1
|
Tawfik H, Puza S, Seemann R, Fleury JB. Transport Properties of Gramicidin A Ion Channel in a Free-Standing Lipid Bilayer Filled With Oil Inclusions. Front Cell Dev Biol 2020; 8:531229. [PMID: 33015051 PMCID: PMC7498540 DOI: 10.3389/fcell.2020.531229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/14/2020] [Indexed: 11/13/2022] Open
Abstract
Ion channels are key proteins in mammalian cell membranes. They have a central role in the physiology of excitable cells such as neurons, muscle, and heart cells. They also play a crucial role in kidney physiology. The gramicidin ion channel is one of the most studied ion channels, in particular it was intensively employed to investigate the lipid–protein interactions in model cell membranes. For example, even though the sequence of gramicidin is extremely hydrophobic, its motion is impaired in membrane bilayer, i.e., it does not rapidly flip to the other membrane leaflet, and low channel activity were observed when gramicidin is added asymmetrically to only one leaflet of a model cell membrane. In this article, we study the transport properties of gramicidin channel in a heterogeneous model membrane. Using microfluidics, we are forming freestanding bilayers as model cell membranes including heterogeneous domains that are created by oil inclusions. The presence of oil inclusions is then demonstrated by measuring the bilayer capacity via a patch-clamp amplifier and fluorescent confocal inspection. Based on electrophysiological and optical measurements Gramicidin A (gA) ion channels are dispersed into the buffer phases on both side of the formed lipid bilayer and insert spontaneously into the bilayer upon formation. The presence of functional Gramicidin A is then demonstrated by measuring conductivity signals. Based on electrophysiological and optical measurements, we explore the consequence of the presence of these oil inclusions on the functionality of incorporated gA ion channels. For low oil concentration, we measure a decrease of gA transport properties due to the reduction of the bilayer tension. For large oil concentration, we measure a saturation of gA transport properties due to an increase of the bilayer thickness.
Collapse
Affiliation(s)
- Harvey Tawfik
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
| | - Sevde Puza
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
| | - Ralf Seemann
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
| | - Jean-Baptiste Fleury
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
| |
Collapse
|
2
|
Chakraborty K, Dutta C, Mukherjee S, Biswas A, Gayen P, George G, Raghothama S, Ghosh S, Dey S, Bhattacharyya D, Sinha Roy R. Engineering Ionophore Gramicidin-Inspired Self-Assembled Peptides for Drug Delivery and Cancer Nanotherapeutics. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Kasturee Chakraborty
- Department of Biological Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 India
| | - Chiranjit Dutta
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 India
| | - Sanchita Mukherjee
- Department of Biological Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 India
| | - Abhijit Biswas
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 India
| | - Paramita Gayen
- Department of Biological Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 India
| | - Gijo George
- NMR Research Centre; Indian Institute of Science; Bangalore 560012 India
| | | | - Snehasish Ghosh
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 India
| | - Souvik Dey
- Department of Biological Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 India
| | - Dhananjay Bhattacharyya
- Computational Science Division; Saha Institute of Nuclear Physics; Kolkata, 1/AF Bidhannagar Kolkata 700064 India
| | - Rituparna Sinha Roy
- Department of Biological Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 India
- Centre for Advanced Functional Materials; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 India
- Centre for Climate and Environmental Studies; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 India
| |
Collapse
|
3
|
Kondrashov OV, Galimzyanov TR, Pavlov KV, Kotova EA, Antonenko YN, Akimov SA. Membrane Elastic Deformations Modulate Gramicidin A Transbilayer Dimerization and Lateral Clustering. Biophys J 2018; 115:478-493. [PMID: 30049405 PMCID: PMC6084527 DOI: 10.1016/j.bpj.2018.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 01/25/2023] Open
Abstract
Gramicidin A (gA) is a short β-helical peptide known to form conducting channels in lipid membranes because of transbilayer dimerization. The gA conducting dimer, being shorter than the lipid bilayer thickness, deforms the membrane in its vicinity, and the bilayer elastic energy contributes to the gA dimer formation energy. Likewise, membrane incorporation of a gA monomer, which is shorter than the lipid monolayer thickness, creates a void, thereby forcing surrounding lipid molecules to tilt to fill it. The energy of membrane deformation was calculated in the framework of the continuum elasticity theory, taking into account splay, tilt, lateral stretching/compression, Gaussian splay deformations, and external membrane tension. We obtained the interaction energy profiles for two gA monomers located either in the same or in the opposite monolayers. The profiles demonstrated the long-range attraction and short-range repulsion behavior of the monomers resulting from the membrane deformation. Analysis of the profile features revealed conditions under which clusters of gA monomers would not dissipate because of diffusion. The calculated dependence of the dimer formation and decay energy barriers on the membrane elastic properties was in good agreement with the available experimental data and suggested an explanation for a hitherto contentious phenomenon.
Collapse
Affiliation(s)
- Oleg V Kondrashov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia; Department of Theoretical Physics, Moscow Institute of Physics and Technology, Dolgoprudniy, Moscow Region, Russia
| | - Timur R Galimzyanov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia; Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology "MISiS," Moscow, Russia
| | - Konstantin V Pavlov
- Laboratory of Electrophysiology, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Elena A Kotova
- Department of Photosynthesis and Fluorescence Research Methods, A. N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Yuri N Antonenko
- Laboratory of Membrane Biophysics, A. N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Sergey A Akimov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia; Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology "MISiS," Moscow, Russia.
| |
Collapse
|
4
|
Reddy DN, Singh S, Ho CMW, Patel J, Schlesinger P, Rodgers S, Doctor A, Marshall GR. Design, synthesis, and biological evaluation of stable β 6.3-Helices: Discovery of non-hemolytic antibacterial peptides. Eur J Med Chem 2018; 149:193-210. [PMID: 29501941 DOI: 10.1016/j.ejmech.2018.02.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 01/26/2018] [Accepted: 02/16/2018] [Indexed: 11/25/2022]
Abstract
Gramicidin A, a topical antibiotic made from alternating L and D amino acids, is characterized by its wide central pore; upon insertion into membranes, it forms channels that disrupts ion gradients. We present helical peptidomimetics with this characteristic wide central pore that have been designed to mimic gramicidin A channels. Mimetics were designed using molecular modeling focused on oligomers of heterochiral dipeptides of proline analogs, in particular azaproline (AzPro). Molecular Dynamics simulations in water confirmed the stability of the designed helices. A sixteen-residue Formyl-(AzPro-Pro)8-NHCH2CH2OH helix was synthesized as well as a full thirty-two residue Cbz-(AzPro-Pro)16-OtBu channels. No liposomal lysis activity was observed suggesting lack of channel formation, possibly due to inappropriate hydrogen-bonding interactions in the membrane. These peptidomimetics also did not hemolyze red blood cells, unlike gramicidin A.
Collapse
Affiliation(s)
- Damodara N Reddy
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Sukrit Singh
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chris M W Ho
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janki Patel
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Paul Schlesinger
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephen Rodgers
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Allan Doctor
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Garland R Marshall
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
5
|
Sani MA, Separovic F. Antimicrobial Peptide Structures: From Model Membranes to Live Cells. Chemistry 2017; 24:286-291. [PMID: 29068097 DOI: 10.1002/chem.201704362] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Indexed: 01/12/2023]
Abstract
The rise in antibiotic resistance has led to a renewed interest in antimicrobial peptides (AMPs) that target membranes. The mode of action of AMPs involves the disruption of the lipid bilayer and leads to growth inhibition and death of the bacteria. However, details at the molecular level of how these peptides kill bacteria and the reasons for the observed differences in selectivity remain unclear. Structural information is crucial for defining the molecular mechanism by which these peptides recognize, self-assemble and interact with a particular lipid membrane. Solid-state NMR is a non-invasive technique that allows the study of the structural details of lipid-peptide and peptide-peptide interactions. Following on from studies of antibiotic and lytic peptides, gramicidin A and melittin, respectively, we investigated maculatin 1.1, an AMP from the skin of Australian tree frogs that acts against Gram-positive bacteria. By using perdeuterated phospholipids and specifically labelled peptides, 2 H, 31 P and {31 P}15 N REDOR solid-state NMR experiments have been used to localize, maculatin 1.1 in neutral and anionic model membranes. However, the structure, location and activity depend on the composition of the model membrane and current advances in solid-state NMR spectroscopy now allow structure determination of AMPs in live bacteria.
Collapse
Affiliation(s)
- Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC, 3010, Australia
| |
Collapse
|
6
|
Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| |
Collapse
|
7
|
Meikle TG, Zabara A, Waddington LJ, Separovic F, Drummond CJ, Conn CE. Incorporation of antimicrobial peptides in nanostructured lipid membrane mimetic bilayer cubosomes. Colloids Surf B Biointerfaces 2017; 152:143-151. [DOI: 10.1016/j.colsurfb.2017.01.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/27/2016] [Accepted: 01/03/2017] [Indexed: 11/28/2022]
|
8
|
Mohamed AA, Zhang L, Dorrah MA, Elmogy M, Yousef HA, Bassal TTM, Duvic B. Molecular characterization of a c-type lysozyme from the desert locust, Schistocerca gregaria (Orthoptera: Acrididae). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 61:60-69. [PMID: 26997372 DOI: 10.1016/j.dci.2016.03.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 06/05/2023]
Abstract
Lysozymes are bacteriolytic peptides that are implicated in the insect nonspecific innate immune responses. In this study, a full-length cDNA encoding a c-type lysozyme from Schistocerca gregaria (SgLys) has been cloned and characterized from the fat body of immune-challenged 5(th) instar. The deduced mature lysozyme is 119 amino acid residues in length, has a calculated molecular mass of 13.4 kDa and an isoelectric point (Ip) of 9.2. SgLys showed high identities with other insect lysozymes, ranging from 41.5% to 93.3% by BLASTp search in NCBI. Eukaryotic in vitro expression of the SgLys ORF (rSgLys) with an apparent molecular mass of ∼16 kDa under SDS-PAGE is close to the calculated molecular weight of the full-length protein. rSgLys displayed growth inhibitory activity against Gram-negative and Gram-positive bacteria. 3D structure modeling of SgLys, based on comparison with that of silkworm lysozyme, and sequence comparison with the helix-loop-helix (α-hairpin) structure of hen egg white lysozyme (HEWL) were employed to interpret the antibacterial potencies. Phylogenetic alignments indicate that SgLys aligns well with insect c-type lysozymes that expressed principally in fat body and hemocytes and whose role has been defined as immune-related. Western blot analysis showed that SgLys expression was highest at 6-12 h post-bacterial challenge and subsequently decreased with time. Transcriptional profiles of SgLys were determined by semi-quantitative RT-PCR analysis. SgLys transcript was upregulated at the highest level in fat body, hemocytes, salivary gland, thoracic muscles, and epidermal tissue. It was expressed in all developmental stages from egg to adult. These data indicate that SgLys is a predominant acute-phase protein that is expressed and upregulated upon immune challenge.
Collapse
Affiliation(s)
- Amr A Mohamed
- Department of Entomology, Faculty of Science, Cairo University, P. O. Box 12613, Giza, Egypt.
| | - Long Zhang
- Key Lab for Biological Control of the Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing, 100193, PR China
| | - Moataza A Dorrah
- Department of Entomology, Faculty of Science, Cairo University, P. O. Box 12613, Giza, Egypt
| | - Mohamed Elmogy
- Department of Entomology, Faculty of Science, Cairo University, P. O. Box 12613, Giza, Egypt
| | - Hesham A Yousef
- Department of Entomology, Faculty of Science, Cairo University, P. O. Box 12613, Giza, Egypt
| | - Taha T M Bassal
- Department of Entomology, Faculty of Science, Cairo University, P. O. Box 12613, Giza, Egypt
| | - Bernard Duvic
- Unité DGIMI UMR INRA-UM 1333, Université Montpellier, Place Eugène Bataillon, Montpellier, France
| |
Collapse
|
9
|
Stevenson P, Tokmakoff A. Distinguishing gramicidin D conformers through two-dimensional infrared spectroscopy of vibrational excitons. J Chem Phys 2015; 142:212424. [PMID: 26049444 PMCID: PMC4401804 DOI: 10.1063/1.4917321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/31/2015] [Indexed: 11/14/2022] Open
Abstract
Gramicidin D is a short peptide which dimerizes to form helical pores, adopting one of two conformations in the process. These conformations differ primarily in number of residues per turn and the hydrogen-bond registry between rungs of the helix. Using amide I 2D infrared (IR) and FTIR, we have demonstrated that it is possible to distinguish between the different conformers of gramicidin D in solution. We show that the spectra observed for this helical peptide bear no resemblance to the spectra of α- or 310-helices and that while the FTIR spectra appear similar to spectra of β-sheets, 2D IR reveals that the observed resonances arise from vibrational modes unlike those observed in β-sheets. We also present an idealized model which reproduces the experimental data with high fidelity. This model is able to explain the polarization-dependence of the experimental 2D IR data. Using this model, we show the coupling between the rungs of the helix dominates the spectra, and as a consequence of this, the number of residues per turn can greatly influence the amide I spectra of gramicidin D.
Collapse
Affiliation(s)
- Paul Stevenson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
| |
Collapse
|
10
|
Abstract
Ion channels provide a conductance pathway for the passive transport of ions across membranes. These functional molecules perform key tasks in biological systems such as neuronal signaling, muscular control, and sensing. Recently, function-oriented synthesis researchers began to focus on ion channels with the goal of modifying the function of existing ion channels (ion selectivity, gating) or creating new channels with novel functions. Both approaches, ion channel engineering and de novo design, have involved synthetic chemists, biochemists, structural biologists, and neurochemists. Researchers characterize the function of ion channels by measuring their conductance in samples of biological membranes (patch clamp) or artificial membranes (planar lipid bilayers). At the single molecule level, these measurements require special attention to the purity of the sample, a challenge that synthetic chemists should be aware of. Ideally, researchers study the function of channels while also acquiring structural data (X-ray, NMR) to understand and predict how synthetic modifications alter channel function. Long-term oriented researchers would like to apply synthetic ion channels to single molecule sensing and to implantat these synthetic systems in living organisms as tools or for the treatment of channelopathies. In this Account, we discuss our own work on synthetic ion channels and explain the shift of our research focus from a de novo design of oligo-THFs and oligo-THF-amino acids to ion channel engineering. We introduce details about two biological lead structures for ion channel engineering: the gramicidin β(6,3) helix as an example of a channel with a narrow ion conductance pathway and the outer membrane porins (OmpF, OmpG) with their open β-barrel structure. The increase and the reversal of ion selectivity of these systems and the hydrophobic match/mismatch of the channel with the phospholipid bilayer are of particular interest. For engineering ion channels, we need to supplement the single-point attachment of a synthetic modulator with the synthesis of a more challenging two-point attachment. The successful function-oriented synthesis of ion channels will require interdisciplinary efforts that include new electrophysiology techniques, efficient synthesis (peptide/protein/organic), and good structural analysis.
Collapse
Affiliation(s)
- Philipp Reiß
- Fachbereich Chemie, Philipps-Universität Marburg, Hans Meerwein Strasse, 35032 Marburg, Germany
| | - Ulrich Koert
- Fachbereich Chemie, Philipps-Universität Marburg, Hans Meerwein Strasse, 35032 Marburg, Germany
| |
Collapse
|
11
|
de Jesus AJ, Allen TW. The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:864-76. [PMID: 22989724 DOI: 10.1016/j.bbamem.2012.09.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/27/2022]
Abstract
Tryptophan (Trp) is abundant in membrane proteins, preferentially residing near the lipid-water interface where it is thought to play a significant anchoring role. Using a total of 3 μs of molecular dynamics simulations for a library of hydrophobic WALP-like peptides, a long poly-Leu α-helix, and the methyl-indole analog, we explore the thermodynamics of the Trp movement in membranes that governs the stability and orientation of transmembrane protein segments. We examine the dominant hydrogen-bonding interactions between the Trp and lipid carbonyl and phosphate moieties, cation-π interactions to lipid choline moieties, and elucidate the contributions to the thermodynamics that serve to localize the Trp, by ~4 kcal/mol, near the membrane glycerol backbone region. We show a striking similarity between the free energy to move an isolated Trp side chain to that found from a wide range of WALP peptides, suggesting that the location of this side chain is nearly independent of the host transmembrane segment. Our calculations provide quantitative measures that explain Trp's role as a modulator of responses to hydrophobic mismatch, providing a deeper understanding of how lipid composition may control a range of membrane active peptides and proteins.
Collapse
|
12
|
Rokitskaya TI, Sorochkina AI, Kovalchuk SI, Egorova NS, Kotova EA, Sychev SV, Antonenko YN. The pH-dependent induction of lipid membrane ionic permeability by N-terminally lysine-substituted analogs of gramicidin A. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:129-38. [DOI: 10.1007/s00249-011-0764-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 09/30/2011] [Accepted: 10/11/2011] [Indexed: 11/29/2022]
|
13
|
Modeling the membrane environment for membrane proteins. Biophys J 2011; 100:2073-4; author reply 2075. [PMID: 21504744 DOI: 10.1016/j.bpj.2011.02.058] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/01/2011] [Accepted: 02/25/2011] [Indexed: 11/24/2022] Open
|
14
|
Jones TL, Fu R, Nielson F, Cross TA, Busath DD. Gramicidin channels are internally gated. Biophys J 2010; 98:1486-93. [PMID: 20409467 DOI: 10.1016/j.bpj.2009.11.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 10/20/2009] [Accepted: 11/12/2009] [Indexed: 11/25/2022] Open
Abstract
Gramicidin channels are archetypal molecular subjects for solid-state NMR studies and investigations of single-channel or cation conductance. Until now, the transitions between on and off conductance states have been thought, based on multichannel studies, to represent monomer <--> dimer reactions. Here we use a single-molecule deposition method (vesicle fusion to a planar bilayer) to show that gramicidin dimer channels do not normally dissociate when conductance terminates. Furthermore, the observation of two 13C peaks in solid-state NMR indicates very stable dichotomous conformations for both the first and second peptide bonds in the monomers, and a two-dimensional chemical exchange spectrum with a 12-s mixing time demonstrates that the Val1 carbonyl conformations exchange slowly, with lifetimes of several seconds. It is proposed that gramicidin channels are gated by small conformational changes in the channel near the permeation pathway. These studies demonstrate how regulation of conformations governing closed <--> open transitions may be achieved and studied at the molecular level.
Collapse
Affiliation(s)
- Tyson L Jones
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah, USA
| | | | | | | | | |
Collapse
|
15
|
Siu SWI, Böckmann RA. Low Free Energy Barrier for Ion Permeation Through Double-Helical Gramicidin. J Phys Chem B 2009; 113:3195-202. [DOI: 10.1021/jp810302k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shirley W. I. Siu
- Theoretical and Computational Membrane Biology, Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, 66041 Saarbrücken, Germany
| | - Rainer A Böckmann
- Theoretical and Computational Membrane Biology, Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, 66041 Saarbrücken, Germany
| |
Collapse
|
16
|
Bajaj VS, Hornstein MK, Kreischer KE, Sirigiri JR, Woskov PP, Mak-Jurkauskas ML, Herzfeld J, Temkin RJ, Griffin RG. 250GHz CW gyrotron oscillator for dynamic nuclear polarization in biological solid state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 189:251-79. [PMID: 17942352 PMCID: PMC2695453 DOI: 10.1016/j.jmr.2007.09.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Revised: 09/03/2007] [Accepted: 09/13/2007] [Indexed: 05/05/2023]
Abstract
In this paper, we describe a 250 GHz gyrotron oscillator, a critical component of an integrated system for magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments at 9T, corresponding to 380 MHz (1)H frequency. The 250 GHz gyrotron is the first gyro-device designed with the goal of seamless integration with an NMR spectrometer for routine DNP enhanced NMR spectroscopy and has operated under computer control for periods of up to 21 days with a 100% duty cycle. Following a brief historical review of the field, we present studies of the membrane protein bacteriorhodopsin (bR) using DNP enhanced multidimensional NMR. These results include assignment of active site resonances in [U-(13)C, (15)N]-bR and demonstrate the utility of DNP for studies of membrane proteins. Next, we review the theory of gyro-devices from quantum mechanical and classical viewpoints and discuss the unique considerations that apply to gyrotron oscillators designed for DNP experiments. We then characterize the operation of the 250 GHz gyrotron in detail, including its long-term stability and controllability. We have measured the spectral purity of the gyrotron emission using both homodyne and heterodyne techniques. Radiation intensity patterns from the corrugated waveguide that delivers power to the NMR probe were measured using two new techniques to confirm pure mode content: a thermometric approach based on the temperature-dependent color of liquid crystalline media applied to a substrate and imaging with a pyroelectric camera. We next present a detailed study of the mode excitation characteristics of the gyrotron. Exploration of the operating characteristics of several fundamental modes reveals broadband continuous frequency tuning of up to 1.8 GHz as a function of the magnetic field alone, a feature that may be exploited in future tunable gyrotron designs. Oscillation of the 250 GHz gyrotron at the second harmonic of cyclotron resonance begins at extremely low beam currents (as low 12 mA) at frequencies between 320 and 365 GHz, suggesting an efficient route for the generation of even higher frequency radiation. The low starting currents were attributed to an elevated cavity Q, which is confirmed by cavity thermal load measurements. We conclude with an appendix containing a detailed description of the control system that safely automates all aspects of the gyrotron operation.
Collapse
Affiliation(s)
- Vikram S. Bajaj
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Melissa K. Hornstein
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Kenneth E. Kreischer
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Jagadishwar R. Sirigiri
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Paul P. Woskov
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | | | - Judith Herzfeld
- Department of Chemistry, Brandeis University, Waltham, MA, 02454
| | - Richard J. Temkin
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139
| |
Collapse
|
17
|
Esbjörner EK, Caesar CEB, Albinsson B, Lincoln P, Nordén B. Tryptophan orientation in model lipid membranes. Biochem Biophys Res Commun 2007; 361:645-50. [PMID: 17692825 DOI: 10.1016/j.bbrc.2007.07.135] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 07/16/2007] [Indexed: 11/28/2022]
Abstract
Tryptophans in membrane proteins display strong preference for the lipid membrane interface and are important for anchoring proteins at the proper longitudinal level. Linear dichroism spectroscopy on indoles in shear-deformed liposomes has been used to show that this positioning is accompanied by an intrinsically adopted orientation, also observed for tryptophans in membrane-bound peptides. Similarities in orientation of different indoles suggest that tryptophan will adopt this orientation independent of the protein it is part of. From the orientation of indole electronic transition moments L(a), L(b) and B(b), a binding model is proposed where the indole long axis is approximately 60-65 degrees from the membrane normal and the indole plane is at an oblique angle. We propose that dipole-dipole interactions and steric constraints in the membrane hydrocarbon region determine positioning and orientation of tryptophans whereas hydrogen bonding and cation-pi interactions with lipid head-groups, though contributing to the membrane affinity of indoles, are less important.
Collapse
Affiliation(s)
- Elin K Esbjörner
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden.
| | | | | | | | | |
Collapse
|
18
|
Davies-Tuck M, Lee TH, Apffel A, Aguilar MI. Hydrophobic and electrostatic forces control the retention of membrane peptides and proteins with an immobilised phosphatidic acid column. J Chromatogr A 2007; 1156:167-73. [PMID: 17397853 DOI: 10.1016/j.chroma.2007.03.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 03/07/2007] [Accepted: 03/15/2007] [Indexed: 11/19/2022]
Abstract
The retention behaviour of four membrane-associated peptides and proteins with an immobilized phosphatidic acid (PA) stationary phase was evaluated. The solutes included the cytolytic peptides gramicidin A and melittin, the integral membrane protein bacteriorhodpsin and cytochrome c, a peripheral membrane protein. Gramicidin has no nett charge and exhibited normal reversed phase-like behaviour which was largely independent of mobile phase pH. In contrast, melittin, which has a positively charged C-terminal tail, exhibited reversed phase like retention at pH 5.4 and 7.4, and was not retained at pH 3 reflecting the influence of electrostatic interactions with the negatively charged phosphatidic acid ligand. Bacteriorhodpsin was eluted at high acetonitrile concentrations at pH 3 and 5.4 and cytochrome c was only eluted at pH 3. Moreover, cytochrome c eluted in the breakthrough peak between 0 and 100% acetonitrile, demonstrating the role of electrostatic interactions with the PA surface. Overall, the results demonstrate that pH can be used to optimize the fractionation and separation of membrane proteins with immobilized lipid stationary phases.
Collapse
Affiliation(s)
- Miranda Davies-Tuck
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic 3800, Australia
| | | | | | | |
Collapse
|
19
|
Siu SWI, Böckmann RA. Electric field effects on membranes: Gramicidin A as a test ground. J Struct Biol 2007; 157:545-56. [PMID: 17116406 DOI: 10.1016/j.jsb.2006.10.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 07/25/2006] [Accepted: 10/03/2006] [Indexed: 11/19/2022]
Abstract
Electric fields due to transmembrane potential differences or ionic gradients across the membrane are presumably crucial for many reactions across membranes or close to membranes like signal transduction, control of ion channels or the generation of neural impulses. Molecular dynamics simulations have been used to study the influence of external electric fields on a mixed gramicidin/phospholipid bilayer system. At high field strengths, formation of membrane electropores occurred both close and distal to the gramicidin. Gramicidin was found to stabilize the membrane adjacent to the protein but also at larger distances of up to 2-3 nm. As a result, membrane pore formation was found to be significantly suppressed for the mixed gramicidin/DMPC system. Moderate field strengths only weakly affected the structure and dynamics of the gramicidin. Spontaneous potassium passage events in external electric fields were observed for both the head-to-head helical conformation as well as for the double helical conformation of gramicidin A. The double-helical conformation was found to facilitate ion passage compared to the head-to-head helical dimer.
Collapse
Affiliation(s)
- Shirley W I Siu
- Saarland University, Center for Bioinformatics Saar, Theoretical and Computational Membrane Biology, P.O. Box 15 11 50, 66041 Saarbrücken, Germany
| | | |
Collapse
|
20
|
Dutseva EA, Antonenko YN, Kotova EA, Pfeifer JR, Koert U. Sensitized photoinactivation of minigramicidin channels in bilayer lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1768:1230-7. [PMID: 17306219 DOI: 10.1016/j.bbamem.2007.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 12/26/2006] [Accepted: 01/10/2007] [Indexed: 11/15/2022]
Abstract
The method of sensitized photoinactivation based on the photosensitized damage of gramicidin A (gA) molecules was applied here to study ionic channels formed by minigramicidin (the 11-residue analogue of gramicidin A) in a planar bilayer lipid membrane (BLM) of different thickness. Irradiation of BLM with a single flash of visible light in the presence of a photosensitizer (aluminum phthalocyanine or Rose Bengal) generating singlet oxygen provoked a decrease in the minigramicidin-induced electric current across BLM, the kinetics of which had the characteristic time of several seconds, as observed with gA. For gA, there is good correlation between the characteristic time of photoinactivation and the single-channel lifetime. In contrast to the covalent dimer of gA characterized by extremely long single-channel lifetime and the absence of current relaxation upon flash excitation, the covalent head-to-head dimer of minigramicidin displayed the flash-induced current decrease with the kinetics being strongly dependent on the membrane thickness. The current decrease became slower both upon increasing the concentration of the minigramicidin covalent dimer and upon including cholesterol in the membrane composition. These data in combination with the quadratic dependence of the current on the peptide concentration can be rationalized by hypothesizing that the macroscopic current across BLM measured at high concentrations of the peptide is provided by dimers of minigramicidin covalent dimers in the double beta(5.7)-helical conformation having the lifetime of about 0.4 s, while single channels with the lifetime of 0.01 s, observed at a very low peptide concentration, correspond to the single-stranded beta(6.3)-helical conformation. Alternatively the results can be explained by clustering of channels at high concentrations of the minigramicidin covalent dimer.
Collapse
Affiliation(s)
- Elena A Dutseva
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | | | | | | | | |
Collapse
|
21
|
Shabany H, Ferdani R, Gokel GW. Hydraphile Synthetic Channel Compounds: Models for Transmembrane, Cation-conducting Transporters. Supramol Chem 2006. [DOI: 10.1080/10610270108029456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Hossein Shabany
- a Bioorganic Chemistry Program and Dept. of Molecular Biology and Pharmacology , Washington University School of Medicine , 660 South Euclid Ave., Campus Box 8103, St. Louis, MO, 63110, USA
| | - Riccardo Ferdani
- a Bioorganic Chemistry Program and Dept. of Molecular Biology and Pharmacology , Washington University School of Medicine , 660 South Euclid Ave., Campus Box 8103, St. Louis, MO, 63110, USA
| | - George W. Gokel
- a Bioorganic Chemistry Program and Dept. of Molecular Biology and Pharmacology , Washington University School of Medicine , 660 South Euclid Ave., Campus Box 8103, St. Louis, MO, 63110, USA
| |
Collapse
|
22
|
Affiliation(s)
- Svetlana Litvinchuk
- a Department of Organic Chemistry , University of Geneva , Geneva, Switzerland
| | - Stefan Matile
- a Department of Organic Chemistry , University of Geneva , Geneva, Switzerland
| |
Collapse
|
23
|
Schröder S, Schrey AK, Knoll A, Reiß P, Ziemer B, Koert U. Tetrahydropyran-Amino Acids: Novel Building Blocks for Gramicidin-Hybrid Ion Channels. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600068] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
24
|
|
25
|
Li Y, Han X, Lai AL, Bushweller JH, Cafiso DS, Tamm LK. Membrane structures of the hemifusion-inducing fusion peptide mutant G1S and the fusion-blocking mutant G1V of influenza virus hemagglutinin suggest a mechanism for pore opening in membrane fusion. J Virol 2005; 79:12065-76. [PMID: 16140782 PMCID: PMC1212637 DOI: 10.1128/jvi.79.18.12065-12076.2005] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influenza virus hemagglutinin (HA)-mediated membrane fusion is initiated by a conformational change that releases a V-shaped hydrophobic fusion domain, the fusion peptide, into the lipid bilayer of the target membrane. The most N-terminal residue of this domain, a glycine, is highly conserved and is particularly critical for HA function; G1S and G1V mutant HAs cause hemifusion and abolish fusion, respectively. We have determined the atomic resolution structures of the G1S and G1V mutant fusion domains in membrane environments. G1S forms a V with a disrupted "glycine edge" on its N-terminal arm and G1V adopts a slightly tilted linear helical structure in membranes. Abolishment of the kink in G1V results in reduced hydrophobic penetration of the lipid bilayer and an increased propensity to form beta-structures at the membrane surface. These results underline the functional importance of the kink in the fusion peptide and suggest a structural role for the N-terminal glycine ridge in viral membrane fusion.
Collapse
Affiliation(s)
- Yinling Li
- Department of Molecular Physiology and Biological Physics, University of Virginia, P.O. Box 800736, Charlottesville, VA 22908-0736, USA
| | | | | | | | | | | |
Collapse
|
26
|
Al-Momani L, Reiss P, Koert U. A lipid dependence in the formation of twin ion channels. Biochem Biophys Res Commun 2005; 328:342-7. [PMID: 15670789 DOI: 10.1016/j.bbrc.2004.12.170] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Indexed: 10/25/2022]
Abstract
A gramicidin A derivative with a polyether linkage between both ethanolamine termini was synthesized and its ion channel properties were studied. The compound showed a duplication in the state of conductance for alkali cations in thick DOPC bilayer membranes, which is interpreted as the occurrence of twin-channels. In thinner DMPC membranes mono-channels were dominant. The influence of hydrophobic coupling on the mono channel/twin channel equilibrium is discussed.
Collapse
Affiliation(s)
- Lo'ay Al-Momani
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein Strasse, D-35032 Marburg, Germany
| | | | | |
Collapse
|
27
|
Abstract
The biological ion channel gramicidin A (gA) was modified by synthetic means to obtain the tail-to-tail linked asymmetric gA-derived dimer compound 3. Single-channel current measurements for 3 in planar lipid bilayers exhibit an Eisenman I ion selectivity for alkali cations. The structural asymmetry does not lead to an observable functional asymmetry. The structure of 3 in solution without and with Cs cations was investigated by 1H-NMR spectroscopy. In CDCl3/CD3OH (1 : 1, v/v), 3 forms a mixture of double-stranded beta-helices. Upon addition of excess CsCl, the double-stranded species are converted completely into one new conformer: the right-handed single-stranded beta-helix. A combination of DQF-COSY and TOCSY was used for the assignment of the 1H-NMR spectrum of the Cs-3 complex in CDCl3/CD3OH (1 : 1, v/v). A total of 69 backbone, 27 long-range, and 64 side-chain distance restraints were obtained from NOESY together with 25 phi and 14 chi1 torsion angles obtained from coupling constants. These data were used as input for structure calculation with dyana built in sybyl 6.8. A final set of 11 structures with an average rmsd for the backbone of 0.45 A was obtained (PDB: 1TKQ). The structure of the Cs-3 complex in solution is equivalent to the bioactive channel conformation in the membrane environment.
Collapse
Affiliation(s)
- Xiulan Xie
- Fachbereich Chemie, Philipps-Universität Marburg, Germany
| | | | | | | | | |
Collapse
|
28
|
Sensitized Photoinactivation of Gramicidin Channels: Technique and Applications. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1554-4516(05)01005-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
|
29
|
Jagannadham MV, Nagaraj R. Conformation of gramicidin a in water: Inference from analysis of hydrogen/deuterium exchange behavior by matrix assisted laser desorption ionization mass spectrometry. Biopolymers 2005; 80:708-13. [PMID: 15887265 DOI: 10.1002/bip.20293] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Gramicidin A (the major component of gramicidin D) is a highly hydrophobic peptide with very little solubility in water. Hence, the conformation of this peptide has been extensively investigated in organic solvents and model membranes, but not in water. The peptide adopts a beta6.3-helical conformation in the monomeric and dimeric forms. We have investigated the conformation of gramicidin A in water by monitoring hydrogen-deuterium exchange by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Our results indicate that gramicidin A is monomeric and exists in a highly folded conformation. The metal ion bound forms are clearly discernible in the monomers. The presence of the dimeric form is not observed. It is unlikely this is due to the operating conditions or the method used, as both hetero- and homodimers in gramicidin D are detected when methanol is used as a solvent. The present study also establishes that the linear gramicidins retain a history of solvent environment when ions are generated by matrix-assisted laser desorption ionization and analyzed by time-of-flight.
Collapse
Affiliation(s)
- M V Jagannadham
- Centre for Cellular and Molecular Biology,Uppal Road,Hyderabad 500 007, India.
| | | |
Collapse
|
30
|
Andronesi OC, Pfeifer JR, Al-Momani L, Ozdirekcan S, Rijkers DTS, Angerstein B, Luca S, Koert U, Killian JA, Baldus M. Probing membrane protein orientation and structure using fast magic-angle-spinning solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2004; 30:253-265. [PMID: 15754053 DOI: 10.1007/s10858-004-3452-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2004] [Accepted: 09/02/2004] [Indexed: 05/24/2023]
Abstract
One and two-dimensional solid-state NMR experiments are discussed that permit probing local structure and overall molecular conformation of membrane-embedded polypeptides under Magic Angle Spinning. The functional dependence of a series of anisotropic recoupling schemes is analyzed using theoretical and numerical methods. These studies lead to the construction of a set of polarization dephasing or transfer units that probe local backbone conformation and overall molecular orientation within the same NMR experiment. Experimental results are shown for a randomly oriented peptide and for two model membrane-peptides reconstituted into lipid bilayers and oriented on polymer films according to a method proposed by Bechinger et al.
Collapse
Affiliation(s)
- O C Andronesi
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Gokel GW, Schlesinger PH, Djedovic NK, Ferdani R, Harder EC, Hu J, Leevy WM, Pajewska J, Pajewski R, Weber ME. Functional, synthetic organic chemical models of cellular ion channels. Bioorg Med Chem 2004; 12:1291-304. [PMID: 15018901 DOI: 10.1016/j.bmc.2003.08.036] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2003] [Revised: 07/31/2003] [Accepted: 08/01/2003] [Indexed: 10/26/2022]
Affiliation(s)
- George W Gokel
- Department of Molecular Biology & Pharmacology, Washington University School of Medicine, 660 South Euclid Ave., Campus Box 8103, St Louis, MO 63110, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
|
33
|
Harms GS, Orr G, Montal M, Thrall BD, Colson SD, Lu HP. Probing conformational changes of gramicidin ion channels by single-molecule patch-clamp fluorescence microscopy. Biophys J 2003; 85:1826-38. [PMID: 12944296 PMCID: PMC1303355 DOI: 10.1016/s0006-3495(03)74611-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2003] [Accepted: 06/04/2003] [Indexed: 10/21/2022] Open
Abstract
Complex conformational changes influence and regulate the dynamics of ion channels. Such conformational changes are stochastic and often inhomogeneous, which makes it extremely difficult, if not impossible, to characterize them by ensemble-averaged experiments or by single-channel recordings of the electric current that report the open-closed events but do not specifically probe the associated conformational changes. Here, we report our studies on ion channel conformational changes using a new approach, patch-clamp fluorescence microscopy, which simultaneously combines single-molecule fluorescence spectroscopy and single-channel current recordings to probe the open-closed transitions and the conformational dynamics of individual ion channels. We demonstrate patch-clamp fluorescence microscopy by measuring gramicidin ion channel conformational changes in a lipid bilayer formed at a patch-clamp micropipette tip under a buffer solution. By measuring single-pair fluorescence resonance energy transfer and fluorescence self-quenching from dye-labeled gramicidin channels, we observed that the efficiency of single-pair fluorescence resonance energy transfer and self-quenching is widely distributed, which reflects a broad distribution of conformations. Our results strongly suggest a hitherto undetectable correlation between the multiple conformational states of the gramicidin channel and its closed and open states in a lipid bilayer.
Collapse
Affiliation(s)
- Greg S Harms
- Pacific Northwest National Laboratory, Fundamental Science Division, Richland, Washington 99352, USA
| | | | | | | | | | | |
Collapse
|
34
|
Vescovi A, Knoll A, Koert U. Synthesis and functional studies of THF-gramicidin hybrid ion channels. Org Biomol Chem 2003; 1:2983-97. [PMID: 12968351 DOI: 10.1039/b303249n] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
THF-gramicidin hybrids 2-4 with the L-THF amino acid 1 in positions 11 and 12 and compounds 5-8 with the D-THF amino acid ent-1 in positions 10 and 11 were synthesized and their ion channel properties were studied by single-channel-current analysis. The replacement of positions 11 and 12 by the L-THF amino acid 1 gave a strongly reduced channel performance. In contrast, replacement of positions 10 and 11 by the D-THF amino acid ent-1 gave rise to new and interesting channel properties. For the permeability ratios, the ion selectivity shifts from Eisenman I towards Eisenman III selectivity and the channels display ms-dynamics. Most remarkable is the asymmetric compound 8, which inserts selectively into a DPhPC membrane and displays voltage-directed gating dynamics.
Collapse
Affiliation(s)
- Andrea Vescovi
- Institut für Chemie, Humboldt-Universität Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | | | | |
Collapse
|
35
|
Abstract
The interaction of biotin-binding proteins with biotinylated gramicidin (gA5XB) was studied by monitoring single-channel activity and sensitized photoinactivation kinetics. It was discovered that the addition of streptavidin or avidin to the bathing solutions of a bilayer lipid membrane (BLM) with incorporated gA5XB induced the opening of a channel characterized by approximately doubled single-channel conductance and extremely long open-state duration. We believe that the deceleration of the photoinactivation kinetics observed here with streptavidin and previously (Rokitskaya, T.I., Y.N. Antonenko, E.A. Kotova, A. Anastasiadis, and F. Separovic. 2000. Biochemistry. 39:13053-13058) with avidin reflects the formation of long-lived channels of this type. Both opening and closing of the double-conductance channels occurred via a transient sub-state of the conductance coinciding with that of the usual single-channel transition. The appearance of the double-conductance channels after the addition of streptavidin was preceded by bursts of fast fluctuations of the current with the open state duration of the individual events of 60 ms. The streptavidin-induced double-conductance channels appeared to be inherent only to the gramicidin analogue with a biotin group linked to the COOH terminus through a long linker arm. Including biotinylated phosphatidylethanolamine into the BLM prevented the formation of the double-conductance channels even with the excess streptavidin. In view of the results obtained here, it is suggested that the double-conductance channel represents a tandem of two neighboring gA5XB channels with their COOH termini being cross-linked by the bound streptavidin at both sides of the BLM. The finding that streptavidin induces the formation of the tandem gramicidin channel comprising two channels functioning in concert is considered to be relevant to the physiologically important phenomenon of ligand-induced receptor oligomerization.
Collapse
|
36
|
Rokitskaya TI, Kotova EA, Antonenko YN. Cytochrome c decelerates channel kinetics of negatively charged gramicidin due to electrostatic interaction. Biochem Biophys Res Commun 2003; 302:865-8. [PMID: 12646251 DOI: 10.1016/s0006-291x(03)00274-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The effect of cytochrome c on the kinetic properties of ion channels formed by O-pyromellitylgramicidin (OPg), the negatively charged analogue of gramicidin A (gA), in bilayer lipid membranes was studied by the method of sensitized photoinactivation. The addition of cytochrome c to both sides of the membrane caused substantial deceleration of the photoinactivation kinetics of OPg channels which expose three negative charges to the aqueous phase at both sides of the membrane. By contrast, the gA photoinactivation kinetics was unaltered by the addition of cytochrome c. Based on the sensitivity of the observed effect to the ionic strength of the bathing solution, the cytochrome c-induced deceleration of the OPg photoinactivation kinetics reflecting the increase in the OPg channel lifetime was ascribed to electrostatic interaction of positive charges of cytochrome c with negative charges of OPg that resulted in channel clustering. Formation of clusters of OPg channels was previously inferred to explain the polylysine effect on the OPg channel kinetics. The decelerating effect of cytochrome c on OPg channels was observed only at a high number of OPg channels in the membrane, thus suggesting that the interaction between cytochrome c and the charged transmembrane protein requires sufficiently high negative charge density on the surface of the membrane.
Collapse
Affiliation(s)
- Tatiana I Rokitskaya
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | | | | |
Collapse
|
37
|
de Groot BL, Tieleman DP, Pohl P, Grubmüller H. Water permeation through gramicidin A: desformylation and the double helix: a molecular dynamics study. Biophys J 2002; 82:2934-42. [PMID: 12023216 PMCID: PMC1302081 DOI: 10.1016/s0006-3495(02)75634-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Multinanosecond molecular dynamics simulations of gramicidin A embedded in a dimyristoylphosphatidylcholine bilayer show a remarkable structural stability for both experimentally determined conformations: the head-to-head helical dimer and the double helix. Water permeability was found to be much higher in the double helical conformation, which is explained by lower hydrogen bond-mediated enthalpic barriers at the channel entrance and its larger pore size. Free-energy perturbation calculations show that the double helical structure is stabilized by the positive charges at the N termini introduced by the desformylation, whereas the helical dimer is destabilized. Together with the recent experimental observation that desformyl gramicidin conducts water hundredfold better than gramicidin, this suggests that desformyl gramicidin A predominantly occurs in the double helical conformation.
Collapse
Affiliation(s)
- Bert L de Groot
- Theoretical Molecular Biophysics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | | | | | | |
Collapse
|
38
|
Arndt HD, Vescovi A, Schrey A, Pfeifer JR, Koert U. Solution phase synthesis and purification of the minigramicidin ion channels and a succinyl-linked gramicidin. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00179-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
39
|
Ibrahim HR, Thomas U, Pellegrini A. A helix-loop-helix peptide at the upper lip of the active site cleft of lysozyme confers potent antimicrobial activity with membrane permeabilization action. J Biol Chem 2001; 276:43767-74. [PMID: 11560930 DOI: 10.1074/jbc.m106317200] [Citation(s) in RCA: 220] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, we have found that partially unfolded lysozyme exerts broad spectrum antimicrobial action in vitro against Gram-negative and Gram-positive bacteria independent of its catalytic activity. In parallel, an internal peptide (residues 98-112) of hen egg white lysozyme, obtained after digestion with clostripain, possessed broad spectrum antimicrobial action in vitro. This internal peptide is part of a helix-loop-helix domain (87-114 sequence of hen lysozyme) located at the upper lip of the active site cleft of lysozyme. The helix-loop-helix (HLH) structures are known motifs commonly found in membrane-active and DNA-binding proteins. To evaluate the contribution of the HLH peptide to the antimicrobial properties of lysozyme, the HLH sequence and its secondary structure derivatives of chicken and human lysozyme were synthesized and tested for antimicrobial activity against several bacterial strains. We found that the full HLH peptide of both chicken and human lysozymes was potently microbicidal against both Gram-positive and Gram-negative bacteria and the fungus Candida albicans. The N-terminal helix of HLH was specifically bactericidal to Gram-positive bacteria, whereas the C-terminal helix was bactericidal to all tested strains. Outer and inner membrane permeabilization studies, as well as measurements of transmembrane electrochemical potentials, provided evidence that HLH peptide and its C-terminal helix domain kill Gram-negative bacteria by crossing the outer membrane via self-promoted uptake and causing damage to the inner membrane through channel formation. The results are discussed in terms of proposed mechanisms for the catalytically independent antimicrobial activity of lysozyme that offer a new strategy for the design of potential antimicrobial drugs in the treatment of infectious diseases.
Collapse
Affiliation(s)
- H R Ibrahim
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
| | | | | |
Collapse
|
40
|
Abstract
Potential step amperometry (chronoamperometry) of the Tl(I)/Tl(Hg) electrochemical reduction process has been used to investigate the underlying mechanisms of gramicidin activity in phospholipid monolayers. The experiments were carried out at gramicidin-modified dioleoyl phosphatidylcholine (DOPC)-coated electrodes. Application of a potential step to the coated electrode system results in a current transient that can be divided into two regions. An initial exponential decay of current corresponds to the inactivation of monomer channel conductance and a longer time scale quasi-steady-state represents the diffusion of ions to a bimolecular surface reaction. Concentrations of monomer conducting channels are relatively low, and the results indicate that two or more forms of gramicidin are in equilibrium with each other in the layer. Aromatic/conjugated compounds incorporated into the monolayer increase the reduction current by decreasing the rate of channel inactivation and increasing the stability of the conducting channel. This effect is positively correlated with the degree of the compound's aromaticity. The anomalous influence of alkali metal ions on the reduction current is consistent with the model of gramicidin being speciated in the monolayer in more than one form. The results have implications on the lability of the peptide conformation in biological membranes and its dependence on lipid environment, solution composition, and applied potential.
Collapse
Affiliation(s)
- A Nelson
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, United Kingdom.
| |
Collapse
|
41
|
Armstrong KM, Quigley EP, Quigley P, Crumrine DS, Cukierman S. Covalently linked gramicidin channels: effects of linker hydrophobicity and alkaline metals on different stereoisomers. Biophys J 2001; 80:1810-8. [PMID: 11259294 PMCID: PMC1301370 DOI: 10.1016/s0006-3495(01)76151-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The direct role of the dioxolane group on the gating and single-channel conductance of different stereoisomers of the dioxolane-linked gramicidin A (gA) channels reconstituted in planar lipid bilayers was investigated. Four different covalently linked gA dimers were synthesized. In two of them, the linker was the conventional dioxolane described previously (SS and RR channels). Two gAs were covalently linked with a novel modified dioxolane group containing a retinal attachment (ret-SS and ret-RR gA dimers). These proteins also formed ion channels in lipid bilayers and were selective for monovalent cations. The presence of the bulky and hydrophobic retinal group immobilizes the dioxolane linker in the bilayer core preventing its rotation into the hydrophilic lumen of the pore. In 1 M HCl the gating kinetics of the SS or RR dimers were indistinguishable from their retinal counterparts; the dwell-time distributions of the open and closed states in the SS and ret-SS were basically the same. In particular, the inactivation of the RR was not prevented by the presence of the retinal group. It is concluded that neither the fast closing events in the SS or RR dimers nor the inactivation of the RR are likely to be a functional consequence of the flipping of the dioxolane inside the pore of the channel. On the other hand, the inactivation of the RR dimer was entirely eliminated when alkaline metals (Cs(+) or K(+)) were the permeating cations in the channel. In fact, the open state of the RR channel became extremely stable, and the gating characteristics of both the SS and RR channels were different from what was seen before with permeating protons. As in HCl, the presence of a retinal in the dioxolane linker did not affect the gating behavior of the SS and RR in Cs(+)- or K(+)-containing solutions. Alternative hypotheses concerning the gating of linked gA dimers are discussed.
Collapse
Affiliation(s)
- K M Armstrong
- Department of Physiology, Loyola University Medical School, Maywood, Illinois 60153, USA
| | | | | | | | | |
Collapse
|
42
|
Gokel GW, Ferdani R, Liu J, Pajewski R, Shabany H, Uetrecht P. Hydraphile channels: models for transmembrane, cation-conducting transporters. Chemistry 2001; 7:33-9. [PMID: 11205025 DOI: 10.1002/1521-3765(20010105)7:1<33::aid-chem33>3.0.co;2-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A completely synthetic, non-peptide channel has been prepared and shown to conduct cations across a phospholipid bilayer membrane. Studies have been undertaken to assess the compound's location within the bilayer and to better understand its function. These studies are described along with background on the design and concept of the channel.
Collapse
Affiliation(s)
- G W Gokel
- Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA.
| | | | | | | | | | | |
Collapse
|
43
|
Fushman D, Ghose R, Cowburn D. The Effect of Finite Sampling on the Determination of Orientational Properties: A Theoretical Treatment with Application to Interatomic Vectors in Proteins. J Am Chem Soc 2000. [DOI: 10.1021/ja001128j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David Fushman
- Contribution from the The Rockefeller University, 1230 York Avenue, New York, New York 10021
| | - Ranajeet Ghose
- Contribution from the The Rockefeller University, 1230 York Avenue, New York, New York 10021
| | - David Cowburn
- Contribution from the The Rockefeller University, 1230 York Avenue, New York, New York 10021
| |
Collapse
|
44
|
Abstract
One major remaining problem in structural biology is to elucidate the structure and mechanism of function of membrane proteins. On the basis of preliminary information from genome projects, it is now estimated that up to 50,000 different membrane proteins may exist in the human being and that virtually every life process proceeds, sooner or later, through a membrane protein. Solid-state NMR spectroscopy in high magnetic field is rapidly developing into a widely applicable tool to describe the structure and help understand the mechanism of function of a membrane protein. Recent work in applied solid-state NMR spectroscopy crosses the boundary between the biological and the physical sciences, and aims at increasing the predictive range of this biophysical method.
Collapse
Affiliation(s)
- H J de Groot
- Leiden Institute of Chemistry, Gorlaeus Laboratories, POB 9502, 2300 RA, Leiden, Netherlands.
| |
Collapse
|
45
|
Abstract
Membrane proteins present a hydrophobic surface to the surrounding lipid, whereas portions protruding into the aqueous milieu expose a polar surface. But how have proteins evolved to deal with the complex environment at the membrane-water interface? Some insights have been provided by high-resolution structures of membrane proteins, and recent studies of the role of individual amino acids in mediating protein-lipid contacts have shed further light on this issue. It now appears clear that the polar-aromatic residues Trp and Tyr have a specific affinity for a region near the lipid carbonyls, whereas positively charged residues extend into the lipid phosphate region.
Collapse
Affiliation(s)
- J A Killian
- Dept of Biochemistry of Membranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | | |
Collapse
|
46
|
Abstract
This review compares and contrasts the structures of several different types of ion channels with known three-dimensional structures, including gramicidin and the family of peptaibol channels, as well as the Streptomyces lividans potassium channel, to reveal common features in their structures that relate to their functional roles in ion binding and transport across membranes. Specifically, the locations of aromatic amino acids, the dimensions of the molecules, the multimeric nature of the channels and the roles of hydrogen bonds in stabilising such structures, the means by which the channels open and close, and the chemical nature of the groups which make up the channel lumen are discussed. The emphasis is on the commonality of features found in model channels, which may ultimately be found in other biological channel structures.
Collapse
Affiliation(s)
- B A Wallace
- Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK.
| |
Collapse
|