1
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van Tilburg M, Hilbers PAJ, Markvoort AJ. On the role of membrane embedding, protein rigidity and transmembrane length in lipid membrane fusion. SOFT MATTER 2023; 19:1791-1802. [PMID: 36786821 DOI: 10.1039/d2sm01582j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The fusion of biological membranes is ubiquitous in natural processes like exo- and endocytosis, intracellular trafficking and viral entry. Membrane fusion is also utilized in artificial biomimetic fusion systems, e.g. for drug delivery. Both the natural and the biomimetic fusion systems rely on a wide range of (artificial) proteins mediating the fusion process. Although the exact mechanisms of these proteins differ, clear analogies in their general behavior can be observed in bringing the membranes in close proximity and mediating the fusion reaction. In our study, we use molecular dynamics simulations with coarse grained models, mimicking the general behavior of fusion proteins (spikes), to systematically examine the effects of specific characteristics of these proteins on the fusion process. The protein characteristics considered are (i) the type of membrane embedding, i.e., either transmembrane or not, (ii) the rigidity, and (iii) the transmembrane domain (TMD) length. The results show essential differences in fusion pathway between monotopic and transmembrane spikes, in which transmembrane spikes seem to inhibit the formation of hemifusion diaphragms, leading to a faster fusion development. Furthermore, we observed that an increased rigidity and a decreased TMD length both proved to contribute to a faster fusion development. Finally, we show that a single spike may suffice to successfully induce a fusion reaction, provided that the spike is sufficiently rigid and attractive. Not only does this shed light on biological fusion of membranes, it also provides clear design rules for artificial membrane fusion systems.
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Affiliation(s)
- Marco van Tilburg
- Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, The Netherlands.
| | - Peter A J Hilbers
- Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, The Netherlands.
- Institute of Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Albert J Markvoort
- Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, The Netherlands.
- Institute of Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
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2
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Shitut S, Shen MJ, Claushuis B, Derks RJE, Giera M, Rozen D, Claessen D, Kros A. Generating Heterokaryotic Cells via Bacterial Cell-Cell Fusion. Microbiol Spectr 2022; 10:e0169322. [PMID: 35862998 PMCID: PMC9430406 DOI: 10.1128/spectrum.01693-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/22/2022] [Indexed: 11/20/2022] Open
Abstract
Fusion of cells is an important and common biological process that leads to the mixing of cellular contents and the formation of multinuclear cells. Cell fusion occurs when distinct membranes are brought into proximity of one another and merge to become one. Fusion holds promise for biotechnological innovations, for instance, for the discovery of urgently needed new antibiotics. Here, we used antibiotic-producing bacteria that can proliferate without their cell wall as a model to investigate cell-cell fusion. We found that fusion between genetically distinct cells yields heterokaryons that are viable, contain multiple selection markers, and show increased antimicrobial activity. The rate of fusion induced using physical and chemical methods was dependent on membrane fluidity, which is related to lipid composition as a function of cellular age. Finally, by using an innovative system of synthetic membrane-associated lipopeptides, we achieved targeted fusion between distinctly marked cells to further enhance fusion efficiency. These results provide a molecular handle to understand and control cell-cell fusion, which can be used in the future for the discovery of new drugs. IMPORTANCE Cell-cell fusion is instrumental in introducing different sets of genes in the same environment, which subsequently leads to diversity. There is need for new protocols to fuse cells of different types together for biotechnological applications like drug discovery. We present here wall-deficient cells as a platform for the same. We identify the fluidity of the membrane as an important characteristic for the process of fusion. We demonstrate a cell-specific approach for fusion using synthetically designed peptides yielding cells with modified antibiotic production profiles. Overall, wall-deficient cells can be a chassis for innovative metabolite production by providing an alternative method for cell-cell fusion.
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Affiliation(s)
- Shraddha Shitut
- Origins Centre, Groningen, the Netherlands
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Meng-Jie Shen
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Bart Claushuis
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Rico J. E. Derks
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Daniel Rozen
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Dennis Claessen
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Alexander Kros
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
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3
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Daudey GA, Shen M, Singhal A, van der Est P, Sevink GJA, Boyle AL, Kros A. Liposome fusion with orthogonal coiled coil peptides as fusogens: the efficacy of roleplaying peptides. Chem Sci 2021; 12:13782-13792. [PMID: 34760163 PMCID: PMC8549789 DOI: 10.1039/d0sc06635d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 09/18/2021] [Indexed: 12/18/2022] Open
Abstract
Biological membrane fusion is a highly specific and coordinated process as a multitude of vesicular fusion events proceed simultaneously in a complex environment with minimal off-target delivery. In this study, we develop a liposomal fusion model system with specific recognition using lipidated derivatives of a set of four de novo designed heterodimeric coiled coil (CC) peptide pairs. Content mixing was only obtained between liposomes functionalized with complementary peptides, demonstrating both fusogenic activity of CC peptides and the specificity of this model system. The diverse peptide fusogens revealed important relationships between the fusogenic efficacy and the peptide characteristics. The fusion efficiency increased from 20% to 70% as affinity between complementary peptides decreased, (from KF ≈ 108 to 104 M−1), and fusion efficiency also increased due to more pronounced asymmetric role-playing of membrane interacting ‘K’ peptides and homodimer-forming ‘E’ peptides. Furthermore, a new and highly fusogenic CC pair (E3/P1K) was discovered, providing an orthogonal peptide triad with the fusogenic CC pairs P2E/P2K and P3E/P3K. This E3/P1k pair was revealed, via molecular dynamics simulations, to have a shifted heptad repeat that can accommodate mismatched asparagine residues. These results will have broad implications not only for the fundamental understanding of CC design and how asparagine residues can be accommodated within the hydrophobic core, but also for drug delivery systems by revealing the necessary interplay of efficient peptide fusogens and enabling the targeted delivery of different carrier vesicles at various peptide-functionalized locations. We developed a liposomal fusion model system with specific recognition using a set of heterodimeric coiled coil peptide pairs. This study unravels important structure–fusogenic efficacy relationships of peptide fusogens.![]()
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Affiliation(s)
- Geert A Daudey
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Mengjie Shen
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Ankush Singhal
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Patrick van der Est
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - G J Agur Sevink
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Aimee L Boyle
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Alexander Kros
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
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4
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Yang J, Firdaus F, Azuar A, Khalil ZG, Marasini N, Capon RJ, Hussein WM, Toth I, Skwarczynski M. Cell-Penetrating Peptides-Based Liposomal Delivery System Enhanced Immunogenicity of Peptide-Based Vaccine against Group A Streptococcus. Vaccines (Basel) 2021; 9:499. [PMID: 34066099 PMCID: PMC8151947 DOI: 10.3390/vaccines9050499] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
Peptide-based vaccine development represents a highly promising strategy for preventing Group A Streptococcus (GAS) infection. However, these vaccines need to be administered with the help of a delivery system and/or immune adjuvant. Cell-penetrating peptides (CPPs) have been used as a powerful tool for delivering various therapeutic agents, including peptides, as they can overcome the permeability barrier of cell membranes. Here, we used CPPs to deliver our lead lipopeptide-based vaccine (LCP-1). CPPs were anchored through a spacer to LCP-1-bearing multilamellar and unilamellar liposomes and administered to Swiss outbred mice. Tat47-57 conjugated to two palmitic acids via a (Gly)6 spacer (to form a liposome-anchoring moiety) was the most efficient system for triggering immune responses when combined with multilamellar liposomes bearing LCP-1. The immunostimulatory potential of a variety of other CPPs was examined following intranasal administration in mice. Among them, LCP-1/liposomes/Tat47-57 and LCP-1/liposomes/KALA induced the highest antibody titers. The antibodies produced showed high opsonic activity against clinically isolated GAS strains D3840 and GC2 203. The use of the CPP-liposome delivery system is a promising strategy for liposome-based GAS vaccine development.
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Affiliation(s)
- Jieru Yang
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (J.Y.); (F.F.); (A.A.); (W.M.H.); (I.T.)
| | - Farrhana Firdaus
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (J.Y.); (F.F.); (A.A.); (W.M.H.); (I.T.)
| | - Armira Azuar
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (J.Y.); (F.F.); (A.A.); (W.M.H.); (I.T.)
| | - Zeinab G. Khalil
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Nirmal Marasini
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Robert J. Capon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Waleed M. Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (J.Y.); (F.F.); (A.A.); (W.M.H.); (I.T.)
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (J.Y.); (F.F.); (A.A.); (W.M.H.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (J.Y.); (F.F.); (A.A.); (W.M.H.); (I.T.)
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5
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Utterström J, Naeimipour S, Selegård R, Aili D. Coiled coil-based therapeutics and drug delivery systems. Adv Drug Deliv Rev 2021; 170:26-43. [PMID: 33378707 DOI: 10.1016/j.addr.2020.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/20/2022]
Abstract
Coiled coils are characterized by an arrangement of two or more α-helices into a superhelix and one of few protein motifs where the sequence-to-structure relationship to a large extent have been decoded and understood. The abundance of both natural and de novo designed coil coils provides a rich molecular toolbox for self-assembly of elaborate bespoke molecular architectures, nanostructures, and materials. Leveraging on the numerous possibilities to tune both affinities and preferences for polypeptide oligomerization, coiled coils offer unique possibilities to design modular and dynamic assemblies that can respond in a predictable manner to biomolecular interactions and subtle physicochemical cues. In this review, strategies to use coiled coils in design of novel therapeutics and advanced drug delivery systems are discussed. The applications of coiled coils for generating drug carriers and vaccines, and various aspects of using coiled coils for controlling and triggering drug release, and for improving drug targeting and drug uptake are described. The plethora of innovative coiled coil-based molecular systems provide new knowledge and techniques for improving efficacy of existing drugs and can facilitate development of novel therapeutic strategies.
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6
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Löffler PMG, Rabe A, Vogel S. Lipid-Modified Peptide Nucleic Acids: Synthesis and Application to Programmable Liposome Fusion. Methods Mol Biol 2021; 2105:75-96. [PMID: 32088865 DOI: 10.1007/978-1-0716-0243-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Peptide nucleic acids (PNAs) can be modified with aliphatic lipid chains and designed to be water soluble and able to spontaneously insert into phospholipid bilayers. Liposomes with 1.5% negatively charged POPG can be driven to fuse and mix their inner content volumes via functionalization with such lipidated peptide nucleic acids (LiPNAs). During fusion, only low amounts of leakage occur (<5%). We describe here the synthesis and purification of such LiPNAs using an automated peptide synthesizer and the preparation of LiPNA functionalized liposomes. Further, we describe the measurement of LiPNA-induced fusion using a fluorescence-based assay for the content mixing between a liposome population with an encapsulated self-quenching fluorescent dye (SRB) and a buffer-filled liposome population.
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Affiliation(s)
- Philipp M G Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Alexander Rabe
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark.
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7
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Akimov SA, Kondrashov OV, Zimmerberg J, Batishchev OV. Ectodomain Pulling Combines with Fusion Peptide Inserting to Provide Cooperative Fusion for Influenza Virus and HIV. Int J Mol Sci 2020; 21:ijms21155411. [PMID: 32751407 PMCID: PMC7432320 DOI: 10.3390/ijms21155411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 12/18/2022] Open
Abstract
Enveloped viruses include the most dangerous human and animal pathogens, in particular coronavirus, influenza virus, and human immunodeficiency virus (HIV). For these viruses, receptor binding and entry are accomplished by a single viral envelope protein (termed the fusion protein), the structural changes of which trigger the remodeling and merger of the viral and target cellular membranes. The number of fusion proteins required for fusion activity is still under debate, and several studies report this value to range from 1 to 9 for type I fusion proteins. Here, we consider the earliest stage of viral fusion based on the continuum theory of membrane elasticity. We demonstrate that membrane deformations induced by the oblique insertion of amphipathic fusion peptides mediate the lateral interaction of these peptides and drive them to form into a symmetric fusion rosette. The pulling force produced by the structural rearrangements of the fusion protein ectodomains gives additional torque, which deforms the membrane and additionally stabilizes the symmetric fusion rosette, thus allowing a reduction in the number of fusion peptides needed for fusion. These findings can resolve the large range of published cooperativity indices for HIV, influenza, and other type I fusion proteins.
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Affiliation(s)
- Sergey A. Akimov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia; (O.V.K.); (O.V.B.)
- Correspondence: ; Tel.: +7-495-955-4776
| | - Oleg V. Kondrashov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia; (O.V.K.); (O.V.B.)
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Oleg V. Batishchev
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia; (O.V.K.); (O.V.B.)
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8
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Lee H. Molecular Simulations of PEGylated Biomolecules, Liposomes, and Nanoparticles for Drug Delivery Applications. Pharmaceutics 2020; 12:E533. [PMID: 32531886 PMCID: PMC7355693 DOI: 10.3390/pharmaceutics12060533] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
Since the first polyethylene glycol (PEG)ylated protein was approved by the FDA in 1990, PEGylation has been successfully applied to develop drug delivery systems through experiments, but these experimental results are not always easy to interpret at the atomic level because of the limited resolution of experimental techniques. To determine the optimal size, structure, and density of PEG for drug delivery, the structure and dynamics of PEGylated drug carriers need to be understood close to the atomic scale, as can be done using molecular dynamics simulations, assuming that these simulations can be validated by successful comparisons to experiments. Starting with the development of all-atom and coarse-grained PEG models in 1990s, PEGylated drug carriers have been widely simulated. In particular, recent advances in computer performance and simulation methodologies have allowed for molecular simulations of large complexes of PEGylated drug carriers interacting with other molecules such as anticancer drugs, plasma proteins, membranes, and receptors, which makes it possible to interpret experimental observations at a nearly atomistic resolution, as well as help in the rational design of drug delivery systems for applications in nanomedicine. Here, simulation studies on the following PEGylated drug topics will be reviewed: proteins and peptides, liposomes, and nanoparticles such as dendrimers and carbon nanotubes.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin 16890, Korea
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9
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Controlled Peptide-Mediated Vesicle Fusion Assessed by Simultaneous Dual-Colour Time-Lapsed Fluorescence Microscopy. Sci Rep 2020; 10:3087. [PMID: 32080270 PMCID: PMC7033240 DOI: 10.1038/s41598-020-59926-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/31/2020] [Indexed: 12/03/2022] Open
Abstract
We have employed a model system, inspired by SNARE proteins, to facilitate membrane fusion between Giant Unilamellar Vesicles (GUVs) and Large Unilamellar Vesicles (LUVs) under physiological conditions. In this system, two synthetic lipopeptide constructs comprising the coiled-coil heterodimer-forming peptides K4, (KIAALKE)4, or E4, (EIAALEK)4, a PEG spacer of variable length, and a cholesterol moiety to anchor the peptides into the liposome membrane replace the natural SNARE proteins. GUVs are functionalized with one of the lipopeptide constructs and the fusion process is triggered by adding LUVs bearing the complementary lipopeptide. Dual-colour time lapse fluorescence microscopy was used to visualize lipid- and content-mixing. Using conventional confocal microscopy, lipid mixing was observed on the lipid bilayer of individual GUVs. In addition to lipid-mixing, content-mixing assays showed a low efficiency due to clustering of K4-functionalized LUVs on the GUVs target membranes. We showed that, through the use of the non-ionic surfactant Tween 20, content-mixing between GUVs and LUVs could be improved, meaning this system has the potential to be employed for drug delivery in biological systems.
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10
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SU YY, LI CY, LI D. Progress in Membrane Fusion and Its Application in Drug Delivery. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61202-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Löffler PMG, Ries O, Vogel S. DNA-Mediated Liposome Fusion Observed by Fluorescence Spectrometry. Methods Mol Biol 2019; 2063:101-118. [PMID: 31667766 DOI: 10.1007/978-1-0716-0138-9_9] [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: 03/12/2023]
Abstract
DNA-programmed and controlled fusion of lipid membranes have recently been optimized to reliably mix the contents between two populations of liposomes, each functionalized with complementary lipidated DNA (LiNA) oligomer. In this chapter we describe a procedure for DNA-controlled fusion of liposomes mediated by LiNAs that are designed to force bilayers into close proximity. Using a self-quenching fluorescent dye (Sulforhodamine B) to monitor both the mixing of the internal volumes and leakage of the dye into the outer volume we measure the efficiency of content mixing in the bulk population, allowing for direct comparison between different LiNA designs. By generating samples for calibration corresponding to different amounts of content mixing, the average number of fusion events per labeled liposome can be estimated.
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Affiliation(s)
- Philipp M G Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Oliver Ries
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark.
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12
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Löffler PMG, Hansen AH, Ries O, Jakobsen U, Rabe A, Sørensen KT, Glud K, Vogel S. Lipidated Polyaza Crown Ethers as Membrane Anchors for DNA-Controlled Content Mixing between Liposomes. Sci Rep 2019; 9:13856. [PMID: 31554826 PMCID: PMC6761097 DOI: 10.1038/s41598-019-49862-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/23/2019] [Indexed: 01/21/2023] Open
Abstract
The ability to manipulate and fuse nano-compartmentalized volumes addresses a demand for spatiotemporal control in the field of synthetic biology, for example in the bottom-up construction of (bio)chemical nanoreactors and for the interrogation of enzymatic reactions in confined space. Herein, we mix entrapped sub-attoliter volumes of liposomes (~135 nm diameter) via lipid bilayer fusion, facilitated by the hybridization of membrane-anchored lipidated oligonucleotides. We report on an improved synthesis of the membrane-anchor phosphoramidites that allows for a flexible choice of lipophilic moiety. Lipid-nucleic acid conjugates (LiNAs) with and without triethylene glycol spacers between anchor and the 17 nt binding sequence were synthesized and their fusogenic potential evaluated. A fluorescence-based content mixing assay was employed for kinetic monitoring of fusion of the bulk liposome populations at different temperatures. Data obtained at 50 °C indicated a quantitative conversion of the limiting liposome population into fused liposomes and an unprecedently high initial fusion rate was observed. For most conditions and designs only low leakage during fusion was observed. These results consolidate LiNA-mediated membrane fusion as a robust platform for programming compartmentalized chemical and enzymatic reactions.
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Affiliation(s)
- Philipp M G Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Anders Højgaard Hansen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Oliver Ries
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Ulla Jakobsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark.,PET & Cyclotron Unit, Department of Nuclear Medicine, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense C, Denmark
| | - Alexander Rabe
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Kristian T Sørensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Kasper Glud
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark.
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13
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Li H, Liu Q, Crielaard BJ, de Vries JW, Loznik M, Meng Z, Yang X, Göstl R, Herrmann A. Fast, Efficient, and Targeted Liposome Delivery Mediated by DNA Hybridization. Adv Healthc Mater 2019; 8:e1900389. [PMID: 31081288 DOI: 10.1002/adhm.201900389] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/26/2019] [Indexed: 12/22/2022]
Abstract
Safety and efficacy, two significant parameters in drug administration, can be improved by site-specific delivery approaches. Here a fast, efficient, and targeted liposome delivery system steered by a DNA hybridization recognition mechanism is presented. For this purpose, lipid-terminated DNA is inserted in both liposome and cell membranes by simple mixing of the components. Cellular accumulation of cargo encapsulated in the liposomal core is substantially enhanced when the DNA sequence on the cell is complementary to that on the liposome. Additionally, in mixed cell populations, liposomes discriminate targets by their complementary DNA sequences. Exposure of cells to low temperature and endocytosis inhibitors suggests a caveolae-dependent endocytosis uptake pathway. Mechanistically, hybridization between DNA strands spatially traps liposomes and cell membranes in close proximity, consequently increases the local liposome concentration, and thereby enhances cellular uptake of liposomes and their payload. This programmable delivery system might contribute to new applications in molecular biology and drug delivery.
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Affiliation(s)
- Hongyan Li
- Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- DWI – Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
| | - Qing Liu
- Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Bart J. Crielaard
- Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jan W. de Vries
- Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Mark Loznik
- DWI – Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- Institute of Technical and Macromolecular ChemistryRWTH Aachen University Worringerweg 2 52074 Aachen Germany
| | - Zhuojun Meng
- Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Xintong Yang
- Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- DWI – Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
| | - Robert Göstl
- DWI – Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
| | - Andreas Herrmann
- Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- DWI – Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- Institute of Technical and Macromolecular ChemistryRWTH Aachen University Worringerweg 2 52074 Aachen Germany
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14
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Interaction of SNARE Mimetic Peptides with Lipid bilayers: Effects of Secondary Structure, Bilayer Composition and Lipid Anchoring. Sci Rep 2019; 9:7708. [PMID: 31118479 PMCID: PMC6531448 DOI: 10.1038/s41598-019-43418-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 04/18/2019] [Indexed: 12/24/2022] Open
Abstract
The coiled-coil forming peptides 'K' enriched in lysine and 'E' enriched in glutamic acid have been used as a minimal SNARE mimetic system for membrane fusion. Here we describe atomistic molecular dynamics simulations to characterize the interactions of these peptides with lipid bilayers for two different compositions. For neutral phosphatidylcholine (PC)/phosphatidylethanolamine (PE) bilayers the peptides experience a strong repulsive barrier against adsorption, also observed in potential of mean force (PMF) profiles calculated with umbrella sampling. For peptide K, a minimum of -12 kBT in the PMF provides an upper bound for the binding free energy whereas no stable membrane bound state could be observed for peptide E. In contrast, the electrostatic interactions with negatively charged phosphatidylglycerol (PG) lipids lead to fast adsorption of both peptides at the head-water interface. Experimental data using fluorescently labeled peptides confirm the stronger binding to PG containing bilayers. Lipid anchors have little effect on the peptide-bilayer interactions or peptide structure, when the peptide also binds to the bilayer in the absence of a lipid anchor. For peptide E, which does not bind to the PC bilayer without a lipid anchor, the presence of such an anchor strengthens the electrostatic interactions between the charged side chains and the zwitterionic head-groups and leads to a stabilization of the peptide's helical fold by the membrane.
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15
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Mazur F, Chandrawati R. Peptide-Mediated Liposome Fusion as a Tool for the Detection of Matrix Metalloproteinases. ACTA ACUST UNITED AC 2019; 3:e1800330. [PMID: 32627412 DOI: 10.1002/adbi.201800330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/11/2019] [Indexed: 11/08/2022]
Abstract
Biological cells continue to inspire the development of technologies toward rapid, sensitive, and selective detection of analytes. Membrane fusion is a key biological event in living cells that involves a highly selective recognition mechanism controlled by different functional proteins. Herein, liposome-liposome fusion mediated by coiled-coil forming peptides JR2EC and JR2KC to mimic biological membrane fusion is reported. The liposome fusion event is monitored through fluorescence generation and this mechanism forms the basis of a detection assay for matrix metalloproteinases (MMPs), which are key homeostatic proteases. Using this approach, a limit of detection of 0.35 µg mL-1 MMP-7 in biological samples is obtained, and this assay does not require washing, separation, or amplification steps. The developed tool could be extended for the detection of other proteolytic enzymes of the MMP family (diagnostic or prognostic markers) and has the potential for screening of peptide libraries against a target of interest.
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Affiliation(s)
- Federico Mazur
- School of Chemical Engineering and Australian Centre for Nanomedicine (ACN), The University of New South Wales (UNSW Sydney), Sydney, NSW, 2052, Australia
| | - Rona Chandrawati
- School of Chemical Engineering and Australian Centre for Nanomedicine (ACN), The University of New South Wales (UNSW Sydney), Sydney, NSW, 2052, Australia
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16
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Daudey G, Schwieger C, Rabe M, Kros A. Influence of Membrane-Fusogen Distance on the Secondary Structure of Fusogenic Coiled Coil Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5501-5508. [PMID: 30908063 PMCID: PMC6484379 DOI: 10.1021/acs.langmuir.8b04195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Liposomal membrane fusion is an important tool to study complex biological fusion mechanisms. We use lipidated derivatives of the specific heterodimeric coiled coil pair E: (EIAALEK)3 and K: (KIAALKE)3 to study and control the fusion of liposomes. In this model system, peptides are tethered to their liposomes via a poly(ethylene glycol) (PEG) spacer and a lipid anchor. The efficiency of the fusion mechanism and function of the peptides is highly affected by the PEG-spacer length and the lipid anchor type. Here, the influence of membrane-fusogen distance on the peptide-membrane interactions and the peptide secondary structures is studied with Langmuir film balance and infrared reflection absorption spectroscopy. We found that the introduction of a spacer to monolayer-tethered peptide E changes its conformation from solvated random coils to homo-oligomers. In contrast, the described peptide-monolayer interaction of peptide K is not affected by the PEG-spacer length. Furthermore, the coexistence of different conformations when both lipopeptides E and K are present at the membrane surface is demonstrated empirically, which has many implications for the design of effective fusogenic recognition units and the field of artificial membrane fusion.
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Affiliation(s)
| | | | - Martin Rabe
- Department
of Interface Chemistry and Surface Engineering, Max-Planck-Institut für Eisenforschung GmbH, 40237 Düsseldorf, Germany
| | - Alexander Kros
- Supramolecular
and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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17
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Zheng T, Chen Y, Shi Y, Feng H. High efficiency liposome fusion induced by reducing undesired membrane peptides interaction. OPEN CHEM 2019. [DOI: 10.1515/chem-2019-0004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractA full membrane fusion model which attains both complete lipid mixing and content mixing liposomal membranes mediated by coiled-coil forming lipopeptides LPK [L-PEG12-(KIAALKE)3] and LPE [L-PEG12-(EIAALEK)3] is presented. The electrostatic effects of lipid anchored peptides on fusion efficiency was investigated. For this, the original amino acid sequence of the membrane bound LPK was varied at its ‘f’-position of the helical structure, i.e. via mutating the anionic glutamate residues by either neutral serines or cationic lysines. Both CD and fluorescence measurements showed that replacing the negatively charged glutamate did not significantly alter the peptide ability to form a coiled coil, but lipid mixing and content mixing assays showed more efficient liposome-liposome fusion resulting in almost quantitative content mixing for the lysine mutated analogue (LPKK) in conjunction with LPE. A mechanism is proposed for a fusion model triggered by membrane destabilizing effects mediated by the membrane destabilizing activety of LPK in cooperation with the electrostatic activity of LPE. This new insight may enlightens the further development of a promising nano carrier tool for biomedical applications.
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Affiliation(s)
- Tingting Zheng
- Shenzhen Key Laboratory for Drug Addiction and Medication Safety, Department of Ultrasound, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, 518036 Shenzhen, Shenzhen, China
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300RA, Leiden, The Netherlands
| | - Yun Chen
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300RA, Leiden, The Netherlands
| | - Yu Shi
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300RA, Leiden, The Netherlands
| | - Huanhuan Feng
- School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China
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18
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Agrawal P, Singh H, Srivastava HK, Singh S, Kishore G, Raghava GPS. Benchmarking of different molecular docking methods for protein-peptide docking. BMC Bioinformatics 2019; 19:426. [PMID: 30717654 PMCID: PMC7394329 DOI: 10.1186/s12859-018-2449-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/29/2018] [Indexed: 11/10/2022] Open
Abstract
Background Molecular docking studies on protein-peptide interactions are a challenging and time-consuming task because peptides are generally more flexible than proteins and tend to adopt numerous conformations. There are several benchmarking studies on protein-protein, protein-ligand and nucleic acid-ligand docking interactions. However, a series of docking methods is not rigorously validated for protein-peptide complexes in the literature. Considering the importance and wide application of peptide docking, we describe benchmarking of 6 docking methods on 133 protein-peptide complexes having peptide length between 9 to 15 residues. The performance of docking methods was evaluated using CAPRI parameters like FNAT, I-RMSD, L-RMSD. Result Firstly, we performed blind docking and evaluate the performance of the top docking pose of each method. It was observed that FRODOCK performed better than other methods with average L-RMSD of 12.46 Å. The performance of all methods improved significantly for their best docking pose and achieved highest average L-RMSD of 3.72 Å in case of FRODOCK. Similarly, we performed re-docking and evaluated the performance of the top and best docking pose of each method. We achieved the best performance in case of ZDOCK with average L-RMSD 8.60 Å and 2.88 Å for the top and best docking pose respectively. Methods were also evaluated on 40 protein-peptide complexes used in the previous benchmarking study, where peptide have length up to 5 residues. In case of best docking pose, we achieved the highest average L-RMSD of 4.45 Å and 2.09 Å for the blind docking using FRODOCK and re-docking using AutoDock Vina respectively. Conclusion The study shows that FRODOCK performed best in case of blind docking and ZDOCK in case of re-docking. There is a need to improve the ranking of docking pose generated by different methods, as the present ranking scheme is not satisfactory. To facilitate the scientific community for calculating CAPRI parameters between native and docked complexes, we developed a web-based service named PPDbench (http://webs.iiitd.edu.in/raghava/ppdbench/). Electronic supplementary material The online version of this article (10.1186/s12859-018-2449-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Piyush Agrawal
- Center for Computation Biology, Indraprastha Institute of Information Technology, Okhla Phase III, New Delhi, 110020, India.,CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Harinder Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | | | - Sandeep Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Gaurav Kishore
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Gajendra P S Raghava
- Center for Computation Biology, Indraprastha Institute of Information Technology, Okhla Phase III, New Delhi, 110020, India. .,CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India.
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19
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Koukalová A, Pokorná Š, Boyle AL, Lopez Mora N, Kros A, Hof M, Šachl R. Distinct roles of SNARE-mimicking lipopeptides during initial steps of membrane fusion. NANOSCALE 2018; 10:19064-19073. [PMID: 30288507 DOI: 10.1039/c8nr05730c] [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
A model system for membrane fusion, inspired by SNARE proteins and based on two complementary lipopeptides CPnE4 and CPnK4, has been recently developed. It consists of cholesterol (C), a poly(ethylene glycol) linker (Pn) and either a cationic peptide K4 (KIAALKE)4 or an anionic peptide E4 (EIAALEK)4. In this paper, fluorescence spectroscopy is used to decipher distinct but complementary roles of these lipopeptides during early stages of membrane fusion. Molecular evidence is provided that different distances of E4 in CPnE4 and K4 in CPnK4 from the bilayer represent an important mechanism, which enables fusion. Whereas E4 is exposed to the bulk and solely promotes membrane binding of CPnK4, K4 loops back to the lipid-water interface where it fulfills two distinct roles: it initiates bilayer contact by binding to CPnE4 containing bilayers; and it initiates fusion by modulating the bilayer properties. The interaction between CPnE4 and CPnK4 is severely down-regulated by binding of K4 to the bilayer and possible only if the lipopeptides approach each other as constituents of different bilayers. When the complementary lipopeptides are localized in the same bilayer, hetero-coiling is disabled. These data provide crucial insights as to how fusion is initiated and highlight the importance of both peptides in this process.
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Affiliation(s)
- Alena Koukalová
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, Prague, 182 23, Czech Republic.
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Peptide-Mediated Liposome Fusion: The Effect of Anchor Positioning. Int J Mol Sci 2018; 19:ijms19010211. [PMID: 29320427 PMCID: PMC5796160 DOI: 10.3390/ijms19010211] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/02/2018] [Accepted: 01/08/2018] [Indexed: 11/17/2022] Open
Abstract
A minimal model system for membrane fusion, comprising two complementary peptides dubbed "E" and "K" joined to a cholesterol anchor via a polyethyleneglycol spacer, has previously been developed in our group. This system promotes the fusion of large unilamellar vesicles and facilitates liposome-cell fusion both in vitro and in vivo. Whilst several aspects of the system have previously been investigated to provide an insight as to how fusion is facilitated, anchor positioning has not yet been considered. In this study, the effects of placing the anchor at either the N-terminus or in the center of the peptide are investigated using a combination of circular dichroism spectroscopy, dynamic light scattering, and fluorescence assays. It was discovered that anchoring the "K" peptide in the center of the sequence had no effect on its structure, its ability to interact with membranes, or its ability to promote fusion, whereas anchoring the 'E' peptide in the middle of the sequence dramatically decreases fusion efficiency. We postulate that anchoring the 'E' peptide in the middle of the sequence disrupts its ability to form homodimers with peptides on the same membrane, leading to aggregation and content leakage.
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