with increasing ion concentrations, and this ion-gate effect appeared to be quite selective, with the most pronounced effects observed among the series of alkaline-earth ions with Ca2+.
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Affiliation(s)
- S Chen
- Department of Chemistry, Southern Illinois University, Carbondale 62901-4409, USA.
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39
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Abstract
Notwithstanding great advances in the engineering and structural analysis of globular proteins, relatively limited success has been achieved with membrane proteins--due largely to their intrinsic high insolubility and the concomitant difficulty in obtaining crystals. Progress with de novo synthesis of model membrane-interactive peptides presents an opportunity to construct simpler peptides with definable structures, and permits one to approach an understanding of the properties of the membrane proteins themselves. In the present article, we review how our laboratory and others have used peptide approaches to assess the detailed interactions of peptides with membranes, and primary folding at membrane surfaces and in membranes. Structural studies of model peptides identified the existence of a "threshold hydrophobicity," which controls spontaneous peptide insertion into membranes. Related studies of the relative helicity of peptides in organic media such as n-butanol indicate that the helical propensity of individual residues--not simply their hydrophobicity--may dictate the conformations of peptides in membranes. The overall experimental results provide fundamental guidelines for membrane protein engineering.
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Affiliation(s)
- L P Liu
- Division of Biochemistry Research, Hospital for Sick Children, Toronto, Ontario, Canada
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40
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Ionov R, El-Abed A, Angelova A, Goldmann M, Peretti P. Asymmetrical ion-channel model inferred from two-dimensional crystallization of a peptide antibiotic. Biophys J 2000; 78:3026-35. [PMID: 10827981 PMCID: PMC1300886 DOI: 10.1016/s0006-3495(00)76841-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The structural organization of ion channels formed in lipid membranes by amphiphilic alpha-helical peptides is deduced by applying direct structural methods to different lipid/alamethicin systems. Alamethicin represents a hydrophobic alpha-helical peptide antibiotic forming voltage-gated ion channels in lipid membranes. Here the first direct evidence for the existence of large-scale two-dimensional crystalline domains of alamethicin helices, oriented parallel to the air/water interface, is presented using synchrotron x-ray diffraction, fluorescence microscopy, and surface pressure/area isotherms. Proofs are obtained that the antibiotic peptide injected into the aqueous phase under phospholipid monolayers penetrates these monolayers, phase separates, and forms domains within the lipid environment, keeping the same, parallel orientation of the alpha-helices with respect to the phospholipid/water interface. A new asymmetrical, "lipid-covered ring" model of the voltage-gated ion channel of alamethicin is inferred from the structural results presented, and the mechanism of ion-channel formation is discussed.
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Affiliation(s)
- R Ionov
- Groupe de Recherche en Physique et Biophysique, Université René Descartes, 75270 Paris Cedex 06, France.
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41
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Borisenko V, Sansom MS, Woolley GA. Protonation of lysine residues inverts cation/anion selectivity in a model channel. Biophys J 2000; 78:1335-48. [PMID: 10692320 PMCID: PMC1300733 DOI: 10.1016/s0006-3495(00)76688-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A dimeric alamethicin analog with lysine at position 18 in the sequence (alm-K18) was previously shown to form stable anion-selective channels in membranes at pH 7.0 [Starostin, A. V., R. Butan, V. Borisenko, D. A. James, H. Wenschuh, M. S. Sansom, and G. A. Woolley. 1999. Biochemistry. 38:6144-6150]. To probe the charge state of the conducting channel and how this might influence cation versus anion selectivity, we performed a series of single-channel selectivity measurements at different pH values. At pH 7.0 and below, only anion-selective channels were found with P(K(+))/P(Cl(-)) = 0. 25. From pH 8-10, a mixture of anion-selective, non-selective, and cation-selective channels was found. At pH > 11 only cation-selective channels were found with P(K(+))/P(Cl(-)) = 4. In contrast, native alamethicin-Q18 channels (with Gln in place of Lys at position 18) were cation-selective (P(K(+))/P(Cl(-)) = 4) at all pH values. Continuum electrostatics calculations were then carried out using an octameric model of the alm-K18 channel embedded in a low dielectric slab to simulate a membrane. Although the calculations can account for the apparent pK(a) of the channel, they fail to correctly predict the degree of selectivity. Although a switch from cation- to anion-selectivity as the channel becomes protonated is indicated, the degree of anion-selectivity is severely overestimated, suggesting that the continuum approach does not adequately represent some aspect of the electrostatics of permeation in these channels. Side-chain conformational changes upon protonation, conformational changes, and deprotonation caused by permeating cations and counterion binding by lysine residues upon protonation are considered as possible sources of the overestimation.
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Affiliation(s)
- V Borisenko
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Canada
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42
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Woolley GA, Starostin AV, Butan R, James DA, Wenschuh H, Sansom MS. Engineering charge selectivity in alamethicin channels. NOVARTIS FOUNDATION SYMPOSIUM 1999; 225:62-9; discussion 69-73. [PMID: 10472048 DOI: 10.1002/9780470515716.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The peptide alamethicin provides a system for engineering ion channel charge selectivity. To define alamethicin charge selectivity experimentally, we measured single-channel current-voltage relationships in KCl gradients using covalently linked peptide dimers. Two factors were found to contribute to the charge selectivity of these channels: (i) the ionic strength of the surrounding solutions; and (ii) the distribution of fixed charge on the peptide. Native alamethicin channels exhibited either cation selectivity or anion selectivity depending on which end of the channel was at the low salt side of the membrane. When the glutamine residue at position 18 in the sequence was replaced with a lysine residue, an anion-selective channel was obtained regardless of which end of the channel was at the low salt side of the membrane.
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Affiliation(s)
- G A Woolley
- Department of Chemistry, University of Toronto, Canada
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43
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Deber CM, Liu LP, Wang C. Perspective: peptides as mimics of transmembrane segments in proteins. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1999; 54:200-5. [PMID: 10517157 DOI: 10.1034/j.1399-3011.1999.00118.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Peptide-based approaches to protein structure within membranes have proven enormously valuable. When one focusses on the detailed manner through which membrane proteins actually traverse the cell bilayer, a simple observation emerges: helical peptide segments of 20 amino acids each constitute the only tangible connection between the inside and outside of the cell. Thus, a major step towards understanding the key relationships between biological function and membrane protein structure can be taken through characterization, by composition, sequence, chain length, hydrophobicity and conformation, of hydrophobic peptides designed as mimics of transmembrane segments.
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Affiliation(s)
- C M Deber
- Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, Canada.
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44
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Duclohier H, Kociolek K, Stasiak M, Leplawy MT, Marshall GR. C-terminally shortened alamethicin on templates: influence of the linkers on conductances. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1420:14-22. [PMID: 10446286 DOI: 10.1016/s0005-2736(99)00047-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In order to test the influence of chemical modifications designed to allow covalent coupling of channel-forming peptide motifs into variable sized oligomers, a series of alamethicin derivatives was prepared. The building block encompassing the N-terminal 1-17 residues of alamethicin behaved normally in the conductance assay on planar lipid bilayers, albeit at higher concentration and with a slightly reduced voltage-dependence. A linker Ac-K-OCH(2)C(6)H(4)CH(3)p attached via the epsilon amino group of lysine to the C-terminus of alamethicin(1-17) increased membrane affinity. The latter was further enhanced in a dimer and a tetramer in which alamethicin(1-17) chains were tethered to di- or tetra-lysine linkers, respectively, but macroscopic current-voltage curves displayed much reduced voltage-dependencies and reversed hysteresis. An usual behaviour with high voltage-dependence was restored with the modified dimer of alamethicin(1-17) in which alanine separated the two consecutive lysine residues in the linker. Of special interest was the development of a 'negative resistance' branch in macroscopic current-voltage curves for low concentrations of this dimer with the more flexible linker. Single channel events displayed only one single open state with fast kinetics and whose conductance matches that of the alamethicin heptamer or octamer.
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Affiliation(s)
- H Duclohier
- UMR 6522 CNRS-Université de Rouen, Institut Fédératif de Recherches Multidisciplinaires sur les Peptides (IFRMP 23), 76821, Mont-Saint-Aignan, Cedex, France.
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45
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Abstract
We have used molecular dynamics simulations, corresponding to a total simulation time of 11 ns, to investigate the effective short-time local diffusion coefficient of potassium and chloride ions in a series of model ion channels. These models, which include channels formed by the fungal peptide alamethicin, by a synthetic leucine-serine peptide, and by the pore-lining M2 helix bundle of the nicotinic acetylcholine receptor, have a range of different secondary structures, diameters and hydrophobicities. We find that the diffusion coefficients of both ions are appreciably reduced in the narrower channels, the extent of the reduction being similar for both the anionic and cationic species. This suggests that a difference in mobility cannot be the source of the ion selectivity exhibited by some of the channels (for example, the leucine-serine peptide). We find no evidence for a reduction in mobility of either ion in the nAChR model. These results are broadly in line with a previous similar study of Na+ ions, and may be useful in Poisson-Nernst-Planck, Eyring rate theory or Brownian dynamics calculations of channel conductance.
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Affiliation(s)
- G R Smith
- Department of Biochemistry, University of Oxford, UK.
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46
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Tieleman DP, Berendsen HJ, Sansom MS. An alamethicin channel in a lipid bilayer: molecular dynamics simulations. Biophys J 1999; 76:1757-69. [PMID: 10096876 PMCID: PMC1300154 DOI: 10.1016/s0006-3495(99)77337-6] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present the results of 2-ns molecular dynamics (MD) simulations of a hexameric bundle of Alm helices in a 1-palmitoyl-2-oleoylphosphatidylcholine bilayer. These simulations explore the dynamic properties of a model of a helix bundle channel in a complete phospholipid bilayer in an aqueous environment. We explore the stability and conformational dynamics of the bundle in a phospholipid bilayer. We also investigate the effect on bundle stability of the ionization state of the ring of Glu18 side chains. If all of the Glu18 side chains are ionised, the bundle is unstable; if none of the Glu18 side chains are ionized, the bundle is stable. pKA calculations suggest that either zero or one ionized Glu18 is present at neutral pH, correlating with the stable form of the helix bundle. The structural and dynamic properties of water in this model channel were examined. As in earlier in vacuo simulations (Breed et al., 1996 .Biophys. J. 70:1643-1661), the dipole moments of water molecules within the pore were aligned antiparallel to the helix dipoles. This contributes to the stability of the helix bundle.
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Affiliation(s)
- D P Tieleman
- BIOSON Research Institute and Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
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47
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Cafiso DS. Chapter 7 Interaction of Natural and Model Peptides with Membranes. CURRENT TOPICS IN MEMBRANES 1999. [DOI: 10.1016/s0070-2161(08)61045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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48
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Smith GR, Sansom MS. Dynamic properties of Na+ ions in models of ion channels: a molecular dynamics study. Biophys J 1998; 75:2767-82. [PMID: 9826599 PMCID: PMC1299950 DOI: 10.1016/s0006-3495(98)77720-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
We present simulation results for the effective diffusion coefficients of a sodium ion in a series of model ion channels of different diameters and hydrophobicities, including models of alamethicin, a leucine-serine peptide, and the M2 helix bundle of the nicotinic acetylcholine receptor. The diffusion coefficient, which in the simulations has a value of 0.15(2) A2ps-1 in bulk water, is found to be reduced to as little as 0.02(1) A2ps-1 in the narrower channels, and to about 0.10(5) A2ps-1 in wider channels such as the nicotinic acetylcholine receptor. It is anticipated that this work will be useful in connection with calculations of channel conductivity using such techniques as the Poisson-Nernst-Planck equation, Eyring rate theory, or Brownian dynamics.
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Affiliation(s)
- G R Smith
- Laboratory of Molecular Biophysics, University of Oxford, Oxford OX1 3QU, United Kingdom
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49
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Affiliation(s)
- M S Sansom
- Laboratory of Molecular Biophysics, University of Oxford, United Kingdom
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50
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Duval D, Riddell FG, Rebuffat S, Platzer N, Bodo B. Ionophoric activity of the antibiotic peptaibol trichorzin PA VI: a 23Na- and 35Cl-NMR study. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1372:370-8. [PMID: 9675337 DOI: 10.1016/s0005-2736(98)00080-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Trichorzin PA VI (Ac Aib1 Ser Ala Aib Iva Gln Aib Val Aib Gly10 Leu Aib Pro Leu Aib Aib Gln Pheol18) is one of the seven main peptaibols forming the natural antibiotic 18-residue peptide mixture biosynthesised by a Trichoderma harzianum strain. Trichorzins exhibit antimycoplasmic activity resulting from membrane permeability perturbations. The membrane permeabilisation process by trichorzin PA VI has been examined in egg yolk phosphatidylcholine large unilamellar vesicles (LUV) and under conditions of ionic equilibrium by 23Na- and 35Cl-NMR experiments conducted in the presence of a chemical shift reagent and a relaxation agent, respectively. In such conditions, trichorzin PA VI exchanges both cations and anions across the vesicle bilayers, indicating the absence of ion- and charge-selectivity, in contrast to antibiotic ionophores, such as monensin or nigericin; the Na+ exchange is not influenced by the ionic strength. The kinetics of the Na+ exchange have been found to be third to fourth order with respect to the peptide concentration. The permeabilisation process of liposomes has been shown to be due to the formation of aggregates of three to four helical peptide monomers arranged into a supramolecular complex including presumably lipid molecules and forming a badly-defined pore in the bilayer. The major mechanism by which ions may exchange through the bilayer involves a long-lasting opening of the pores allowing complete exchange of the internal and external media in an 'all or nothing mode'.
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Affiliation(s)
- D Duval
- Laboratoire de Chimie des Substances Naturelles, URA CNRS 401, GDR CNRS 790, Muséum National d'Histoire Naturelle, 63 rue Buffon, 75231 Paris Cedex 05, France
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