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Mu Y, Wang Z, Song L, Ma K, Chen Y, Li P, Yan Z. Modulating lipid bilayer permeability and structure: Impact of hydrophobic chain length, C-3 hydroxyl group, and double bond in sphingosine. J Colloid Interface Sci 2024; 674:513-526. [PMID: 38943912 DOI: 10.1016/j.jcis.2024.06.171] [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: 02/19/2024] [Revised: 06/14/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
Sphingosine, an amphiphilic molecule, plays a pivotal role as the core structure of sphingolipids, essential constituents of cell membranes. Its unique capability to enhance the permeability of lipid membranes profoundly influences crucial life processes. The molecular structure of sphingosine dictates its mode of entry into lipid bilayers and governs its interactions with lipids, thereby determining membrane permeability. However, the incomplete elucidation of the relationship between the molecular structure of sphingosine and the permeability of lipid membranes persists due to challenges associated with synthesizing sphingosine molecules. A series of sphingosine-derived molecules, featuring diverse hydrophobic chain lengths and distinct headgroup structure, were meticulously designed and successfully synthesized. These molecules were employed to investigate the permeability of large unilamellar vesicles, functioning as model lipid bilayers. With a decrease in the hydrophobic chain length of sphingosine from C15 to C11, the transient leakage ratio of vesicle contents escalated from ∼ 13 % to ∼ 28 %. Although the presence of double bond did not exert a pronounced influence on transient leakage, it significantly affected the continuous leakage ratio. Conversely, modifying the chirality of the C-3 hydroxyl group gives the opposite result. Notably, methylation at the C-3 hydroxyl significantly elevates transient leakage while suppressing the continuous leakage ratio. Additionally, sphingosines that significantly affect vesicle permeability tend to have a more pronounced impact on cell viability. Throughout this leakage process, the charge state of sphingosine-derived molecule aggregates in the solution emerged as a pivotal factor influencing vesicle permeability. Fluorescence lifetime experiments further revealed discernible variations in the effect of sphingosine molecular structure on the mobility of hydrophobic regions within lipid bilayers. These observed distinctions emphasize the impact of molecular structure on intermolecular interactions, extending to the microscopic architecture of membranes, and underscore the significance of subtle alterations in molecular structure and their associated aggregation behaviors in governing membrane permeability.
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Affiliation(s)
- Yonghang Mu
- State Key Laboratory of Heavy Oil Processing, College of Chemistry and Chemical Engineering, China University of Petroleum, Qingdao 266580, China
| | - Zi Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemistry and Chemical Engineering, China University of Petroleum, Qingdao 266580, China.
| | - Linhua Song
- State Key Laboratory of Heavy Oil Processing, College of Chemistry and Chemical Engineering, China University of Petroleum, Qingdao 266580, China
| | - Kun Ma
- ISIS Facility, Rutherford Appleton Laboratory, STFC, Chilton, Didcot, Oxon OX11 0QX, UK
| | - Yao Chen
- ISIS Facility, Rutherford Appleton Laboratory, STFC, Chilton, Didcot, Oxon OX11 0QX, UK
| | - Peixun Li
- ISIS Facility, Rutherford Appleton Laboratory, STFC, Chilton, Didcot, Oxon OX11 0QX, UK
| | - Zifeng Yan
- State Key Laboratory of Heavy Oil Processing, College of Chemistry and Chemical Engineering, China University of Petroleum, Qingdao 266580, China.
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2
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Nehls C, Schröder M, Haubenthal T, Haas A, Gutsmann T. The mechanistic basis of the membrane-permeabilizing activities of the virulence-associated protein A (VapA) from Rhodococcus equi. Mol Microbiol 2024; 121:578-592. [PMID: 38308564 DOI: 10.1111/mmi.15233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/05/2024]
Abstract
Pathogenic Rhodococcus equi release the virulence-associated protein A (VapA) within macrophage phagosomes. VapA permeabilizes phagosome and lysosome membranes and reduces acidification of both compartments. Using biophysical techniques, we found that VapA interacts with model membranes in four steps: (i) binding, change of mechanical properties, (ii) formation of specific membrane domains, (iii) permeabilization within the domains, and (iv) pH-specific transformation of domains. Biosensor data revealed that VapA binds to membranes in one step at pH 6.5 and in two steps at pH 4.5 and decreases membrane fluidity. The integration of VapA into lipid monolayers was only significant at lateral pressures <20 mN m-1 indicating preferential incorporation into membrane regions with reduced integrity. Atomic force microscopy of lipid mono- and bilayers showed that VapA increased the surface heterogeneity of liquid disordered domains. Furthermore, VapA led to the formation of a new microstructured domain type and, at pH 4.5, to the formation of 5 nm high domains. VapA binding, its integration and lipid domain formation depended on lipid composition, pH, protein concentration and lateral membrane pressure. VapA-mediated permeabilization is clearly distinct from that caused by classical microbial pore formers and is a key contribution to the multiplication of Rhodococcus equi in phagosomes.
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Affiliation(s)
- Christian Nehls
- Division of Biophysics, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Kiel Nano, Surface and Interface Science KiNSIS, Kiel University, Kiel, Germany
| | - Marcel Schröder
- Division of Biophysics, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | | | - Albert Haas
- Cell Biology Institute, University of Bonn, Bonn, Germany
| | - Thomas Gutsmann
- Division of Biophysics, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Kiel Nano, Surface and Interface Science KiNSIS, Kiel University, Kiel, Germany
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3
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Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S, Suzuki H, Kambara F, Fukasawa G, Cooney A, Di Michele L, Elani Y, Matsuura T, Kawano R. Lipid vesicle-based molecular robots. LAB ON A CHIP 2024; 24:996-1029. [PMID: 38239102 PMCID: PMC10898420 DOI: 10.1039/d3lc00860f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.
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Affiliation(s)
- Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoji Iwabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Misa Yamaji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoko Fujita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Harune Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Fumika Kambara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Genki Fukasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Aileen Cooney
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
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4
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Hohmann T, Chowdhary S, Ataka K, Er J, Dreyhsig GH, Heberle J, Koksch B. Introducing Aliphatic Fluoropeptides: Perspectives on Folding Properties, Membrane Partition and Proteolytic Stability. Chemistry 2023; 29:e202203860. [PMID: 36722398 DOI: 10.1002/chem.202203860] [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: 12/09/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/02/2023]
Abstract
A de novo designed class of peptide-based fluoropolymers composed of fluorinated aliphatic amino acids as main components is reported. Structural characterization provided insights into fluorine-induced alterations on β-strand to α-helix transition upon an increase in SDS content and revealed the unique formation of PPII structures for trifluorinated fluoropeptides. A combination of circular dichroism, fluorescence-based leaking assays and surface enhanced infrared absorption spectroscopy served to examine the insertion and folding processes into unilamellar vesicles. While partitioning into lipid bilayers, the degree of fluorination conducts a decrease in α-helical content. Furthermore, this study comprises a report on the proteolytic stability of peptides exclusively built up by fluorinated amino acids and proved all sequences to be enzymatically degradable despite the degree of fluorination. Herein presented fluoropeptides as well as the distinctive properties of these artificial and polyfluorinated foldamers with enzyme-degradable features will play a crucial role in the future development of fluorinated peptide-based biomaterials.
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Affiliation(s)
- Thomas Hohmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Suvrat Chowdhary
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Jasmin Er
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Gesa Heather Dreyhsig
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
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5
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Ghimire J, Guha S, Nelson BJ, Morici LA, Wimley WC. The Remarkable Innate Resistance of Burkholderia bacteria to Cationic Antimicrobial Peptides: Insights into the Mechanism of AMP Resistance. J Membr Biol 2022; 255:503-511. [PMID: 35435452 PMCID: PMC9576820 DOI: 10.1007/s00232-022-00232-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/24/2022] [Indexed: 12/29/2022]
Abstract
Gram-negative bacteria belonging to the genus Burkholderia are remarkably resistant to broad-spectrum, cationic, antimicrobial peptides (AMPs). It has been proposed that this innate resistance is related to changes in the outer membrane lipopolysaccharide (OM LPS), including the constitutive, essential modification of outer membrane Lipid A phosphate groups with cationic 4-amino-4-deoxy-arabinose. This modification reduces the overall negative charge on the OM LPS which may change the OM structure and reduce the binding, accumulation, and permeation of cationic AMPs. Similarly, the Gram-negative pathogen Pseudomonas aeruginosa can quickly become resistant to many AMPs by multiple mechanisms, frequently, including activation of the arn operon, which leads, transiently, to the same modification of Lipid A. We recently discovered a set of synthetically evolved AMPs that do not invoke any resistance in P. aeruginosa over multiple passages and thus are apparently not inhibited by aminorabinosylation of Lipid A in P. aeruginosa. Here we test these resistance-avoiding peptides, within a set of 18 potent AMPs, against Burkholderia thailandensis. We find that none of the AMPs tested have measurable activity against B. thailandensis. Some were inactive at concentrations as high as 150 μM, despite all having sterilizing activity at ≤ 10 μM against a panel of common, human bacterial pathogens, including P. aeruginosa. We speculate that the constitutive modification of Lipid A in members of the Burkholderia genus is only part of a broader set of modifications that change the architecture of the OM to provide such remarkable levels of resistance to cationic AMPs.
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Affiliation(s)
- Jenisha Ghimire
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112
| | - Shantanu Guha
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112
| | - Benjamin J. Nelson
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112
| | - Lisa A. Morici
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, 70112
| | - William C. Wimley
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112,To whom correspondence should be addressed at
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6
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Parayath NN, Gandham SK, Amiji MM. Tumor-targeted miRNA nanomedicine for overcoming challenges in immunity and therapeutic resistance. Nanomedicine (Lond) 2022; 17:1355-1373. [PMID: 36255330 PMCID: PMC9706370 DOI: 10.2217/nnm-2022-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
miRNA are critical messengers in the tumor microenvironment (TME) that influence various processes leading to immune suppression, tumor progression, metastasis and resistance. Strategies to modulate miRNAs in the TME have important implications in overcoming these challenges. However, miR delivery to specific cells in the TME has been challenging. This review discusses nanomedicine strategies to achieve cell-specific delivery of miRNAs. The key goal of delivery is to activate the tumor immune landscape as well as to prevent chemotherapy resistance. Specifically, the use of hyaluronic acid-based nanoparticle miRNA delivery to the TME is discussed. The discussion is focused on miRNA-125b for reprogramming tumor-associated macrophages to overcome immunosuppression and miRNA-let-7b to overcome resistance to anticancer chemotherapeutics because both these miRNAs have been extensively evaluated for delivery with hyaluronic acid-based delivery systems.
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Affiliation(s)
- Neha N Parayath
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Srujan K Gandham
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Mansoor M Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA,Department of Chemical Engineering, College of Engineering, Northeastern University, Boston, MA 02115, USA,Author for correspondence: Tel.: +1 617 373 3137;
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7
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Chen CH, Bepler T, Pepper K, Fu D, Lu TK. Synthetic molecular evolution of antimicrobial peptides. Curr Opin Biotechnol 2022; 75:102718. [PMID: 35395425 DOI: 10.1016/j.copbio.2022.102718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 01/18/2023]
Abstract
As we learn more about how peptide structure and activity are related, we anticipate that antimicrobial peptides will be engineered to have strong potency and distinct functions and that synthetic peptides will have new biomedical applications, such as treatments for emerging infectious diseases. As a result of the enormous number of possible amino acid sequences and the low-throughput nature of antimicrobial peptide assays, computational tools for peptide design and optimization are needed for direct experimentation toward obtaining functional sequences. Recent developments in computational tools have improved peptide design, saving labor, reagents, costs, and time. At the same time, improvements in peptide synthesis and experimental platforms continue to reduce the cost and increase the throughput of peptide-drug screening. In this review, we discuss the current methods of peptide design and engineering, including in silico methods and peptide synthesis and screening, and highlight areas of potential improvement.
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Affiliation(s)
- Charles H Chen
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Tristan Bepler
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Simons Machine Learning Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Karen Pepper
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Debbie Fu
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Timothy K Lu
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Senti Biosciences, South San Francisco, CA 94080, USA.
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8
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Design of Membrane Active Peptides Considering Multi-Objective Optimization for Biomedical Application. MEMBRANES 2022; 12:membranes12020180. [PMID: 35207101 PMCID: PMC8880019 DOI: 10.3390/membranes12020180] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023]
Abstract
A multitude of membrane active peptides exists that divides into subclasses, such as cell penetrating peptides (CPPs) capable to enter eukaryotic cells or antimicrobial peptides (AMPs) able to interact with prokaryotic cell envelops. Peptide membrane interactions arise from unique sequence motifs of the peptides that account for particular physicochemical properties. Membrane active peptides are mainly cationic, often primary or secondary amphipathic, and they interact with membranes depending on the composition of the bilayer lipids. Sequences of these peptides consist of short 5–30 amino acid sections derived from natural proteins or synthetic sources. Membrane active peptides can be designed using computational methods or can be identified in screenings of combinatorial libraries. This review focuses on strategies that were successfully applied to the design and optimization of membrane active peptides with respect to the fact that diverse features of successful peptide candidates are prerequisites for biomedical application. Not only membrane activity but also degradation stability in biological environments, propensity to induce resistances, and advantageous toxicological properties are crucial parameters that have to be considered in attempts to design useful membrane active peptides. Reliable assay systems to access the different biological characteristics of numerous membrane active peptides are essential tools for multi-objective peptide optimization.
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9
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Ranade SS, Ramalingam R. Hydrogen bonds in anoplin peptides aid in identification of a structurally stable therapeutic drug scaffold. J Mol Model 2020; 26:155. [PMID: 32451705 DOI: 10.1007/s00894-020-04380-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 04/07/2020] [Indexed: 12/30/2022]
Abstract
Multi-drug resistance is a major issue faced by the global pharmaceutical industry. Short antimicrobial peptides such as anoplins can be used to replace antibiotics, thus mitigating this issue. Antimicrobial activity, non-toxicity, and structural stability are essential features of a therapeutic drug. Antimicrobial activity and toxicity to human erythrocytes have been previously reported for anoplin and anoplin R5K T8W. This study attempts to identify a therapeutic peptide drug scaffold between these peptides by examining their structural stability, mainly based on the hydrogen bonds (H-bond) found in their structures. The static structure of anoplin R5K T8W displayed lower H-bond distances than anoplin, thereby exhibiting enhanced structural stability. Dynamic stability studies revealed that conformers of anoplin R5K T8W exhibited lower hydrogen bond distances (HBDs), higher H-bond occupancies, and higher radial distribution function (RDF) of H-bonds in comparison with conformers of anoplin. Furthermore, conformers of anoplin R5K T8W generated using 50-ns molecular dynamics simulation displayed lower conformational free energy than anoplin, thus establishing its higher structural stability. Overall, anoplin R5K T8W can be claimed as a promising scaffold that may be used for therapeutic purposes. In conclusion, H-bonds play a major role in structural stability and may aid in identification of a therapeutic peptide scaffold. Graphical abstract.
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Affiliation(s)
- Shruti Sunil Ranade
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, 632014, India
| | - Rajasekaran Ramalingam
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, 632014, India.
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10
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Effects of CGA-N12 on the membrane structure of Candida tropicalis cells. Biochem J 2020; 477:1813-1825. [DOI: 10.1042/bcj20190939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 01/08/2023]
Abstract
The antimicrobial peptide CGA-N12 (NH2-ALQGAKERAHQQ-COOH) is an active peptide derived from chromogranin A (CGA) and consists of the 65th to 76th amino acids of the N-terminus. The results of our previous studies showed that CGA-N12 exerts anti-Candida activity by inducing apoptosis without destroying the integrity of cell membranes. In this study, the effect of CGA-N12 on the cell membrane structure of Candida tropicalis was investigated. CGA-N12 resulted in the dissipation of the membrane potential, the increase in membrane fluidity, and the outflow of potassium ions in C. tropicalis without significantly changing the ergosterol level. Fluorescence quenching was applied to evaluate the membrane channel characteristics induced by CGA-N12 through detection of the following: membrane permeability of hydrated Cl− (ϕ ≈ 0.66 nm) using the membrane-impermeable halogen anion-selective fluorescent dye lucigenin, passage of the membrane-impermeable dye carboxyfluorescein (CF) (ϕ ≈ 1 nm) through the membrane, and membrane permeation of H3O+ based on the membrane non-permeable pH-sensitive fluorescent dye 8-hydroxypyrene-1,3,6-trisulfonic acid, trisodium salt (HPTS). In conclusion, CGA-N12 can induce the formation of non-selective ion channels <1 nm in diameter in the membranes of C. tropicalis, resulting in the leakage of potassium ions, chloride ions, and protons, among others, leading to dissipation of the membrane potential. As a result, the fluidity of membranes is increased without destroying the synthesis of ergosterol is not affected.
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11
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Sandomenico A, Caporale A, Doti N, Cross S, Cruciani G, Chambery A, De Falco S, Ruvo M. Synthetic Peptide Libraries: From Random Mixtures to In Vivo Testing. Curr Med Chem 2020; 27:997-1016. [PMID: 30009695 DOI: 10.2174/0929867325666180716110833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/22/2018] [Accepted: 06/29/2018] [Indexed: 01/13/2023]
Abstract
Combinatorially generated molecular repertoires have been largely used to identify novel bioactive compounds. Ever more sophisticated technological solutions have been proposed to simplify and speed up such process, expanding the chemical diversity space and increasing the prospect to select new molecular entities with specific and potent activities against targets of therapeutic relevance. In this context, random mixtures of oligomeric peptides were originally used and since 25 years they represent a continuous source of bioactive molecules with potencies ranging from the sub-nM to microM concentration. Synthetic peptide libraries are still employed as starting "synthetic broths" of structurally and chemically diversified molecular fragments from which lead compounds can be extracted and further modified. Thousands of studies have been reported describing the application of combinatorial mixtures of synthetic peptides with different complexity and engrafted on diverse structural scaffolds for the identification of new compounds which have been further developed and also tested in in vivo models of relevant diseases. We briefly review some of the most used methodologies for library preparation and screening and the most recent case studies appeared in the literature where compounds have reached at least in vivo testing in animal or similar models. Recent technological advancements in biotechnology, engineering and computer science have suggested new options to facilitate the discovery of new bioactive peptides. In this instance, we anticipate here a new approach for the design of simple but focused tripeptide libraries against druggable cavities of therapeutic targets and its complementation with existing approaches.
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Affiliation(s)
- Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Andrea Caporale
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Nunzianna Doti
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Simon Cross
- Molecular Discovery Ltd, Unit 501 Centennial Park, Centennial Avenue Elstree, Borehamwood, Hertfordshire WD6 3FG, United Kingdom
| | - Gabriele Cruciani
- Molecular Discovery Ltd, Unit 501 Centennial Park, Centennial Avenue Elstree, Borehamwood, Hertfordshire WD6 3FG, United Kingdom.,Dipartimento di Chimica, Biologia e Biotecnologia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Angela Chambery
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy
| | - Sandro De Falco
- Istituto di Genetica e Biofisica del CNR, via Pietro Castellino, 111, 80131, Napoli, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
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12
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Wimley WC, Hristova K. The Mechanism of Membrane Permeabilization by Peptides: Still an Enigma. Aust J Chem 2019; 73:96-103. [PMID: 32341596 DOI: 10.1071/ch19449] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Peptide-induced permeabilization of lipid vesicles has been measured for decades and has provided many insights into the sequence-structure-function relationships of membrane-active peptides. However, researchers in the field have noted that many experiments show transient permeabilization, in which a burst of leakage occurs immediately after peptide addition, followed by a slowdown or cessation of leakage before all contents have been released. This widely observed, but rarely studied, phenomenon is not explained by standard equilibrium pore models that are commonly invoked in both experimental and computational studies. Here we discuss observations of transient permeabilization, and we outline a pathway towards understanding this enigmatic phenomenon.
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Affiliation(s)
- William C Wimley
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218
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13
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Nguyen MHL, DiPasquale M, Rickeard BW, Doktorova M, Heberle FA, Scott HL, Barrera FN, Taylor G, Collier CP, Stanley CB, Katsaras J, Marquardt D. Peptide-Induced Lipid Flip-Flop in Asymmetric Liposomes Measured by Small Angle Neutron Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11735-11744. [PMID: 31408345 PMCID: PMC7393738 DOI: 10.1021/acs.langmuir.9b01625] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Despite the prevalence of lipid transbilayer asymmetry in natural plasma membranes, most biomimetic model membranes studied are symmetric. Recent advances have helped to overcome the difficulties in preparing asymmetric liposomes in vitro, allowing for the examination of a larger set of relevant biophysical questions. Here, we investigate the stability of asymmetric bilayers by measuring lipid flip-flop with time-resolved small-angle neutron scattering (SANS). Asymmetric large unilamellar vesicles with inner bilayer leaflets containing predominantly 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and outer leaflets composed mainly of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) displayed slow spontaneous flip-flop at 37 ◦C (half-time, t1/2 = 140 h). However, inclusion of peptides, namely, gramicidin, alamethicin, melittin, or pHLIP (i.e., pH-low insertion peptide), accelerated lipid flip-flop. For three of these peptides (i.e., pHLIP, alamethicin, and melittin), each of which was added externally to preformed asymmetric vesicles, we observed a completely scrambled bilayer in less than 2 h. Gramicidin, on the other hand, was preincorporated during the formation of the asymmetric liposomes and showed a time resolvable 8-fold increase in the rate of lipid asymmetry loss. These results point to a membrane surface-related (e.g., adsorption/insertion) event as the primary driver of lipid scrambling in the asymmetric model membranes of this study. We discuss the implications of membrane peptide binding, conformation, and insertion on lipid asymmetry.
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Affiliation(s)
- Michael H. L. Nguyen
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
| | - Mitchell DiPasquale
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
| | - Brett W. Rickeard
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
| | - Milka Doktorova
- Department of Integrative Biology and Pharmacology,
University of Texas Health Science Center at Houston, Houston, Texas 77225, United
States
| | - Frederick A. Heberle
- Department of Integrative Biology and Pharmacology,
University of Texas Health Science Center at Houston, Houston, Texas 77225, United
States
- Center for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
| | - Haden L. Scott
- Center for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biochemistry & Cellular and
Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United
States
| | - Francisco N. Barrera
- Department of Biochemistry & Cellular and
Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United
States
| | - Graham Taylor
- The Bredesen Center, University of Tennessee,
Knoxville, Tennessee 37996, United States
| | - Charles P. Collier
- The Bredesen Center, University of Tennessee,
Knoxville, Tennessee 37996, United States
- Center for Nanophase Materials Sciences, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Christopher B. Stanley
- Neutron Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - John Katsaras
- Large Scale Structures Group, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
- Shull Wollan Center, a Joint Institute for Neutron
Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United
States
- Department of Physics and Astronomy, University of
Tennessee, Knoxville, Tennessee 37996, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
- Department of Physics, University of Windsor, Windsor, N9B
3P4 ON Canada
- Corresponding Author:
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14
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Comparative mode of action of the antimicrobial peptide melimine and its derivative Mel4 against Pseudomonas aeruginosa. Sci Rep 2019; 9:7063. [PMID: 31068610 PMCID: PMC6506473 DOI: 10.1038/s41598-019-42440-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/18/2019] [Indexed: 12/16/2022] Open
Abstract
Melimine and Mel4 are chimeric cationic peptides with broad-spectrum antimicrobial activity. They have been shown to be highly biocompatible in animal models and human clinical trials. The current study examined the mechanism of action of these two antimicrobial peptides against P. aeruginosa. The effect of the peptides of endotoxin neutralization, and their interactions with cytoplasmic membranes using DiSC(3)-5 and Sytox green, Syto-9 and PI dyes were analysed. Release of ATP and DNA/RNA were determined using ATP luminescence and increase in OD260 nm. The bacteriolytic ability of the peptides was determined by measuring decreases in OD620 nm. Both the peptides neutralized LPS suggesting their interaction with lipid A. Cytoplasmic membrane was disrupted within 30 seconds, which correlated with reductions in cellular viability. At 2 minutes melimine or Mel4, released 75% and 36% cellular ATP respectively (P < 0.001). Membrane permeabilization started 5 minutes with simultaneous release of DNA/RNA. Flow cytometry demonstrated 52% and 18% bacteria were stained with PI after 30 minutes. Overall, melimine showed higher capacity for membrane disruption compared to Mel4 (P < 0.001). The findings of this study have been summarized as a timeline of bactericidal activity, suggesting that the peptides permeabilized P. aeruginosa within 5 minutes, started lysis within 2 hours of exposure.
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15
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Guha S, Ghimire J, Wu E, Wimley WC. Mechanistic Landscape of Membrane-Permeabilizing Peptides. Chem Rev 2019; 119:6040-6085. [PMID: 30624911 DOI: 10.1021/acs.chemrev.8b00520] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Membrane permeabilizing peptides (MPPs) are as ubiquitous as the lipid bilayer membranes they act upon. Produced by all forms of life, most membrane permeabilizing peptides are used offensively or defensively against the membranes of other organisms. Just as nature has found many uses for them, translational scientists have worked for decades to design or optimize membrane permeabilizing peptides for applications in the laboratory and in the clinic ranging from antibacterial and antiviral therapy and prophylaxis to anticancer therapeutics and drug delivery. Here, we review the field of membrane permeabilizing peptides. We discuss the diversity of their sources and structures, the systems and methods used to measure their activities, and the behaviors that are observed. We discuss the fact that "mechanism" is not a discrete or a static entity for an MPP but rather the result of a heterogeneous and dynamic ensemble of structural states that vary in response to many different experimental conditions. This has led to an almost complete lack of discrete three-dimensional active structures among the thousands of known MPPs and a lack of useful or predictive sequence-structure-function relationship rules. Ultimately, we discuss how it may be more useful to think of membrane permeabilizing peptides mechanisms as broad regions of a mechanistic landscape rather than discrete molecular processes.
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Affiliation(s)
- Shantanu Guha
- Department of Biochemistry and Molecular Biology Tulane University School of Medicine , New Orleans , Louisiana 70112 , United States
| | - Jenisha Ghimire
- Department of Biochemistry and Molecular Biology Tulane University School of Medicine , New Orleans , Louisiana 70112 , United States
| | - Eric Wu
- Department of Biochemistry and Molecular Biology Tulane University School of Medicine , New Orleans , Louisiana 70112 , United States
| | - William C Wimley
- Department of Biochemistry and Molecular Biology Tulane University School of Medicine , New Orleans , Louisiana 70112 , United States
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16
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Pittman AE, Marsh BP, King GM. Conformations and Dynamic Transitions of a Melittin Derivative That Forms Macromolecule-Sized Pores in Lipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8393-8399. [PMID: 29933696 DOI: 10.1021/acs.langmuir.8b00804] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Systematically evolved from the primary active component of bee venom, MelP5 is a lipophilic peptide with important physical properties that differ from wild-type melittin, including the ability to create large equilibrium pores in lipid bilayers at low peptide to lipid ratios. Self-assembly into stable membrane spanning pores makes MelP5 a promising candidate for future applications in the pharmaceutical arena. Despite significant interest, little is known about the mechanism by which MelP5 remodels the lipid bilayer upon binding. We demonstrate by direct atomic force microscope imaging of supported lipid bilayers in solution that MelP5 remodels 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) in one of two ways. It creates either highly localized voids in the bilayer or diffuse nonlocalized thinning. Thinning of the bilayer was measured to be 3.0 ± 1.4 Å (mean ± standard deviation) below the surface of the upper leaflet of the bilayer. Pores, defined as highly localized voids in the bilayer, exhibited several sizes. Approximately 20% of pores exhibited large footprint areas (47 ± 20 nm2) which appear capable of passing bulky macromolecules. The peptide-effected bilayer was observed to reversibly exchange between membrane-thinned and pore states in an apparent dynamic equilibrium. Analysis of time-lapsed images suggested upper and lower bounds (0.2 < τ < 180 s) on the characteristic time scale of transitions between the membrane-thinned and pore states. Moreover, pores were found to colocalize with membrane-thinned regions, a novel observation that is consistent with the notion of cooperativity among membrane-bound peptides when forming pores.
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17
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Synthetic molecular evolution of hybrid cell penetrating peptides. Nat Commun 2018; 9:2568. [PMID: 29967329 PMCID: PMC6028423 DOI: 10.1038/s41467-018-04874-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 05/24/2018] [Indexed: 12/26/2022] Open
Abstract
Peptides and analogs such as peptide nucleic acids (PNA) are promising tools and therapeutics, but the cell membrane remains a barrier to intracellular targets. Conjugation to classical cell penetrating peptides (CPPs) such as pTat48–60 (tat) and pAntp43–68 (penetratin) facilitates delivery; however, efficiencies are low. Lack of explicit design principles hinders rational improvement. Here, we use synthetic molecular evolution (SME) to identify gain-of-function CPPs with dramatically improved ability to deliver cargoes to cells at low concentration. A CPP library containing 8192 tat/penetratin hybrid peptides coupled to an 18-residue PNA is screened using the HeLa pTRE-LucIVS2 splice correction reporter system. The daughter CPPs identified are one to two orders of magnitude more efficient than the parent sequences at delivery of PNA, and also deliver a dye cargo and an anionic peptide cargo. The significant increase in performance following a single iteration of SME demonstrates the power of this approach to peptide sequence optimization. Therapeutic peptide nucleic acids can be delivered into cells by conjugation to cell penetrating peptides (CPPs), but efficiency is usually low. Here the authors use synthetic molecular evolution and a luciferase-based library screen to generate new CPPs with improved efficiency and lower toxicity.
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18
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Largo E, Gladue DP, Torralba J, Aguilella VM, Alcaraz A, Borca MV, Nieva JL. Mutation-induced changes of transmembrane pore size revealed by combined ion-channel conductance and single vesicle permeabilization analyses. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1015-1021. [PMID: 29317201 DOI: 10.1016/j.bbamem.2018.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/25/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023]
Abstract
Permeabilization of the Endoplasmic Reticulum (ER) is instrumental in the progression of host-cell infection by many viral pathogens. We have described that permeabilization of ER model membranes by the pore-forming domain of the Classical Swine Fever Virus (CSFV) p7 protein depends on two sequence determinants: the C-terminal transmembrane helix, and the preceding polar loop that regulates its activity. Here, by combining ion-channel activity measurements in planar lipid bilayers with imaging of single Giant Unilamellar Vesicles (GUVs), we demonstrate that point substitutions directed to conserved residues within these regions affect ER-like membrane permeabilization following distinct mechanisms. Whereas the polar loop appeared to be involved in protein insertion and oligomerization, substitution of residues predicted to face the lumen of the pore inhibited large conducting channels (>1 nS) over smaller ones (120 pS). Quantitative analyses of the ER-GUV distribution as a function of the solute size revealed a selective inhibition for the permeation of solutes with sizes larger than 4 kDa, further demonstrating that the mutation targeting the transmembrane helix prevented formation of the large pores. Collectively, our data support the idea that the pore-forming domain of p7 may assemble into finite pores with approximate diameters of 1 and 5 nm. Moreover, the observation that the mutation interfering with formation of the larger pores can hamper virus production without affecting ER localization or homo-oligomerization, suggests prospective strategies to block/attenuate pestiviruses.
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Affiliation(s)
- Eneko Largo
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain
| | - Douglas P Gladue
- Plum Island Animal Disease Center, ARS, USDA, Greenport, NY 11944, USA
| | - Johana Torralba
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain
| | - Vicente M Aguilella
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain
| | - Manuel V Borca
- Plum Island Animal Disease Center, ARS, USDA, Greenport, NY 11944, USA
| | - José L Nieva
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain.
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19
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Chen M, Balhara V, Jaimes Castillo AM, Balsevich J, Johnston LJ. Interaction of saponin 1688 with phase separated lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1263-1272. [PMID: 28389202 DOI: 10.1016/j.bbamem.2017.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/14/2017] [Accepted: 03/31/2017] [Indexed: 12/12/2022]
Abstract
Saponins are a diverse family of naturally occurring plant triterpene or steroid glycosides that have a wide range of biological activities. They have been shown to permeabilize membranes and in some cases membrane disruption has been hypothesized to involve saponin/cholesterol complexes. We have examined the interaction of steroidal saponin 1688-1 with lipid membranes that contain cholesterol and have a mixture of liquid-ordered (Lo) and liquid-disordered (Ld) phases as a model for lipid rafts in cellular membranes. A combination of atomic force microscopy (AFM) and fluorescence was used to probe the effect of saponin on the bilayer. The results demonstrate that saponin forms defects in the membrane and also leads to formation of small aggregates on the membrane surface. Although most of the membrane damage occurs in the liquid-disordered phase, fluorescence results demonstrate that saponin localizes in both ordered and disordered membrane phases, with a modest preference for the disordered regions. Similar effects are observed for both direct incorporation of saponin in the lipid mixture used to make vesicles/bilayers and for incubation of saponin with preformed bilayers. The results suggest that the initial sites of interaction are at the interface between the domains and surrounding disordered phase. The preference for saponin localization in the disordered phase may reflect the ease of penetration of saponin into a less ordered membrane, rather than the actual cholesterol concentration in the membrane. Dye leakage assays indicate that a high concentration of saponin is required for membrane permeabilization consistent with the supported lipid bilayer experiments.
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Affiliation(s)
- Maohui Chen
- Measurement Science and Standards, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Vinod Balhara
- Measurement Science and Standards, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | | | - John Balsevich
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK S7N 0W9, Canada
| | - Linda J Johnston
- Measurement Science and Standards, National Research Council Canada, Ottawa, ON K1A 0R6, Canada.
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20
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Li J, Koh JJ, Liu S, Lakshminarayanan R, Verma CS, Beuerman RW. Membrane Active Antimicrobial Peptides: Translating Mechanistic Insights to Design. Front Neurosci 2017; 11:73. [PMID: 28261050 PMCID: PMC5306396 DOI: 10.3389/fnins.2017.00073] [Citation(s) in RCA: 329] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/31/2017] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial peptides (AMPs) are promising next generation antibiotics that hold great potential for combating bacterial resistance. AMPs can be both bacteriostatic and bactericidal, induce rapid killing and display a lower propensity to develop resistance than do conventional antibiotics. Despite significant progress in the past 30 years, no peptide antibiotic has reached the clinic yet. Poor understanding of the action mechanisms and lack of rational design principles have been the two major obstacles that have slowed progress. Technological developments are now enabling multidisciplinary approaches including molecular dynamics simulations combined with biophysics and microbiology toward providing valuable insights into the interactions of AMPs with membranes at atomic level. This has led to increasingly robust models of the mechanisms of action of AMPs and has begun to contribute meaningfully toward the discovery of new AMPs. This review discusses the detailed action mechanisms that have been put forward, with detailed atomistic insights into how the AMPs interact with bacterial membranes. The review further discusses how this knowledge is exploited toward developing design principles for novel AMPs. Finally, the current status, associated challenges, and future directions for the development of AMP therapeutics are discussed.
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Affiliation(s)
- Jianguo Li
- Ocular Chemistry and Anti-Infectives, Singapore Eye Research InstituteSingapore, Singapore
- Agency for Science, Technology and Research (ASTAR), Bioinformatics InstituteSingapore, Singapore
- Duke-NUS Graduate Medical School, SRP Neuroscience and BDSingapore, Singapore
| | - Jun-Jie Koh
- Ocular Chemistry and Anti-Infectives, Singapore Eye Research InstituteSingapore, Singapore
| | - Shouping Liu
- Ocular Chemistry and Anti-Infectives, Singapore Eye Research InstituteSingapore, Singapore
| | | | - Chandra S. Verma
- Ocular Chemistry and Anti-Infectives, Singapore Eye Research InstituteSingapore, Singapore
- Agency for Science, Technology and Research (ASTAR), Bioinformatics InstituteSingapore, Singapore
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
- School of Biological Sciences, Nanyang Technological UniversitySingapore, Singapore
| | - Roger W. Beuerman
- Ocular Chemistry and Anti-Infectives, Singapore Eye Research InstituteSingapore, Singapore
- Duke-NUS Graduate Medical School, SRP Neuroscience and BDSingapore, Singapore
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21
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Murray B, Pearson CS, Aranjo A, Cherupalla D, Belfort G. Mechanism of Four de Novo Designed Antimicrobial Peptides. J Biol Chem 2016; 291:25706-25715. [PMID: 27738105 DOI: 10.1074/jbc.m116.733816] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/11/2016] [Indexed: 11/06/2022] Open
Abstract
As pathogenic bacteria become resistant to traditional antibiotics, alternate approaches such as designing and testing new potent selective antimicrobial peptides (AMP) are increasingly attractive. However, whereas much is known regarding the relationship between the AMP sequence and potency, less research has focused on developing links between AMP properties, such as design and structure, with mechanisms. Here we use four natural AMPs of varying known secondary structures and mechanisms of lipid bilayer disruption as controls to determine the mechanisms of four rationally designed AMPs with similar secondary structures and rearranged amino acid sequences. Using a Quartz Crystal Microbalance with Dissipation, we were able to differentiate between molecular models of AMP actions such as barrel-stave pore formation, toroidal pore formation, and peptide insertion mechanisms by quantifying differential frequencies throughout an oscillating supported lipid bilayer. Barrel-stave pores were identified by uniform frequency modulation, whereas toroidal pores possessed characteristic changes in oscillation frequency throughout the bilayer. The resulting modes of action demonstrate that rearrangement of an amino acid sequence of the AMP resulted in identical overall mechanisms, and that a given secondary structure did not necessarily predict mechanism. Also, increased mass addition to Gram-positive mimetic membranes from AMP disruption corresponded with lower minimum inhibitory concentrations against the Gram-positive Staphylococcus aureus.
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Affiliation(s)
- Brian Murray
- From the Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - C Seth Pearson
- From the Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Alexa Aranjo
- From the Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Dinesh Cherupalla
- From the Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Georges Belfort
- From the Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
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22
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Samuel R, Gillmor S. Membrane phase characteristics control NA-CATH activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1974-1982. [PMID: 27216315 DOI: 10.1016/j.bbamem.2016.05.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 04/06/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022]
Abstract
Our studies presented in this report focus on the behavior of NA-CATH, an α-helical cathelicidin antimicrobial peptide, originally discovered in the Naja atra snake. It has demonstrated high potency against gram-positive and gram-negative bacteria with minimal hemolysis. Here we examine the kinetics, behaviors and potential mechanisms of the peptide in the presence of membrane liposome, modeling Escherichia coli, whose membrane exhibits distinct lipid phases. To understand NA-CATH interactions, the role of lipid phases is critical. We test three different lipid compositions to detangle the effect of phase on NA-CATH's activity using a series of leakage experiments. From these studies, we observe that NA-CATH changes from membrane disruption to pore-based lysing, depending on phases and lipid composition. This behavior also plays a major role in its kinetics.
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Affiliation(s)
- Robin Samuel
- Department of Chemistry, George Washington University, Washington, DC 20052, United States
| | - Susan Gillmor
- Department of Chemistry, George Washington University, Washington, DC 20052, United States.
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23
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He J, Krauson AJ, Wimley WC. Toward the de novo design of antimicrobial peptides: Lack of correlation between peptide permeabilization of lipid vesicles and antimicrobial, cytolytic, or cytotoxic activity in living cells. Biopolymers 2016; 102:1-6. [PMID: 23893525 DOI: 10.1002/bip.22281] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/04/2013] [Accepted: 04/19/2013] [Indexed: 11/09/2022]
Abstract
We previously performed a lipid vesicle-based, high-throughput screen on a 26-residue combinatorial peptide library that was designed de novo to yield membrane-permeabilizing peptides that fold into β-sheets. The most active and soluble library members that were identified permeabilized lipid vesicles detectably, but not with high potency. Nonetheless, they were broad-spectrum, membrane-permeabilizing antibiotics with minimum sterilizing activity at low µM concentrations. In an expansion of that work, we recently performed an iterative screen in which an active consensus sequence from that first-generation library was used as a template to design a second-generation library which was then screened against lipid vesicles at very high stringency. Compared to the consensus sequence from the first library, the most active second-generation peptides are highly potent, equilibrium pore-formers in synthetic lipid vesicles. Here, we use these first- and second-generation families of peptides to test the hypothesis that a large increase in potency in bacteria-like lipid vesicles will correlate with a large improvement in antimicrobial activity. The results do not support the hypothesis. Despite a 20-fold increase in potency against bacteria-like lipid vesicles, the second-generation peptides are only slightly more active against bacteria, and at the same time, are also more toxic against mammalian cells. The results suggest that a "pipeline" strategy toward the optimization of antimicrobial peptides could begin with a vesicle-based screen for identifying families with broad-spectrum activity, but will also need to include screening or optimization steps that are done under conditions that are more directly relevant to possible therapeutic applications.
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Affiliation(s)
- Jing He
- Department of Biochemistry SL43, Tulane University School of Medicine, New Orleans, LA, 70112
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24
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Du H, Samuel RL, Massiah MA, Gillmor SD. The structure and behavior of the NA-CATH antimicrobial peptide with liposomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015. [DOI: 10.1016/j.bbamem.2015.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Yamada T, Signorelli S, Cannistraro S, Beattie CW, Bizzarri AR. Chirality switching within an anionic cell-penetrating peptide inhibits translocation without affecting preferential entry. Mol Pharm 2014; 12:140-9. [PMID: 25478723 DOI: 10.1021/mp500495u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Multiple substitution of d- for l-amino acids decreases the intracellular uptake of cationic cell penetrating peptides (CPP) in a cell line-dependent manner. We show here that a single d-amino acid substitution can decrease the overall uptake of the anionic, amphipathic CPP, p28, into cancer and histologically matched normal cell lines, while not altering the preferential uptake of p28 into cancer cells. The decrease appears dependent on the position of the d-substitution within the peptide and the ability of the substituted d-amino acid to alter chirality. We also suggest that when d-substitution alters the ratio of α-helix to β-sheet content of an anionic CPP, its translocation across the cell membrane is altered, reducing overall entry. These observations may have a significant effect on the design of future d-substituted analogues of cell penetrating peptides.
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Affiliation(s)
- Tohru Yamada
- Division of Surgical Oncology, Department of Surgery, University of Illinois College of Medicine , Chicago, Illinois 60612, United States
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26
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Lipkin RB, Lazaridis T. Implicit Membrane Investigation of the Stability of Antimicrobial Peptide β-Barrels and Arcs. J Membr Biol 2014; 248:469-86. [PMID: 25430621 DOI: 10.1007/s00232-014-9759-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 11/18/2014] [Indexed: 12/31/2022]
Abstract
Previous simulations showed that the β-hairpin antimicrobial peptide (AMP) protegrin-1 can form stable octameric β-barrels and tetrameric arcs (half barrels) in both implicit and explicit membranes. Here, we extend this investigation to several AMPs of similar structure: tachyplesin, androctonin, polyphemusin, gomesin, and the retrocyclin θ-defensin. These peptides form short β-hairpins stabilized by 2-3 disulfide bonds. We also examine synthetic β-sheet peptides selected from a combinatorial library for their ability or inability to form pores in lipid membranes. When heptameric, octameric, and decameric β-barrels and tetrameric arcs of these peptides were embedded in pre-formed neutral or anionic lipid pores (i.e., pores in neutral or anionic membranes, respectively), a variety of behaviors and membrane binding energies were observed. Due to the cationic charge of the peptides, more favorable transfer energies and more stable binding were observed in anionic than neutral pores. The synthetic peptides bound very strongly and formed stable barrels and arcs in both neutral and anionic pores. The natural AMPs exhibited unfavorable or marginally favorable binding energy and kinetic stability in neutral pores, consistent with the lower hemolytic activity of some of them compared with protegrin-1. Binding to anionic pores was more favorable, but significant distortions of the barrel or arc structures were sometimes noted. These results are discussed in light of the available experimental data. The diversity of behaviors obtained makes it unlikely that the barrel and arc mechanisms are valid for the entire family of β-hairpin AMPs.
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Affiliation(s)
- Richard B Lipkin
- Department of Chemistry, City College of the City University of New York, 160 Convent Ave., New York, NY, 10031, USA
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27
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Salazar VA, Rubin J, Moussaoui M, Pulido D, Nogués MV, Venge P, Boix E. Protein post-translational modification in host defense: the antimicrobial mechanism of action of human eosinophil cationic protein native forms. FEBS J 2014; 281:5432-46. [PMID: 25271100 DOI: 10.1111/febs.13082] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 09/17/2014] [Accepted: 09/26/2014] [Indexed: 02/06/2023]
Abstract
Knowledge on the contribution of protein glycosylation in host defense antimicrobial peptides is still scarce. We have studied here how the post-translational modification pattern modulates the antimicrobial activity of one of the best characterized leukocyte granule proteins. The human eosinophil cationic protein (ECP), an eosinophil specific granule protein secreted during inflammation and infection, can target a wide variety of pathogens. Previous work in human eosinophil extracts identified several ECP native forms and glycosylation heterogeneity was found to contribute to the protein biological properties. In this study we analyze for the first time the antimicrobial activity of the distinct native proteins purified from healthy donor blood. Low and heavy molecular weight forms were tested on Escherichia coli cell cultures and compared with the recombinant non-glycosylated protein. Further analysis on model membranes provided an insight towards an understanding of the protein behavior at the cytoplasmic membrane level. The results highlight the significant reduction in protein toxicity and bacteria agglutination activity for heavy glycosylated fractions. Notwithstanding, the lower glycosylated fraction mostly retains the lipopolysaccharide binding affinity together with the cytoplasmic membrane depolarization and membrane leakage activities. From structural analysis we propose that heavy glycosylation interferes with the protein self-aggregation, hindering the cell agglutination and membrane disruption processes. The results suggest the contribution of post-translational modifications to the antimicrobial role of ECP in host defense.
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Affiliation(s)
- Vivian A Salazar
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Spain
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28
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He J, Starr CG, Wimley WC. A lack of synergy between membrane-permeabilizing cationic antimicrobial peptides and conventional antibiotics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:8-15. [PMID: 25268681 DOI: 10.1016/j.bbamem.2014.09.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 09/16/2014] [Accepted: 09/20/2014] [Indexed: 01/20/2023]
Abstract
The rapid rise in morbidity and mortality from drug-resistant pathogenic bacteria has generated elevated interest in combination therapy using antimicrobial agents. Antimicrobial peptides (AMPs) are a candidate drug class to advance the development of combination therapies. Although the literature is ambiguous, the generic membrane disrupting activity of AMPs could enable them to synergize with conventional small molecule antibiotics by increasing access to the cell and by triggering membrane damage mediators. We used a novel assay to measure interactions, expressed as fractional inhibitory concentration (FIC), between four conventional antibiotics in combination with four well-characterized, membrane permeabilizing AMPs, against three species of Gram negative and Gram positive bacteria, giving 40 total pair-wise measurements of FIC with statistical uncertainties. We chose a set of AMPs that are known to dramatically disrupt the membranes of both Gram negative and Gram positive bacteria. Yet none of the membrane permeabilizing antimicrobial peptides interacted synergistically with any of the conventional antibiotic drugs in any organism. Large-scale membrane disruption and permeabilization by AMPs is not sufficient to drive them to act synergistically with chemical antibiotics in either Gram negative or Gram positive microbes.
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Affiliation(s)
- Jing He
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Charles G Starr
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - William C Wimley
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA.
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29
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Rapsch K, Bier FF, von Nickisch-Rosenegk M. Rational design of artificial β-strand-forming antimicrobial peptides with biocompatible properties. Mol Pharm 2014; 11:3492-502. [PMID: 25192319 DOI: 10.1021/mp500271c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Because the intensive use of antibiotics has led to a large variety of resistant bacterial strains, therapeutic measures have become increasingly challenging. In order to ensure reliable treatment of diseases, alternative antimicrobial agents need to be explored. In this context, antimicrobial peptides have been discussed as novel bioactive molecules, which, however, may be limited in their applicability due to their high manufacturing costs and poor pharmacokinetic properties. Consequently, the design of artificial antimicrobial peptides featuring two flanking cationic regions and a hydrophobic center is presented. These sequences led to distinct antimicrobial activity on the same order of magnitude as that of naturally occurring reference peptides but with less cytotoxic or cytostatic drawbacks. Furthermore, a deletion and substitution library revealed the minimal sequence requirements. By analysis of the computed 3D structures of these peptides, a single characteristic β-strand was identified. This structural motif was pivotal for antimicrobial activity. Consequently, an optimized peptide sequence with antimicrobial and biocompatible properties was derived, and its application was demonstrated in a mixed culture experiment. Thus, it was shown that the optimized artificial antimicrobial peptide is suitable as a therapeutic agent and may be used as template for the development of new antimicrobial peptides with unique secondary structures.
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Affiliation(s)
- Karsten Rapsch
- Fraunhofer Institute for Biomedical Engineering IBMT , Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam, Germany
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30
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Choi H, Lee DG. Antifungal activity and pore-forming mechanism of astacidin 1 against Candida albicans. Biochimie 2014; 105:58-63. [PMID: 24955933 DOI: 10.1016/j.biochi.2014.06.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/13/2014] [Indexed: 11/16/2022]
Abstract
In a previous report, a novel antibacterial peptide astacidin 1 (FKVQNQHGQVVKIFHH) was isolated from hemocyanin of the freshwater crayfish Pacifastacus leniusculus. In this study, the antifungal activity and mechanism of astacidin 1 were evaluated. Astacidin 1 exhibited antifungal activity against Candida albicans, Trichosporon beigelii, Malassezia furfur, and Trichophyton rubrum. Also, astacidin 1 had fungal cell selectivity in human erythrocytes without causing hemolysis. To understand the antifungal mechanism, membrane studies were done against C. albicans and T. beigelii. Flow cytometric analysis and K(+) measurement showed membrane damage, resulting in membrane permeabilization and K(+) release-induced membrane depolarization. Furthermore, the calcein leakage from liposomes mimicking C. albicans membrane demonstrated that the membrane-active action was driven by pore-forming mechanism. Live cell imaging using fluorescein isothiocyanate-labeled dextrans of various sizes suggested that the radii of pores formed in the C. albicans membrane were 1.4-2.3 nm. Therefore, the present study suggests that astacidin 1 exerts its antifungal effect by damaging the fungal membrane via pore formation.
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Affiliation(s)
- Hyemin Choi
- School of Life Sciences, BK 21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu 702-701, Republic of Korea
| | - Dong Gun Lee
- School of Life Sciences, BK 21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu 702-701, Republic of Korea.
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31
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Koller D, Lohner K. The role of spontaneous lipid curvature in the interaction of interfacially active peptides with membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2250-9. [PMID: 24853655 DOI: 10.1016/j.bbamem.2014.05.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 01/28/2023]
Abstract
Research on antimicrobial peptides is in part driven by urgent medical needs such as the steady increase in pathogens being resistant to antibiotics. Despite the wealth of information compelling structure-function relationships are still scarce and thus the interfacial activity model has been proposed to bridge this gap. This model also applies to other interfacially active (membrane active) peptides such as cytolytic, cell penetrating or antitumor peptides. One parameter that is strongly linked to interfacial activity is the spontaneous lipid curvature, which is experimentally directly accessible. We discuss different parameters such as H-bonding, electrostatic repulsion, changes in monolayer surface area and lateral pressure that affect induction of membrane curvature, but also vice versa how membrane curvature triggers peptide response. In addition, the impact of membrane lipid composition on the formation of curved membrane structures and its relevance for diverse mode of action of interfacially active peptides and in turn biological activity are described. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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Affiliation(s)
- Daniel Koller
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Schmiedlstraße 6, A-8042 Graz, Austria.
| | - Karl Lohner
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Schmiedlstraße 6, A-8042 Graz, Austria.
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32
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Human neutrophil peptide 1 variants bearing arginine modified cationic side chains: effects on membrane partitioning. Biophys Chem 2014; 190-191:32-40. [PMID: 24820901 DOI: 10.1016/j.bpc.2014.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/14/2014] [Accepted: 04/15/2014] [Indexed: 11/22/2022]
Abstract
α-Defensins (e.g. human neutrophil peptides, HNPs) have a broad spectrum bactericidal activity contributing to human innate immunity. The positive charge of amino acid side chains is responsible for the first interaction of cationic antimicrobial peptides with negatively charged bacterial membranes. α-Defensins contain a high content of Arg residues compared to Lys. In this paper, different peptide analogs including substitution of Arg-14 respectively with N(G)-N(G')-asymmetric dimethyl-l-arginine (ADMA), N(G)-N(G')-symmetric dimethyl-l-arginine (SDMA) and Lys (R14K and R15KR14KR15K) variants have been studied to test the role of Arg guanidino group and the localized cationic charge of Lys for interaction with lipid membranes. Our findings show that all the variants have a decreased disruptive activity against the bilayer. The methylated analogs show a reduction in membrane partitioning due to the lack of their ability to form hydrogen bonds. Comparison with the native HNP-1 peptide has been discussed.
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33
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Wiedman G, Fuselier T, He J, Searson PC, Hristova K, Wimley WC. Highly efficient macromolecule-sized poration of lipid bilayers by a synthetically evolved peptide. J Am Chem Soc 2014; 136:4724-31. [PMID: 24588399 PMCID: PMC3985440 DOI: 10.1021/ja500462s] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Indexed: 12/30/2022]
Abstract
Peptides that self-assemble, at low concentration, into bilayer-spanning pores which allow the passage of macromolecules would be beneficial in multiple areas of biotechnology. However, there are few, if any, natural or designed peptides that have this property. Here we show that the 26-residue peptide "MelP5", a synthetically evolved gain-of-function variant of the bee venom lytic peptide melittin identified in a high-throughput screen for small molecule leakage, enables the passage of macromolecules across bilayers under conditions where melittin and other pore-forming peptides do not. In surface-supported bilayers, MelP5 forms unusually high conductance, equilibrium pores at peptide:lipid ratios as low as 1:25000. The increase in bilayer conductance due to MelP5 is dramatically higher, per peptide, than the increase due to the parent sequence of melittin or other peptide pore formers. Here we also develop two novel assays for macromolecule leakage from vesicles, and we use them to characterize MelP5 pores in bilayers. We show that MelP5 allows the passage of macromolecules across vesicle membranes at peptide:lipid ratios as low as 1:500, and under conditions where neither osmotic lysis nor gross vesicle destabilization occur. The macromolecule-sized, equilibrium pores formed by MelP5 are unique as neither melittin nor other pore-forming peptides release macromolecules significantly under the same conditions. MelP5 thus appears to belong to a novel functional class of peptide that could form the foundation of multiple potential biotechnological applications.
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Affiliation(s)
- Gregory Wiedman
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
- Institute
for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Taylor Fuselier
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Jing He
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Peter C. Searson
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
- Institute
for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kalina Hristova
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
- Institute
for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - William C. Wimley
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
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34
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Pink DA, Hasan FM, Quinn BE, Winterhalter M, Mohan M, Gill TA. Interaction of protamine with gram‐negative bacteria membranes: possible alternative mechanisms of internalization in
Escherichia coli
,
Salmonella typhimurium
and
Pseudomonas aeruginosa. J Pept Sci 2014; 20:240-50. [DOI: 10.1002/psc.2610] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 11/14/2013] [Accepted: 12/02/2013] [Indexed: 11/08/2022]
Affiliation(s)
- David. A. Pink
- Department of Physics St. Francis Xavier University Antigonish NS B2G 2W5 Canada
| | - Fida M. Hasan
- Department of Process Engineering and Applied Science Dalhousie University Halifax NS B3J 2X4 Canada
| | - Bonnie E. Quinn
- Department of Physics St. Francis Xavier University Antigonish NS B2G 2W5 Canada
| | | | - Mukund Mohan
- Department of Process Engineering and Applied Science Dalhousie University Halifax NS B3J 2X4 Canada
| | - Tom A. Gill
- Department of Process Engineering and Applied Science Dalhousie University Halifax NS B3J 2X4 Canada
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35
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Balhara V, Schmidt R, Gorr SU, DeWolf C. Membrane selectivity and biophysical studies of the antimicrobial peptide GL13K. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2193-203. [DOI: 10.1016/j.bbamem.2013.05.027] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/24/2013] [Accepted: 05/27/2013] [Indexed: 01/27/2023]
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36
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He J, Kauffman WB, Fuselier T, Naveen SK, Voss TG, Hristova K, Wimley WC. Direct cytosolic delivery of polar cargo to cells by spontaneous membrane-translocating peptides. J Biol Chem 2013; 288:29974-86. [PMID: 23983125 DOI: 10.1074/jbc.m113.488312] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Direct cellular entry of potentially useful polar compounds into cells is prevented by the hydrophobic barrier of the membrane. Toward circumventing this barrier, we used high throughput screening to identify a family of peptides that carry membrane-impermeant cargos across synthetic membranes. Here we characterize the plasma membrane translocation of these peptides with polar cargos under a variety of conditions. The spontaneous membrane-translocating peptides (SMTPs) delivered the zwitterionic, membrane-impermeant dye tetramethylrhodamine (TAMRA) into cells even when the conditions were not permissive for endocytosis. They also delivered the larger, anionic membrane-impermeant dye Alexa Fluor 546 but did not deliver a quantum dot nanoparticle. Under all conditions, the SMTP-cargo filled the cytoplasm with a diffuse, non-punctate fluorescence that was partially excluded from the nucleus. D-amino acid peptides behaved identically in vitro, ruling out proteolysis as an important factor in the diffuse cellular distribution. Thus, cytosolic delivery of SMTP-cargo conjugates is dominated by direct membrane translocation. This is in sharp contrast to Arg9-TAMRA, a representative highly cationic, cell-penetrating peptide, which entered cells only when endocytosis was permitted. Arg9-TAMRA triggered large scale endocytosis and did not appreciably escape the endosomal compartments in the 1-h timescales we studied. When injected into mice, SMTP-TAMRA conjugates were found in many tissues even after 2 h. Unconjugated TAMRA was rapidly cleared and did not become systemically distributed. SMTPs are a platform that could improve delivery of many polar compounds to cells, in the laboratory or in the clinic, including those that would otherwise be rejected as drugs because they are membrane-impermeant.
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Affiliation(s)
- Jing He
- From the Departments of Biochemistry and
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37
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Domingues TM, Mattei B, Seelig J, Perez KR, Miranda A, Riske KA. Interaction of the antimicrobial peptide gomesin with model membranes: a calorimetric study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8609-8618. [PMID: 23755822 DOI: 10.1021/la401596s] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Gomesin is a potent cationic antimicrobial peptide (z = +6) isolated from the Brazilian spider Acanthoscurria gomesiana . The interaction of gomesin with large unilamellar vesicles composed of a 1:1 mixture of zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) phospholipids is studied with isothermal titration calorimetry (ITC). In parallel, light scattering and optical microscopy are used to assess peptide-induced vesicle aggregation. The ability of gomesin to permeabilize the membrane is examined with fluorescence spectroscopy of the leakage of 5,6-carboxyfluorescein (CF). Vesicles coated with 3 mol % 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (PE-PEG) lipids are also investigated to assess the influence of peptide-induced vesicle aggregation in the activity of gomesin. The ITC and light scattering titrations are done in two ways: lipid into peptide and peptide into lipid injections. Although some differences arise between the two setups, the basic interaction of gomesin with anionic vesicles is preserved. A surface partition model combined with the Gouy-Chapman theory is put forward to fit the ITC results. The intrinsic binding constant of gomesin is found to be K ≈ 10(3) M(-1). The interaction of gomesin with anionic membranes is highly exothermic and enthalpy-driven. Binding of gomesin is virtually always accompanied by vesicle aggregation and changes in membrane permeability, leading to CF leakage. Addition of PE-PEG to the membrane strongly attenuates vesicle aggregation but does not significantly change the mode of action of gomesin. The results point to a strong interaction of gomesin with the membrane surface, causing membrane rupture without a deep penetration into the bilayer core.
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Affiliation(s)
- Tatiana M Domingues
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, Brazil
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38
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Krauson AJ, He J, Wimley AW, Hoffmann AR, Wimley WC. Synthetic molecular evolution of pore-forming peptides by iterative combinatorial library screening. ACS Chem Biol 2013; 8:823-31. [PMID: 23394375 DOI: 10.1021/cb300598k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We previously reported the de novo design of a combinatorial peptide library that was subjected to high-throughput screening to identify membrane-permeabilizing antimicrobial peptides that have β-sheet-like secondary structure. Those peptides do not form discrete pores in membranes but instead partition into membrane interfaces and cause transient permeabilization by membrane disruption, but only when present at high concentration. In this work, we used a consensus sequence from that initial screen as a template to design an iterative, second generation library. In the 24-26-residue, 16,200-member second generation library we varied six residues. Two diad repeat motifs of alternating polar and nonpolar amino acids were preserved to maintain a propensity for non-helical secondary structure. We used a new high-throughput assay to identify members that self-assemble into equilibrium pores in synthetic lipid bilayers. This screen was done at a very stringent peptide to lipid ratio of 1:1000 where most known membrane-permeabilizing peptides, including the template peptide, are not active. In a screen of 10,000 library members we identified 16 (~0.2%) that are equilibrium pore-formers at this high stringency. These rare and highly active peptides, which share a common sequence motif, are as potent as the most active pore-forming peptides known. Furthermore, they are not α-helical, which makes them unusual, as most of the highly potent pore-forming peptides are amphipathic α-helices. Here we demonstrate that this synthetic molecular evolution-based approach, taken together with the new high-throughput tools we have developed, enables the identification, refinement, and optimization of unique membrane active peptides.
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Affiliation(s)
- Aram J. Krauson
- Department of Biochemistry
and Molecular Biology SL43, Tulane University School of Medicine, New Orleans,
Louisiana 70112, United States
| | - Jing He
- Department of Biochemistry
and Molecular Biology SL43, Tulane University School of Medicine, New Orleans,
Louisiana 70112, United States
| | - Andrew W. Wimley
- Department of Biochemistry
and Molecular Biology SL43, Tulane University School of Medicine, New Orleans,
Louisiana 70112, United States
| | - Andrew R. Hoffmann
- Department of Biochemistry
and Molecular Biology SL43, Tulane University School of Medicine, New Orleans,
Louisiana 70112, United States
| | - William C. Wimley
- Department of Biochemistry
and Molecular Biology SL43, Tulane University School of Medicine, New Orleans,
Louisiana 70112, United States
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39
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Moiset G, Cirac AD, Stuart MCA, Marrink SJ, Sengupta D, Poolman B. Dual action of BPC194: a membrane active peptide killing bacterial cells. PLoS One 2013; 8:e61541. [PMID: 23620763 PMCID: PMC3631201 DOI: 10.1371/journal.pone.0061541] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 03/10/2013] [Indexed: 11/30/2022] Open
Abstract
Membrane active peptides can perturb the lipid bilayer in several ways, such as poration and fusion of the target cell membrane, and thereby efficiently kill bacterial cells. We probe here the mechanistic basis of membrane poration and fusion caused by membrane-active, antimicrobial peptides. We show that the cyclic antimicrobial peptide, BPC194, inhibits growth of Gram-negative bacteria and ruptures the outer and inner membrane at the onset of killing, suggesting that not just poration is taking place at the cell envelope. To simplify the system and to better understand the mechanism of action, we performed Förster resonance energy transfer and cryogenic transmission electron microscopy studies in model membranes and show that the BPC194 causes fusion of vesicles. The fusogenic action is accompanied by leakage as probed by dual-color fluorescence burst analysis at a single liposome level. Atomistic molecular dynamics simulations reveal how the peptides are able to simultaneously perturb the membrane towards porated and fused states. We show that the cyclic antimicrobial peptides trigger both fusion and pore formation and that such large membrane perturbations have a similar mechanistic basis.
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Affiliation(s)
- Gemma Moiset
- Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB) and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Anna D. Cirac
- Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB) and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
- Institute of Computational Chemistry, University of Girona, Campus Montivili, Girona, Spain
| | - Marc C. A. Stuart
- Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB) and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Siewert-Jan Marrink
- Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB) and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Durba Sengupta
- Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB) and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, India
- * E-mail: (BP); (DS)
| | - Bert Poolman
- Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB) and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
- * E-mail: (BP); (DS)
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40
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Xia L, Zhang F, Liu Z, Ma J, Yang J. Expression and characterization of cecropinXJ, a bioactive antimicrobial peptide from Bombyx mori (Bombycidae, Lepidoptera) in Escherichia coli.. Exp Ther Med 2013; 5:1745-1751. [PMID: 23837066 PMCID: PMC3702707 DOI: 10.3892/etm.2013.1056] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/22/2013] [Indexed: 12/31/2022] Open
Abstract
Insect antimicrobial peptides (AMPs) have a broad antimicrobial spectrum. To aid the characterization of the gene function and further applications, we cloned the gene of cecropinXJ into the prokaryotic expression vector pET32a and expressed cecropinXJ in Escherichia coli BL2l (DE3). Following induction by isopropyl-β-D-thiogalactoside (IPTG), a 25 kDa fusion peptide of cecropinXJ with a tagged thioredoxin (Trx) protein was highly expressed in E. coli. The yield was 10 mg/l culture medium following purification on nickel-nitrilotriacetic acid (Ni-NTA) metal affinity chromatography matrices. The purified recombinant antibacterial peptide, cecropinXJ, retained a high stability against Staphylococcus aureus over a temperature range from 4 to 100°C and a pH range from pH 2.0 to 12.0. The minimum inhibitory concentration (MIC) of the fusion protein against S. aureus was 0.4 μM. The recombinant cecropinXJ is also cytotoxic to several types of human cancer cells.
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Affiliation(s)
- Lijie Xia
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang 830046, P.R. China
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Xia L, Liu Z, Ma J, Sun S, Yang J, Zhang F. Expression, purification and characterization of cecropin antibacterial peptide from Bombyx mori in Saccharomyces cerevisiae. Protein Expr Purif 2013; 90:47-54. [PMID: 23500722 DOI: 10.1016/j.pep.2013.02.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 02/19/2013] [Accepted: 02/20/2013] [Indexed: 01/14/2023]
Abstract
CecropinXJ is a cationic antimicrobial peptide originally isolated from the larvae of Bombyx mori. In this study, an antibacterial peptide gene of cecropinXJ was cloned into the pYES2/CT/α Factor expression vector and expressed in the Saccharomyces cerevisiae INVSc1 strain. Following an induction of recombinant protein expression in yeast for 120 h, the maximum amount of total secreted protein was 1.437 g/L. The percentage of recombinant cecropinXJ was estimated to be 79.45% of the total protein. After purification with Ni-NTA agarose column, recombinant cecropinXJ was noted to exert strong antimicrobial activities against a broad-spectrum of microorganisms, including Gram-negative and Gram-positive bacteria. Its minimal inhibitory concentration (MIC) against Escherichia coli ATCC25922 was 0.81 μM. In addition, transmission electron microscopy (TEM) analysis indicated that the surfaces of the treated pathogens underwent obvious morphological changes compared with the untreated controls, suggesting that this antimicrobial peptide exerts its action by directly disrupting membranes of microorganisms. CecropinXJ had a small hemolytic effect on red blood cells even with a peptide concentration of 200 μM. Thus, cecropinXJ acts selectively on bacterial membranes. Purified recombinant antibacterial peptide, cecropinXJ, retained a high stability against E. coli ATCC25922 over a temperature range from 4 °C to 100 °C and a pH range from pH 2.0 to 12.0. Taken together, this study demonstrates that recombinant cecropinXJ can be produced in large quantities in yeast with genetic engineering methods, and that it has strong and rapid antimicrobial activities against all of microorganisms tested. Our results suggest that cecropinXJ is a potential candidate for therapy.
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Affiliation(s)
- Lijie Xia
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, PR China
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Bonucci A, Balducci E, Pistolesi S, Pogni R. The defensin–lipid interaction: Insights on the binding states of the human antimicrobial peptide HNP-1 to model bacterial membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:758-64. [DOI: 10.1016/j.bbamem.2012.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 10/08/2012] [Accepted: 11/08/2012] [Indexed: 01/13/2023]
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Lorin A, Noël M, Provencher MÈ, Turcotte V, Cardinal S, Lagüe P, Voyer N, Auger M. Determining the mode of action involved in the antimicrobial activity of synthetic peptides: a solid-state NMR and FTIR study. Biophys J 2012; 103:1470-9. [PMID: 23062339 DOI: 10.1016/j.bpj.2012.08.055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/20/2012] [Accepted: 08/28/2012] [Indexed: 10/27/2022] Open
Abstract
We have previously shown that leucine to lysine substitution(s) in neutral synthetic crown ether containing 14-mer peptide affect the peptide structure and its ability to permeabilize bilayers. Depending on the substitution position, the peptides adopt mainly either a α-helical structure able to permeabilize dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylglycerol (DMPG) vesicles (nonselective peptides) or an intermolecular β-sheet structure only able to permeabilize DMPG vesicles (selective peptides). In this study, we have used a combination of solid-state NMR and Fourier transform infrared spectroscopy to investigate the effects of nonselective α-helical and selective intermolecular β-sheet peptides on both types of bilayers. (31)P NMR results indicate that both types of peptides interact with the headgroups of DMPC and DMPG bilayers. (2)H NMR and Fourier transform infrared results reveal an ordering of the hydrophobic core of bilayers when leakage is noted, i.e., for DMPG vesicles in the presence of both types of peptides and DMPC vesicles in the presence of nonselective peptides. However, selective peptides have no significant effect on the ordering of DMPC acyl chains. The ability of these 14-mer peptides to permeabilize lipid vesicles therefore appears to be related to their ability to increase the order of the bilayer hydrophobic core.
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Affiliation(s)
- Aurélien Lorin
- Département de chimie, PROTEO (Regroupement Québécois de Recherche sur la Fonction, la Structure et l'Ingénierie des Protéines), CERMA (Centre de Recherche sur les Matériaux Avancés), Université Laval, Québec, Québec, Canada
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Krauson AJ, He J, Wimley WC. Gain-of-function analogues of the pore-forming peptide melittin selected by orthogonal high-throughput screening. J Am Chem Soc 2012; 134:12732-41. [PMID: 22731650 DOI: 10.1021/ja3042004] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We recently developed an orthogonal, high-throughput assay to identify peptides that self-assemble into potent, equilibrium pores in synthetic lipid bilayers. Here, we use this assay as a high-throughput screen to select highly potent pore-forming peptides from a 7776-member rational combinatorial peptide library based on the sequence of the natural pore-forming peptide toxin melittin. In the library we varied ten critical residues in the melittin sequence, chosen to test specific structural hypotheses about the mechanism of pore formation. Using the new high-throughput assay, we screened the library for gain-of-function sequences at a peptide to lipid ratio of 1:1000 where native melittin is not active. More than 99% of the library sequences were also inactive under these conditions. A small number of library members (0.1%) were highly active. From these we identified 14 potent, gain-of-function, pore-forming sequences. These sequences differed from melittin in only 2-6 amino acids out of 26. Some native residues were highly conserved and others were consistently changed. The two factors that were essential for gain-of-function were the preservation of melittin's proline-dependent break in the middle of the helix and the improvement and extension the amphipathic nature of the α-helix. In particular the highly cationic carboxyl-terminal sequence of melittin, is consistently changed in the gain-of-function variants to a sequence that it is capable of participating in an extended amphipathic α-helix. The most potent variants reside in a membrane-spanning orientation, in contrast to the parent melittin, which is predominantly surface bound. This structural information, taken together with the high-throughput tools developed for this work, enable the identification, refinement and optimization of pore-forming peptides for many potential applications.
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Affiliation(s)
- Aram J Krauson
- Department of Biochemistry, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
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Bai Y, Liu S, Li J, Lakshminarayanan R, Sarawathi P, Tang C, Ho D, Verma C, Beuerman RW, Pervushin K. Progressive structuring of a branched antimicrobial peptide on the path to the inner membrane target. J Biol Chem 2012; 287:26606-17. [PMID: 22700968 DOI: 10.1074/jbc.m112.363259] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In recent years, interest has grown in the antimicrobial properties of certain natural and non-natural peptides. The strategy of inserting a covalent branch point in a peptide can improve its antimicrobial properties while retaining host biocompatibility. However, little is known regarding possible structural transitions as the peptide moves on the access path to the presumed target, the inner membrane. Establishing the nature of the interactions with the complex bacterial outer and inner membranes is important for effective peptide design. Structure-activity relationships of an amphiphilic, branched antimicrobial peptide (B2088) are examined using environment-sensitive fluorescent probes, electron microscopy, molecular dynamics simulations, and high resolution NMR in solution and in condensed states. The peptide is reconstituted in bacterial outer membrane lipopolysaccharide extract as well as in a variety of lipid media mimicking the inner membrane of Gram-negative pathogens. Progressive structure accretion is observed for the peptide in water, LPS, and lipid environments. Despite inducing rapid aggregation of bacteria-derived lipopolysaccharides, the peptide remains highly mobile in the aggregated lattice. At the inner membranes, the peptide undergoes further structural compaction mediated by interactions with negatively charged lipids, probably causing redistribution of membrane lipids, which in turn results in increased membrane permeability and bacterial lysis. These findings suggest that peptides possessing both enhanced mobility in the bacterial outer membrane and spatial structure facilitating its interactions with the membrane-water interface may provide excellent structural motifs to develop new antimicrobials that can overcome antibiotic-resistant Gram-negative pathogens.
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Affiliation(s)
- Yang Bai
- Singapore Eye Research Institute, Singapore 168751
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Lin J, Motylinski J, Krauson AJ, Wimley WC, Searson PC, Hristova K. Interactions of membrane active peptides with planar supported bilayers: an impedance spectroscopy study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:6088-96. [PMID: 22416892 DOI: 10.1021/la300274n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Membrane active peptides exert their biological effects by interacting directly with a cell's lipid bilayer membrane. These therapeutically promising peptides have demonstrated a variety of activities including antimicrobial, cytolytic, membrane translocating, and cell penetrating activities. Here, we use electrochemical impedance spectroscopy (EIS) on polymer-cushioned supported lipid bilayers constructed on single crystal silicon to study two pairs of closely related membrane active peptides selected from rationally designed, combinatorial libraries to have different activities in lipid bilayers: translocation, permeabilization, or no activity. Using EIS, we observed that binding of a membrane translocating peptide to the lipid bilayer resulted in a small decrease in membrane resistance followed by a recovery back to the original value. The recovery may be directly attributable to peptide translocation. A nontranslocating peptide did not decrease the resistance. The other pair, two membrane permeabilizing peptides, caused an exponential decrease of membrane resistance in a concentration-dependent manner. This permeabilization of the supported bilayer occurs at peptide to lipid ratios as much as 1000-fold lower than that needed to observe effects in vesicle leakage assays and gives new insights into the fundamental peptide-bilayer interactions involved in membrane permeabilization.
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Affiliation(s)
- Janice Lin
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Scorciapino MA, Pirri G, Vargiu AV, Ruggerone P, Giuliani A, Casu M, Buerck J, Wadhwani P, Ulrich AS, Rinaldi AC. A novel dendrimeric peptide with antimicrobial properties: structure-function analysis of SB056. Biophys J 2012; 102:1039-48. [PMID: 22404926 DOI: 10.1016/j.bpj.2012.01.048] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 01/17/2012] [Accepted: 01/30/2012] [Indexed: 01/15/2023] Open
Abstract
The novel antimicrobial peptide with a dimeric dendrimer scaffold, SB056, was empirically optimized by high-throughput screening. This procedure produced an intriguing primary sequence whose structure-function analysis is described here. The alternating pattern of hydrophilic and hydrophobic amino acids suggests the possibility that SB056 is a membrane-active peptide that forms amphiphilic β-strands in a lipid environment. Circular dichroism confirmed that the cationic SB056 folds as β-sheets in the presence of anionic vesicles. Lipid monolayer surface pressure experiments revealed unusual kinetics of monolayer penetration, which suggest lipid-induced aggregation as a membranolytic mechanism. NMR analyses of the linear monomer and the dendrimeric SB056 in water and in 30% trifluoroethanol, on the other hand, yielded essentially unstructured conformations, supporting the excellent solubility and storage properties of this compound. However, simulated annealing showed that many residues lie in the β-region of the Ramachandran plot, and molecular-dynamics simulations confirmed the propensity of this peptide to fold as a β-type conformation. The excellent solubility in water and the lipid-induced oligomerization characteristics of this peptide thus shed light on its mechanism of antimicrobial action, which may also be relevant for systems that can form toxic β-amyloid fibrils when in contact with cellular membranes. Functionally, SB056 showed high activity against Gram-negative bacteria and some limited activity against Gram-positive bacteria. Its potency against Gram-negative strains was comparable (on a molar basis) to that of colistin and polymyxin B, with an even broader spectrum of activity than numerous other reference compounds.
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Affiliation(s)
- Mariano A Scorciapino
- Department of Chemical Sciences, Istituto Officina dei Materiali del Consiglio Nazionale delle Ricerche, UOS SLACS, Italy
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Lorin A, Noël M, Provencher MÈ, Turcotte V, Masson C, Cardinal S, Lagüe P, Voyer N, Auger M. Revisiting peptide amphiphilicity for membrane pore formation. Biochemistry 2011; 50:9409-20. [PMID: 21942823 DOI: 10.1021/bi201335t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
It has previously been shown that an amphipathic de novo designed peptide made of 10 leucines and four phenylalanines substituted with crown ethers induces vesicle leakage without selectivity. To gain selectivity against negatively charged dimyristoylphosphatidylglycerol (DMPG) bilayers, one or two leucines of the peptide were substituted with positively charged residues at each position. All peptides induce significant calcein leakage of DMPG vesicles. However, some peptides do not induce significant leakage of zwitterionic dimyristoylphosphatidylcholine vesicles and are thus active against only bacterial model membranes. The intravesicular leakage is induced by pore formation instead of membrane micellization. Nonselective peptides are mostly helical, while selective peptides mainly adopt an intermolecular β-sheet structure. This study therefore demonstrates that the position of the lysine residues significantly influences the secondary structure and bilayer selectivity of an amphipathic 14-mer peptide, with β-sheet peptides being more selective than helical peptides.
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Affiliation(s)
- Aurélien Lorin
- Département de chimie, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Centre de recherche sur les matériaux avancés, Université Laval, Québec, Québec, Canada G1V 0A6
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Bocchinfuso G, Bobone S, Mazzuca C, Palleschi A, Stella L. Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides. Cell Mol Life Sci 2011; 68:2281-301. [PMID: 21584808 PMCID: PMC11114703 DOI: 10.1007/s00018-011-0719-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 10/18/2022]
Abstract
Since their initial discovery, 30 years ago, antimicrobial peptides (AMPs) have been intensely investigated as a possible solution to the increasing problem of drug-resistant bacteria. The interaction of antimicrobial peptides with the cellular membrane of bacteria is the key step of their mechanism of action. Fluorescence spectroscopy can provide several structural details on peptide-membrane systems, such as partition free energy, aggregation state, peptide position and orientation in the bilayer, and the effects of the peptides on the membrane order. However, these "low-resolution" structural data are hardly sufficient to define the structural requirements for the pore formation process. Molecular dynamics simulations, on the other hand, provide atomic-level information on the structure and dynamics of the peptide-membrane system, but they need to be validated experimentally. In this review we summarize the information that can be obtained by both approaches, highlighting their versatility and complementarity, suggesting that their synergistic application could lead to a new level of insight into the mechanism of membrane destabilization by AMPs.
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Affiliation(s)
- Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Sara Bobone
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Claudia Mazzuca
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Antonio Palleschi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- IRCCS Neuromed, 86077 Pozzilli, IS Italy
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- IRCCS Neuromed, 86077 Pozzilli, IS Italy
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Destabilization exerted by peptides derived from the membrane-proximal external region of HIV-1 gp41 in lipid vesicles supporting fluid phase coexistence. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1797-805. [PMID: 21316335 DOI: 10.1016/j.bbamem.2011.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 02/01/2011] [Accepted: 02/04/2011] [Indexed: 11/22/2022]
Abstract
The human immunodeficiency virus (HIV) envelope is enriched in cholesterol and sphingomyelin, two lipids that sustain the formation of laterally segregated liquid-ordered fluid domains in model systems. Several evidences indicate that the high lipid order existing at the envelope may play a role in HIV pathogenesis. A putative mechanism might involve the modulation of the membrane-perturbing function of the gp41 membrane-proximal external region (MPER). To test such hypothesis, we investigate here the effect of lipid phase coexistence on the membrane-restructuring properties of NpreTM and CpreTM, two peptides based on the amino- and carboxy-terminal MPER sequences, respectively. Fluid phase coexistence elicited the fusogenic activity of NpreTM at high membrane doses and stimulated "graded" leakage at low doses. By comparison, the effect on CpreTM was restricted to an enhancement of "all-or-none" leakage that was consistent with the promotion of its surface aggregation. Confocal microscopy of single vesicles revealed the preference of both peptides for liquid-disordered domains. Accordingly, we speculate that confinement into envelope fluid nanodomains might boost the distinct capacities of HIV MPER hydrophobic modules for inducing membrane defects during fusion.
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