1
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Miura Y. The conformational properties of alamethicin in ethanol studied by NMR. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:267-276. [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] [MESH Headings] [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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Molecular dynamics simulations to study the role of biphenylalanine in promoting the antibacterial activity of ultrashort peptides. J Mol Graph Model 2022; 117:108282. [PMID: 35961218 DOI: 10.1016/j.jmgm.2022.108282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/14/2022] [Accepted: 07/24/2022] [Indexed: 01/14/2023]
Abstract
The hydrophobic amino acid biphenylalanine (B) plays a key role in the antibacterial activity of ultrashort peptides. In this study, the interactions of tetrapeptide BRBR-NH2 (BRBR) and pentapeptide BRBRB-NH2 (BRBRB) with dioleoylphosphatidylcholine/dioleoylphosphatidylglycerol (DOPC/DOPG) mixed model membrane were studied by molecular dynamics simulation to assess the role of biphenylalanine in promoting the antibacterial activity of ultrashort peptides. At low peptide concentrations, both peptides presented amphiphilic conformations; residues B of the pentapeptide approached the membrane faster than those of the tetrapeptide and made more contacts with the membrane; BRBRB exhibited stronger membrane affinity than BRBR. However, due to the low peptide concentrations, the effects of these two peptides on the membrane were not significantly different. At high peptide concentrations, the strong affinity of BRBRB made it have more interaction with membrane than BRBR and most residues B of BRBRB inserted into the membrane; BRBRB was more prone to aggregation and caused the membrane more disordered and thinner than BRBR. Hydrophobic residues often act as anchors in the antibacterial activity of ultrashort antimicrobial peptides. Adding a hydrophobic residue B to the C-terminal of BRBR could improve the ability of the peptide to "grasp" the membrane. At high peptide concentrations, the addition of residue B might enhance the antibacterial activity of the peptide. Thus, our results will be helpful in designing efficient antibacterial drugs.
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3
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Phyo P, Zhao X, Templeton AC, Xu W, Cheung JK, Su Y. Understanding molecular mechanisms of biologics drug delivery and stability from NMR spectroscopy. Adv Drug Deliv Rev 2021; 174:1-29. [PMID: 33609600 DOI: 10.1016/j.addr.2021.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/20/2021] [Accepted: 02/07/2021] [Indexed: 02/06/2023]
Abstract
Protein therapeutics carry inherent limitations of membrane impermeability and structural instability, despite their predominant role in the modern pharmaceutical market. Effective formulations are needed to overcome physiological and physicochemical barriers, respectively, for improving bioavailability and stability. Knowledge of membrane affinity, cellular internalization, encapsulation, and release of drug-loaded carrier vehicles uncover the structural basis for designing and optimizing biopharmaceuticals with enhanced delivery efficiency and therapeutic efficacy. Understanding stabilizing and destabilizing interactions between protein drugs and formulation excipients provide fundamental mechanisms for ensuring the stability and quality of biological products. This article reviews the molecular studies of biologics using solution and solid-state NMR spectroscopy on structural attributes pivotal to drug delivery and stability. In-depth investigation of the structure-function relationship of drug delivery systems based on cell-penetrating peptides, lipid nanoparticles and polymeric colloidal, and biophysical and biochemical stability of peptide, protein, monoclonal antibody, and vaccine, as the integrative efforts on drug product design, will be elaborated.
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Affiliation(s)
- Pyae Phyo
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Xi Zhao
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Allen C Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Jason K Cheung
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States.
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4
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Understanding the antimicrobial activity of water soluble γ-cyclodextrin/alamethicin complex. Colloids Surf B Biointerfaces 2018; 172:451-458. [DOI: 10.1016/j.colsurfb.2018.08.065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/06/2018] [Accepted: 08/29/2018] [Indexed: 02/03/2023]
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5
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Abbasi F, Alvarez-Malmagro J, Su Z, Leitch JJ, Lipkowski J. Pore Forming Properties of Alamethicin in Negatively Charged Floating Bilayer Lipid Membranes Supported on Gold Electrodes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:13754-13765. [PMID: 30265810 DOI: 10.1021/acs.langmuir.8b02554] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Electrochemical impedance spectroscopy (EIS), atomic force microscopy (AFM), and photon polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) were employed to investigate the formation of alamethicin pores in negatively charged bilayers composed of a mixture of 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) and egg-PG floating at gold (111) electrode surfaces modified by self-assembled monolayers of 1-thio-β-d-glucose (β-Tg). The EIS data showed that the presence of alamethicin decreases the membrane resistivity by about 1 order of magnitude. PM-IRRAS measurements provided information about the tilt angles of peptide helical axis with respect to the bilayer normal. The small tilt angles obtained for the peptide helical axis prove that the alamethicin molecules were inserted into the DMPC/egg-PG membranes. The tilt angles decreased when negative potentials were applied, which correlates with the observed decrease in membrane resistivity, indicating that ion pore formation is assisted by the transmembrane potential. Molecular resolution AFM images provided visual evidence that alamethicin molecules aggregate forming hexagonal porous 2D lattices with periodicities of 2.0 ± 0.2 nm. The pore formation by alamethicin in the negatively charged membrane was compared with the interaction of this peptide with a bilayer formed by zwitterionic lipids. The comparison of these results showed that alamethicin preferentially forms ion translocating pores in negatively charged phospholipid membranes.
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Affiliation(s)
- Fatemeh Abbasi
- Department of Chemistry , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | | | - ZhangFei Su
- Department of Chemistry , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - J Jay Leitch
- Department of Chemistry , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Jacek Lipkowski
- Department of Chemistry , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
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6
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Conjugates and nano-delivery of antimicrobial peptides for enhancing therapeutic activity. J Drug Deliv Sci Technol 2018. [DOI: 10.1016/j.jddst.2017.12.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Mizuguchi T, Matubayasi N. Free-Energy Analysis of Peptide Binding in Lipid Membrane Using All-Atom Molecular Dynamics Simulation Combined with Theory of Solutions. J Phys Chem B 2018; 122:3219-3229. [DOI: 10.1021/acs.jpcb.7b08241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomoko Mizuguchi
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- Institute for the Promotion of University Strategy, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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8
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Zhang MK, Lyu Y, Zhu X, Wang JP, Jin ZY, Narsimhan G. Enhanced solubility and antimicrobial activity of alamethicin in aqueous solution by complexation with γ-cyclodextrin. J Funct Foods 2018. [DOI: 10.1016/j.jff.2017.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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9
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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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10
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Das S, Ben Haj Salah K, Wenger E, Martinez J, Kotarba J, Andreu V, Ruiz N, Savini F, Stella L, Didierjean C, Legrand B, Inguimbert N. Enhancing the Antimicrobial Activity of Alamethicin F50/5 by Incorporating N-terminal Hydrophobic Triazole Substituents. Chemistry 2017; 23:17964-17972. [DOI: 10.1002/chem.201703569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Sanjit Das
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
| | - Khoubaib Ben Haj Salah
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
| | - Emmanuel Wenger
- CRM2 (UMR UL-CNRS 7036) Faculté des Sciences et Technologies; Université de Lorraine; 70239 Boulevard des Aiguillettes 54506 Vandoeuvre-lès-Nancy France)
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; Université de Montpellier; 15 avenue Charles Flahault, BP 14491 34093 Montpellier Cedex 5 France
| | | | | | - Nicolas Ruiz
- Laboratoire Mer Molécules Santé.; Université de Nantes, UFR de Sciences pharmaceutiques et biologiques; 9 rue Bias-BP 61112 44035 Nantes France
| | - Filippo Savini
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma, Tor Vergata; Via della Ricerca Scientifica 00133 Roma Italy)
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma, Tor Vergata; Via della Ricerca Scientifica 00133 Roma Italy)
| | - Claude Didierjean
- CRM2 (UMR UL-CNRS 7036) Faculté des Sciences et Technologies; Université de Lorraine; 70239 Boulevard des Aiguillettes 54506 Vandoeuvre-lès-Nancy France)
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; Université de Montpellier; 15 avenue Charles Flahault, BP 14491 34093 Montpellier Cedex 5 France
| | - Nicolas Inguimbert
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
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11
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Booth V, Warschawski DE, Santisteban NP, Laadhari M, Marcotte I. Recent progress on the application of 2H solid-state NMR to probe the interaction of antimicrobial peptides with intact bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1500-1511. [PMID: 28844739 DOI: 10.1016/j.bbapap.2017.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 07/13/2017] [Accepted: 07/25/2017] [Indexed: 10/19/2022]
Abstract
Discoveries relating to innate immunity and antimicrobial peptides (AMPs) granted Bruce Beutler and Jules Hoffmann a Nobel prize in medicine in 2011, and opened up new avenues for the development of therapies against infections, and even cancers. The mechanisms by which AMPs interact with, and ultimately disrupt, bacterial cell membranes is still, to a large extent, incompletely understood. Up until recently, this mechanism was studied using model lipid membranes that failed to reproduce the complexity of molecular interactions present in real cells comprising lipids but also membrane proteins, a cell wall containing peptidoglycan or lipopolysaccharides, and other molecules. In this review, we focus on recent attempts to study, at the molecular level, the interaction between cationic AMPs and intact bacteria, by 2H solid-state NMR. Specifically-labeled lipids allow us to focus on the interaction of AMPs with the heart of the bacterial membrane, and measure the lipid order and its variation upon interaction with various peptides. We will review the important parameters to consider in such a study, and summarize the results obtained in the past 5years on various peptides, in particular aurein 1.2, caerin 1.1, MSI-78 and CA(1-8)M(1-10). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Valerie Booth
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada; Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada
| | - Dror E Warschawski
- UMR 7099, CNRS - Université Paris Diderot, IBPC, 13 rue Pierre et Marie Curie, F-75005 Paris, France; Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montréal H3C 3P8, Canada
| | - Nury P Santisteban
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada
| | - Marwa Laadhari
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montréal H3C 3P8, Canada
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montréal H3C 3P8, Canada.
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12
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Wimmer R, Uggerhøj LE. Determination of Structure and Micellar Interactions of Small Antimicrobial Peptides by Solution-State NMR. Methods Mol Biol 2017; 1548:73-88. [PMID: 28013498 DOI: 10.1007/978-1-4939-6737-7_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
NMR spectroscopy is a well-established technique to determine the structure of peptides and small proteins in solution, also when bound to detergent micelles or phospholipid bicelles. The structure of the peptide alone is, however, not conveying the full picture, if the peptide is bound to a micelle, since it does not tell anything about the orientation of the peptide in the micelle. This article describes how to obtain that information together with information on peptide structure.
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Affiliation(s)
- Reinhard Wimmer
- Department of Chemistry and Bioscience, University of Aalborg, Frederik Bajers vej 7H, 9220, Aalborg, Denmark.
| | - Lars Erik Uggerhøj
- Department of Chemistry and Bioscience, University of Aalborg, Frederik Bajers vej 7H, 9220, Aalborg, Denmark
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13
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Xiang N, Lyu Y, Zhu X, Bhunia AK, Narsimhan G. Methodology for identification of pore forming antimicrobial peptides from soy protein subunits β-conglycinin and glycinin. Peptides 2016; 85:27-40. [PMID: 27612614 DOI: 10.1016/j.peptides.2016.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/31/2016] [Accepted: 09/05/2016] [Indexed: 01/07/2023]
Abstract
Antimicrobial peptides (AMPs) inactivate microbial cells through pore formation in cell membrane. Because of their different mode of action compared to antibiotics, AMPs can be effectively used to combat drug resistant bacteria in human health. AMPs can also be used to replace antibiotics in animal feed and immobilized on food packaging films. In this research, we developed a methodology based on mechanistic evaluation of peptide-lipid bilayer interaction to identify AMPs from soy protein. Production of AMPs from soy protein is an attractive, cost-saving alternative for commercial consideration, because soy protein is an abundant and common protein resource. This methodology is also applicable for identification of AMPs from any protein. Initial screening of peptide segments from soy glycinin (11S) and soy β-conglycinin (7S) subunits was based on their hydrophobicity, hydrophobic moment and net charge. Delicate balance between hydrophilic and hydrophobic interactions is necessary for pore formation. High hydrophobicity decreases the peptide solubility in aqueous phase whereas high hydrophilicity limits binding of the peptide to the bilayer. Out of several candidates chosen from the initial screening, two peptides satisfied the criteria for antimicrobial activity, viz. (i) lipid-peptide binding in surface state and (ii) pore formation in transmembrane state of the aggregate. This method of identification of antimicrobial activity via molecular dynamics simulation was shown to be robust in that it is insensitive to the number of peptides employed in the simulation, initial peptide structure and force field. Their antimicrobial activity against Listeria monocytogenes and Escherichia coli was further confirmed by spot-on-lawn test.
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Affiliation(s)
- Ning Xiang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States
| | - Yuan Lyu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States
| | - Xiao Zhu
- Research Computing, Rosen Center for Advanced Computing, Purdue University, West Lafayette, IN 47907, United States
| | - Arun K Bhunia
- Department of Food Science, Purdue University, West Lafayette, IN 47907, United States; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, United States
| | - Ganesan Narsimhan
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States.
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14
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Kobayashi H, Nagao S, Hirota S. Characterization of the Cytochrome c
Membrane-Binding Site Using Cardiolipin-Containing Bicelles with NMR. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hisashi Kobayashi
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama, Ikoma Nara 630-0192 Japan
| | - Satoshi Nagao
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama, Ikoma Nara 630-0192 Japan
| | - Shun Hirota
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama, Ikoma Nara 630-0192 Japan
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15
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Kobayashi H, Nagao S, Hirota S. Characterization of the Cytochrome c Membrane-Binding Site Using Cardiolipin-Containing Bicelles with NMR. Angew Chem Int Ed Engl 2016; 55:14019-14022. [PMID: 27723218 DOI: 10.1002/anie.201607419] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/16/2016] [Indexed: 12/12/2022]
Abstract
Cytochrome (cyt) c transports electrons from Complex III to Complex IV in mitochondria. Cyt c is ordinarily anchored to the mitochondrial membrane through interaction with cardiolipin (CL), however its release into the cytosol initiates apoptosis. The cyt c interaction site with CL-containing bicelles was characterized by NMR spectroscopy. Chemical shift perturbations in cyt c signals upon interaction with bicelles revealed that a relatively wide region, which includes the A-site, the CXXCH motif, and the N- and C-terminal helices, and contains multiple Lys residues, interacts cooperatively with CL. The specific cyt c-CL interaction increased with increasing CL molecules in the bicelles. The location of the cyt c interaction site for CL was similar to those for Complex III and Complex IV, thus indicating that cyt c recognizes lipids and partner proteins in a similar way. In addition to elucidating the cyt c membrane-binding site, these results provide insight into the dynamic aspect of cyt c interactions in mitochondria.
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Affiliation(s)
- Hisashi Kobayashi
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Satoshi Nagao
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
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16
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Kabelka I, Vácha R. Optimal conditions for opening of membrane pore by amphiphilic peptides. J Chem Phys 2015; 143:243115. [DOI: 10.1063/1.4933229] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Ivo Kabelka
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Robert Vácha
- Faculty of Science and CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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17
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Wondraczek L, Tyystjärvi E, Méndez-Ramos J, Müller FA, Zhang Q. Shifting the Sun: Solar Spectral Conversion and Extrinsic Sensitization in Natural and Artificial Photosynthesis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2015; 2:1500218. [PMID: 27774377 PMCID: PMC5063168 DOI: 10.1002/advs.201500218] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/07/2015] [Indexed: 05/22/2023]
Abstract
Solar energy harvesting is largely limited by the spectral sensitivity of the employed energy conversion system, where usually large parts of the solar spectrum do not contribute to the harvesting scheme, and where, of the contributing fraction, the full potential of each photon is not efficiently used in the generation of electrical or chemical energy. Extrinsic sensitization through photoluminescent spectral conversion has been proposed as a route to at least partially overcome this problem. Here, we discuss this approach in the emerging context of photochemical energy harvesting and storage through natural or artificial photosynthesis. Clearly contrary to application in photovoltaic energy conversion, implementation of solar spectral conversion for extrinsic sensitization of a photosynthetic machinery is very straightforward, and-when compared to intrinsic sensitization-less-strict limitations with regard to quantum coherence are seen. We now argue the ways in which extrinsic sensitization through photoluminescent spectral converters will-and will not-play its role in the area of ultra-efficient photosynthesis, and also illustrate how such extrinsic sensitization requires dedicated selection of specific conversion schemes and design strategies on system scale.
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Affiliation(s)
- Lothar Wondraczek
- Otto Schott Institute of Materials Research University of Jena Jena 07743 Germany; Centre for Energy and Environmental Chemistry (CEEC)University of Jena Jena 07743 Germany
| | - Esa Tyystjärvi
- Department of Biochemistry and Food Chemistry University of Turku 20014 Turku Finland
| | - Jorge Méndez-Ramos
- Department of Physics University La Laguna 38206 La Laguna Tenerife Spain
| | - Frank A Müller
- Otto Schott Institute of Materials Research University of Jena Jena 07743 Germany; Centre for Energy and Environmental Chemistry (CEEC)University of Jena Jena 07743 Germany
| | - Qinyuan Zhang
- State Key Laboratory of Luminescent Materials and Devices Institute of Optical Communication Materials South China University of Technology Guangzhou 510640 P.R. China
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18
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Bobone S, De Zotti M, Bortolotti A, Biondi B, Ballano G, Palleschi A, Toniolo C, Formaggio F, Stella L. The fluorescence and infrared absorption probepara-cyanophenylalanine: Effect of labeling on the behavior of different membrane-interacting peptides. Biopolymers 2015; 104:521-32. [DOI: 10.1002/bip.22674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/30/2015] [Accepted: 05/04/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Sara Bobone
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Marta De Zotti
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Annalisa Bortolotti
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Gema Ballano
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Claudio Toniolo
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Lorenzo Stella
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
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19
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Nagao T, Mishima D, Javkhlantugs N, Wang J, Ishioka D, Yokota K, Norisada K, Kawamura I, Ueda K, Naito A. Structure and orientation of antibiotic peptide alamethicin in phospholipid bilayers as revealed by chemical shift oscillation analysis of solid state nuclear magnetic resonance and molecular dynamics simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2789-98. [PMID: 26248014 DOI: 10.1016/j.bbamem.2015.07.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/01/2015] [Accepted: 07/31/2015] [Indexed: 11/26/2022]
Abstract
The structure, topology and orientation of membrane-bound antibiotic alamethicin were studied using solid state nuclear magnetic resonance (NMR) spectroscopy. (13)C chemical shift interaction was observed in [1-(13)C]-labeled alamethicin. The isotropic chemical shift values indicated that alamethicin forms a helical structure in the entire region. The chemical shift anisotropy of the carbonyl carbon of isotopically labeled alamethicin was also analyzed with the assumption that alamethicin molecules rotate rapidly about the bilayer normal of the phospholipid bilayers. It is considered that the adjacent peptide planes form an angle of 100° or 120° when it forms α-helix or 310-helix, respectively. These properties lead to an oscillation of the chemical shift anisotropy with respect to the phase angle of the peptide plane. Anisotropic data were acquired for the 4 and 7 sites of the N- and C-termini, respectively. The results indicated that the helical axes for the N- and C-termini were tilted 17° and 32° to the bilayer normal, respectively. The chemical shift oscillation curves indicate that the N- and C-termini form the α-helix and 310-helix, respectively. The C-terminal 310-helix of alamethicin in the bilayer was experimentally observed and the unique bending structure of alamethicin was further confirmed by measuring the internuclear distances of [1-(13)C] and [(15)N] doubly-labeled alamethicin. Molecular dynamics simulation of alamethicin embedded into dimyristoyl phophatidylcholine (DMPC) bilayers indicates that the helical axes for α-helical N- and 310-helical C-termini are tilted 12° and 32° to the bilayer normal, respectively, which is in good agreement with the solid state NMR results.
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Affiliation(s)
- Takashi Nagao
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Daisuke Mishima
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Namsrai Javkhlantugs
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan; Center for Nanoscience and Nanotechnology, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Jun Wang
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Daisuke Ishioka
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kiyonobu Yokota
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazushi Norisada
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazuyoshi Ueda
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
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20
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Hansen SK, Bertelsen K, Paaske B, Nielsen NC, Vosegaard T. Solid-state NMR methods for oriented membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:48-85. [PMID: 26282196 DOI: 10.1016/j.pnmrs.2015.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Oriented-sample solid-state NMR represents one of few experimental methods capable of characterising the membrane-bound conformation of proteins in the cell membrane. Since the technique was developed 25 years ago, the technique has been applied to study the structure of helix bundle membrane proteins and antimicrobial peptides, characterise protein-lipid interactions, and derive information on dynamics of the membrane anchoring of membrane proteins. We will review the major developments in various aspects of oriented-sample solid-state NMR, including sample-preparation methods, pulse sequences, theory required to interpret the experiments, perspectives for and guidelines to new experiments, and a number of representative applications.
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Affiliation(s)
- Sara K Hansen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Berit Paaske
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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21
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Tošner Z, Andersen R, Stevensson B, Edén M, Nielsen NC, Vosegaard T. Computer-intensive simulation of solid-state NMR experiments using SIMPSON. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 246:79-93. [PMID: 25093693 DOI: 10.1016/j.jmr.2014.07.002] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/08/2014] [Accepted: 07/13/2014] [Indexed: 06/03/2023]
Abstract
Conducting large-scale solid-state NMR simulations requires fast computer software potentially in combination with efficient computational resources to complete within a reasonable time frame. Such simulations may involve large spin systems, multiple-parameter fitting of experimental spectra, or multiple-pulse experiment design using parameter scan, non-linear optimization, or optimal control procedures. To efficiently accommodate such simulations, we here present an improved version of the widely distributed open-source SIMPSON NMR simulation software package adapted to contemporary high performance hardware setups. The software is optimized for fast performance on standard stand-alone computers, multi-core processors, and large clusters of identical nodes. We describe the novel features for fast computation including internal matrix manipulations, propagator setups and acquisition strategies. For efficient calculation of powder averages, we implemented interpolation method of Alderman, Solum, and Grant, as well as recently introduced fast Wigner transform interpolation technique. The potential of the optimal control toolbox is greatly enhanced by higher precision gradients in combination with the efficient optimization algorithm known as limited memory Broyden-Fletcher-Goldfarb-Shanno. In addition, advanced parallelization can be used in all types of calculations, providing significant time reductions. SIMPSON is thus reflecting current knowledge in the field of numerical simulations of solid-state NMR experiments. The efficiency and novel features are demonstrated on the representative simulations.
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Affiliation(s)
- Zdeněk Tošner
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark; NMR Laboratory, Department of Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-128 43, Czech Republic.
| | - Rasmus Andersen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Baltzar Stevensson
- Physical Chemistry Division, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mattias Edén
- Physical Chemistry Division, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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22
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Castro TG, Micaêlo NM. Conformational and thermodynamic properties of non-canonical α,α-dialkyl glycines in the peptaibol Alamethicin: molecular dynamics studies. J Phys Chem B 2014; 118:9861-70. [PMID: 25091499 DOI: 10.1021/jp505400q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we investigate the structure, dynamic and thermodynamic properties of noncanonical disubstituted amino acids (α,α-dialkyl glycines), also known as non-natural amino acids, in the peptaibol Alamethicin. The amino acids under study are Aib (α-amino isobutyric acid or α-methyl alanine), Deg (α,α-diethyl glycine), Dpg (α,α-dipropyl glycine), Dibg (α,α-di-isobutyl glycine), Dhg (α,α-dihexyl glycine), DΦg (α,α-diphenyl glycine), Dbzg (α,α-dibenzyl glycine), Ac6c (α,α-cyclohexyl glycine), and Dmg (α,α-dihydroxymethyl glycine). It is hypothesized that these amino acids are able to induce well-defined secondary structure in peptidomimetics. To test this hypothesis, new peptidomimetics of Alamethicin were constructed by replacing the native Aib positions of Alamethicin by one or more new α,α-dialkyl glycines. Dhg and Ac6c demonstrated the capacity to induce well-defined α-helical structures. Dhg and Ac6c also promote the thermodynamic stabilization of these peptides in a POPC model membrane and are better alternatives to the Aib in Alamethicin. These noncanonical amino acids also improved secondary structure properties, revealing preorganization in water and maintenance of α helical structure in POPC. We show that it is possible to optimize the helicity and thermodynamic properties of native Alamethicin, and we suggest that these amino acids could be incorporated in other peptides with similar structural effect.
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Affiliation(s)
- Tarsila G Castro
- Departamento de Química, Escola de Ciências, Universidade do Minho , Largo do Paço, Braga 4704-553, Portugal
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23
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Di Luca M, Maccari G, Nifosì R. Treatment of microbial biofilms in the post-antibiotic era: prophylactic and therapeutic use of antimicrobial peptides and their design by bioinformatics tools. Pathog Dis 2014; 70:257-70. [PMID: 24515391 DOI: 10.1111/2049-632x.12151] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/22/2014] [Accepted: 01/30/2014] [Indexed: 12/14/2022] Open
Abstract
The treatment for biofilm infections is particularly challenging because bacteria in these conditions become refractory to antibiotic drugs. The reduced effectiveness of current therapies spurs research for the identification of novel molecules endowed with antimicrobial activities and new mechanisms of antibiofilm action. Antimicrobial peptides (AMPs) have been receiving increasing attention as potential therapeutic agents, because they represent a novel class of antibiotics with a wide spectrum of activity and a low rate in inducing bacterial resistance. Over the past decades, a large number of naturally occurring AMPs have been identified or predicted from various organisms as effector molecules of the innate immune system playing a crucial role in the first line of defense. Recent studies have shown the ability of some AMPs to act against microbial biofilms, in particular during early phases of biofilm development. Here, we provide a review of the antimicrobial peptides tested on biofilms, highlighting their advantages and disadvantages for prophylactic and therapeutic applications. In addition, we describe the strategies and methods for de novo design of potentially active AMPs and discuss how informatics and computational tools may be exploited to improve antibiofilm effectiveness.
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24
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Vácha R, Frenkel D. Simulations suggest possible novel membrane pore structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:1304-1310. [PMID: 24059441 DOI: 10.1021/la402727a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Amphiphilic proteins and peptides can induce the formation of stable and metastable pores in membranes. Using coarse-grained simulations, we have studied the factors that affect structure of peptide-stabilized pores. Our simulations are able to reproduce the formation of the well-known barrel-stave or toroidal pores, but in addition, we find evidence for a novel "double-belt" pore structure: in this structure the peptides that coat the membrane pore are oriented parallel to the membrane plane. To check the predictions of our coarse-grained model, we have performed more detailed simulations, using the MARTINI force field. These simulations show that the double-belt structure is stable up to at least the microsecond time scale.
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Affiliation(s)
- Robert Vácha
- National Centre for Biomolecular Research, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University , Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
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25
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Biomimetic Membrane Supported at a Metal Electrode Surface. ADVANCES IN PLANAR LIPID BILAYERS AND LIPOSOMES 2014. [DOI: 10.1016/b978-0-12-418698-9.00001-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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26
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Relini A, Marano N, Gliozzi A. Misfolding of amyloidogenic proteins and their interactions with membranes. Biomolecules 2013; 4:20-55. [PMID: 24970204 PMCID: PMC4030986 DOI: 10.3390/biom4010020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/13/2013] [Accepted: 12/17/2013] [Indexed: 01/07/2023] Open
Abstract
In this paper, we discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. Many of these proteins are implicated in serious illnesses such as Alzheimer’s disease and Parkinson’s disease. Misfolding of amyloidogenic proteins leads to the formation of polymorphic oligomers and fibrils. Oligomeric aggregates are widely thought to be the toxic species, however, fibrils also play a role in membrane damage. We focus on the structure of these aggregates and their interactions with model membranes. Study of interactions of amlyoidogenic proteins with model and natural membranes has shown the importance of the lipid bilayer in protein misfolding and aggregation and has led to the development of several models for membrane permeabilization by the resulting amyloid aggregates. We discuss several of these models: formation of structured pores by misfolded amyloidogenic proteins, extraction of lipids, interactions with receptors in biological membranes, and membrane destabilization by amyloid aggregates perhaps analogous to that caused by antimicrobial peptides.
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Affiliation(s)
- Annalisa Relini
- Department of Physics, University of Genoa, Genoa 16146, Italy.
| | - Nadia Marano
- Department of Physics, University of Genoa, Genoa 16146, Italy.
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27
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Kredics L, Szekeres A, Czifra D, Vágvölgyi C, Leitgeb B. Recent results in alamethicin research. Chem Biodivers 2013; 10:744-71. [PMID: 23681724 DOI: 10.1002/cbdv.201200390] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 12/20/2022]
Affiliation(s)
- László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged.
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28
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Bortolus M, De Zotti M, Formaggio F, Maniero AL. Alamethicin in bicelles: Orientation, aggregation, and bilayer modification as a function of peptide concentration. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2620-7. [DOI: 10.1016/j.bbamem.2013.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/24/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022]
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29
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Solution NMR studies on the orientation of membrane-bound peptides and proteins by paramagnetic probes. Molecules 2013; 18:7407-35. [PMID: 23799448 PMCID: PMC6269851 DOI: 10.3390/molecules18077407] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/13/2013] [Accepted: 06/20/2013] [Indexed: 12/24/2022] Open
Abstract
Many peptides and proteins are attached to or immersed in a biological membrane. In order to understand their function not only the structure but also their topology in the membrane is important. Solution NMR spectroscopy is one of the most often used approaches to determine the orientation and localization of membrane-bound peptides and proteins. Here we give an application-oriented overview on the use of paramagnetic probes for the investigation of membrane-bound peptides and proteins. The examples discussed range from the large pool of antimicrobial peptides, bacterial toxins, cell penetrating peptides to domains of larger proteins or the calcium regulating protein phospholamban. Topological information is obtained in all these examples by the use of either attached or freely mobile paramagnetic tags. For some examples information obtained from the paramagnetic probes was included in the structure determination.
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30
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Kumara Swamy SK, Karczmarska A, Makowska-Janusik M, Kassiba A, Dittmer J. Solid-State NMR Correlation Experiments and Distance Measurements in Paramagnetic Metalorganics Exemplified by Cu-Cyclam. Chemphyschem 2013; 14:1864-70. [DOI: 10.1002/cphc.201300119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Indexed: 11/11/2022]
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31
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Abstract
Antimicrobial peptides (AMPs) provide a primordial source of immunity, conferring upon eukaryotic cells resistance against bacteria, protozoa, and viruses. Despite a few examples of anionic peptides, AMPs are usually relatively short positively charged polypeptides, consisting of a dozen to about a hundred amino acids, and exhibiting amphipathic character. Despite significant differences in their primary and secondary structures, all AMPs discovered to date share the ability to interact with cellular membranes, thereby affecting bilayer stability, disrupting membrane organization, and/or forming well-defined pores. AMPs selectively target infectious agents without being susceptible to any of the common pathways by which these acquire resistance, thereby making AMPs prime candidates to provide therapeutic alternatives to conventional drugs. However, the mechanisms of AMP actions are still a matter of intense debate. The structure-function paradigm suggests that a better understanding of how AMPs elicit their biological functions could result from atomic resolution studies of peptide-lipid interactions. In contrast, more strict thermodynamic views preclude any roles for three-dimensional structures. Indeed, the design of selective AMPs based solely on structural parameters has been challenging. In this chapter, we will focus on selected AMPs for which studies on the corresponding AMP-lipid interactions have helped reach an understanding of how AMP effects are mediated. We will emphasize the roles of both liquid- and solid-state NMR spectroscopy for elucidating the mechanisms of action of AMPs.
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32
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Méndez-Ramos J, Acosta-Mora P, Ruiz-Morales JC, Hernández T, Borges ME, Esparza P. Turning into the blue: materials for enhancing TiO2 photocatalysis by up-conversion photonics. RSC Adv 2013. [DOI: 10.1039/c3ra44342f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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33
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Yamaguchi T, Uno T, Uekusa Y, Yagi-Utsumi M, Kato K. Ganglioside-embedding small bicelles for probing membrane-landing processes of intrinsically disordered proteins. Chem Commun (Camb) 2013; 49:1235-7. [DOI: 10.1039/c2cc38016a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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34
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Li J, Liu S, Lakshminarayanan R, Bai Y, Pervushin K, Verma C, Beuerman RW. Molecular simulations suggest how a branched antimicrobial peptide perturbs a bacterial membrane and enhances permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:1112-21. [PMID: 23274275 DOI: 10.1016/j.bbamem.2012.12.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 12/03/2012] [Accepted: 12/18/2012] [Indexed: 11/29/2022]
Abstract
A covalently, branched antimicrobial peptide (BAMP) B2088 demonstrating enhanced antimicrobial effects and without additional toxicity when compared to its linear counterpart, has been developed. Atomistic molecular dynamics simulations have been used to investigate the mode of interaction of B2088 with model bacterial and mammalian membranes. These simulations suggest that both long-range electrostatic interactions and short-range hydrogen bonding play important roles in steering B2088 toward the negatively charged membranes. The reason why B2088 is selective towards the bacterial membrane is postulated to be the greater density of negative charges on the bacterial membrane which enables rapid accumulation of B2088 on the bacterial membrane to a high surface concentration, stabilizing it through excess hydrogen bond formation. The majority of hydrogen bonds are seen between the side chains of the basic residues (Arg or Lys) with the PO4 groups of lipids. In particular, formation of the bidentate hydrogen bonds between the guanidinium group of Arg and PO4 groups are found to be more favorable, both geometrically and energetically. Moreover, the planar gaunidinium group and its hydrophobic character enable the Arg side chains to solvate into the hydrophobic membrane. Structural perturbation of the bacterial membrane is found to be concentration dependent and is significant at higher concentrations of B2088, resulting in a large number of water translocations across the bacterial membrane. These simulations enhance our understanding of the action mechanism of a covalently branched antimicrobial peptide with model membranes and provide practical guidance for the design of new antimicrobial peptides.
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Affiliation(s)
- Jianguo Li
- Singapore Eye Research Institute, Singapore, Singapore
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35
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Dürr UN, Gildenberg M, Ramamoorthy A. The magic of bicelles lights up membrane protein structure. Chem Rev 2012; 112:6054-74. [PMID: 22920148 PMCID: PMC3497859 DOI: 10.1021/cr300061w] [Citation(s) in RCA: 266] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Indexed: 12/12/2022]
Affiliation(s)
| | - Melissa Gildenberg
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055,
United States
| | - Ayyalusamy Ramamoorthy
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055,
United States
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36
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Hill EH, Stratton K, Whitten DG, Evans DG. Molecular dynamics simulation study of the interaction of cationic biocides with lipid bilayers: aggregation effects and bilayer damage. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:14849-14854. [PMID: 23036095 DOI: 10.1021/la303158c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A novel class of phenylene ethynylene polyelectrolyte oligomers (OPEs) has been found to be effective biocidal agents against a variety of pathogens. The mechanism of attack is not yet fully understood. Recent studies have shown that OPEs cause catastrophic damage to large unilamellar vesicles. This study uses classical molecular dynamics (MD) simulations to understand how OPEs interact with model lipid bilayers. All-atom molecular dynamics simulations show that aggregates of OPEs inserted into the membrane cause significant structural damage and create a channel, or pore, that allows significant leakage of water through the membrane on the 0.1 μs time scale.
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Affiliation(s)
- Eric H Hill
- The Nanoscience and Microsystems Program, University of New Mexico, Albuquerque, New Mexico 87131, United States
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37
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Bertelsen K, Dorosz J, Hansen SK, Nielsen NC, Vosegaard T. Mechanisms of peptide-induced pore formation in lipid bilayers investigated by oriented 31P solid-state NMR spectroscopy. PLoS One 2012; 7:e47745. [PMID: 23094079 PMCID: PMC3475706 DOI: 10.1371/journal.pone.0047745] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 09/17/2012] [Indexed: 01/30/2023] Open
Abstract
There is a considerable interest in understanding the function of antimicrobial peptides (AMPs), but the details of their mode of action is not fully understood. This motivates extensive efforts in determining structural and mechanistic parameters for AMP’s interaction with lipid membranes. In this study we show that oriented-sample 31P solid-state NMR spectroscopy can be used to probe the membrane perturbations and -disruption by AMPs. For two AMPs, alamethicin and novicidin, we observe that the majority of the lipids remain in a planar bilayer conformation but that a number of lipids are involved in the peptide anchoring. These lipids display reduced dynamics. Our study supports previous studies showing that alamethicin adopts a transmembrane arrangement without significant disturbance of the surrounding lipids, while novicidin forms toroidal pores at high concentrations leading to more extensive membrane disturbance.
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Affiliation(s)
- Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, University of Aarhus, Aarhus, Denmark
| | - Jerzy Dorosz
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, University of Aarhus, Aarhus, Denmark
| | - Sara Krogh Hansen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, University of Aarhus, Aarhus, Denmark
| | - Niels Chr. Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, University of Aarhus, Aarhus, Denmark
- * E-mail: (NCN); (TV)
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, University of Aarhus, Aarhus, Denmark
- Department of Engineering, School of Engineering, University of Aarhus, Aarhus, Denmark
- * E-mail: (NCN); (TV)
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38
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Nakata S, Shiota T, Kumazawa N, Denda M. Interaction between a monosaccharide and a phospholipid molecular layer. Colloids Surf A Physicochem Eng Asp 2012. [DOI: 10.1016/j.colsurfa.2012.04.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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39
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Hjørringgaard CU, Vad BS, Matchkov VV, Nielsen SB, Vosegaard T, Nielsen NC, Otzen DE, Skrydstrup T. Cyclodextrin-scaffolded alamethicin with remarkably efficient membrane permeabilizing properties and membrane current conductance. J Phys Chem B 2012; 116:7652-9. [PMID: 22676384 DOI: 10.1021/jp2098679] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial resistance to classical antibiotics is a serious medical problem, which continues to grow. Small antimicrobial peptides represent a potential solution and are increasingly being developed as novel therapeutic agents. Many of these peptides owe their antibacterial activity to the formation of trans-membrane ion-channels resulting in cell lysis. However, to further develop the field of peptide antibiotics, a thorough understanding of their mechanism of action is needed. Alamethicin belongs to a class of peptides called peptaibols and represents one of these antimicrobial peptides. To examine the dynamics of assembly and to facilitate a thorough structural evaluation of the alamethicin ion-channels, we have applied click chemistry for the synthesis of templated alamethicin multimers covalently attached to cyclodextrin-scaffolds. Using oriented circular dichroism, calcein release assays, and single-channel current measurements, the α-helices of the templated multimers were demonstrated to insert into lipid bilayers forming highly efficient and remarkably stable ion-channels.
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Affiliation(s)
- Claudia U Hjørringgaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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40
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Roos C, Kai L, Proverbio D, Ghoshdastider U, Filipek S, Dötsch V, Bernhard F. Co-translational association of cell-free expressed membrane proteins with supplied lipid bilayers. Mol Membr Biol 2012; 30:75-89. [PMID: 22716775 DOI: 10.3109/09687688.2012.693212] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Routine strategies for the cell-free production of membrane proteins in the presence of detergent micelles and for their efficient co-translational solubilization have been developed. Alternatively, the expression in the presence of rationally designed lipid bilayers becomes interesting in particular for biochemical studies. The synthesized membrane proteins would be directed into a more native-like environment and cell-free expression of transporters, channels or other membrane proteins in the presence of supplied artificial membranes could allow their subsequent functional analysis without any exposure to detergents. In addition, lipid-dependent effects on activity and stability of membrane proteins could systematically be studied. However, in contrast to the generally efficient detergent solubilization, the successful stabilization of membrane proteins with artificial membranes appears to be more difficult. A number of strategies have therefore been explored in order to optimize the co-translational association of membrane proteins with different forms of supplied lipid bilayers including liposomes, bicelles, microsomes or nanodiscs. In this review, we have compiled the current state-of-the-art of this technology and we summarize parameters which have been indicated as important for the co-translational association of cell-free synthesized membrane proteins with supplied membranes.
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Affiliation(s)
- Christian Roos
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Germany
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41
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Kraft JF, Vestergaard M, Schiøtt B, Thøgersen L. Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations. J Chem Theory Comput 2012; 8:1556-69. [DOI: 10.1021/ct200921u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johan F. Kraft
- Center for Insoluble Protein
Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO), Department
of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Mikkel Vestergaard
- Center for Insoluble Protein
Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO), Department
of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein
Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO), Department
of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Lea Thøgersen
- Centre for Membrane Pumps in
Cells and Disease (PUMPKIN), Bioinformatics Research Centre, C.F. Møllers Alle 8, DK-8000 Aarhus C,
Denmark
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42
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Lorieau JL, Louis JM, Bax A. Whole-body rocking motion of a fusion peptide in lipid bilayers from size-dispersed 15N NMR relaxation. J Am Chem Soc 2011; 133:14184-7. [PMID: 21848255 PMCID: PMC3168931 DOI: 10.1021/ja2045309] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biological membranes present a highly fluid environment, and integration of proteins within such membranes is itself highly dynamic: proteins diffuse laterally within the plane of the membrane and rotationally about the normal vector of this plane. We demonstrate that whole-body motions of proteins within a lipid bilayer can be determined from NMR (15)N relaxation rates collected for different-sized bicelles. The importance of membrane integration and interaction is particularly acute for proteins and peptides that function on the membrane itself, as is the case for pore-forming and fusion-inducing proteins. For the influenza hemagglutinin fusion peptide, which lies on the surface of membranes and catalyzes the fusion of membranes and vesicles, we found large-amplitude, rigid-body wobbling motions on the nanosecond time scale relative to the lipid bilayer. This behavior complements prior analyses where data were commonly interpreted in terms of a static oblique angle of insertion for the fusion peptide with respect to the membrane. Quantitative disentanglement of the relative motions of two interacting objects by systematic variation of the size of one is applicable to a wide range of systems beyond protein-membrane interactions.
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Affiliation(s)
- Justin L Lorieau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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43
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Woo HJ, Wallqvist A. Spontaneous buckling of lipid bilayer and vesicle budding induced by antimicrobial peptide magainin 2: a coarse-grained simulation study. J Phys Chem B 2011; 115:8122-9. [PMID: 21651300 DOI: 10.1021/jp2023023] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular mechanisms of the action of antimicrobial peptides on bacterial membranes were studied by large scale coarse-grained simulations of magainin 2-dipalmitoylphosphatidylcholine/palmitoyloleoylphosphatidylglycerol (DPPC/POPG) mixed bilayer systems with spatial extents up to 0.1 μm containing up to 1600 peptides. Equilibrium simulations exhibit disordered toroidal pores stabilized by peptides. However, when a layer of peptides is placed near the lipid head groups on one side of the bilayer only, their incorporation leads to a spontaneous buckling of the bilayer. This buckling is followed by the formation of a quasi-spherical vesicular bud connected to the bilayer by a narrow neck. The mean curvature of the budding region is consistent with what is expected based on the dependence of the area per lipid on the peptide-to-lipid ratio in equilibrium simulations. Our simulations suggest that the incorporation of antimicrobial peptides on the exterior surface of a vesicle or a bacterial cell leads to buckling and vesicle budding, presumably accompanied by nucleations of giant transient pores of sizes that are much larger than indicated by equilibrium measurements and simulations.
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Affiliation(s)
- Hyung-June Woo
- Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, United States.
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44
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Balleza D. Toward understanding protocell mechanosensation. ORIGINS LIFE EVOL B 2011; 41:281-304. [PMID: 21080073 DOI: 10.1007/s11084-010-9225-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 10/20/2010] [Indexed: 01/11/2023]
Abstract
Mechanosensitive (MS) channels can prevent bacterial bursting during hypo-osmotic shocks by responding to increases in lateral tension at the membrane level through an integrated and coordinated opening mechanism. Mechanical regulation in protocells could have been one of the first mechanisms to evolve in order to preserve their integrity against changing environmental conditions. How has the rich functional diversity found in present cells been created throughout evolution, and what did the primordial MS channels look like? This review has been written with the aim of identifying which factors may have been important for the appearance of the first osmotic valve in a prebiotic context, and what this valve may have been like. It highlights the mechanical properties of lipid bilayers, the association of peptides as aggregates in membranes, and the conservation of sequence motifs as central aspects to understand the evolution of proteins that gate below the tension required for spontaneous pore formation and membrane rupture. The arguments developed here apply to both MscL and MscS homologs, but could be valid to mechano-susceptible proteins in general.
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Affiliation(s)
- Daniel Balleza
- Unidad de Biofísica, CSIC-UPV/EHU, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Spain.
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45
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Nakata S, Ikeguchi A, Shiota T, Komori R, Kumazawa N, Tsutsumi M, Denda M. Interactions between Sex Hormones and a 1,2-Di-O-myristoyl-sn-glycero-3-phosphocholine Molecular Layer: Characteristics of the Liposome, Surface Area versus Surface Pressure of the Monolayer, and Microscopic Observation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2011. [DOI: 10.1246/bcsj.20100256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Bertelsen K, Vad B, Nielsen EH, Hansen SK, Skrydstrup T, Otzen DE, Vosegaard T, Nielsen NC. Long-term-stable ether-lipid vs conventional ester-lipid bicelles in oriented solid-state NMR: altered structural information in studies of antimicrobial peptides. J Phys Chem B 2011; 115:1767-74. [PMID: 21309516 DOI: 10.1021/jp110866g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, ether lipids have been introduced as long-term stable alternatives to the more natural, albeit easier degradable, ester lipids in the preparation of oriented lipid bilayers and bicelles for oriented-sample solid-state NMR spectroscopy. Here we report that ether lipids such as the frequently used 14-O-PC (1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine) may induce significant changes in the structure and dynamics, including altered interaction between peptides and lipids relative to what is observed with the more conventionally used DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) bilayers. Such effects are demonstrated for the antimicrobial peptide novicidin, for which 2D separate-local-field NMR and circular dichroism experiments reveal significant structural/conformational differences for the peptide in the two different lipid systems. Likewise, we observe altered secondary structure and different temperature-dependent membrane anchoring for the antimicrobial peptide alamethicin depending on whether the peptide is reconstituted into ester or ether lipids. Such observations are not particularly surprising considering the significant difference of the lipids in the phosphorus headgroup and they may provide important new insight into the delicate peptide-membrane interactions in the systems studied. In contrast, these observations reinforce the need to carefully consider potential structural changes in addition to long-term stability prior to the selection of membrane environment of membrane proteins in the analysis of their structure and dynamics. In more general terms, the results underscore the necessity in structural biology to address both the protein and its environments in studies relating structure to function.
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Affiliation(s)
- Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
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47
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Butterfield SM, Lashuel HA. Amyloidogenic protein-membrane interactions: mechanistic insight from model systems. Angew Chem Int Ed Engl 2011; 49:5628-54. [PMID: 20623810 DOI: 10.1002/anie.200906670] [Citation(s) in RCA: 482] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The toxicity of amyloid-forming proteins is correlated with their interactions with cell membranes. Binding events between amyloidogenic proteins and membranes result in mutually disruptive structural perturbations, which are associated with toxicity. Membrane surfaces promote the conversion of amyloid-forming proteins into toxic aggregates, and amyloidogenic proteins, in turn, compromise the structural integrity of the cell membrane. Recent studies with artificial model membranes have highlighted the striking resemblance of the mechanisms of membrane permeabilization of amyloid-forming proteins to those of pore-forming toxins and antimicrobial peptides.
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Affiliation(s)
- Sara M Butterfield
- Laboratory of Molecular Neurobiology and Neuroproteomics, Swiss Federal Institute of Technology Lausanne (EPFL), SV-BMI-LMNN AI2351, 1015 Lausanne, Switzerland
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48
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Dorosz J, Gofman Y, Kolusheva S, Otzen D, Ben-Tal N, Nielsen NC, Jelinek R. Membrane interactions of novicidin, a novel antimicrobial peptide: phosphatidylglycerol promotes bilayer insertion. J Phys Chem B 2010; 114:11053-60. [PMID: 20690652 DOI: 10.1021/jp1052248] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novicidin is an antimicrobial peptide derived from ovispirin, a cationic peptide which originated from the ovine cathelicidin SMAP-29. Novicidin, however, has been designed to minimize the cytotoxic properties of SMAP-29 and ovisipirin toward achieving potential therapeutic applications. We present an analysis of membrane interactions and lipid bilayer penetration of novicidin, using an array of biophysical techniques and biomimetic membrane assemblies, complemented by Monte Carlo (MC) simulations. The data indicate that novicidin interacts minimally with zwitterionic bilayers, accounting for its low hemolytic activity. Negatively charged phosphatidylglycerol, on the other hand, plays a significant role in initiating membrane binding of novicidin, and promotes peptide insertion into the interface between the lipid headgroups and the acyl chains. The significant insertion into bilayers containing negative phospholipids might explain the enhanced antibacterial properties of novicidin. Overall, this study highlights two distinct outcomes for membrane interactions of novicidin, and points to a combination between electrostatic attraction to the lipid/water interface and penetration into the subsurface lipid headgroups region as important determinants for the biological activity of novicidin.
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Affiliation(s)
- Jerzy Dorosz
- Department of Chemistry and Ilse Katz Institute for Nanotechnology, Ben Gurion University, Beer Sheva 84105, Israel
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49
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Raschle T, Hiller S, Etzkorn M, Wagner G. Nonmicellar systems for solution NMR spectroscopy of membrane proteins. Curr Opin Struct Biol 2010; 20:471-9. [PMID: 20570504 DOI: 10.1016/j.sbi.2010.05.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 05/09/2010] [Indexed: 01/28/2023]
Abstract
Integral membrane proteins play essential roles in many biological processes, such as energy transduction, transport of molecules, and signaling. The correct function of membrane proteins is likely to depend strongly on the chemical and physical properties of the membrane. However, membrane proteins are not accessible to many biophysical methods in their native cellular membrane. A major limitation for their functional and structural characterization is thus the requirement for an artificial environment that mimics the native membrane to preserve the integrity and stability of the membrane protein. Most commonly employed are detergent micelles, which can however be detrimental to membrane protein activity and stability. Here, we review recent developments for alternative, nonmicellar solubilization techniques, with a particular focus on their application to solution NMR studies. We discuss the use of amphipols and lipid bilayer systems, such as bicelles and nanolipoprotein particles (NLPs). The latter show great promise for structural studies in near native membranes.
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50
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Butterfield S, Lashuel H. Wechselwirkungen zwischen amyloidogenen Proteinen und Membranen: Modellsysteme liefern mechanistische Einblicke. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906670] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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