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Quagliarini E, Renzi S, Digiacomo L, Giulimondi F, Sartori B, Amenitsch H, Tassinari V, Masuelli L, Bei R, Cui L, Wang J, Amici A, Marchini C, Pozzi D, Caracciolo G. Microfluidic Formulation of DNA-Loaded Multicomponent Lipid Nanoparticles for Gene Delivery. Pharmaceutics 2021; 13:1292. [PMID: 34452253 PMCID: PMC8400491 DOI: 10.3390/pharmaceutics13081292] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/30/2021] [Accepted: 08/14/2021] [Indexed: 01/07/2023] Open
Abstract
In recent years, lipid nanoparticles (LNPs) have gained considerable attention in numerous research fields ranging from gene therapy to cancer immunotherapy and DNA vaccination. While some RNA-encapsulating LNP formulations passed clinical trials, DNA-loaded LNPs have been only marginally explored so far. To fulfil this gap, herein we investigated the effect of several factors influencing the microfluidic formulation and transfection behavior of DNA-loaded LNPs such as PEGylation, total flow rate (TFR), concentration and particle density at the cell surface. We show that PEGylation and post-synthesis sample concentration facilitated formulation of homogeneous and small size LNPs with high transfection efficiency and minor, if any, cytotoxicity on human Embryonic Kidney293 (HEK-293), spontaneously immortalized human keratinocytes (HaCaT), immortalized keratinocytes (N/TERT) generated from the transduction of human primary keratinocytes, and epidermoid cervical cancer (CaSki) cell lines. On the other side, increasing TFR had a detrimental effect both on the physicochemical properties and transfection properties of LNPs. Lastly, the effect of particle concentration at the cell surface on the transfection efficiency (TE) and cell viability was largely dependent on the cell line, suggesting that its case-by-case optimization would be necessary. Overall, we demonstrate that fine tuning formulation and microfluidic parameters is a vital step for the generation of highly efficient DNA-loaded LNPs.
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Affiliation(s)
- Erica Quagliarini
- Department of Chemistry, “Sapienza” University of Rome, 00185 Rome, Italy;
| | - Serena Renzi
- Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (S.R.); (L.D.); (F.G.); (V.T.)
| | - Luca Digiacomo
- Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (S.R.); (L.D.); (F.G.); (V.T.)
| | - Francesca Giulimondi
- Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (S.R.); (L.D.); (F.G.); (V.T.)
| | - Barbara Sartori
- Institute of inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria; (B.S.); (H.A.)
| | - Heinz Amenitsch
- Institute of inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria; (B.S.); (H.A.)
| | - Valentina Tassinari
- Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (S.R.); (L.D.); (F.G.); (V.T.)
| | - Laura Masuelli
- Department of Experimental Medicine, “Sapienza” University of Rome, 00185 Rome, Italy;
| | - Roberto Bei
- Department of Clinical Sciences and Translational Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Lishan Cui
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (L.C.); (J.W.); (A.A.); (C.M.)
| | - Junbiao Wang
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (L.C.); (J.W.); (A.A.); (C.M.)
| | - Augusto Amici
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (L.C.); (J.W.); (A.A.); (C.M.)
| | - Cristina Marchini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (L.C.); (J.W.); (A.A.); (C.M.)
| | - Daniela Pozzi
- Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (S.R.); (L.D.); (F.G.); (V.T.)
| | - Giulio Caracciolo
- Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (S.R.); (L.D.); (F.G.); (V.T.)
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Dargel C, Gräbitz-Bräuer F, Geisler R, Fandrich P, Hannappel Y, Porcar L, Hellweg T. Stable DOPG/Glycyrrhizin Vesicles with a Wide Range of Mixing Ratios: Structure and Stability as Seen by Scattering Experiments and Cryo-TEM. Molecules 2021; 26:molecules26164959. [PMID: 34443547 PMCID: PMC8399256 DOI: 10.3390/molecules26164959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/24/2022] Open
Abstract
Phosphatidylglycerols represent a large share of the lipids in the plasmamembrane of procaryotes. Therefore, this study investigates the role of charged lipids in the plasma membrane with respect to the interaction of the antiviral saponin glycyrrhizin with such membranes. Glycyrrhizin is a natural triterpenic-based surfactant found in licorice. Vesicles made of 1,2-dioleoyl-sn-glycero-3-phospho-rac-(1’-glycerol) (DOPG)/glycyrrhizin are characterized by small-angle scattering with neutrons and X-rays (SANS and SAXS). Small-angle scattering data are first evaluated by the model-independent modified Kratky–Porod method and afterwards fitted by a model describing the shape of small unilamellar vesicles (SUV) with an internal head-tail contrast. Complete miscibility of DOPG and glycyrrhizin was revealed even at a ratio of lipid:saponin of 1:1. Additional information about the chain-chain correlation distance of the lipid/saponin mixtures in the SUV structures is obtained from wide-angle X-ray scattering (WAXS).
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Affiliation(s)
- Carina Dargel
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (C.D.); (F.G.-B.); (R.G.); (P.F.); (Y.H.)
| | - Friederike Gräbitz-Bräuer
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (C.D.); (F.G.-B.); (R.G.); (P.F.); (Y.H.)
| | - Ramsia Geisler
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (C.D.); (F.G.-B.); (R.G.); (P.F.); (Y.H.)
| | - Pascal Fandrich
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (C.D.); (F.G.-B.); (R.G.); (P.F.); (Y.H.)
| | - Yvonne Hannappel
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (C.D.); (F.G.-B.); (R.G.); (P.F.); (Y.H.)
| | - Lionel Porcar
- Institut Laue-Langevin, 71 Avenue des Martyrs CS 20156, CEDEX 9, 38042 Grenoble, France;
| | - Thomas Hellweg
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (C.D.); (F.G.-B.); (R.G.); (P.F.); (Y.H.)
- Correspondence: ; Tel.: +49-0521-106-2055
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Ionic environment, thickness and line tension as determinants of phase separation in whole Purified Myelin Membranes monolayers. Colloids Surf B Biointerfaces 2021; 207:112027. [PMID: 34388613 DOI: 10.1016/j.colsurfb.2021.112027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/14/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
Purified myelin membranes (PMM) were spread as monomolecular films at the air/aqueous solution interface, and visualized by Brewster Angle Microscopy (BAM) at different lateral pressures (π) on three specific aqueous solutions: absence of salts, physiological conditions and presence of calcium. Coexistence of Liquid-Expanded (LE) and Liquid Ordered (LO) phases persisted up to collapse in the presence of salts, whereas monolayers became homogeneous at π ≥ 35-40 mN/m when salts are absent. This PMM phase-mixing behavior in monolayers is similar to the previously reported behavior of PMM multilamellar vesicles. Reflectivities (Rp) of p-polarized light from both phases were assessed throughout the whole π -range, and film thicknesses (t) were calculated from the Rp values and measured film refractive indices (n). The LO phase was found to be more reflective and thicker than the LE phase at π ≤ 15 mN/m, but less reflective and thinner at higher π. We also determined the line tension (λ) of PMM monolayers at the domain boundaries from the rate of domain shape relaxation, which turned out to be of the order of picoNewtons (pN) and decreased as π increased. A correlation between λ and thickness differences (Δt) was found, suggesting that Δt is a molecular determinant for λ in PMM monolayers. Both λ and Δt were found to increase markedly when calcium was present in the subphase. This result corroborates the concept of divalent cations as a stabilizing factor for phase separation, in line with earlier studies on this mixture forming multilamellar membrane arrangements.
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Frewein MPK, Doktorova M, Heberle FA, Scott HL, Semeraro EF, Porcar L, Pabst G. Structure and Interdigitation of Chain-Asymmetric Phosphatidylcholines and Milk Sphingomyelin in the Fluid Phase. Symmetry (Basel) 2021; 13:1441. [PMID: 35530371 PMCID: PMC9075682 DOI: 10.3390/sym13081441] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We addressed the frequent occurrence of mixed-chain lipids in biological membranes and their impact on membrane structure by studying several chain-asymmetric phosphatidylcholines and the highly asymmetric milk sphingomyelin. Specifically, we report trans-membrane structures of the corresponding fluid lamellar phases using small-angle X-ray and neutron scattering, which were jointly analyzed in terms of a membrane composition-specific model, including a headgroup hydration shell. Focusing on terminal methyl groups at the bilayer center, we found a linear relation between hydrocarbon chain length mismatch and the methyl-overlap for phosphatidylcholines, and a non-negligible impact of the glycerol backbone-tilting, letting the sn1-chain penetrate deeper into the opposing leaflet by half a CH2 group. That is, penetration-depth differences due to the ester-linked hydrocarbons at the glycerol backbone, previously reported for gel phase structures, also extend to the more relevant physiological fluid phase, but are significantly reduced. Moreover, milk sphingomyelin was found to follow the same linear relationship suggesting a similar tilt of the sphingosine backbone. Complementarily performed molecular dynamics simulations revealed that there is always a part of the lipid tails bending back, even if there is a high interdigitation with the opposing chains. The extent of this back-bending was similar to that in chain symmetric bilayers. For both cases of adaptation to chain length mismatch, chain-asymmetry has a large impact on hydrocarbon chain ordering, inducing disorder in the longer of the two hydrocarbons.
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Affiliation(s)
- Moritz P. K. Frewein
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
- Institut Laue-Langevin, 38043 Grenoble, France
- BioTechMed Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Frederick A. Heberle
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Haden L. Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Enrico F. Semeraro
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
- BioTechMed Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | | | - Georg Pabst
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
- BioTechMed Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
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55
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Freire RV, Pillco-Valencia Y, da Hora GC, Ramstedt M, Sandblad L, Soares TA, Salentinig S. Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles: Combining in silico tools and experimental methods. J Colloid Interface Sci 2021; 596:352-363. [DOI: 10.1016/j.jcis.2021.03.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 01/21/2023]
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Calcium mediated DNA binding in non-lamellar structures formed by DOPG/glycerol monooleate. Chem Phys Lipids 2021; 239:105118. [PMID: 34280362 DOI: 10.1016/j.chemphyslip.2021.105118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/28/2021] [Accepted: 07/14/2021] [Indexed: 11/21/2022]
Abstract
In order to test an encapsulation method of short fragmented DNA (∼ 20-300 bp), we study the solubilisation in 150 mM solution of NaCl of a cubic phase formed by glycerol monooleate (GMO) with negatively charged dioleoylphosphatidylglycerol (DOPG) up to the level of unilamellar vesicles and, subsequently, the restoration of the cubic phase using Ca2+ cations. We performed small angle X-ray and neutron scattering (SAXS and SANS) to follow structural changes in DOPG/GMO mixtures induced by increasing DOPG content. The cubic phase (Pn3m space group) is preserved up to ∼ 11 mol% of DOPG in DOPG/GMO. Above 20 mol%, the SANS curves are typical of unilamellar vesicles. The thickness of the DOPG/GMO lipid bilayer (dL) decreases slightly with increasing fraction of DOPG. The addition of 15 mM of CaCl2 solution shields the electrostatic repulsions of DOPG molecules, increases slightly dL and restores the cubic structures in the mixtures up to ∼ 37 mol% of DOPG. Zeta potential shows negative surface charge. The analysis of the data provides the radius of the water nano-channels of the formed non-lamellar structures. We discuss their dimensions with respect to DNA binding. In addition, Ca2+ mediates DNA - DOPG/GMO binding. The formed hexagonal phase, HII, binds less of DNA in comparison with cubic phases (∼ 6 wt% and ∼ 20 wt% of the total amount, respectively). The studied system can be utilized as anionic QII delivery vector for genetic material.
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Lira RB, Leomil FSC, Melo RJ, Riske KA, Dimova R. To Close or to Collapse: The Role of Charges on Membrane Stability upon Pore Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004068. [PMID: 34105299 PMCID: PMC8188222 DOI: 10.1002/advs.202004068] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/14/2020] [Indexed: 05/28/2023]
Abstract
Resealing of membrane pores is crucial for cell survival. Membrane surface charge and medium composition are studied as defining regulators of membrane stability. Pores are generated by electric field or detergents. Giant vesicles composed of zwitterionic and negatively charged lipids mixed at varying ratios are subjected to a strong electric pulse. Interestingly, charged vesicles appear prone to catastrophic collapse transforming them into tubular structures. The spectrum of destabilization responses includes the generation of long-living submicroscopic pores and partial vesicle bursting. The origin of these phenomena is related to the membrane edge tension, which governs pore closure. This edge tension significantly decreases as a function of the fraction of charged lipids. Destabilization of charged vesicles upon pore formation is universal-it is also observed with other poration stimuli. Disruption propensity is enhanced for membranes made of lipids with higher degree of unsaturation. It can be reversed by screening membrane charge in the presence of calcium ions. The observed findings in light of theories of stability and curvature generation are interpreted and mechanisms acting in cells to prevent total membrane collapse upon poration are discussed. Enhanced membrane stability is crucial for the success of electroporation-based technologies for cancer treatment and gene transfer.
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Affiliation(s)
- Rafael B. Lira
- Departamento de BiofísicaUniversidade Federal de São PauloSão Paulo04039‐032Brazil
- Department of Theory and BiosystemsMax Planck Institute of Colloids and InterfacesPotsdam14424Germany
- Present address:
Moleculaire BiofysicaZernike InstituutRijksuniversiteitGroningen9747 AGThe Netherlands
| | | | - Renan J. Melo
- Instituto de FísicaUniversidade de São PauloSão Paulo05508‐090Brazil
| | - Karin A. Riske
- Departamento de BiofísicaUniversidade Federal de São PauloSão Paulo04039‐032Brazil
| | - Rumiana Dimova
- Department of Theory and BiosystemsMax Planck Institute of Colloids and InterfacesPotsdam14424Germany
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Li M, Sun W, Tyurin VA, DeLucia M, Ahn J, Kagan VE, van der Wel PCA. Activation of Cytochrome C Peroxidase Function Through Coordinated Foldon Loop Dynamics upon Interaction with Anionic Lipids. J Mol Biol 2021; 433:167057. [PMID: 34033821 DOI: 10.1016/j.jmb.2021.167057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Cardiolipin (CL) is a mitochondrial anionic lipid that plays important roles in the regulation and signaling of mitochondrial apoptosis. CL peroxidation catalyzed by the assembly of CL-cytochrome c (cyt c) complexes at the inner mitochondrial membrane is a critical checkpoint. The structural changes in the protein, associated with peroxidase activation by CL and different anionic lipids, are not known at a molecular level. To better understand these peripheral protein-lipid interactions, we compare how phosphatidylglycerol (PG) and CL lipids trigger cyt c peroxidase activation, and correlate functional differences to structural and motional changes in membrane-associated cyt c. Structural and motional studies of the bound protein are enabled by magic angle spinning solid state NMR spectroscopy, while lipid peroxidase activity is assayed by mass spectrometry. PG binding results in a surface-bound state that preserves a nativelike fold, which nonetheless allows for significant peroxidase activity, though at a lower level than binding its native substrate CL. Lipid-specific differences in peroxidase activation are found to correlate to corresponding differences in lipid-induced protein mobility, affecting specific protein segments. The dynamics of omega loops C and D are upregulated by CL binding, in a way that is remarkably controlled by the protein:lipid stoichiometry. In contrast to complete chemical denaturation, membrane-induced protein destabilization reflects a destabilization of select cyt c foldons, while the energetically most stable helices are preserved. Our studies illuminate the interplay of protein and lipid dynamics in the creation of lipid peroxidase-active proteolipid complexes implicated in early stages of mitochondrial apoptosis.
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Affiliation(s)
- Mingyue Li
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wanyang Sun
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Maria DeLucia
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Institute for Regenerative Medicine, IM Sechenov, Moscow State Medical University, Moscow 119146, Russian Federation
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
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Häffner SM, Parra-Ortiz E, Browning KL, Jørgensen E, Skoda MWA, Montis C, Li X, Berti D, Zhao D, Malmsten M. Membrane Interactions of Virus-like Mesoporous Silica Nanoparticles. ACS NANO 2021; 15:6787-6800. [PMID: 33724786 DOI: 10.1021/acsnano.0c10378] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In the present study, we investigated lipid membrane interactions of silica nanoparticles as carriers for the antimicrobial peptide LL-37 (LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES). In doing so, smooth mesoporous nanoparticles were compared to virus-like mesoporous nanoparticles, characterized by a "spiky" external surface, as well as to nonporous silica nanoparticles. For this, we employed a combination of neutron reflectometry, ellipsometry, dynamic light scattering, and ζ-potential measurements for studies of bacteria-mimicking bilayers formed by palmitoyloleoylphosphatidylcholine/palmitoyloleoylphosphatidylglycerol. The results show that nanoparticle topography strongly influences membrane binding and destabilization. We found that virus-like particles are able to destabilize such lipid membranes, whereas the corresponding smooth silica nanoparticles are not. This effect of particle spikes becomes further accentuated after loading of such particles with LL-37. Thus, peptide-loaded virus-like nanoparticles displayed more pronounced membrane disruption than either peptide-loaded smooth nanoparticles or free LL-37. The structural basis of this was clarified by neutron reflectometry, demonstrating that the virus-like nanoparticles induce trans-membrane defects and promote incorporation of LL-37 throughout both bilayer leaflets. The relevance of such effects of particle spikes for bacterial membrane rupture was further demonstrated by confocal microscopy and live/dead assays on Escherichia coli bacteria. Taken together, these findings demonstrate that topography influences the interaction of nanoparticles with bacteria-mimicking lipid bilayers, both in the absence and presence of antimicrobial peptides, as well as with bacteria. The results also identify virus-like mesoporous nanoparticles as being of interest in the design of nanoparticles as delivery systems for antimicrobial peptides.
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Affiliation(s)
| | - Elisa Parra-Ortiz
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Kathryn L Browning
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Elin Jørgensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Maximilian W A Skoda
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell, Oxfordshire OX11 0QX, United Kingdom
| | - Costanza Montis
- CSGI and Department of Chemistry "Ugo Schiff″, University of Florence, IT-50019 Sesto Fiorentino, Italy
| | - Xiaomin Li
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, People's Republic of China
| | - Debora Berti
- CSGI and Department of Chemistry "Ugo Schiff″, University of Florence, IT-50019 Sesto Fiorentino, Italy
| | - Dongyuan Zhao
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, People's Republic of China
| | - Martin Malmsten
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Department of Physical Chemistry 1, University of Lund, SE-22100 Lund, Sweden
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Mink C, Strandberg E, Wadhwani P, Melo MN, Reichert J, Wacker I, Castanho MARB, Ulrich AS. Overlapping Properties of the Short Membrane-Active Peptide BP100 With (i) Polycationic TAT and (ii) α-helical Magainin Family Peptides. Front Cell Infect Microbiol 2021; 11:609542. [PMID: 33981626 PMCID: PMC8107365 DOI: 10.3389/fcimb.2021.609542] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/09/2021] [Indexed: 01/04/2023] Open
Abstract
BP100 is a short, designer-made membrane-active peptide with multiple functionalities: antimicrobial, cell-penetrating, and fusogenic. Consisting of five lysines and 6 hydrophobic residues, BP100 was shown to bind to lipid bilayers as an amphipathic α-helix, but its mechanism of action remains unclear. With these features, BP100 embodies the characteristics of two distinctly different classes of membrane-active peptides, which have been studied in detail and where the mechanism of action is better understood. On the one hand, its amphiphilic helical structure is similar to the pore forming magainin family of antimicrobial peptides, though BP100 is much too short to span the membrane. On the other hand, its length and high charge density are reminiscent of the HIV-TAT family of cell penetrating peptides, for which inverted micelles have been postulated as translocation intermediates, amongst other mechanisms. Assays were performed to test the antimicrobial and hemolytic activity, the induced leakage and fusion of lipid vesicles, and cell uptake. From these results the functional profiles of BP100, HIV-TAT, and the magainin-like peptides magainin 2, PGLa, MSI-103, and MAP were determined and compared. It is observed that the activity of BP100 resembles most closely the much longer amphipathic α-helical magainin-like peptides, with high antimicrobial activity along with considerable fusogenic and hemolytic effects. In contrast, HIV-TAT shows almost no antimicrobial, fusogenic, or hemolytic effects. We conclude that the amphipathic helix of BP100 has a similar membrane-based activity as magainin-like peptides and may have a similar mechanism of action.
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Affiliation(s)
- Christian Mink
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), KIT, Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), KIT, Karlsruhe, Germany
| | - Manuel N Melo
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | - Irene Wacker
- Cryo EM, Centre for Advanced Materials, Universität Heidelberg, Heidelberg, Germany
| | - Miguel A R B Castanho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Anne S Ulrich
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Biological Interfaces (IBG-2), KIT, Karlsruhe, Germany
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61
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Guo R, Sumner J, Qian S. Structure of Diisobutylene Maleic Acid Copolymer (DIBMA) and Its Lipid Particle as a “Stealth” Membrane-Mimetic for Membrane Protein Research. ACS APPLIED BIO MATERIALS 2021; 4:4760-4768. [DOI: 10.1021/acsabm.0c01626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Rong Guo
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Grinnell College, Grinnell, Iowa 50112, United States
| | - Jacob Sumner
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Yu Y, Krämer A, Venable RM, Brooks BR, Klauda JB, Pastor RW. CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids. J Chem Theory Comput 2021; 17:1581-1595. [PMID: 33620194 PMCID: PMC8130185 DOI: 10.1021/acs.jctc.0c01327] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Long-range Lennard-Jones (LJ) interactions have been incorporated into the CHARMM36 (C36) lipid force field (FF) using the LJ particle-mesh Ewald (LJ-PME) method in order to remove the inconsistency of bilayer and monolayer properties arising from the exclusion of long-range dispersion [Yu, Y.; Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. J. Chem. Theory Comput. 2021, 10.1021/acs.jctc.0c01326. (preceding article in this issue)]. The new FF is denoted C36/LJ-PME. While the first optimization was based on three phosphatidylcholines (PCs), this work extends the validation and parametrization to more lipids including PC, phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and ether lipids. The agreement with experimental structure data is excellent for PC, PE, and ether lipids. C36/LJ-PME also compares favorably with scattering data of PG bilayers but less so with NMR deuterium order parameters of 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DMPG) at 303.15 K, indicating a need for future optimization regarding PG-specific parameters. Frequency dependence of NMR T1 spin-lattice relaxation times is well-described by C36/LJ-PME, and the overall agreement with experiment is comparable to C36. Lipid diffusion is slower than C36 due to the added long-range dispersion causing a higher viscosity, although it is still too fast compared to experiment after correction for periodic boundary conditions. When using a 10 Å real-space cutoff, the simulation speed of C36/LJ-PME is roughly equal to C36. While more lipids will be incorporated into the FF in the future, C36/LJ-PME can be readily used for common lipids and extends the capability of the CHARMM FF by supporting monolayers and eliminating the cutoff dependence.
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Affiliation(s)
- Yalun Yu
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Andreas Krämer
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jeffery B Klauda
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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63
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Malekkhaiat Häffner S, Parra-Ortiz E, Skoda MWA, Saerbeck T, Browning KL, Malmsten M. Composition effects on photooxidative membrane destabilization by TiO 2 nanoparticles. J Colloid Interface Sci 2021; 584:19-33. [PMID: 33039680 DOI: 10.1016/j.jcis.2020.09.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 11/30/2022]
Abstract
Membrane interactions and photooxidative membrane destabilization of titanium dioxide (TiO2) nanoparticles were investigated, focusing on the effects of membrane composition, notably phospholipid headgroup charge and presence of cholesterol. For this, we employed a battery of state-of-the-art methods for studies of bilayers formed by zwitterionic palmitoyloleoylphosphatidylcholine (POPC) containing also polyunsaturated palmitoylarachidonoylphosphocholine (PAPC), as well as its mixtures with anionic palmitoyloleoylphosphatidylglycerol (POPG) and cholesterol. It was found that the TiO2 nanoparticles display close to zero charge at pH 7.4, resulting in aggregation. At pH 3.4, in contrast, the 6 nm TiO2 nanoparticles are well dispersed due to a strongly positive ζ-potential. Mirroring this pH dependence, TiO2 nanoparticles were observed to bind to negatively charged lipid bilayers at pH 3.4, but much less so at pH 7.4. While nanoparticle binding has some destabilizing effect alone, illumination with ultraviolet (UV) light accentuates membrane destabilization, a result of oxidative stress caused by generated reactive oxygen species (ROS). Neutron reflectivity (NR), quartz crystal microbalance (QCM), and small-angle X-ray scattering (SAXS) results all demonstrate that membrane composition strongly influences membrane interactions and photooxidative destabilization of lipid bilayers. In particular, the presence of anionic POPG makes the bilayers more sensitive to oxidative destabilization, whereas a stabilizing effect was observed in the presence of cholesterol. Also, structural aspects of peroxidation were found to depend strongly on membrane composition, notably the presence of anionic phospholipids. The results show that membrane interactions and UV-induced ROS generation act in concert and need to be considered together to understand effects of lipid membrane composition on UV-triggered oxidative destabilization by TiO2 nanoparticles, e.g., in the context of oxidative damage of bacteria and cells.
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Affiliation(s)
| | - E Parra-Ortiz
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - M W A Skoda
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell, Oxfordshire OX11 OQX, UK
| | - T Saerbeck
- Institut Laue-Langevin, CS 20156, 38042 Grenoble Cedex 9, France
| | - K L Browning
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - M Malmsten
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark; Department of Physical Chemistry 1, University of Lund, SE-22100 Lund, Sweden
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64
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Pluhackova K, Horner A. Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity. BMC Biol 2021; 19:4. [PMID: 33441107 PMCID: PMC7807449 DOI: 10.1186/s12915-020-00936-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Lipid-protein interactions stabilize protein oligomers, shape their structure, and modulate their function. Whereas in vitro experiments already account for the functional importance of lipids by using natural lipid extracts, in silico methods lack behind by embedding proteins in single component lipid bilayers. However, to accurately complement in vitro experiments with molecular details at very high spatio-temporal resolution, molecular dynamics simulations have to be performed in natural(-like) lipid environments. RESULTS To enable more accurate MD simulations, we have prepared four membrane models of E. coli polar lipid extract, a typical model organism, each at all-atom (CHARMM36) and coarse-grained (Martini3) representations. These models contain all main lipid headgroup types of the E. coli inner membrane, i.e., phosphatidylethanolamines, phosphatidylglycerols, and cardiolipins, symmetrically distributed between the membrane leaflets. The lipid tail (un)saturation and propanylation stereochemistry represent the bacterial lipid tail composition of E. coli grown at 37∘C until 3/4 of the log growth phase. The comparison of the Simple three lipid component models to the complex 14-lipid component model Avanti over a broad range of physiologically relevant temperatures revealed that the balance of lipid tail unsaturation and propanylation in different positions and inclusion of lipid tails of various length maintain realistic values for lipid mobility, membrane area compressibility, lipid ordering, lipid volume and area, and the bilayer thickness. The only Simple model that was able to satisfactory reproduce most of the structural properties of the complex Avanti model showed worse agreement of the activation energy of basal water permeation with the here performed measurements. The Martini3 models reflect extremely well both experimental and atomistic behavior of the E. coli polar lipid extract membranes. Aquaporin-1 embedded in our native(-like) membranes causes partial lipid ordering and membrane thinning in its vicinity. Moreover, aquaporin-1 attracts and temporarily binds negatively charged lipids, mainly cardiolipins, with a distinct cardiolipin binding site in the crevice at the contact site between two monomers, most probably stabilizing the tetrameric protein assembly. CONCLUSIONS The here prepared and validated membrane models of E. coli polar lipids extract revealed that lipid tail complexity, in terms of double bond and cyclopropane location and varying lipid tail length, is key to stabilize membrane properties over a broad temperature range. In addition, they build a solid basis for manifold future simulation studies on more realistic lipid membranes bridging the gap between simulations and experiments.
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Affiliation(s)
- Kristyna Pluhackova
- Department of Biosystems Science and Engineering, Eidgenössiche Technische Hochschule (ETH) Zürich, Mattenstr. 26, Basel, 4058, Switzerland.
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
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Qian S, Sharma VK, Clifton LA. Understanding the Structure and Dynamics of Complex Biomembrane Interactions by Neutron Scattering Techniques. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:15189-15211. [PMID: 33300335 DOI: 10.1021/acs.langmuir.0c02516] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The membrane is one of the key structural materials of biology at the cellular level. Composed predominantly of a bilayer of lipids with embedded and bound proteins, it defines the boundaries of the cell and many organelles essential to life and therefore is involved in almost all biological processes. Membrane-specific interactions, such as drug binding to a membrane receptor or the interactions of an antimicrobial compound with the lipid matrix of a pathogen membrane, are of interest across the scientific disciplines. Herein we present a review, aimed at nonexperts, of the major neutron scattering techniques used in membrane studies: small-angle neutron scattering, neutron membrane diffraction, neutron reflectometry, quasielastic neutron scattering, and neutron spin echo. Neutron scattering techniques are well suited to studying biological membranes. The nondestructive nature of cold neutrons means that samples can be measured for long periods without fear of beam damage from ultraviolet, electron, or X-ray radiation, and neutron beams are highly penetrating, thus offering flexibility in samples and sample environments. Most important is the strong difference in neutron scattering lengths between the two most abundant forms of hydrogen, protium and deuterium. Changing the relative amounts of protium/deuterium in a sample allows the production of a series of neutron scattering data sets, enabling the observation of differing components within complex membrane architectures. This approach can be as simple as using the naturally occurring neutron contrast between different biomolecules to study components in a complex by changing the solution H2O/D2O ratio or as complex as selectively labeling individual components with hydrogen isotopes. This review presents an overview of each experimental technique with the neutron instrument configuration, related sample preparation and sample environment, and data analysis, highlighted by a special emphasis on using prominent neutron contrast to understand structure and dynamics. This review gives researchers a practical introduction to the often enigmatic suite of neutron beamlines, thereby lowering the barrier to taking advantage of these large-facility techniques to achieve new understandings of membranes and their interactions with other molecules.
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Affiliation(s)
- Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Veerendra Kumar Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Luke A Clifton
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, U.K. OX11 0QX
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66
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Antosiewicz JM, Długosz M. Constant-pH Brownian Dynamics Simulations of a Protein near a Charged Surface. ACS OMEGA 2020; 5:30282-30298. [PMID: 33251463 PMCID: PMC7689933 DOI: 10.1021/acsomega.0c04817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/04/2020] [Indexed: 05/04/2023]
Abstract
We have developed a rigid-body Brownian dynamics algorithm that allows for simulations of a globular protein suspended in an ionic solution confined by a charged planar boundary, with an explicit treatment of pH-dependent protein protonation equilibria and their couplings to the electrostatic potential of the plane. Electrostatic interactions are described within a framework of the continuum Poisson-Boltzmann model, whereas protein-plane hydrodynamic interactions are evaluated based on analytical expressions for the position- and orientation-dependent near-wall friction tensor of a spheroid. The algorithm was applied to simulate near-surface diffusion of lysozyme in solutions having pH in the range 4-10 and ionic strengths of 10 and 150 mM. As a reference, we performed Brownian dynamics simulations in which the protein is assigned a fixed, most probable protonation state, appropriate for given solution conditions and unaffected by the presence of the charged plane, and Brownian dynamics simulations in which the protein probes possible protonation states with the pH-dependent probability, but these variations are not coupled to the electric field generated by the boundary. We show that electrostatic interactions with the negatively charged plane substantially modify probabilities of different protonation states of lysozyme and shift protonation equilibria of both acidic and basic amino acid side chains toward higher pH values. Consequently, equilibrium energy distributions, equilibrium position-orientation distributions, and functions that characterize rotational dynamics, which for a protein with multiple ionization sites, such as lysozyme, in the presence of a charged obstacle are pH-dependent, are significantly affected by the approach taken to incorporate the solution pH into simulations.
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67
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Faizi HA, Reeves CJ, Georgiev VN, Vlahovska PM, Dimova R. Fluctuation spectroscopy of giant unilamellar vesicles using confocal and phase contrast microscopy. SOFT MATTER 2020; 16:8996-9001. [PMID: 32966528 DOI: 10.1039/d0sm00943a] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A widely used method to measure the bending rigidity of bilayer membranes is fluctuation spectroscopy, which analyses the thermally-driven membrane undulations of giant unilamellar vesicles recorded with either phase-contrast or confocal microscopy. Here, we analyze the fluctuations of the same vesicle using both techniques and obtain consistent values for the bending modulus. We discuss the factors that may lead to discrepancies.
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Affiliation(s)
- Hammad A Faizi
- Department of Mechanical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, USA. and Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany.
| | - Cody J Reeves
- Department of Engineering Sciences and Applied Mathematics, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, USA
| | - Vasil N Georgiev
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany.
| | - Petia M Vlahovska
- Department of Mechanical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, USA. and Department of Engineering Sciences and Applied Mathematics, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, USA
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany.
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68
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Nielsen JE, König N, Yang S, Skoda MWA, Maestro A, Dong H, Cárdenas M, Lund R. Lipid membrane interactions of self-assembling antimicrobial nanofibers: effect of PEGylation. RSC Adv 2020; 10:35329-35340. [PMID: 35515685 PMCID: PMC9056946 DOI: 10.1039/d0ra07679a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/11/2020] [Indexed: 12/18/2022] Open
Abstract
Supramolecular assembly and PEGylation (attachment of a polyethylene glycol polymer chain) of peptides can be an effective strategy to develop antimicrobial peptides with increased stability, antimicrobial efficacy and hemocompatibility. However, how the self-assembly properties and PEGylation affect their lipid membrane interaction is still an unanswered question. In this work, we use state-of-the-art small angle X-ray and neutron scattering (SAXS/SANS) together with neutron reflectometry (NR) to study the membrane interaction of a series of multidomain peptides, with and without PEGylation, known to self-assemble into nanofibers. Our approach allows us to study both how the structure of the peptide and the membrane are affected by the peptide-lipid interactions. When comparing self-assembled peptides with monomeric peptides that are not able to undergo assembly due to shorter chain length, we found that the nanofibers interact more strongly with the membrane. They were found to insert into the core of the membrane as well as to absorb as intact fibres on the surface. Based on the presented results, PEGylation of the multidomain peptides leads to a slight net decrease in the membrane interaction, while the distribution of the peptide at the interface is similar to the non-PEGylated peptides. Based on the structural information, we showed that nanofibers were partially disrupted upon interaction with phospholipid membranes. This is in contrast with the considerable physical stability of the peptide in solution, which is desirable for an extended in vivo circulation time.
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Affiliation(s)
| | - Nico König
- Department of Chemistry, University of Oslo 0315 Oslo Norway .,Jülich Centre for Neutron Science (JCNS) and Institute for Complex Systems (ICS), Forschungszentrum Jülich GmbH 52425 Jülich Germany
| | - Su Yang
- Department of Chemistry & Biochemistry, The University of Texas at Arlington Arlington Texas 76019 USA
| | - Maximilian W A Skoda
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory Harwell Science and Innovation Campus, Didco Oxfordshire OX11 OQX UK
| | | | - He Dong
- Department of Chemistry & Biochemistry, The University of Texas at Arlington Arlington Texas 76019 USA
| | - Marité Cárdenas
- Biofilms Research Center for Biointerfaces, Department of Biomedical Science, Health and Society, Malmö University 20506 Malmö Sweden
| | - Reidar Lund
- Department of Chemistry, University of Oslo 0315 Oslo Norway
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69
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Yu Y, Klauda JB. Update of the CHARMM36 United Atom Chain Model for Hydrocarbons and Phospholipids. J Phys Chem B 2020; 124:6797-6812. [PMID: 32639155 DOI: 10.1021/acs.jpcb.0c04795] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accurate lipid force field (FF) parameters used in molecular dynamics (MD) simulations are crucial for understanding the properties of lipid-containing systems and biological processes related to lipids. The last update of the CHARMM36 united atom chain model (C36UA) was in 2013 [Lee, S. J. Phys. Chem. B 2014, 118, 547 556]; it utilized CHARMM36 (C36) lipid FF parameters for headgroups and OPLS-UA Lennard-Jones (LJ) parameters for tails. Simulations with the FF were able to reproduce many experimental observables of lipid bilayers accurately, but to be more applicable for a wide range of lipids, additional FF parameter optimization was needed. In this work, we present an update of the model, named C36UAr. The parameterization included the LJ parameters for hydrocarbons and related dihedrals. Bulk liquid properties (density, heat of vaporization, isothermal compressibility, and diffusion constant) of model compounds were used as targets for the LJ parameter fitting, and dihedrals were fit to either quantum mechanical (QM) or potential of mean force (PMF) calculations using C36. Thermodynamic reweighting was used to further improve the parameters. Bilayer simulations of various lipid headgroups (phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol) and tails (saturated, monounsaturated, and polyunsaturated) were performed to validate the model, and significant improvements were seen in bilayer properties, including surface area, membrane thicknesses, NMR deuterium order parameters, and density profiles. C36UAr was also compared to the hydrogen mass repartitioning (HMR) method. The high accuracy and competitive efficiency shown in this study make C36UAr one of the best choices for studies of membrane structure and membrane-associated proteins.
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70
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Doktorova M, Kučerka N, Kinnun JJ, Pan J, Marquardt D, Scott HL, Venable RM, Pastor RW, Wassall SR, Katsaras J, Heberle FA. Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data. J Phys Chem B 2020; 124:5186-5200. [PMID: 32468822 DOI: 10.1021/acs.jpcb.0c03389] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å2, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å2 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.
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Affiliation(s)
- Milka Doktorova
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.,Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, 814 99 Bratislava, Slovakia
| | - Jacob J Kinnun
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Haden L Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Stephen R Wassall
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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71
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Gao Y, Lee J, Widmalm G, Im W. Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Enterobacterial Common Antigen. J Phys Chem B 2020; 124:5948-5956. [DOI: 10.1021/acs.jpcb.0c03353] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ya Gao
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
- Department of Biological Sciences, Department of Chemistry, and Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jumin Lee
- Department of Biological Sciences, Department of Chemistry, and Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Wonpil Im
- Department of Biological Sciences, Department of Chemistry, and Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
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72
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Strandberg E, Bentz D, Wadhwani P, Bürck J, Ulrich AS. Terminal charges modulate the pore forming activity of cationic amphipathic helices. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183243. [DOI: 10.1016/j.bbamem.2020.183243] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/14/2020] [Accepted: 02/18/2020] [Indexed: 11/15/2022]
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73
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Membrane interactions of antimicrobial peptide-loaded microgels. J Colloid Interface Sci 2020; 562:322-332. [DOI: 10.1016/j.jcis.2019.12.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 12/16/2022]
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74
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Marquardt D, Heberle FA, Pan J, Cheng X, Pabst G, Harroun TA, Kučerka N, Katsaras J. The structures of polyunsaturated lipid bilayers by joint refinement of neutron and X-ray scattering data. Chem Phys Lipids 2020; 229:104892. [PMID: 32061581 DOI: 10.1016/j.chemphyslip.2020.104892] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/18/2020] [Accepted: 02/10/2020] [Indexed: 11/29/2022]
Abstract
We present the detailed structural analysis of polyunsaturated fatty acid-containing phospholipids namely, 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC) and 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC). A newly developed molecular dynamics (MD) simulation parsing scheme for lipids containing fatty acids with multiple double bonds was implemented into the scattering density profile (SDP) model to simultaneously refine differently contrasted neutron and X-ray scattering data. SDP analyses of scattering data at 30 °C yielded lipid areas of 71.1 Å2 and 70.4 Å2 for PDPC and SDPC bilayers, respectively, and a model free analysis of PDPC at 30 °C resulted in a lipid area of 72 Å2. In addition to bilayer structural parameters, using area-constrained MD simulations we determined the area compressibility modulus, KA, to be 246.4 mN/m, a value similar to other neutral phospholipids.
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Affiliation(s)
- Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada; Department of Physics, University of Windsor, Windsor, ON, Canada.
| | | | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL USA
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, OH, USA
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, 8010 Graz, Austria
| | - Thad A Harroun
- Department of Physics, Brock University, St. Catharines, ON, Canada
| | - Norbert Kučerka
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Russia and Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Slovakia
| | - John Katsaras
- Department of Physics, Brock University, St. Catharines, ON, Canada; The Bredesen Center, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Large Scale Structures Group, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA.
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75
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Bacteriocin enterocin CRL35 is a modular peptide that induces non-bilayer states in bacterial model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183135. [DOI: 10.1016/j.bbamem.2019.183135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 10/07/2019] [Accepted: 11/04/2019] [Indexed: 11/17/2022]
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76
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Jacoby G, Portnaya I, Danino D, Diamant H, Beck R. Delayed nucleation in lipid particles. SOFT MATTER 2020; 16:247-255. [PMID: 31777911 DOI: 10.1039/c9sm01834d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Metastable states in first-order phase-transitions have been traditionally described by classical nucleation theory (CNT). However, recently an increasing number of systems displaying such a transition have not been successfully modelled by CNT. The delayed crystallization of phospholipids upon super-cooling is an interesting case, since the extended timescales allow access into the dynamics. Herein, we demonstrate the controllable behavior of the long-lived metastable liquid-crystalline phase of dilauroyl-phosphatidylethanolamine (DLPE), arranged in multi-lamellar vesicles, and the ensuing cooperative transition to the crystalline state. Experimentally, we find that the delay in crystallization is a bulk phenomenon, which is tunable and can be manipulated to span two orders of magnitude in time by changing the quenching temperature, solution salinity, or adding a secondary phospholipid. Our results reveal the robust persistence of the metastability, and showcase the apparent deviation from CNT. This distinctive suppression of the transition may be explained by the resistance of the multi-lamellar vesicle to deformations caused by nucleated crystalline domains. Since phospholipids are used as a platform for drug-delivery, a programmable design of cargo hold and release can be of great benefit.
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Affiliation(s)
- Guy Jacoby
- The Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel.
| | - Irina Portnaya
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Dganit Danino
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Haim Diamant
- The Raymond and Beverly School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roy Beck
- The Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel.
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77
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Gilbile D, Docto D, Kingi D, Kurniawan J, Monahan D, Tang A, Kuhl T. How Well Can You Tailor the Charge of Lipid Vesicles? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:15960-15969. [PMID: 31608647 PMCID: PMC9044797 DOI: 10.1021/acs.langmuir.9b02163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Knowledge and control of surface charge or potential is important for tailoring colloidal interactions. In this work, we compare widely used zeta potential (ζ) measurements of charged lipid vesicle surface potential to direct measurements using the surface force apparatus (SFA). Our measurements show good agreement between the two techniques. On varying the fraction of anionic lipids dimyristoylphosphatidylserine (DMPS) or dimyristoylphosphatidylglycerol (DMPG) mixed with zwitterionic dimyristoylphosphatidylcholine (DMPC) from 0 to 100 mol % we observed a near-linear increase in membrane surface charge or potential up to 20-30 mol % charged lipids beyond which charge saturation occurred in physiological (high) salt conditions. Similarly, in low salt concentrations, a linear increase in charge/potential was found but only up to ∼5-10 mol % charged lipids beyond which the surface charge or potential leveled off. While a lower degree of ionization is expected due to the lower dielectric constant (ε ∼ 4) of the lipid acyl chain environment, increasing intramembrane electrostatic repulsion between neighboring charged lipid head groups at higher charge loading contributes to charge suppression. Measured potentials in physiological salt solutions were consistent with predictions using the Gouy-Chapman-Stern-Grahame (GCSG) model of the electrical double layer with Langmuir binding of counterions, but in low salt conditions, the model significantly overestimated the surface charge/potential. The much lower ionization in low salt (maximum ∼1-2% of total lipids ionized) instead was consistent with counterion condensation at the bilayer surface which limited the charge that could be obtained. The strong interplay between membrane composition, lipid headgroup ionization, electrolyte concentration, and solution pH complicates exact prediction and tuning of membrane surface charge for applications. However, the theoretical frameworks used here can provide guidelines to understand this interplay and establish a range of achievable potentials for a system and predict the response to triggers like pH and salt concentration changes.
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78
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Elmer-Dixon MM, Hoody J, Steele HBB, Becht DC, Bowler BE. Cardiolipin Preferentially Partitions to the Inner Leaflet of Mixed Lipid Large Unilamellar Vesicles. J Phys Chem B 2019; 123:9111-9122. [DOI: 10.1021/acs.jpcb.9b07690] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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79
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Scott HL, Skinkle A, Kelley EG, Waxham MN, Levental I, Heberle FA. On the Mechanism of Bilayer Separation by Extrusion, or Why Your LUVs Are Not Really Unilamellar. Biophys J 2019; 117:1381-1386. [PMID: 31586522 DOI: 10.1016/j.bpj.2019.09.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/18/2019] [Accepted: 09/10/2019] [Indexed: 11/18/2022] Open
Abstract
Extrusion through porous filters is a widely used method for preparing biomimetic model membranes. Of primary importance in this approach is the efficient production of single bilayer (unilamellar) vesicles that eliminate the influence of interlamellar interactions and strictly define the bilayer surface area available to external reagents such as proteins. Submicroscopic vesicles produced using extrusion are widely assumed to be unilamellar, and large deviations from this assumption would impact interpretations from many model membrane experiments. Using three probe-free methods-small angle X-ray and neutron scattering and cryogenic electron microscopy-we report unambiguous evidence of extensive multilamellarity in extruded vesicles composed of neutral phosphatidylcholine lipids, including for the common case of neutral lipids dispersed in physiological buffer and extruded through 100-nm diameter pores. In such preparations, only ∼35% of lipids are externally accessible and this fraction is highly dependent on preparation conditions. Charged lipids promote unilamellarity as does decreasing solvent ionic strength, indicating the importance of electrostatic interactions in determining the lamellarity of extruded vesicles. Smaller extrusion pore sizes also robustly increase the fraction of unilamellar vesicles, suggesting a role for membrane bending. Taken together, these observations suggest a mechanistic model for extrusion, wherein the formation of unilamellar vesicles involves competition between bilayer bending and adhesion energies. The findings presented here have wide-ranging implications for the design and interpretation of model membrane studies, especially ensemble-averaged observations relying on the assumption of unilamellarity.
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Affiliation(s)
- Haden L Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Allison Skinkle
- Department of Biosciences, Rice University, Houston, Texas; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas
| | - Elizabeth G Kelley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas.
| | - Frederick A Heberle
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas.
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80
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Marzuoli I, Margreitter C, Fraternali F. Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description. J Chem Theory Comput 2019; 15:5175-5193. [PMID: 31433640 PMCID: PMC7377650 DOI: 10.1021/acs.jctc.9b00509] [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] [Indexed: 12/15/2022]
Abstract
![]()
Membranes
are a crucial component of both bacterial and mammalian
cells, being involved in signaling, transport, and compartmentalization.
This versatility requires a variety of lipid species to tailor the
membrane’s behavior as needed, increasing the complexity of
the system. Molecular dynamics simulations have been successfully
applied to study model membranes and their interactions with proteins,
elucidating some crucial mechanisms at the atomistic detail and thus
complementing experimental techniques. An accurate description of
the functional interplay of the diverse membrane components crucially
depends on the selected parameters that define the adopted force field.
A coherent parameterization for lipids and proteins is therefore needed.
In this work, we propose and validate new lipid head group parameters
for the GROMOS 54A8 force field, making use of recently published
parametrizations for key chemical moieties present in lipids. We make
use additionally of a new canonical set of partial charges for lipids,
chosen to be consistent with the parameterization of soluble molecules
such as proteins. We test the derived parameters on five phosphocholine
model bilayers, composed of lipid patches four times larger than the
ones used in previous studies, and run 500 ns long simulations of
each system. Reproduction of experimental data like area per lipid
and deuterium order parameters is good and comparable with previous
parameterizations, as well as the description of liquid crystal to
gel-phase transition. On the other hand, the orientational behavior
of the head groups is more realistic for this new parameter set, and
this can be crucial in the description of interactions with other
polar molecules. For that reason, we tested the interaction of the
antimicrobial peptide lactoferricin with two model membranes showing
that the new parameters lead to a weaker peptide–membrane binding
and give a more realistic outcome in comparing binding to antimicrobial
versus mammal membranes.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Christian Margreitter
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
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81
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Faizi HA, Frey SL, Steinkühler J, Dimova R, Vlahovska PM. Bending rigidity of charged lipid bilayer membranes. SOFT MATTER 2019; 15:6006-6013. [PMID: 31298256 DOI: 10.1039/c9sm00772e] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We experimentally investigate the effect of lipid charge on the stiffness of bilayer membranes. The bending rigidity of membranes with composition 0-100 mol% of charged lipids, in the absence and presence of salt at different concentrations, is measured with the flicker spectroscopy method, using the shape fluctuations of giant unilamellar vesicles. The analysis considers both the mean squared amplitudes and the time autocorrelations of the shape modes. Our results show that membrane charge increases the bending rigidity relative to the charge-free membrane. The effect is diminished by the addition of monovalent salt to the suspending solutions. The trend shown by the membrane bending rigidity correlates with zeta potential measurements, confirming charge screening at different salt concentrations. The experimental results in the presence of salt are in good agreement with existing theories of membrane stiffening by surface charge.
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Affiliation(s)
- Hammad A Faizi
- Department of Mechanical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, USA
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82
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A biophysical study of the interactions between the antimicrobial peptide indolicidin and lipid model systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1355-1364. [DOI: 10.1016/j.bbamem.2019.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/22/2019] [Accepted: 04/07/2019] [Indexed: 12/19/2022]
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83
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Talandashti R, Mahdiuni H, Jafari M, Mehrnejad F. Molecular Basis for Membrane Selectivity of Antimicrobial Peptide Pleurocidin in the Presence of Different Eukaryotic and Prokaryotic Model Membranes. J Chem Inf Model 2019; 59:3262-3276. [DOI: 10.1021/acs.jcim.9b00245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Reza Talandashti
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, P.O. Box 14395-1561, Tehran, Iran
| | - Hamid Mahdiuni
- Bioinformatics Lab., Department of Biology, School of Sciences, Razi University, P.O. Box 67149-67346, Kermanshah, Iran
| | - Majid Jafari
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, P.O. Box 14395-1561, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, P.O. Box 14395-1561, Tehran, Iran
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84
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Schott-Verdugo S, Gohlke H. PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building. J Chem Inf Model 2019; 59:2522-2528. [PMID: 31120747 DOI: 10.1021/acs.jcim.9b00269] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present PACKMOL-Memgen, a simple-to-use, generalized workflow for automated building of membrane-protein-lipid-bilayer systems based on open-source tools including Packmol, memembed, pdbremix, and AmberTools. Compared with web-interface-based related tools, PACKMOL-Memgen allows setup of multiple configurations of a system in a user-friendly and efficient manner within minutes. The generated systems are well-packed and thus well-suited as starting configurations in MD simulations under periodic boundary conditions, requiring only moderate equilibration times. PACKMOL-Memgen is distributed with AmberTools and runs on most computing platforms, and its output can also be used for CHARMM or adapted to other molecular-simulation packages.
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Affiliation(s)
- Stephan Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , 40225 Düsseldorf , Germany.,Centro de Bioinformática y Simulación Molecular (CBSM), Faculty of Engineering , Universidad de Talca , 1 Poniente 1141 , Casilla 721 , Talca , Chile
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , 40225 Düsseldorf , Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems-Structural Biochemistry (ICS 6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
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85
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McCluskey AR, Grant J, Symington AR, Snow T, Doutch J, Morgan BJ, Parker SC, Edler KJ. An introduction to classical molecular dynamics simulation for experimental scattering users. J Appl Crystallogr 2019; 52:665-668. [PMID: 31236095 PMCID: PMC6557182 DOI: 10.1107/s1600576719004333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/30/2019] [Indexed: 11/10/2022] Open
Abstract
Classical molecular dynamics simulations are a common component of multi-modal analyses of scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a 'black box' analysis technique. This article describes an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open-source software repository, which can be freely copied, modified and redistributed by educators. The topics covered in this OER include classical atomistic modelling, parameterizing interatomic potentials, molecular dynamics simulations, typical sources of error and some of the approaches to using simulations in the analysis of scattering data.
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Affiliation(s)
- Andrew R. McCluskey
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
- Diamond Light Source, Harwell Campus, Didcot OX11 0DE, UK
| | - James Grant
- Computing Services, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Adam R. Symington
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tim Snow
- Diamond Light Source, Harwell Campus, Didcot OX11 0DE, UK
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - James Doutch
- ISIS Facility, Rutherford Appleton Laboratory, STFC, Chilton, Didcot OX11 0QX, UK
| | - Benjamin J. Morgan
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Stephen C. Parker
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Karen J. Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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86
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Losasso V, Hsiao YW, Martelli F, Winn MD, Crain J. Modulation of Antimicrobial Peptide Potency in Stressed Lipid Bilayers. PHYSICAL REVIEW LETTERS 2019; 122:208103. [PMID: 31172786 DOI: 10.1103/physrevlett.122.208103] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Indexed: 06/09/2023]
Abstract
It is shown that the tendency of an archetypal antimicrobial peptide to insert into and perforate a simple lipid bilayer is strongly modulated by tensile stress in the membrane. The results, obtained through molecular dynamics simulations, have been demonstrated with several lipid compositions and appear to be general, although quantitative details differ. The findings imply that the potency of antimicrobial peptides may not be a purely intrinsic chemical property and, instead, depends on the mechanical state of the target membrane.
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Affiliation(s)
- Valeria Losasso
- Daresbury Laboratory, STFC, Daresbury, Warrington, England WA4 4AD, United Kingdom
| | - Ya-Wen Hsiao
- Daresbury Laboratory, STFC, Daresbury, Warrington, England WA4 4AD, United Kingdom
| | - Fausto Martelli
- IBM Research, Hartree Centre, Daresbury, England WA4 4AD, United Kingdom
| | - Martyn D Winn
- Daresbury Laboratory, STFC, Daresbury, Warrington, England WA4 4AD, United Kingdom
| | - Jason Crain
- IBM Research, Hartree Centre, Daresbury, England WA4 4AD, United Kingdom
- Dept. of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, England
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87
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Vasquez-Montes V, Vargas-Uribe M, Pandey NK, Rodnin MV, Langen R, Ladokhin AS. Lipid-modulation of membrane insertion and refolding of the apoptotic inhibitor Bcl-xL. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:691-700. [PMID: 31004798 DOI: 10.1016/j.bbapap.2019.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023]
Abstract
Bcl-xL is a member of the Bcl-2 family of apoptotic regulators, responsible for inhibiting the permeabilization of the mitochondrial outer membrane, and a promising anti-cancer target. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (a) a soluble folded conformation, (b) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (c) refolded membrane-inserted conformations, for which no structural data are available. Previous studies established that in the cell Bcl-xL exists in a dynamic equilibrium between soluble and membranous states, however, no direct evidence exists in support of either anchored or inserted conformation of the membranous state in vivo. In this in vitro study, we employed a combination of fluorescence and EPR spectroscopy to characterize structural features of the bilayer-inserted conformation of Bcl-xL and the lipid modulation of its membrane insertion transition. Our results indicate that the core hydrophobic helix α6 inserts into the bilayer without adopting a transmembrane orientation. This insertion disrupts the packing of Bcl-xL and releases the regulatory N-terminal BH4 domain (α1) from the rest of the protein structure. Our data demonstrate that both insertion and refolding of Bcl-xL are modulated by lipid composition, which brings the apparent pKa of insertion to the threshold of physiological pH. We hypothesize that conformational rearrangements associated with the bilayer insertion of Bcl-xL result in its switching to a so-called non-canonical mode of apoptotic inhibition. Presented results suggest that the alteration in lipid composition before and during apoptosis can serve as an additional factor regulating the permeabilization of the mitochondrial outer membrane.
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Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Mauricio Vargas-Uribe
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Nitin K Pandey
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ralf Langen
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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88
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Ruokonen SK, Ekholm FS, Wiedmer SK. Assessing the Interactions of Auristatin Derivatives with Mixed Phospholipid-Sodium Dodecyl Sulfate Aggregate Dispersions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5232-5240. [PMID: 30889955 PMCID: PMC6727603 DOI: 10.1021/acs.langmuir.9b00116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/09/2019] [Indexed: 06/09/2023]
Abstract
The aim of this study was to assess what properties of the pseudostationary phases in electrokinetic capillary chromatography affect the interactions between monomethyl auristatin E (MMAE) and hydrophilically modified structural analogues thereof with various lipophilic phases. MMAE is a widely used cytotoxic agent in antibody-drug conjugates (ADC), which are used as selective biopharmaceutical drugs in the treatment of cancers. MMAE and its derivatives are highly lipophilic, yet they fail to interact with biomimicking phosphatidylcholine-phosphatidylserine liposomes. To reveal what properties affect the interaction of the auristatin derivatives with cell plasma membrane-mimicking vesicles, capillary electrokinetic chromatography was used with four different types of micellar and vesicular pseudostationary phases: pure vesicles, mixed vesicles, mixed micelles, and pure micelles. Vesicular phases were composed of pure phospholipids [dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC)] and phospholipid-surfactant mixtures [sodium dodecyl sulfate, (SDS) with DMPC and DLPC] while the micellar phases comprised pure surfactant (SDS) and surfactant-phospholipid mixtures (SDS-DMPC and SDS-DLPC). In addition, differential scanning calorimetry and dynamic light scattering were used to monitor the aggregate composition. Our data shows that the interaction between hydrophobic auristatin derivatives and hydrophobic pseudostationary phases critically depends on the type, size, and hydrogen bonding capability of the pseudostationary phases.
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Affiliation(s)
- Suvi-Katriina Ruokonen
- Department
of Chemistry, A. I. Virtasen
aukio 1, POB 55, 00014 University of Helsinki, Helsinki, Finland
| | - Filip S. Ekholm
- Department
of Chemistry, A. I. Virtasen
aukio 1, POB 55, 00014 University of Helsinki, Helsinki, Finland
- Glykos Finland Ltd., Viikinkaari 6, 00790 Helsinki, Finland
| | - Susanne K. Wiedmer
- Department
of Chemistry, A. I. Virtasen
aukio 1, POB 55, 00014 University of Helsinki, Helsinki, Finland
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89
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Shahane G, Ding W, Palaiokostas M, Orsi M. Physical properties of model biological lipid bilayers: insights from all-atom molecular dynamics simulations. J Mol Model 2019; 25:76. [PMID: 30806797 DOI: 10.1007/s00894-019-3964-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/07/2019] [Indexed: 02/04/2023]
Abstract
The physical properties of lipid bilayers are sensitive to the specific type and composition of the lipids that make up the many different types of cell membranes. Studying model bilayers of representative heterogeneous compositions can provide key insights into membrane functionality. In this work, we use atomistic molecular dynamics simulations to characterize key properties in a number of bilayer membranes of varying composition. We first examine basic properties, such as lipid area, volume, and bilayer thickness, of simple, homogeneous bilayers comprising several lipid types, which are prevalent in biological membranes. Such lipids are then used in simulations of heterogeneous systems representative of bacterial, mammalian, and cancer membranes. Our analysis is especially focused on depth-dependent, transmembrane profiles; in particular, we calculate lateral pressure and dipole potential profiles, two fundamental properties which play key roles in a large number of biological functions.
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Affiliation(s)
- Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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90
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Dedic J, Rocha S, Okur HI, Wittung-Stafshede P, Roke S. Membrane-Protein-Hydration Interaction of α-Synuclein with Anionic Vesicles Probed via Angle-Resolved Second-Harmonic Scattering. J Phys Chem B 2019; 123:1044-1049. [PMID: 30625272 DOI: 10.1021/acs.jpcb.8b11096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amyloid formation of the protein α-synuclein promotes neurodegeneration in Parkinson's disease. The normal function of α-synuclein includes synaptic vesicle transport and fusion, and the protein binds strongly to negatively charged vesicles in vitro. Here, we demonstrate that nonresonant angle-resolved second-harmonic scattering detects α-synuclein binding to liposomes through changes in water orientational correlations and can thus be used as a high-accuracy and high-throughput label-free probe of protein-liposome interactions. The obtained results support a binding model in which the N-terminus of α-synuclein adopts an α-helical conformation that lies flat on the vesicle surface while the negatively charged C-terminus remains in solution.
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Affiliation(s)
- Jan Dedic
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), Institute of Materials Science (IMX), School of Engineering (STI), Lausanne Centre for Ultrafast Science (LACUS) , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Sandra Rocha
- Department of Biology and Biological Engineering , Chalmers University of Technology , 412 96 Gothenburg , Sweden
| | - Halil I Okur
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), Institute of Materials Science (IMX), School of Engineering (STI), Lausanne Centre for Ultrafast Science (LACUS) , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering , Chalmers University of Technology , 412 96 Gothenburg , Sweden
| | - Sylvie Roke
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), Institute of Materials Science (IMX), School of Engineering (STI), Lausanne Centre for Ultrafast Science (LACUS) , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
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91
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Pfeiffer T, De Nicola A, Montis C, Carlà F, van der Vegt NFA, Berti D, Milano G. Nanoparticles at Biomimetic Interfaces: Combined Experimental and Simulation Study on Charged Gold Nanoparticles/Lipid Bilayer Interfaces. J Phys Chem Lett 2019; 10:129-137. [PMID: 30563321 DOI: 10.1021/acs.jpclett.8b03399] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The poor understanding of the interaction of nanomaterials with biologically relevant interfaces is recognized as one of the major issues currently limiting the development of nanomedicine. The central purpose of this study is to compare experimental (confocal microscopy, fluorescence correlation spectroscopy, X-ray reflectivity) and computational (molecular dynamics simulations) results to thoroughly describe the interaction of cationic gold nanoparticles (AuNPs) with mixed zwitterionic/anionic lipid membranes. The adhesion of AuNPs to the lipid membrane is investigated on different length scales from a structural and dynamical point of view; with this approach, a series of complex phenomena, spanning from lipid extraction, localized membrane disruption, lateral phase separation, and slaved diffusion, are characterized and interpreted from a molecular level to macroscopic observations.
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Affiliation(s)
- Tobias Pfeiffer
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie , Technische Universität Darmstadt , Alarich-Weiss-Straße 10 , Darmstadt 64289 , Germany
| | - Antonio De Nicola
- Department of Organic Materials Science , Yamagata University , 4-3-16 Jonan Yonezawa , Yamagata-ken 992-8510 , Japan
| | - Costanza Montis
- Department of Chemistry "Ugo Schiff" and CSGI , University of Florence , via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy
| | - Francesco Carlà
- European Synchrotron Radiation Facility , CS 40220 , Grenoble Cedex 9, France
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie , Technische Universität Darmstadt , Alarich-Weiss-Straße 10 , Darmstadt 64289 , Germany
| | - Debora Berti
- Department of Chemistry "Ugo Schiff" and CSGI , University of Florence , via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy
| | - Giuseppe Milano
- Department of Organic Materials Science , Yamagata University , 4-3-16 Jonan Yonezawa , Yamagata-ken 992-8510 , Japan
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92
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McCluskey AR, Sanchez-Fernandez A, Edler KJ, Parker SC, Jackson AJ, Campbell RA, Arnold T. Bayesian determination of the effect of a deep eutectic solvent on the structure of lipid monolayers. Phys Chem Chem Phys 2019; 21:6133-6141. [DOI: 10.1039/c9cp00203k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A novel reflectometry analysis method reveals the structure of lipid monolayers at the air-DES interface.
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Affiliation(s)
| | | | | | | | - Andrew J. Jackson
- European Spallation Source
- SE-211 00 Lund
- Sweden
- Department of Physical Chemistry
- Lund University
| | - Richard A. Campbell
- Division of Pharmacy and Optometry
- University of Manchester
- Manchester
- UK
- Institut Laue-Langevin
| | - Thomas Arnold
- Department of Chemistry
- University of Bath
- Bath
- UK
- Diamond Light Source
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93
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Poger D, Pöyry S, Mark AE. Could Cardiolipin Protect Membranes against the Action of Certain Antimicrobial Peptides? Aurein 1.2, a Case Study. ACS OMEGA 2018; 3:16453-16464. [PMID: 30613806 PMCID: PMC6312644 DOI: 10.1021/acsomega.8b02710] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
The activity of a host of antimicrobial peptides has been examined against a range of lipid bilayers mimicking bacterial and eukaryotic membranes. Despite this, the molecular mechanisms and the nature of the physicochemical properties underlying the peptide-lipid interactions that lead to membrane disruption are yet to be fully elucidated. In this study, the interaction of the short antimicrobial peptide aurein 1.2 was examined in the presence of an anionic cardiolipin-containing lipid bilayer using molecular dynamics simulations. Aurein 1.2 is known to interact strongly with anionic lipid membranes. In the simulations, the binding of aurein 1.2 was associated with buckling of the lipid bilayer, the degree of which varied with the peptide concentration. The simulations suggest that the intrinsic properties of cardiolipin, especially the fact that it promotes negative membrane curvature, may help protect membranes against the action of peptides such as aurein 1.2 by counteracting the tendency of the peptide to induce positive curvature in target membranes.
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Affiliation(s)
- David Poger
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sanja Pöyry
- Department
of Physics, Tampere University of Technology, POB 692, F1-33720 Tampere, Finland
| | - Alan E. Mark
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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94
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Manna S, Wu Y, Wang Y, Koo B, Chen L, Petrochenko P, Dong Y, Choi S, Kozak D, Oktem B, Xu X, Zheng J. Probing the mechanism of bupivacaine drug release from multivesicular liposomes. J Control Release 2018; 294:279-287. [PMID: 30576748 DOI: 10.1016/j.jconrel.2018.12.029] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/16/2018] [Accepted: 12/16/2018] [Indexed: 10/27/2022]
Abstract
The mechanism of drug release from complex dosage forms, such as multivesicular liposomes (MVLs), is complex and oftentimes sensitive to the release environment. This challenges the design and development of an appropriate in vitro release test (IVRT) method. In this study, a commercial bupivacaine MVL product was selected as a model product and an IVRT method was developed using a modified USP 2 apparatus in conjunction with reverse-dialysis membranes. This setup allowed the use of in situ UV-Vis probes to continuously monitor the drug concentration during release. In comparison to the traditional sample-and-separate methods, the new method allowed for better control of the release conditions allowing for study of the drug release mechanism. Bupivacaine (BPV) MVLs exhibited distinct tri-phasic release characteristics comprising of an initial burst release, lag phase and a secondary release. Temperature, pH, agitation speed and release media composition were observed to impact the mechanism and rate of BPV release from MVLs. The size and morphology of the MVLs as well as their inner vesicle compartments were analyzed using cryogenic-scanning electron microscopy (cryo-SEM), confocal laser scanning microscopy and laser diffraction, where the mean diameters of the MVLs and their inner "polyhedral" vesicles were found to be 23.6 ± 11.5 μm and 1.52 ± 0.44 μm, respectively. Cryo-SEM results further showed a decrease in particle size and loss of internal "polyhedral" structure of the MVLs over the duration of release, indicating erosion and rearrangement of the lipid layers. Based on these results a potential MVL drug release mechanism was proposed, which may assist with the future development of more biorelevant IVRT method for similar formulations.
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Affiliation(s)
- Soumyarwit Manna
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Yong Wu
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Yan Wang
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Bonhye Koo
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Lynn Chen
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Peter Petrochenko
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Yixuan Dong
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Stephanie Choi
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Darby Kozak
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Berk Oktem
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Xiaoming Xu
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Jiwen Zheng
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD 20993, USA.
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95
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Florek OB, Clifton LA, Wilde M, Arnold T, Green RJ, Frazier RA. Lipid composition in fungal membrane models: effect of lipid fluidity. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1233-1244. [PMID: 30605137 DOI: 10.1107/s2059798318009440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/01/2018] [Indexed: 12/25/2022]
Abstract
The creation of effective fungal membrane models for neutron and X-ray reflectometry experiments is a key step in the development of new antifungal pharmaceuticals and agrochemicals to allow in vitro investigation of their mode of interaction with target cells. The structure of the obtained models depends on the properties of the lipids used and the final composition of the leaflets, and can be subject to the spontaneous translocation of phospholipids across the bilayer. The effect of phospholipid acyl-chain unsaturation and the presence of steroids in the membrane on the bilayer asymmetry were examined by means of neutron reflectometry. The measurements showed that membrane stability was higher if a zwitterionic, saturated acyl-chain phospholipid is present as the inner leaflet. Furthermore, membrane asymmetry was higher in the case of fully saturated lipid systems. As a result, membrane models consisting of fully saturated acyl chains within the inner leaflet are recommended as the starting point for subsequent studies of antifungal interactions owing to the simplicity of the models and their relative stability, thus allowing better control over the exact lipid composition facing the tested antifungal.
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Affiliation(s)
- Olga B Florek
- Department of Food and Nutritional Sciences, University of Reading, PO Box 226, Whiteknights, Reading RG6 6AP, England
| | - Luke A Clifton
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Marleen Wilde
- Reading School of Pharmacy, University of Reading, PO Box 226, Whiteknights, Reading RG6 6AP, England
| | - Thomas Arnold
- I07, Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Rebecca J Green
- Reading School of Pharmacy, University of Reading, PO Box 226, Whiteknights, Reading RG6 6AP, England
| | - Richard A Frazier
- Department of Food and Nutritional Sciences, University of Reading, PO Box 226, Whiteknights, Reading RG6 6AP, England
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96
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Zhang X, Barraza KM, Upton KT, Beauchamp JL. Subtle Changes in Lipid Environment Have Profound Effects on Membrane Oxidation Chemistry. J Am Chem Soc 2018; 140:17492-17498. [DOI: 10.1021/jacs.8b08610] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xinxing Zhang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), College of Chemistry, Nankai University, Tianjin 300071, China
- Noyes Laboratory of Chemical Physics and the Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Kevin M. Barraza
- Noyes Laboratory of Chemical Physics and the Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Kathleen T. Upton
- Noyes Laboratory of Chemical Physics and the Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - J. L. Beauchamp
- Noyes Laboratory of Chemical Physics and the Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
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97
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Nielsen JE, Bjørnestad VA, Lund R. Resolving the structural interactions between antimicrobial peptides and lipid membranes using small-angle scattering methods: the case of indolicidin. SOFT MATTER 2018; 14:8750-8763. [PMID: 30358793 DOI: 10.1039/c8sm01888j] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Using small angle X-ray and neutron scattering (SAXS/SANS) and detailed theoretical modelling we have elucidated the structure of the antimicrobial peptide, indolicidin, and the interaction with model lipid membranes of different anionic lipid compositions mimicking typical charge densities found in the cytoplasmic membrane of bacteria. First, we show that indolicidin displays a predominantly disordered, random chain conformation in solution with a small fraction (≈1%) of fiber-like nanostructures that are not dissolved at higher temperatures. The peptide is shown to strongly interact with the membranes at all charge densities without significantly perturbing the lipid bilayer structure. Instead, the results show that indolicidin inserts into the outer leaflet of the lipid vesicles causing a reduced local order of the lipid packing. This result is supported by an observed change in the melting point of the lipids upon addition of the peptide, as seen by differential scanning calorimetry experiments. The peptide does not to our observation affect the thickness of the membrane or form distinct structural pores in the membrane at physiologically relevant concentrations as has been previously suggested as an important mode of action. Finally, using sophisticated contrast variation SANS, we show that the peptide does not affect the random lateral distribution of anionic lipids in the membrane. Together, these results demonstrate that the structural aspects of the mode of action of antimicrobial peptides can be elucidated in detail using SAS techniques with liposomes as model systems.
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98
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Li A, Schertzer JW, Yong X. Molecular dynamics modeling of Pseudomonas aeruginosa outer membranes. Phys Chem Chem Phys 2018; 20:23635-23648. [PMID: 30191217 DOI: 10.1039/c8cp04278k] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pseudomonas aeruginosa is a common Gram-negative bacterium and opportunistic human pathogen. The distinctive structure of its outer membrane (OM) and outer membrane vesicles (OMVs) plays a fundamental role in bacterial virulence, colonization ability, and antibiotic resistance. To provide critical insights into OM and OMV functionality, we conducted an all-atom molecular dynamics study of asymmetric membranes that are biologically relevant to P. aeruginosa. We hybridized a GLYCAM06-based lipopolysaccharides force field with the Stockholm lipids force field (Slipids) to model bilayer membranes with Lipid A molecules in one leaflet and physiologically relevant phospholipid molecules in the other, including 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG), and 1,2-dioleoyl-sn-glycero-3-phosphoglycerol (DOPG). In particular, a membrane with phospholipid composition representing the P. aeruginosa OM was constructed and modeled by mixing the physiologically dominant components. The detailed structure of membranes was characterized by area per lipid, transmembrane mass and charge densities, radial distribution function (RDF), deuterium order parameter (SCD) of acyl chains, and inclination angles of phosphates and disaccharide in Lipid A. The membrane fluidity in equilibrium and the hydration of functional groups were probed and characterized quantitatively. The consistent properties of the Lipid A leaflets in different membranes demonstrate its compatibility with various phospholipids present in the P. aeruginosa OM. The more ordered acyl chains of Lipid A compared to the cytoplasmic cell membrane contribute to the low permeability of bacterial outer membrane. The findings of this computational investigation of P. aeruginosa OM will further the understanding of microbial pathogenesis and enable future study of OMV biogenesis.
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Affiliation(s)
- Ao Li
- Department of Mechanical Engineering, Binghamton University, The State University of New York, Binghamton, New York 13902, USA.
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99
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Characterization of self-assembled hybrid siloxane-phosphocholine bilayers. Chem Phys Lipids 2018; 216:1-8. [PMID: 30098944 DOI: 10.1016/j.chemphyslip.2018.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/24/2018] [Accepted: 07/31/2018] [Indexed: 01/25/2023]
Abstract
We have synthesized six new hybrid siloxane phosphocholines (SiPCs) and examined their self-assembly behaviour in aqueous dispersions. Employing small angle X-ray scattering we have characterized SiPC bilayers. SiPCs exhibit differential self-assembly behaviour that results from the interplay between the siloxane fatty acid in the sn-2 position and the differing chain length fatty acids in the sn-1 position. SiPCs that possess a fatty acid chain of a C8-C14 chain length in the sn-1 position form unilamellar vesicles. Extending the fatty acid chain length to C16 and C18 allows for the formation of both unilamellar and multilamellar vesicles. We propose that the preferential formation of unilamellar vesicles is the result of an enhanced hydrophobic effect imparted by siloxane chains at the termini of lipid tails.
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100
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Steinkühler J, De Tillieux P, Knorr RL, Lipowsky R, Dimova R. Charged giant unilamellar vesicles prepared by electroformation exhibit nanotubes and transbilayer lipid asymmetry. Sci Rep 2018; 8:11838. [PMID: 30087440 PMCID: PMC6081385 DOI: 10.1038/s41598-018-30286-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/24/2018] [Indexed: 12/22/2022] Open
Abstract
Giant unilamellar vesicles (GUVs) are increasingly used as a versatile research tool to investigate membrane structure, morphology and phase state. In these studies, GUV preparation is typically enhanced by an externally applied electric field, a process called electroformation. We find that upon osmotic deflation, GUVs electroformed from charged and neutral lipids exhibit inward pointing lipid nanotubes, suggesting negative spontaneous curvature of the membrane. By quenching a fluorescent analog of the charged lipid, zeta potential measurements and experiments with the lipid marker annexin A5, we show that electroformed GUVs exhibit an asymmetric lipid distribution across the bilayer leaflets. The asymmetry is lost either after storing electroformed GUVs at room temperature for one day or by applying higher voltages and temperatures during electroformation. GUVs having the same lipid composition but grown via gel-assisted swelling do not show asymmetric lipid distribution. We discuss possible mechanisms for the generation and relaxation of lipid asymmetry, as well as implications for studies using electroformed vesicles. The observed effects allow to control the molecular assembly of lipid bilayer leaflets. Vesicle tubulation as reported here is an example of protein-free reshaping of membranes and is caused by compositional lipid asymmetry between leaflets.
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Affiliation(s)
- Jan Steinkühler
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany
| | - Philippe De Tillieux
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany
- Department of Electrical Engineering, Polytechnique Montreal, Montreal, Quebec, H3T 1J4, Canada
| | - Roland L Knorr
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany
| | - Reinhard Lipowsky
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany
| | - Rumiana Dimova
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany.
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