1
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Miura Y. The conformational properties of alamethicin in ethanol studied by NMR. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024:10.1007/s00249-024-01711-1. [PMID: 38849514 DOI: 10.1007/s00249-024-01711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
Alamethicin, a peptide consisted of 20 amino acid residues, has been known to function as an antibiotic. The peptides self-associate in biological membranes, form an ion channel, and then induce cell death by leaking intracellular contents through a transmembrane pore of an ion channel. We investigated conformation and its thermal stability of alamethicin-A6 and -U6 in ethanol using proton nuclear magnetic resonance (NMR) spectroscopy; alamethicin-A6 and -U6 have the amino acid sequences of UPUAUAQUVUGLUPVUUQQO and UPUAUUQUVUGLUPVUUQQO, respectively, where U and O represent α-aminoisobutyric acid and phenylalaninol, respectively. As indicated by the under bars in the sequences, only the residue 6 differs between the alamethicins. We show that the alamethicins in ethanol form helix conformation in the region of the residues 2-11 and a non-regular conformation in the regions of the N- and C-termini, and that the helices are maintained up to 66 °C at least. Conformations in the region of the residues 12-18 of the alamethicins, however, are not well identified due to the lack of NMR data. In addition, we demonstrate that the amide proton chemical shift temperature coefficients' method, which is known as an indicator for intramolecular hydrogen bonds in peptides and proteins in aqueous solutions, can be also applied to the alamethicins in ethanol. Further, we show that the conformation around the C-terminus of alamethicin-A6 is restrained by intramolecular hydrogen bonds, whereas that of alamethicin-U6 is either restrained or unrestrained by intramolecular hydrogen bonds; the alamethicin-U6 molecules having the restrained and unrestrained conformations coexist in ethanol. We discuss the two types of conformations using a model chain consisting of particles linked by rigid bonds called as the free jointed chain.
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Affiliation(s)
- Yoshinori Miura
- Center for Advanced Instrumental Analysis, Kyushu University, Kasuga, 816-8580, Japan.
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2
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Andrä J, Aisenbrey C, Sudheendra US, Prudhon M, Brezesinski G, Zschech C, Willumeit-Römer R, Leippe M, Gutsmann T, Bechinger B. Structural analysis of the NK-lysin-derived peptide NK-2 upon interaction with bacterial membrane mimetics consisting of phosphatidylethanolamine and phosphatidylglycerol. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184267. [PMID: 38159877 DOI: 10.1016/j.bbamem.2023.184267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
NK-2 is an antimicrobial peptide derived from helices 3 and 4 of the pore-forming protein of natural killer cells, NK-lysin. It has potent activities against Gram-negative and Gram-positive bacteria, fungi and protozoan parasites without being toxic to healthy human cells. In biophysical assays its membrane activities were found to require phosphatidylglycerol (PG) and phosphatidylethanolamine (PE), lipids which dominate the composition of bacterial membranes. Here the structure and activities of NK-2 in binary mixtures of different PE/PG composition were investigated. CD spectroscopy reveals that a threshold concentration of 50 % PG is needed for efficient membrane association of NK-2 concomitant with a random coil - helix transition. Association with PE occurs but is qualitatively different when compared to PG membranes. Oriented solid-state NMR spectroscopy of NK-2 specifically labelled with 15N indicates that the NK-2 helices are oriented parallel to the PG bilayer surface. Upon reduction of the PG content to 20 mol% interactions are weaker and/or an in average more tilted orientation is observed. Fluorescence spectroscopy of differently labelled lipids is in agreement of an interfacial localisation of both helices where the C-terminal end is in a less hydrophobic environment. By inserting into the membrane interface and interacting differently with PE and PG the peptides probably induce high curvature strain which result in membrane openings and rupture.
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Affiliation(s)
- Jörg Andrä
- Department of Biotechnology, Faculty of Life Sciences, Hamburg University of Applied Sciences, Hamburg, Germany.
| | | | - U S Sudheendra
- University of Strasbourg / CNRS, UMR7177, Chemistry Institute, Strasbourg, France
| | - Marc Prudhon
- University of Strasbourg / CNRS, UMR7177, Chemistry Institute, Strasbourg, France
| | - Gerald Brezesinski
- Department of Physics, TU Darmstadt, Darmstadt, Germany; Department of Interfaces, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Claudia Zschech
- Department of Interfaces, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | | | - Matthias Leippe
- Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Thomas Gutsmann
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Burkhard Bechinger
- University of Strasbourg / CNRS, UMR7177, Chemistry Institute, Strasbourg, France; Institut Universitaire de France, 75005 Paris, France.
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3
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Saad A, Bechinger B. Solid-state NMR spectroscopy for structural studies of polypeptides and lipids in extended physiological membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184162. [PMID: 37949788 DOI: 10.1016/j.bbamem.2023.184162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/18/2023] [Accepted: 04/26/2023] [Indexed: 11/12/2023]
Abstract
Solid-state NMR is a quickly developing technique that allows one to obtain structural information at atomic resolution in extended lipid bilayers in a rather unique manner. Two approaches have been developed for membrane proteins and peptides namely magic angle sample spinning and the use of uniaxially oriented membrane samples. The state-of-the-art of both approaches will be introduced and the perspectives of solid-state NMR spectroscopy in the context of other structural biology techniques, pressing biomedical questions and membrane biophysics will be discussed.
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Affiliation(s)
- Ahmad Saad
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France; Institut Universitaire de France, 75005 Paris, France.
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4
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Roversi D, Troiano C, Salnikov E, Giordano L, Riccitelli F, De Zotti M, Casciaro B, Loffredo MR, Park Y, Formaggio F, Mangoni ML, Bechinger B, Stella L. Effects of antimicrobial peptides on membrane dynamics: A comparison of fluorescence and NMR experiments. Biophys Chem 2023; 300:107060. [PMID: 37336097 DOI: 10.1016/j.bpc.2023.107060] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Antimicrobial peptides (AMPs) represent a promising class of compounds to fight resistant infections. They are commonly thought to kill bacteria by perturbing the permeability of their cell membranes. However, bacterial killing requires a high coverage of the cell surface by bound peptides, at least in the case of cationic and amphipathic AMPs. Therefore, it is conceivable that peptide accumulation on the bacterial membranes might interfere with vital cellular functions also by perturbing bilayer dynamics, a hypothesis that has been termed "sand in the gearbox". Here we performed a systematic study of such possible effects, for two representative peptides (the cationic cathelicidin PMAP-23 and the peptaibol alamethicin), employing fluorescence and NMR spectroscopies. These approaches are commonly applied to characterize lipid order and dynamics, but sample different time-scales and could thus report on different membrane properties. In our case, fluorescence anisotropy measurements on liposomes labelled with probes localized at different depths in the bilayer showed that both peptides perturb membrane fluidity and order. Pyrene excimer-formation experiments showed a peptide-induced reduction in lipid lateral mobility. Finally, laurdan fluorescence indicated that peptide binding reduces water penetration below the headgroups region. Comparable effects were observed also in fluorescence experiments performed directly on live bacterial cells. By contrast, the fatty acyl chain order parameters detected by deuterium NMR spectroscopy remained virtually unaffected by addition of the peptides. The apparent discrepancy between the two techniques confirms previous sporadic observations and is discussed in terms of the different characteristic times of the two approaches. The perturbation of membrane dynamics in the ns timescale, indicated by the multiple fluorescence approaches reported here, could contribute to the antimicrobial activity of AMPs, by affecting the function of membrane proteins, which is strongly dependent on the physicochemical properties of the bilayer.
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Affiliation(s)
- Daniela Roversi
- Department of Chemical Science and Technology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Cassandra Troiano
- Department of Chemical Science and Technology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Evgeniy Salnikov
- RMN et Biophysique des membranes, Institut de Chimie de Strasbourg, CNRS/UMR 7177, Université de Strasbourg, 4, rue Blaise Pascal, Strasbourg 67000, France
| | - Lorenzo Giordano
- Department of Chemical Science and Technology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Francesco Riccitelli
- Department of Chemical Science and Technology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Bruno Casciaro
- Department of Biochemical Sciences, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome 00185, Italy
| | - Maria Rosa Loffredo
- Department of Biochemical Sciences, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome 00185, Italy
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, Republic of Korea
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Maria Luisa Mangoni
- Department of Biochemical Sciences, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome 00185, Italy
| | - Burkhard Bechinger
- RMN et Biophysique des membranes, Institut de Chimie de Strasbourg, CNRS/UMR 7177, Université de Strasbourg, 4, rue Blaise Pascal, Strasbourg 67000, France; Institut Universitaire de France, Paris 75005, France
| | - Lorenzo Stella
- Department of Chemical Science and Technology, University of Rome Tor Vergata, Rome 00133, Italy.
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5
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Somberg NH, Wu WW, Medeiros-Silva J, Dregni AJ, Jo H, DeGrado WF, Hong M. SARS-CoV-2 Envelope Protein Forms Clustered Pentamers in Lipid Bilayers. Biochemistry 2022; 61:2280-2294. [PMID: 36219675 PMCID: PMC9583936 DOI: 10.1021/acs.biochem.2c00464] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/26/2022] [Indexed: 11/30/2022]
Abstract
The SARS-CoV-2 envelope (E) protein is a viroporin associated with the acute respiratory symptoms of COVID-19. E forms cation-selective ion channels that assemble in the lipid membrane of the endoplasmic reticulum Golgi intermediate compartment. The channel activity of E is linked to the inflammatory response of the host cell to the virus. Like many viroporins, E is thought to oligomerize with a well-defined stoichiometry. However, attempts to determine the E stoichiometry have led to inconclusive results and suggested mixtures of oligomers whose exact nature might vary with the detergent used. Here, we employ 19F solid-state nuclear magnetic resonance and the centerband-only detection of exchange (CODEX) technique to determine the oligomeric number of E's transmembrane domain (ETM) in lipid bilayers. The CODEX equilibrium value, which corresponds to the inverse of the oligomeric number, indicates that ETM assembles into pentamers in lipid bilayers, without any detectable fraction of low-molecular-weight oligomers. Unexpectedly, at high peptide concentrations and in the presence of the lipid phosphatidylinositol, the CODEX data indicate that more than five 19F spins are within a detectable distance of about 2 nm, suggesting that the ETM pentamers cluster in the lipid bilayer. Monte Carlo simulations that take into account peptide-peptide and peptide-lipid interactions yielded pentamer clusters that reproduced the CODEX data. This supramolecular organization is likely important for E-mediated virus assembly and budding and for the channel function of the protein.
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Affiliation(s)
- Noah H. Somberg
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Westley W. Wu
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, University of California, San Francisco, San Francisco, CA 94158
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, University of California, San Francisco, San Francisco, CA 94158
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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6
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Salnikov E, Bechinger B. Effect of lipid saturation on the topology and oligomeric state of helical membrane polypeptides. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184001. [PMID: 35817122 DOI: 10.1016/j.bbamem.2022.184001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Natural liquid crystalline membranes are made up of many different lipids carrying a mixture of saturated and unsaturated fatty acyl chains. Whereas in the past considerable attention has been paid to cholesterol content, the phospholipid head groups and the membrane surface charge the detailed fatty acyl composition was often considered less important. However, recent investigations indicate that the detailed fatty acyl chain composition has pronounced effects on the oligomerization of the transmembrane helical anchoring domains of the MHC II receptor or the membrane alignment of the cationic antimicrobial peptide PGLa. In contrast the antimicrobial peptides magainin 2 and alamethicin are less susceptible to lipid saturation. Using histidine-rich LAH4 designer peptides the high energetic contributions of lipid saturation in stabilizing transmembrane helical alignments are quantitatively evaluated. These observations can have important implications for the biological regulation of membrane proteins and should be taken into considerations during biophysical or structural experiments.
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Affiliation(s)
- Evgeniy Salnikov
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France; Institut Universitaire de France, France.
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7
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Du Y, Su Y. 19F Solid-state NMR characterization of pharmaceutical solids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 120:101796. [PMID: 35688018 DOI: 10.1016/j.ssnmr.2022.101796] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Solid-state NMR has been increasingly recognized as a high-resolution and versatile spectroscopic tool to characterize drug substances and products. However, the analysis of pharmaceutical materials is often carried out at natural isotopic abundance and a relatively low drug loading in multi-component systems and therefore suffers from challenges of low sensitivity. The fact that fluorinated therapeutics are well represented in pipeline drugs and commercial products offers an excellent opportunity to utilize fluorine as a molecular probe for pharmaceutical analysis. We aim to review recent advancements of 19F magic angle spinning NMR methods in modern drug research and development. Applications to polymorph screening at the micromolar level, structural elucidation, and investigation of molecular interactions at the Ångström to submicron resolution in drug delivery, stability, and quality will be discussed.
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Affiliation(s)
- Yong Du
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, United States
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, United States; Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, IN, 47907, United States; Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, United States; Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, United States.
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8
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Salnikov E, Aisenbrey C, Bechinger B. Lipid saturation and head group composition have a pronounced influence on the membrane insertion equilibrium of amphipathic helical polypeptides. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183844. [PMID: 34954200 DOI: 10.1016/j.bbamem.2021.183844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022]
Abstract
The histidine-rich peptides of the LAH4 family were designed using cationic antimicrobial peptides such as magainin and PGLa as templates. The LAH4 amphipathic helical sequences exhibit a multitude of interesting biological properties such as antimicrobial activity, cell penetration of a large variety of cargo and lentiviral transduction enhancement. The parent peptide associates with lipid bilayers where it changes from an orientation along the membrane interface into a transmembrane configuration in a pH-dependent manner. Here we show that LAH4 adopts a transmembrane configuration in fully saturated DMPC membranes already at pH 3.5, i.e. much below the pKa of the histidines whereas the transition pH in POPC correlates closely with histidine neutralization. In contrast in POPG membranes the in-planar configuration is stabilized by about one pH unit. The differences in pH can be converted into energetic contributions for the in-plane to transmembrane transition equilibrium, where the shift in the transition pH due to lipid saturation corresponds to energies which are otherwise obtained by the exchange of several cationic with hydrophobic residues. A similar dependence on lipid saturation has also been observed when the PGLa and magainin antimicrobial peptides interact within lipid bilayers suggesting that the quantitative evaluation presented in this paper also applies to other membrane polypeptides.
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Affiliation(s)
- Evgeniy Salnikov
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France
| | - Christopher Aisenbrey
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France; Institut Universitaire de France, France.
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9
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Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
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10
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Shcherbakov AA, Medeiros-Silva J, Tran N, Gelenter MD, Hong M. From Angstroms to Nanometers: Measuring Interatomic Distances by Solid-State NMR. Chem Rev 2021; 122:9848-9879. [PMID: 34694769 DOI: 10.1021/acs.chemrev.1c00662] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Internuclear distances represent one of the main structural constraints in molecular structure determination using solid-state NMR spectroscopy, complementing chemical shifts and orientational restraints. Although a large number of magic-angle-spinning (MAS) NMR techniques have been available for distance measurements, traditional 13C and 15N NMR experiments are inherently limited to distances of a few angstroms due to the low gyromagnetic ratios of these nuclei. Recent development of fast MAS triple-resonance 19F and 1H NMR probes has stimulated the design of MAS NMR experiments that measure distances in the 1-2 nm range with high sensitivity. This review describes the principles and applications of these multiplexed multidimensional correlation distance NMR experiments, with an emphasis on 19F- and 1H-based distance experiments. Representative applications of these long-distance NMR methods to biological macromolecules as well as small molecules are reviewed.
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Affiliation(s)
- Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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11
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Rima M, Rima M, Fajloun Z, Sabatier JM, Bechinger B, Naas T. Antimicrobial Peptides: A Potent Alternative to Antibiotics. Antibiotics (Basel) 2021; 10:1095. [PMID: 34572678 PMCID: PMC8466391 DOI: 10.3390/antibiotics10091095] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 01/07/2023] Open
Abstract
Antimicrobial peptides constitute one of the most promising alternatives to antibiotics since they could be used to treat bacterial infections, especially those caused by multidrug-resistant pathogens. Many antimicrobial peptides, with various activity spectra and mechanisms of actions, have been described. This review focuses on their use against ESKAPE bacteria, especially in biofilm treatments, their synergistic activity, and their application as prophylactic agents. Limitations and challenges restricting therapeutic applications are highlighted, and solutions for each challenge are evaluated to analyze whether antimicrobial peptides could replace antibiotics in the near future.
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Affiliation(s)
- Mariam Rima
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, 94270 Le Kremlin-Bicetre, France;
| | - Mohamad Rima
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, EDST, Lebanese University, Tripoli 1300, Lebanon; (M.R.); (Z.F.)
| | - Ziad Fajloun
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, EDST, Lebanese University, Tripoli 1300, Lebanon; (M.R.); (Z.F.)
- Department of Biology, Faculty of Sciences III, Lebanese University, Tripoli 1300, Lebanon
| | - Jean-Marc Sabatier
- Institut de Neuro Physiopathologie, UMR7051, Aix-Marseille Université, Faculté de Pharmacie, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Burkhard Bechinger
- Institut de Chimie de Strasbourg, CNRS, UMR7177, University of Strasbourg, 67008 Strasbourg, France;
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Thierry Naas
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, 94270 Le Kremlin-Bicetre, France;
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicetre, France
- French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, 94270 Le Kremlin-Bicetre, France
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12
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Golysheva EA, Boyle AL, Biondi B, Ruzza P, Kros A, Raap J, Toniolo C, Formaggio F, Dzuba SA. Probing the E/K Peptide Coiled-Coil Assembly by Double Electron-Electron Resonance and Circular Dichroism. Biochemistry 2020; 60:19-30. [PMID: 33320519 DOI: 10.1021/acs.biochem.0c00773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Double electron-electron resonance (DEER, also known as PELDOR) and circular dichroism (CD) spectroscopies were explored for the purpose of studying the specificity of the conformation of peptides induced by their assembly into a self-recognizing system. The E and K peptides are known to form a coiled-coil heterodimer. Two paramagnetic TOAC α-amino acid residues were incorporated into each of the peptides (denoted as K** and E**), and a three-dimensional structural investigation in the presence or absence of their unlabeled counterparts E and K was performed. The TOAC spin-labels, replacing two Ala residues in each compound, are covalently and quasi-rigidly connected to the peptide backbone. They are known not to disturb the native structure, so that any conformational change can easily be monitored and assigned. DEER spectroscopy enables the measurement of the intramolecular electron spin-spin distance distribution between the two TOAC labels, within a length range of 1.5-8 nm. This method allows the individual conformational changes for the K**, K**/E, E**, and E**/K molecules to be investigated in glassy frozen solutions. Our data reveal that the conformations of the E** and K** peptides are strongly influenced by the presence of their counterparts. The results are discussed with those from CD spectroscopy and with reference to the already reported nuclear magnetic resonance data. We conclude that the combined DEER/TOAC approach allows us to obtain accurate and reliable information about the conformation of the peptides before and after their assembly into coiled-coil heterodimers. Applications of this induced fit method to other two-component, but more complex, systems, like a receptor and antagonists, a receptor and a hormone, and an enzyme and a ligand, are discussed.
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Affiliation(s)
- Elena A Golysheva
- Novosibirsk State University, Novosibirsk 630090, Russian Federation.,V. V. Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk 630090, Russian Federation
| | - Aimee L Boyle
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Paolo Ruzza
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Alexander Kros
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Sergei A Dzuba
- Novosibirsk State University, Novosibirsk 630090, Russian Federation.,V. V. Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk 630090, Russian Federation
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13
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Juhl DW, Glattard E, Lointier M, Bampilis P, Bechinger B. The Reversible Non-covalent Aggregation Into Fibers of PGLa and Magainin 2 Preserves Their Antimicrobial Activity and Synergism. Front Cell Infect Microbiol 2020; 10:526459. [PMID: 33102247 PMCID: PMC7554302 DOI: 10.3389/fcimb.2020.526459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/18/2020] [Indexed: 01/29/2023] Open
Abstract
Magainin 2 and PGLa are antimicrobial peptides found together in frog skin secretions. When added as a mixture they show an order of magnitude increase in antibacterial activity and in model membrane permeation assays. Here we demonstrate that both peptides can form fibers with beta-sheet/turn signature in ATR-FTIR- and CD-spectroscopic analyses, but with different morphologies in EM images. Whereas, fiber formation results in acute reduction of the antimicrobial activity of the individual peptides, the synergistic enhancement of activity remains for the equimolar mixture of PGLa and magainin 2 also after fibril formation. The biological significance and potential applications of such supramolecular aggregates are discussed.
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Affiliation(s)
- Dennis Wilkens Juhl
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Elise Glattard
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Morane Lointier
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Panos Bampilis
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
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14
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Highly synergistic antimicrobial activity of magainin 2 and PGLa peptides is rooted in the formation of supramolecular complexes with lipids. Sci Rep 2020; 10:11652. [PMID: 32669585 PMCID: PMC7363891 DOI: 10.1038/s41598-020-68416-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/22/2020] [Indexed: 11/21/2022] Open
Abstract
Magainin 2 and PGLa are cationic, amphipathic antimicrobial peptides which when added as equimolar mixture exhibit a pronounced synergism in both their antibacterial and pore-forming activities. Here we show for the first time that the peptides assemble into defined supramolecular structures along the membrane interface. The resulting mesophases are quantitatively described by state-of-the art fluorescence self-quenching and correlation spectroscopies. Notably, the synergistic behavior of magainin 2 and PGLa correlates with the formation of hetero-domains and an order-of-magnitude increased membrane affinity of both peptides. Enhanced membrane association of the peptide mixture is only observed in the presence of phophatidylethanolamines but not of phosphatidylcholines, lipids that dominate bacterial and eukaryotic membranes, respectively. Thereby the increased membrane-affinity of the peptide mixtures not only explains their synergistic antimicrobial activity, but at the same time provides a new concept to increase the therapeutic window of combinatorial drugs.
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15
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Furlan AL, Laurin Y, Botcazon C, Rodríguez-Moraga N, Rippa S, Deleu M, Lins L, Sarazin C, Buchoux S. Contributions and Limitations of Biophysical Approaches to Study of the Interactions between Amphiphilic Molecules and the Plant Plasma Membrane. PLANTS 2020; 9:plants9050648. [PMID: 32443858 PMCID: PMC7285231 DOI: 10.3390/plants9050648] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 12/20/2022]
Abstract
Some amphiphilic molecules are able to interact with the lipid matrix of plant plasma membranes and trigger the immune response in plants. This original mode of perception is not yet fully understood and biophysical approaches could help to obtain molecular insights. In this review, we focus on such membrane-interacting molecules, and present biophysically grounded methods that are used and are particularly interesting in the investigation of this mode of perception. Rather than going into overly technical details, the aim of this review was to provide to readers with a plant biochemistry background a good overview of how biophysics can help to study molecular interactions between bioactive amphiphilic molecules and plant lipid membranes. In particular, we present the biomimetic membrane models typically used, solid-state nuclear magnetic resonance, molecular modeling, and fluorescence approaches, because they are especially suitable for this field of research. For each technique, we provide a brief description, a few case studies, and the inherent limitations, so non-specialists can gain a good grasp on how they could extend their toolbox and/or could apply new techniques to study amphiphilic bioactive compound and lipid interactions.
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Affiliation(s)
- Aurélien L. Furlan
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Yoann Laurin
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Camille Botcazon
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Technologie de Compiègne, 60200 Compiègne, France;
| | - Nely Rodríguez-Moraga
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Sonia Rippa
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Technologie de Compiègne, 60200 Compiègne, France;
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Sébastien Buchoux
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
- Correspondence: ; Tel.: +33-(0)3-2282-7473
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16
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Munusamy S, Conde R, Bertrand B, Munoz-Garay C. Biophysical approaches for exploring lipopeptide-lipid interactions. Biochimie 2020; 170:173-202. [PMID: 31978418 PMCID: PMC7116911 DOI: 10.1016/j.biochi.2020.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 01/19/2020] [Indexed: 02/07/2023]
Abstract
In recent years, lipopeptides (LPs) have attracted a lot of attention in the pharmaceutical industry due to their broad-spectrum of antimicrobial activity against a variety of pathogens and their unique mode of action. This class of compounds has enormous potential for application as an alternative to conventional antibiotics and for pest control. Understanding how LPs work from a structural and biophysical standpoint through investigating their interaction with cell membranes is crucial for the rational design of these biomolecules. Various analytical techniques have been developed for studying intramolecular interactions with high resolution. However, these tools have been barely exploited in lipopeptide-lipid interactions studies. These biophysical approaches would give precise insight on these interactions. Here, we reviewed these state-of-the-art analytical techniques. Knowledge at this level is indispensable for understanding LPs activity and particularly their potential specificity, which is relevant information for safe application. Additionally, the principle of each analytical technique is presented and the information acquired is discussed. The key challenges, such as the selection of the membrane model are also been briefly reviewed. A brief overview of topics to understand the generalities of lipopeptide (LP) science. Main analytical techniques used to reveal the interaction and the distorting effect of LP on artificial membranes. Guidelines for selecting of the most adequate membrane models for the given analytical technique.
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Affiliation(s)
- Sathishkumar Munusamy
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Renaud Conde
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico.
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17
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Accelerated Molecular Dynamics Applied to the Peptaibol Folding Problem. Int J Mol Sci 2019; 20:ijms20174268. [PMID: 31480404 PMCID: PMC6747184 DOI: 10.3390/ijms20174268] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/24/2019] [Accepted: 08/27/2019] [Indexed: 01/18/2023] Open
Abstract
The use of enhanced sampling molecular dynamics simulations to facilitate the folding of proteins is a relatively new approach which has quickly gained momentum in recent years. Accelerated molecular dynamics (aMD) can elucidate the dynamic path from the unfolded state to the near-native state, “flattened” by introducing a non-negative boost to the potential. Alamethicin F30/3 (Alm F30/3), chosen in this study, belongs to the class of peptaibols that are 7–20 residue long, non-ribosomally synthesized, amphipathic molecules that show interesting membrane perturbing activity. The recent studies undertaken on the Alm molecules and their transmembrane channels have been reviewed. Three consecutive simulations of ~900 ns each were carried out where N-terminal folding could be observed within the first 100 ns, while C-terminal folding could only be achieved almost after 800 ns. It took ~1 μs to attain the near-native conformation with stronger potential boost which may take several μs worth of classical MD to produce the same results. The Alm F30/3 hexamer channel was also simulated in an E. coli mimicking membrane under an external electric field that correlates with previous experiments. It can be concluded that aMD simulation techniques are suited to elucidate peptaibol structures and to understand their folding dynamics.
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18
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Salnikov ES, De Zotti M, Bobone S, Mazzuca C, Raya J, Siano AS, Peggion C, Toniolo C, Stella L, Bechinger B. Trichogin GA IV Alignment and Oligomerization in Phospholipid Bilayers. Chembiochem 2019; 20:2141-2150. [PMID: 31125169 DOI: 10.1002/cbic.201900263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Indexed: 12/21/2022]
Abstract
Trichogin GA IV is a short peptaibol with antimicrobial activity. This uncharged, but amphipathic, sequence is aligned at the membrane interface and undergoes a transition to an aggregated state that inserts more deeply into the membrane, an assembly that predominates at a peptide-to-lipid ratio (P/L) of 1:20. In this work, the natural trichogin sequence was prepared and reconstituted into oriented lipid bilayers. The 15 N NMR chemical shift is indicative of a well-defined alignment of the peptide parallel to the membrane surface at P/Ls of 1:120 and 1:20. When the P/L is increased to 1:8, an additional peptide topology is observed that is indicative of a heterogeneous orientation, with helix alignments ranging from around the magic angle to perfectly in-plane. The topological preference of the trichogin helix for an orientation parallel to the membrane surface was confirmed by attenuated total reflection FTIR spectroscopy. Furthermore, 19 F CODEX experiments were performed on a trichogin sequence with 19 F-Phe at position 10. The CODEX decay is in agreement with a tetrameric complex, in which the 19 F sites are about 9-9.5 Å apart. Thus, a model emerges in which the monomeric peptide aligns along the membrane surface. When the peptide concentration increases, first dimeric and then tetrameric assemblies form, made up from helices oriented predominantly parallel to the membrane surface. The formation of these aggregates correlates with the release of vesicle contents including relatively large molecules.
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Affiliation(s)
- Evgeniy S Salnikov
- Institut de Chimie, University of Strasbourg, CNRS, UMR 7177, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Marta De Zotti
- ICB, Padova Unit, CNR', Department of Chemistry, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Claudia Mazzuca
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Jesus Raya
- Institut de Chimie, University of Strasbourg, CNRS, UMR 7177, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Alvaro S Siano
- Departamento de Química Organica, Facultad de Bioquímica y Ciencias Biologicas, Universidad Nacional del Litoral, Ciudad Universitaria UNL, Ruta Nacional N° 168, Km 472, Santa Fe, 3000, Argentina
| | - Cristina Peggion
- ICB, Padova Unit, CNR', Department of Chemistry, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Claudio Toniolo
- ICB, Padova Unit, CNR', Department of Chemistry, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Burkhard Bechinger
- Institut de Chimie, University of Strasbourg, CNRS, UMR 7177, 4, rue Blaise Pascal, 67070, Strasbourg, France
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19
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Aisenbrey C, Marquette A, Bechinger B. The Mechanisms of Action of Cationic Antimicrobial Peptides Refined by Novel Concepts from Biophysical Investigations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1117:33-64. [PMID: 30980352 DOI: 10.1007/978-981-13-3588-4_4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Even 30 years after the discovery of magainins, biophysical and structural investigations on how these peptides interact with membranes can still bear surprises and add new interesting detail to how these peptides exert their antimicrobial action. Early on, using oriented solid-state NMR spectroscopy, it was found that the amphipathic helices formed by magainins are active when being oriented parallel to the membrane surface. More recent investigations indicate that this in-planar alignment is also found when PGLa and magainin in combination exert synergistic pore-forming activities, where studies on the mechanism of synergistic interaction are ongoing. In a related manner, the investigation of dimeric antimicrobial peptide sequences has become an interesting topic of research which bears promise to refine our views how antimicrobial action occurs. The molecular shape concept has been introduced to explain the effects of lipids and peptides on membrane morphology, locally and globally, and in particular of cationic amphipathic helices that partition into the membrane interface. This concept has been extended in this review to include more recent ideas on soft membranes that can adapt to external stimuli including membrane-disruptive molecules. In this manner, the lipids can change their shape in the presence of low peptide concentrations, thereby maintaining the bilayer properties. At higher peptide concentrations, phase transitions occur which lead to the formation of pores and membrane lytic processes. In the context of the molecular shape concept, the properties of lipopeptides, including surfactins, are shortly presented, and comparisons with the hydrophobic alamethicin sequence are made.
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Affiliation(s)
| | - Arnaud Marquette
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France. .,Faculté de chimie, Institut le Bel, Strasbourg, France.
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20
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Das S, Ben Haj Salah K, Djibo M, Inguimbert N. Peptaibols as a model for the insertions of chemical modifications. Arch Biochem Biophys 2018; 658:16-30. [DOI: 10.1016/j.abb.2018.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/05/2018] [Accepted: 09/18/2018] [Indexed: 12/13/2022]
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21
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Lipid-Mediated Interactions between the Antimicrobial Peptides Magainin 2 and PGLa in Bilayers. Biophys J 2018; 115:1033-1044. [PMID: 30195937 DOI: 10.1016/j.bpj.2018.08.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/13/2018] [Accepted: 08/06/2018] [Indexed: 01/02/2023] Open
Abstract
A synergistic enhancement of activities has been described for the amphipathic cationic antimicrobial peptides magainin 2 and PGLa when tested in antimicrobial assays or in biophysical experiments using model membranes. In the presence of magainin 2, PGLa changes from an in-planar alignment parallel to the membrane surface to a more transmembrane orientation when investigated in membranes made from fully saturated PC or PC/PG, but not when one of the fatty acyl chains is unsaturated. Such lipid-mediated changes in the membrane topology of polypeptide domains could provide an interesting mechanism for the regulation of membrane proteins. Here we investigated the PGLa topology in a wide variety of membranes made of saturated or unsaturated PE, PC, and/or PG using 15N solid-state NMR spectroscopy. In contrast to predictions made by previous models the data show that membrane curvature has only a minor effect on PGLa realignment. Furthermore, using 2H solid-state NMR spectroscopy of deuterated phospholipid fatty acyl chains the order parameters of the lipids were investigated in the presence of PGLa, magainin, or equimolar peptide mixtures. Both peptides cause a pronounced decrease in the order parameters when oriented parallel to the membrane surface, an effect that reverts when PGLa flips into transmembrane alignments. Taken together, these data are suggestive that the magainin-induced disordering of fatty acyl chains provides an important driving force for PGLa realignment.
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22
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Marquette A, Bechinger B. Biophysical Investigations Elucidating the Mechanisms of Action of Antimicrobial Peptides and Their Synergism. Biomolecules 2018; 8:E18. [PMID: 29670065 PMCID: PMC6023007 DOI: 10.3390/biom8020018] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 01/30/2023] Open
Abstract
Biophysical and structural investigations are presented with a focus on the membrane lipid interactions of cationic linear antibiotic peptides such as magainin, PGLa, LL37, and melittin. Observations made with these peptides are distinct as seen from data obtained with the hydrophobic peptide alamethicin. The cationic amphipathic peptides predominantly adopt membrane alignments parallel to the bilayer surface; thus the distribution of polar and non-polar side chains of the amphipathic helices mirror the environmental changes at the membrane interface. Such a membrane partitioning of an amphipathic helix has been shown to cause considerable disruptions in the lipid packing arrangements, transient openings at low peptide concentration, and membrane disintegration at higher peptide-to-lipid ratios. The manifold supramolecular arrangements adopted by lipids and peptides are represented by the 'soft membranes adapt and respond, also transiently' (SMART) model. Whereas molecular dynamics simulations provide atomistic views on lipid membranes in the presence of antimicrobial peptides, the biophysical investigations reveal interesting details on a molecular and supramolecular level, and recent microscopic imaging experiments delineate interesting sequences of events when bacterial cells are exposed to such peptides. Finally, biophysical studies that aim to reveal the mechanisms of synergistic interactions of magainin 2 and PGLa are presented, including unpublished isothermal titration calorimetry (ITC), circular dichroism (CD) and dynamic light scattering (DLS) measurements that suggest that the peptides are involved in liposome agglutination by mediating intermembrane interactions. A number of structural events are presented in schematic models that relate to the antimicrobial and synergistic mechanism of amphipathic peptides when they are aligned parallel to the membrane surface.
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Affiliation(s)
- Arnaud Marquette
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France.
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France.
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23
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Roos M, Wang T, Shcherbakov AA, Hong M. Fast Magic-Angle-Spinning 19F Spin Exchange NMR for Determining Nanometer 19F- 19F Distances in Proteins and Pharmaceutical Compounds. J Phys Chem B 2018; 122:2900-2911. [PMID: 29486126 PMCID: PMC6312665 DOI: 10.1021/acs.jpcb.8b00310] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Internuclear distances measured using NMR provide crucial constraints of three-dimensional structures but are often restricted to about 5 Å due to the weakness of nuclear-spin dipolar couplings. For studying macromolecular assemblies in biology and materials science, distance constraints beyond 1 nm will be extremely valuable. Here we present an extensive and quantitative analysis of the feasibility of 19F spin exchange NMR for precise and robust measurements of interatomic distances up to 1.6 nm at a magnetic field of 14.1 T, under 20-40 kHz magic-angle spinning (MAS). The measured distances are comparable to those achievable from paramagnetic relaxation enhancement but have higher precision, which is better than ±1 Å for short distances and ±2 Å for long distances. For 19F spins with the same isotropic chemical shift but different anisotropic chemical shifts, intermediate MAS frequencies of 15-25 kHz without 1H irradiation accelerate spin exchange. For spectrally resolved 19F-19F spin exchange, 1H-19F dipolar recoupling significantly speeds up 19F-19F spin exchange. On the basis of data from five fluorinated synthetic, pharmaceutical, and biological compounds, we obtained two general curves for spin exchange between CF groups and between CF3 and CF groups. These curves allow 19F-19F distances to be extracted from the measured spin exchange rates after taking into account 19F chemical shifts. These results demonstrate the robustness of 19F spin exchange NMR for distance measurements in a wide range of biological and chemical systems.
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Affiliation(s)
- Matthias Roos
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Tuo Wang
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Alexander A Shcherbakov
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Mei Hong
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
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24
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Forbrig E, Staffa JK, Salewski J, Mroginski MA, Hildebrandt P, Kozuch J. Monitoring the Orientational Changes of Alamethicin during Incorporation into Bilayer Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2373-2385. [PMID: 29353482 DOI: 10.1021/acs.langmuir.7b04265] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Antimicrobial peptides (AMPs) are the first line of defense after contact of an infectious invader, for example, bacterium or virus, with a host and an integral part of the innate immune system of humans. Their broad spectrum of biological functions ranges from cell membrane disruption over facilitation of chemotaxis to interaction with membrane-bound or intracellular receptors, thus providing novel strategies to overcome bacterial resistances. Especially, the clarification of the mechanisms and dynamics of AMP incorporation into bacterial membranes is of high interest, and different mechanistic models are still under discussion. In this work, we studied the incorporation of the peptaibol alamethicin (ALM) into tethered bilayer lipid membranes on electrodes in combination with surface-enhanced infrared absorption (SEIRA) spectroscopy. This approach allows monitoring the spontaneous and potential-induced ion channel formation of ALM in situ. The complex incorporation kinetics revealed a multistep mechanism that points to peptide-peptide interactions prior to penetrating the membrane and adopting the transmembrane configuration. On the basis of the anisotropy of the backbone amide I and II infrared absorptions determined by density functional theory calculations, we employed a mathematical model to evaluate ALM reorientations monitored by SEIRA spectroscopy. Accordingly, ALM was found to adopt inclination angles of ca. 69°-78° and 21° in its interfacially adsorbed and transmembrane incorporated states, respectively. These orientations can be stabilized efficiently by the dipolar interaction with lipid head groups or by the application of a potential gradient. The presented potential-controlled mechanistic study suggests an N-terminal integration of ALM into membranes as monomers or parallel oligomers to form ion channels composed of parallel-oriented helices, whereas antiparallel oligomers are barred from intrusion.
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Affiliation(s)
- Enrico Forbrig
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Jana K Staffa
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Johannes Salewski
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Jacek Kozuch
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
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Syryamina VN, De Zotti M, Toniolo C, Formaggio F, Dzuba SA. Alamethicin self-assembling in lipid membranes: concentration dependence from pulsed EPR of spin labels. Phys Chem Chem Phys 2018; 20:3592-3601. [DOI: 10.1039/c7cp07298h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antimicrobial action of the peptide antibiotic alamethicin (Alm) is commonly related to peptide self-assembling resulting in the formation of voltage-dependent channels in bacterial membranes, which induces ion permeation.
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Affiliation(s)
- Victoria N. Syryamina
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
| | - Marta De Zotti
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Claudio Toniolo
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Fernando Formaggio
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
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