1
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Caselli L, Parra-Ortiz E, Micciulla S, Skoda MWA, Häffner SM, Nielsen EM, van der Plas MJA, Malmsten M. Boosting Membrane Interactions and Antimicrobial Effects of Photocatalytic Titanium Dioxide Nanoparticles by Peptide Coating. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309496. [PMID: 38402437 DOI: 10.1002/smll.202309496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/30/2024] [Indexed: 02/26/2024]
Abstract
Photocatalytic nanoparticles offer antimicrobial effects under illumination due to the formation of reactive oxygen species (ROS), capable of degrading bacterial membranes. ROS may, however, also degrade human cell membranes and trigger toxicity. Since antimicrobial peptides (AMPs) may display excellent selectivity between human cells and bacteria, these may offer opportunities to effectively "target" nanoparticles to bacterial membranes for increased selectivity. Investigating this, photocatalytic TiO2 nanoparticles (NPs) are coated with the AMP LL-37, and ROS generation is found by C11-BODIPY to be essentially unaffected after AMP coating. Furthermore, peptide-coated TiO2 NPs retain their positive ζ-potential also after 1-2 h of UV illumination, showing peptide degradation to be sufficiently limited to allow peptide-mediated targeting. In line with this, quartz crystal microbalance measurements show peptide coating to promote membrane binding of TiO2 NPs, particularly so for bacteria-like anionic and cholesterol-void membranes. As a result, membrane degradation during illumination is strongly promoted for such membranes, but not so for mammalian-like membranes. The mechanisms of these effects are elucidated by neutron reflectometry. Analogously, LL-37 coating promoted membrane rupture by TiO2 NPs for Gram-negative and Gram-positive bacteria, but not for human monocytes. These findings demonstrate that AMP coating may selectively boost the antimicrobial effects of photocatalytic NPs.
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Affiliation(s)
- Lucrezia Caselli
- Department of Pharmacy, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Department of Physical Chemistry 1, Lund University, Lund, SE-22100, Sweden
| | - Elisa Parra-Ortiz
- Department of Pharmacy, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Novonesis, Biologiens Vej 2, Lyngby, DK-2800 Kgs, Denmark
| | - Samantha Micciulla
- Institut Laue-Langevin, CS 20156, Grenoble Cedex 9, 38042, France
- Laboratoire Interdisciplinaire de Physique (LIPhy), Saint Martin d'Hères, 38402, France
- Centre National de la Recherche Scientifique (CNRS), Saint-Martin-d'Hères, Auvergne-Rhône-Alpes, France
| | - Maximilian W A Skoda
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell, OX11 0QX, UK
| | - Sara Malekkhaiat Häffner
- Department of Pharmacy, University of Copenhagen, Copenhagen, DK-2100, Denmark
- RISE Research Institutes of Sweden, Malvinas väg 3, Stockholm, 114 86, Sweden
| | | | | | - Martin Malmsten
- Department of Pharmacy, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Department of Physical Chemistry 1, Lund University, Lund, SE-22100, Sweden
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2
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Caselli L, Köhler S, Schirone D, Humphreys B, Malmsten M. Conformational control of antimicrobial peptide amphiphilicity: consequences for boosting membrane interactions and antimicrobial effects of photocatalytic TiO 2 nanoparticles. Phys Chem Chem Phys 2024; 26:16529-16539. [PMID: 38828872 DOI: 10.1039/d4cp01724b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
This study reports on the effects of conformationally controlled amphiphilicity of antimicrobial peptides (AMPs) on their ability to coat TiO2 nanoparticles (NPs) and boost the photocatalytic antimicrobial effects of such NPs. For this, TiO2 NPs were combined with AMP EFK17 (EFKRIVQRIKDFLRNLV), displaying a disordered conformation in aqueous solution but helix formation on interaction with bacterial membranes. The membrane-bound helix is amphiphilic, with all polar and charged amino acid residues located at one side and all non-polar and hydrophobic residues on the other. In contrast, the d-enantiomer variant EFK17-d (E(dF)KR(dI)VQR(dI)KD(dF)LRNLV) is unable to form the amphiphilic helix on bacterial membrane interaction, whereas the W-residues in EFK17-W (EWKRWVQRWKDFLRNLV) boost hydrophobic interactions of the amphiphilic helix. Circular dichroism results showed the effects displayed for the free peptide, to also be present for peptide-coated TiO2 NPs, causing peptide binding to decrease in the order EFK17-W > EFK17 > EFK17-d. Notably, the formation of reactive oxygen species (ROS) by the TiO2 NPs was essentially unaffected by the presence of peptide coating, for all the peptides investigated, and the coatings stabilized over hours of UV exposure. Photocatalytic membrane degradation from TiO2 NPs coated with EFK17-W and EFK17 was promoted for bacteria-like model bilayers containing anionic phosphatidylglycerol but suppressed in mammalian-like bilayers formed by zwitterionic phosphatidylcholine and cholesterol. Structural aspects of these effects were further investigated by neutron reflectometry with clear variations observed between the bacteria- and mammalian-like model bilayers for the three peptides. Mirroring these results in bacteria-like model membranes, combining TiO2 NPs with EFK17-W and EFK17, but not with non-adsorbing EFK17-d, resulted in boosted antimicrobial effects of the resulting cationic composite NPs already in darkness, effects enhanced further on UV illumination.
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Affiliation(s)
- Lucrezia Caselli
- Department of Physical Chemistry 1, Lund University, SE-22100 Lund, Sweden.
| | - Sebastian Köhler
- LINXS Institute of Advanced Neutron and X-ray Science, Scheelevagen 19, 22370 Lund, Sweden
| | - Davide Schirone
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden
| | - Ben Humphreys
- Institut Laue-Langevin, CS 20156, 38042 Grenoble Cedex 9, France
| | - Martin Malmsten
- Department of Physical Chemistry 1, Lund University, SE-22100 Lund, Sweden.
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark
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3
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Paez‐Perez M, Kuimova MK. Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules. Angew Chem Int Ed Engl 2024; 63:e202311233. [PMID: 37856157 PMCID: PMC10952837 DOI: 10.1002/anie.202311233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
The viscosity and crowding of biological environment are considered vital for the correct cellular function, and alterations in these parameters are known to underly a number of pathologies including diabetes, malaria, cancer and neurodegenerative diseases, to name a few. Over the last decades, fluorescent molecular probes termed molecular rotors proved extremely useful for exploring viscosity, crowding, and underlying molecular interactions in biologically relevant settings. In this review, we will discuss the basic principles underpinning the functionality of these probes and will review advances in their use as sensors for lipid order, protein crowding and conformation, temperature and non-canonical nucleic acid structures in live cells and other relevant biological settings.
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Affiliation(s)
- Miguel Paez‐Perez
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
| | - Marina K. Kuimova
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
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4
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Turbant F, Machiels Q, Waeytens J, Wien F, Arluison V. The Amyloid Assembly of the Bacterial Hfq Is Lipid-Driven and Lipid-Specific. Int J Mol Sci 2024; 25:1434. [PMID: 38338713 PMCID: PMC10855545 DOI: 10.3390/ijms25031434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Under specific conditions, some proteins can self-assemble into fibrillar structures called amyloids. Initially, these proteins were associated with neurodegenerative diseases in eucaryotes. Nevertheless, they have now been identified in the three domains of life. In bacteria, they are involved in diverse biological processes and are usually useful for the cell. For this reason, they are classified as "functional amyloids". In this work, we focus our analysis on a bacterial functional amyloid called Hfq. Hfq is a pleiotropic regulator that mediates several aspects of genetic expression, mainly via the use of small noncoding RNAs. Our previous work showed that Hfq amyloid-fibrils interact with membranes. This interaction influences Hfq amyloid structure formation and stability, but the specifics of the lipid on the dynamics of this process is unknown. Here, we show, using spectroscopic methods, how lipids specifically drive and modulate Hfq amyloid assembly or, conversely, its disassembly. The reported effects are discussed in light of the consequences for bacterial cell life.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Quentin Machiels
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- SDV Department, Université Paris Cité, 75006 Paris, France
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5
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Aceves-Luna H, Glossman-Mitnik D, Flores-Holguín N. Permeability of antioxidants through a lipid bilayer model with coarse-grained simulations. J Biomol Struct Dyn 2023:1-19. [PMID: 37768552 DOI: 10.1080/07391102.2023.2262044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
Abstract
Oxidative stress caused by pollution and lifestyle changes causes an excess of free radicals that react chemically with cell constituents leading to irreversible damage. There are molecules known as antioxidants that reduce the levels of free radicals. Some pigments of fruits and vegetables known as anthocyanins have antioxidant properties. Their interaction with the cell membrane becomes a crucial step in studying these substances. In this research, molecular dynamics simulations, particularly, coarse-grained molecular dynamics (CGMD) were used. This technique aims to replace functional groups with corresponding beads that represent their level of polarity and affinities to other chemical groups. Also, umbrella sampling was carried out to obtain free energy profiles that describe well the orientation and location of antioxidants in a membrane considering Trolox, Cyanidin, Gallic Acid, and Resveratrol molecules to study the structural effects they cause on it. It was concluded in this study that an antioxidant when crossing the membrane does not cause either damage to the structural properties or the loss of packing and stratification of phospholipids. it was also observed that the most reactive part of the molecules could easily approach area A prone to lipid oxidation, which can describe the antioxidant capacity of these molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hugo Aceves-Luna
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, Mexico
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, Mexico
| | - Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, Mexico
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6
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Paez-Perez M, Dent MR, Brooks NJ, Kuimova MK. Viscosity-Sensitive Membrane Dyes as Tools To Estimate the Crystalline Structure of Lipid Bilayers. Anal Chem 2023; 95:12006-12014. [PMID: 37526607 PMCID: PMC10433245 DOI: 10.1021/acs.analchem.3c01747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/12/2023] [Indexed: 08/02/2023]
Abstract
Lipid membranes are crucial for cellular integrity and regulation, and tight control of their structural and mechanical properties is vital to ensure that they function properly. Fluorescent probes sensitive to the membrane's microenvironment are useful for investigating lipid membrane properties; however, there is currently a lack of quantitative correlation between the exact parameters of lipid organization and a readout from these dyes. Here, we investigate this relationship for "molecular rotors", or microviscosity sensors, by simultaneously measuring their fluorescence lifetime to determine the membrane viscosity, while using X-ray diffraction to determine the membrane's structural properties. Our results reveal a phase-dependent correlation between the membrane's structural parameters and mechanical properties measured by a BODIPY-based molecular rotor, giving excellent predictive power for the structural descriptors of the lipid bilayer. We also demonstrate that differences in membrane thickness between different lipid phases are not a prerequisite for the formation of lipid microdomains and that this requirement can be disrupted by the presence of line-active molecules. Our results underpin the use of membrane-sensitive dyes as reporters of the structure of lipid membranes.
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Affiliation(s)
- Miguel Paez-Perez
- MSRH, Department of Chemistry, Imperial College London, Wood Lane, London W12 0BZ, U.K.
| | - Michael R. Dent
- MSRH, Department of Chemistry, Imperial College London, Wood Lane, London W12 0BZ, U.K.
| | - Nicholas J. Brooks
- MSRH, Department of Chemistry, Imperial College London, Wood Lane, London W12 0BZ, U.K.
| | - Marina K. Kuimova
- MSRH, Department of Chemistry, Imperial College London, Wood Lane, London W12 0BZ, U.K.
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7
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Mrđenović D, Tang ZX, Pandey Y, Su W, Zhang Y, Kumar N, Zenobi R. Regioselective Tip-Enhanced Raman Spectroscopy of Lipid Membranes with Sub-Nanometer Axial Resolution. NANO LETTERS 2023; 23:3939-3946. [PMID: 37096805 DOI: 10.1021/acs.nanolett.3c00689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Noninvasive and label-free analysis of cell membranes at the nanoscale is essential to comprehend vital cellular processes. However, conventional analytical tools generally fail to meet this challenge due to the lack of required sensitivity and/or spatial resolution. Herein, we demonstrate that tip-enhanced Raman spectroscopy (TERS) is a powerful nanoanalytical tool to analyze dipalmitoylphosphatidylcholine (DPPC) bilayers and human cell membranes with submolecular resolution in the vertical direction. Unlike the far-field Raman measurements, TERS spectra of the DPPC bilayers reproducibly exhibited a uniquely shaped C-H band. These unique spectral features were also reproducibly observed in the TERS spectrum of human pancreatic cancer cells. Spectral deconvolution and DFT simulations confirmed that the TERS signal primarily originated from vibrations of the CH3 groups in the choline headgroup of the lipids. The reproducible TERS results obtained in this study unequivocally demonstrate the ultrahigh sensitivity of TERS for nanoanalysis of lipid membranes under ambient conditions.
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Affiliation(s)
- Dušan Mrđenović
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Zi-Xi Tang
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, 96 Jinzhai Road, 230026 Hefei, Anhui, People's Republic of China
| | - Yashashwa Pandey
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Weitao Su
- School of Sciences, Hangzhou Dianzi University, 310018 Hangzhou, People's Republic of China
| | - Yao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, 96 Jinzhai Road, 230026 Hefei, Anhui, People's Republic of China
| | - Naresh Kumar
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
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8
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Sharma KD, Heberle FA, Waxham MN. Visualizing lipid membrane structure with cryo-EM: past, present, and future. Emerg Top Life Sci 2023; 7:55-65. [PMID: 36606590 PMCID: PMC10355340 DOI: 10.1042/etls20220090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023]
Abstract
The development of electron cryomicroscopy (cryo-EM) has evolved immensely in the last several decades and is now well-established in the analysis of protein structure both in isolation and in their cellular context. This review focuses on the history and application of cryo-EM to the analysis of membrane architecture. Parallels between the levels of organization of protein structure are useful in organizing the discussion of the unique parameters that influence membrane structure and function. Importantly, the timescales of lipid motion in bilayers with respect to the timescales of sample vitrification is discussed and reveals what types of membrane structure can be reliably extracted in cryo-EM images of vitrified samples. Appreciating these limitations, a review of the application of cryo-EM to examine the lateral organization of ordered and disordered domains in reconstituted and biologically derived membranes is provided. Finally, a brief outlook for further development and application of cryo-EM to the analysis of membrane architecture is provided.
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Affiliation(s)
- Karan D. Sharma
- Department of Chemistry, University of Tennessee, Knoxville, TN
| | | | - M. Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, TX
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9
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Vo A, Murphy M, Phan P, Stone T, Prabhu R. Molecular Dynamics Simulation of Membrane Systems in the context of Traumatic Brain Injury. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023. [DOI: 10.1016/j.cobme.2023.100453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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10
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Nanoscale Bending Dynamics in Mixed-Chain Lipid Membranes. Symmetry (Basel) 2023. [DOI: 10.3390/sym15010191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Lipids that have two tails of different lengths are found throughout biomembranes in nature, yet the effects of this asymmetry on the membrane properties are not well understood, especially when it comes to the membrane dynamics. Here we study the nanoscale bending fluctuations in model mixed-chain 14:0–18:0 PC (MSPC) and 18:0–14:0 PC (SMPC) lipid bilayers using neutron spin echo (NSE) spectroscopy. We find that despite the partial interdigitation that is known to persist in the fluid phase of these membranes, the collective fluctuations are enhanced on timescales of tens of nanoseconds, and the chain-asymmetric lipid bilayers are softer than an analogous chain-symmetric lipid bilayer with the same average number of carbons in the acyl tails, di-16:0 PC (DPPC). Quantitative comparison of the NSE results suggests that the enhanced bending fluctuations at the nanosecond timescales are consistent with experimental and computational studies that showed the compressibility moduli of chain-asymmetric lipid membranes are 20% to 40% lower than chain-symmetric lipid membranes. These studies add to growing evidence that the partial interdigitation in mixed-chain lipid membranes is highly dynamic in the fluid phase and impacts membrane dynamic processes from the molecular to mesoscopic length scales without significantly changing the bilayer thickness or area per lipid.
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11
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Asfia S, Seemann R, Fleury JB. Phospholipids diffusion on the surface of model lipid droplets. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184074. [PMID: 36283490 DOI: 10.1016/j.bbamem.2022.184074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022]
Abstract
Lipid droplets (LD) are organelles localized in the membrane of the Endoplasmic Reticulum (ER) that play an important role in metabolic functions. They consist of a core of neutral lipids surrounded by a monolayer of phosphoplipids and proteins resembling an oil-in-water emulsion droplet. Many studies have focused on the biophysical properties of these LDs. However, despite numerous efforts, we are lacking information on the mobility of phospholipids on the LDs surface, although they may play a key role in the protein distribution. In this article, we developed a microfluidic setup that allows the formation of a triolein-buffer interface decorated with a phospholipid monolayer. Using this setup, we measured the motility of phospholipid molecules by performing Fluorescent Recovery After Photobleaching (FRAP) experiments for different lipidic compositions. The results of the FRAP measurements reveal that the motility of phospholipids is controlled by the monolayer packing decorating the interface.
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Affiliation(s)
- Shima Asfia
- Universitüt des Saarlandes, Experimental Physics and Center for Biophysics, 66123 Saarbrücken, Germany
| | - Ralf Seemann
- Universitüt des Saarlandes, Experimental Physics and Center for Biophysics, 66123 Saarbrücken, Germany
| | - Jean-Baptiste Fleury
- Universitüt des Saarlandes, Experimental Physics and Center for Biophysics, 66123 Saarbrücken, Germany.
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12
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Hashiba K, Sato Y, Taguchi M, Sakamoto S, Otsu A, Maeda Y, Shishido T, Murakawa M, Okazaki A, Harashima H. Branching Ionizable Lipids Can Enhance the Stability, Fusogenicity, and Functional Delivery of mRNA. SMALL SCIENCE 2022. [DOI: 10.1002/smsc.202200071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Kazuki Hashiba
- Nucleic Acid Medicine Business Division Nitto Denko Corporation 1-1-2, Shimohozumi Ibaraki Osaka 567-8680 Japan
| | - Yusuke Sato
- Laboratory for Molecular Design of Pharmaceutics, Faculty of Pharmaceutical Sciences Hokkaido University Kita-12, Nishi-6 Kita-Ku Sapporo 060-0812 Japan
| | - Masamitsu Taguchi
- Nucleic Acid Medicine Business Division Nitto Denko Corporation 1-1-2, Shimohozumi Ibaraki Osaka 567-8680 Japan
| | - Sachiko Sakamoto
- Nucleic Acid Medicine Business Division Nitto Denko Corporation 1-1-2, Shimohozumi Ibaraki Osaka 567-8680 Japan
| | - Ayaka Otsu
- Nucleic Acid Medicine Business Division Nitto Denko Corporation 1-1-2, Shimohozumi Ibaraki Osaka 567-8680 Japan
| | - Yoshiki Maeda
- Nucleic Acid Medicine Business Division Nitto Denko Corporation 1-1-2, Shimohozumi Ibaraki Osaka 567-8680 Japan
| | - Takuya Shishido
- Nucleic Acid Medicine Business Division Nitto Denko Corporation 1-1-2, Shimohozumi Ibaraki Osaka 567-8680 Japan
| | - Masao Murakawa
- Nucleic Acid Medicine Business Division Nitto Denko Corporation 1-1-2, Shimohozumi Ibaraki Osaka 567-8680 Japan
| | - Arimichi Okazaki
- Nucleic Acid Medicine Business Division Nitto Denko Corporation 1-1-2, Shimohozumi Ibaraki Osaka 567-8680 Japan
| | - Hideyoshi Harashima
- Laboratory for Molecular Design of Pharmaceutics, Faculty of Pharmaceutical Sciences Hokkaido University Kita-12, Nishi-6 Kita-Ku Sapporo 060-0812 Japan
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13
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Parra-Ortiz E, Caselli L, Agnoletti M, Skoda MWA, Li X, Zhao D, Malmsten M. Mesoporous silica as a matrix for photocatalytic titanium dioxide nanoparticles: lipid membrane interactions. NANOSCALE 2022; 14:12297-12312. [PMID: 35960150 DOI: 10.1039/d2nr01958b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In the present study, we investigate the combined interaction of mesoporous silica (SiO2) and photocatalytic titanium dioxide (TiO2) nanoparticles with lipid membranes, using neutron reflectometry (NR), cryo-transmission electron microscopy (cryo-TEM), fluorescence oxidation assays, dynamic light scattering (DLS), and ζ-potential measurements. Based on DLS, TiO2 nanoparticles were found to display strongly improved colloidal stability at physiological pH of skin (pH 5.4) after incorporation into either smooth or spiky ("virus-like") mesoporous silica nanoparticles at low pH, the latter demonstrated by cryo-TEM. At the same time, such matrix-bound TiO2 nanoparticles retain their ability to destabilize anionic bacteria-mimicking lipid membranes under UV-illumination. Quenching experiments indicated both hydroxyl and superoxide radicals to contribute to this, while NR showed that free TiO2 nanoparticles and TiO2 loaded into mesoporous silica nanoparticles induced comparable effects on supported lipid membranes, including membrane thinning, lipid removal, and formation of a partially disordered outer membrane leaflet. By comparing effects for smooth and virus-like mesoporous nanoparticles as matrices for TiO2 nanoparticles, the interplay between photocatalytic and direct membrane binding effects were elucidated. Taken together, the study outlines how photocatalytic nanoparticles can be readily incorporated into mesoporous silica nanoparticles for increased colloidal stability and yet retain most of their capacity for photocatalytic destabilization of lipid membranes, and with maintained mechanisms for oxidative membrane destabilization. As such, the study provides new mechanistic information to the widely employed, but poorly understood, practice of loading photocatalytic nanomaterials onto/into matrix materials for increased performance.
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Affiliation(s)
- Elisa Parra-Ortiz
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Lucrezia Caselli
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Monica Agnoletti
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Maximilian W A Skoda
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, OX11 0QX Harwell, Oxfordshire, UK
| | - Xiaomin Li
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, 200433 Shanghai, P. R. China
| | - Dongyuan Zhao
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, 200433 Shanghai, P. R. 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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14
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Supakijsilp A, He J, Lin X, Ye J. Molecular dynamics simulation insights into the cellular uptake of elastic nanoparticles through human pulmonary surfactant. RSC Adv 2022; 12:24222-24231. [PMID: 36128539 PMCID: PMC9403708 DOI: 10.1039/d2ra03670c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
The interaction between inhaled nanoparticles (NPs) and the pulmonary surfactant (PS) monolayer has drawn significant attention due to its potential in drug delivery design and application for respiratory therapeutics in active and passive cellular uptake pathways. Even though much attention has been given to explore the interaction between NPs and the PS monolayer, the effects of the NP elasticity on the translocation across the PS monolayer have not been thoroughly studied. Here, we performed a series of coarse-grained (CG) molecular dynamics simulations to study active or passive cellular uptake pathways of three NPs with different elasticities through a PS monolayer. The differences between active and passive pathways underly the enhanced targeting ability by ligand-receptor interaction (L-R interaction). In the active or passive cellular uptake pathways, it is found that the increase in stiffness level leads to a higher penetrability of NPs at the same time range. The soft NP has always been withheld inside the PS monolayer due to the lowest level of elasticity, while the other two types of NPs penetrate through the PS monolayer as the simulation progresses toward the end. The NPs in the active cellular uptake pathways take a longer time to penetrate the PS monolayer, resulting in a longer average penetration distance of approximately 40.55% and a higher average number of contacts, approximately 36.11%, than passive cellular uptake pathways, due to the L-R interaction. Moreover, it demonstrates that NPs in active cellular uptake pathways have a significantly higher targeting ability with the PS monolayer. We conclude that the level of NP elasticities has a substantial link to the penetrability in active or passive cellular uptake pathways. These results provide valuable insights into drug delivery and nanoprobe design for inhaled NPs within the lungs.
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Affiliation(s)
- Akkaranunt Supakijsilp
- School of Biomedical Engineering, Shanghai Jiao Tong University Shanghai 200030 P. R. China
| | - Jing He
- School of Biomedical Engineering, Shanghai Jiao Tong University Shanghai 200030 P. R. China
| | - Xubo Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University Beijing 100191 P. R. China
| | - Jian Ye
- School of Biomedical Engineering, Shanghai Jiao Tong University Shanghai 200030 P. R. China
- Institute of Medical Robotics, Shanghai Jiao Tong University Shanghai 200240 P. R. China
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15
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Górecki K, Hansen JS, Li P, Nayeri N, Lindkvist-Petersson K, Gourdon P. Microfluidic-Derived Detection of Protein-Facilitated Copper Flux Across Lipid Membranes. Anal Chem 2022; 94:11831-11837. [PMID: 35969432 PMCID: PMC9434548 DOI: 10.1021/acs.analchem.2c02081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
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Measurement of protein-facilitated copper flux across
biological
membranes is a considerable challenge. Here, we demonstrate a straightforward
microfluidic-derived approach for visualization and measurement of
membranous Cu flux. Giant unilamellar vesicles, reconstituted with
the membrane protein of interest, are prepared, surface-immobilized,
and assessed using a novel quencher–sensor reporter system
for detection of copper. With the aid of a syringe pump, the external
buffer is exchanged, enabling consistent and precise exchange of solutes,
without causing vesicle rupture or uneven local metal concentrations
brought about by rapid mixing. This approach bypasses common issues
encountered when studying heavy metal-ion flux, thereby providing
a new platform for in vitro studies of metal homeostasis
aspects that are critical for all cells, health, and disease.
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Affiliation(s)
- Kamil Górecki
- Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund SE-22100, Sweden
| | - Jesper S Hansen
- Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund SE-22100, Sweden
| | - Ping Li
- Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund SE-22100, Sweden
| | - Niloofar Nayeri
- Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund SE-22100, Sweden
| | - Karin Lindkvist-Petersson
- Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund SE-22100, Sweden
| | - Pontus Gourdon
- Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund SE-22100, Sweden.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
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16
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Tourte M, Coffinet S, Wörmer L, Lipp JS, Hinrichs KU, Oger PM. The Exploration of the Thermococcus barophilus Lipidome Reveals the Widest Variety of Phosphoglycolipids in Thermococcales. Front Microbiol 2022; 13:869479. [PMID: 35865931 PMCID: PMC9294538 DOI: 10.3389/fmicb.2022.869479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
One of the most distinctive characteristics of archaea is their unique lipids. While the general nature of archaeal lipids has been linked to their tolerance to extreme conditions, little is known about the diversity of lipidic structures archaea are able to synthesize, which hinders the elucidation of the physicochemical properties of their cell membrane. In an effort to widen the known lipid repertoire of the piezophilic and hyperthermophilic model archaeon Thermococcus barophilus, we comprehensively characterized its intact polar lipid (IPL), core lipid (CL), and polar head group compositions using a combination of cutting-edge liquid chromatography and mass spectrometric ionization systems. We tentatively identified 82 different IPLs based on five distinct CLs and 10 polar head group derivatives of phosphatidylhexoses, including compounds reported here for the first time, e.g., di-N-acetylhexosamine phosphatidylhexose-bearing lipids. Despite having extended the knowledge on the lipidome, our results also indicate that the majority of T. barophilus lipids remain inaccessible to current analytical procedures and that improvements in lipid extraction and analysis are still required. This expanded yet incomplete lipidome nonetheless opens new avenues for understanding the physiology, physicochemical properties, and organization of the membrane in this archaeon as well as other archaea.
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Affiliation(s)
- Maxime Tourte
- Univ. Lyon, Univ. Lyon 1, CNRS, UMR 5240, Villeurbanne, France
- Univ. Lyon, INSA Lyon, CNRS, UMR 5240, Villeurbanne, France
| | - Sarah Coffinet
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Lars Wörmer
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Julius S. Lipp
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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17
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Designer phospholipids – structural retrieval, chemo-/bio- synthesis and isotopic labeling. Biotechnol Adv 2022; 60:108025. [DOI: 10.1016/j.biotechadv.2022.108025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/12/2022] [Accepted: 07/26/2022] [Indexed: 11/23/2022]
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18
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Wallis JG, Bengtsson JD, Browse J. Molecular Approaches Reduce Saturates and Eliminate trans Fats in Food Oils. FRONTIERS IN PLANT SCIENCE 2022; 13:908608. [PMID: 35720592 PMCID: PMC9205222 DOI: 10.3389/fpls.2022.908608] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 05/29/2023]
Abstract
Vegetable oils composed of triacylglycerols (TAG) are a major source of calories in human diets. However, the fatty acid compositions of these oils are not ideal for human nutrition and the needs of the food industry. Saturated fatty acids contribute to health problems, while polyunsaturated fatty acids (PUFA) can become rancid upon storage or processing. In this review, we first summarize the pathways of fatty acid metabolism and TAG synthesis and detail the problems with the oil compositions of major crops. Then we describe how transgenic expression of desaturases and downregulation of the plastid FatB thioesterase have provided the means to lower oil saturates. The traditional solution to PUFA rancidity uses industrial chemistry to reduce PUFA content by partial hydrogenation, but this results in the production of trans fats that are even more unhealthy than saturated fats. We detail the discoveries in the biochemistry and molecular genetics of oil synthesis that provided the knowledge and tools to lower oil PUFA content by blocking their synthesis during seed development. Finally, we describe the successes in breeding and biotechnology that are giving us new, high-oleic, low PUFA varieties of soybean, canola and other oilseed crops.
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Affiliation(s)
| | | | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
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19
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Castillo SR, Rickeard BW, DiPasquale M, Nguyen MHL, Lewis-Laurent A, Doktorova M, Kav B, Miettinen MS, Nagao M, Kelley EG, Marquardt D. Probing the Link between Pancratistatin and Mitochondrial Apoptosis through Changes in the Membrane Dynamics on the Nanoscale. Mol Pharm 2022; 19:1839-1852. [PMID: 35559658 DOI: 10.1021/acs.molpharmaceut.1c00926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pancratistatin (PST) is a natural antiviral alkaloid that has demonstrated specificity toward cancerous cells and explicitly targets the mitochondria. PST initiates apoptosis while leaving healthy, noncancerous cells unscathed. However, the manner by which PST induces apoptosis remains elusive and impedes the advancement of PST as a natural anticancer therapeutic agent. Herein, we use neutron spin-echo (NSE) spectroscopy, molecular dynamics (MD) simulations, and supporting small angle scattering techniques to study PST's effect on membrane dynamics using biologically representative model membranes. Our data suggests that PST stiffens the inner mitochondrial membrane (IMM) by being preferentially associated with cardiolipin, which would lead to the relocation and release of cytochrome c. Second, PST has an ordering effect on the lipids and disrupts their distribution within the IMM, which would interfere with the maintenance and functionality of the active forms of proteins in the electron transport chain. These previously unreported findings implicate PST's effect on mitochondrial apoptosis.
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Affiliation(s)
- Stuart R Castillo
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Brett W Rickeard
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Mitchell DiPasquale
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Michael H L Nguyen
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Aislyn Lewis-Laurent
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, United States
| | - Batuhan Kav
- Max-Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany.,Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Julich, Julich 52428, Germany
| | | | - Michihiro Nagao
- National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland 20899, United States.,Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States.,Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Elizabeth G Kelley
- National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland 20899, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada.,Department of Physics, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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20
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Zhou T, Wu Z, Das S, Eslami H, Müller-Plathe F. How Ethanolic Disinfectants Disintegrate Coronavirus Model Membranes: A Dissipative Particle Dynamics Simulation Study. J Chem Theory Comput 2022; 18:2597-2615. [PMID: 35286098 PMCID: PMC8938819 DOI: 10.1021/acs.jctc.1c01120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Indexed: 01/03/2023]
Abstract
We have developed dissipative particle dynamics models for pure dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and dimyristoylphosphatidylcholine (DMPC) as well as their binary and ternary mixed membranes, as coronavirus model membranes. The stabilities of pure and mixed membranes, surrounded by aqueous solutions containing up to 70 mol % ethanol (alcoholic disinfectants), have been investigated at room temperature. We found that aqueous solutions containing 5-10 mol % ethanol already have a significant weakening effect on the pure and mixed membranes. The magnitude of the effect depends on the membrane composition and the ethanol concentration. Ethanol permeabilizes the membrane, causing its lateral swelling and thickness shrinking and reducing the orientational order of the hydrocarbon tail of the bilayer. The free energy barrier for the permeation of ethanol in the bilayers is considerably reduced by the ethanol uptake. The rupture-critical ethanol concentrations causing the membrane failure are 20.7, 27.5, and 31.7 mol % in the aqueous phase surrounding pure DMPC, DOPC, and DPPC membranes, respectively. Characterizing the failure of lipid membranes by a machine-learning neural network framework, we found that all mixed binary and/or ternary membranes disrupt when immersed in an aqueous solution containing a rupture-critical ethanol concentration, ranging from 20.7 to 31.7 mol %, depending on the composition of the membrane; the DPPC-rich membranes are more intact, while the DMPC-rich membranes are least intact. Due to the tight packing of long, saturated hydrocarbon tails in DPPC, increasing the DPPC content of the mixed membrane increases its stability against the disinfectant. At high DPPC concentrations, where the DOPC and DMPC molecules are confined between the DPPC lipids, the ordered hydrocarbon tails of DPPC also induce order in the DOPC and DMPC molecules and, hence, stabilize the membrane more. Our simulations on pure and mixed membranes of a diversity of compositions reveal that a maximum ethanol concentration of 32 mol % (55 wt %) in the alcohol-based disinfectants is enough to disintegrate any membrane composed of these three lipids.
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Affiliation(s)
- Tianhang Zhou
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Zhenghao Wu
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Shubhadip Das
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Hossein Eslami
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
- College of Sciences, Persian Gulf
University, Boushehr 75168, Iran
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
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21
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Paul B, Weeratunga S, Tillu VA, Hariri H, Henne WM, Collins BM. Structural Predictions of the SNX-RGS Proteins Suggest They Belong to a New Class of Lipid Transfer Proteins. Front Cell Dev Biol 2022; 10:826688. [PMID: 35223850 PMCID: PMC8864675 DOI: 10.3389/fcell.2022.826688] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
Recent advances in protein structure prediction using machine learning such as AlphaFold2 and RosettaFold presage a revolution in structural biology. Genome-wide predictions of protein structures are providing unprecedented insights into their architecture and intradomain interactions, and applications have already progressed towards assessing protein complex formation. Here we present detailed analyses of the sorting nexin proteins that contain regulator of G-protein signalling domains (SNX-RGS proteins), providing a key example of the ability of AlphaFold2 to reveal novel structures with previously unsuspected biological functions. These large proteins are conserved in most eukaryotes and are known to associate with lipid droplets (LDs) and sites of LD-membrane contacts, with key roles in regulating lipid metabolism. They possess five domains, including an N-terminal transmembrane domain that anchors them to the endoplasmic reticulum, an RGS domain, a lipid interacting phox homology (PX) domain and two additional domains named the PXA and PXC domains of unknown structure and function. Here we report the crystal structure of the RGS domain of sorting nexin 25 (SNX25) and show that the AlphaFold2 prediction closely matches the experimental structure. Analysing the full-length SNX-RGS proteins across multiple homologues and species we find that the distant PXA and PXC domains in fact fold into a single unique structure that notably features a large and conserved hydrophobic pocket. The nature of this pocket strongly suggests a role in lipid or fatty acid binding, and we propose that these molecules represent a new class of conserved lipid transfer proteins.
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Affiliation(s)
- Blessy Paul
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Saroja Weeratunga
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Vikas A. Tillu
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Hanaa Hariri
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - W. Mike Henne
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
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22
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Nimer R, Kamel G, Obeidat MA, Dahabiyeh LA. Investigating the molecular structure of plasma in type 2 diabetes mellitus and diabetic nephropathy by synchrotron Fourier-transform infrared microspectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120259. [PMID: 34388428 DOI: 10.1016/j.saa.2021.120259] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Diabetes mellitus (DM) is associated with a high incidence of morbidity and mortality which, in many cases, is derived from the progressive kidney dysfunction due to diabetic nephropathy (DN). In this study, synchrotron-Fourier-transform infrared (SR-FTIR) microspectroscopy was used to identify molecular changes in the lipid and protein regions in the plasma of patients with different stages of DN (mild, moderate, severe and end-stage), and patients with type 2 diabetes mellitus (T2DM) without DN. Our results revealed different conformational changes in the proteins secondary structure between DN stages, and between DN and T2DM groups illustrated by peak shifts and intensity alterations. End-stage DN showed the highest CH2/CH3 ratio and intensity of the carbonyl group in protein-carbonyl region compared to other DN stages indicating high level of unsaturation and lipid peroxidation and oxidation conditions. Moreover, end-stage DN group was characterized by a decrease in amide I and amide II absorption signals which reflected a sign of hypoalbuminemia. When compared to T2DM, DN group demonstrated a higher oxidation state as confirmed via the high intensity of the carbonyl group and the high level of malondialdehyde. The current study highlights the promising role of SR-FTIR microspectroscopy as a new sensitive analytical approach that can be used to provide better understanding of the pathophysiology of DN, and guide the development of new preventive therapies and treatments.
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Affiliation(s)
- Refat Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, 22110 Irbid, Jordan.
| | - Gihan Kamel
- SESAME Synchrotron (Synchrotron-light for Experimental Science and Applications in the Middle East), 19252 Allan, Jordan; Department of Physics, Faculty of Science, Helwan University, Cairo, Egypt
| | - Motaz A Obeidat
- Department of Internal Medicine, Nephrology Division, Jordan University of Science and Technology, Irbid, Jordan
| | - Lina A Dahabiyeh
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, 11942 Amman, Jordan.
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23
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Amyloid-beta peptide (25-35) triggers a reorganization of lipid membranes driven by temperature changes. Sci Rep 2021; 11:21990. [PMID: 34754013 PMCID: PMC8578324 DOI: 10.1038/s41598-021-01347-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/27/2021] [Indexed: 11/08/2022] Open
Abstract
The amyloid-beta peptide (Aβ) is considered a key factor in Alzheimer's disease (AD) ever since the discovery of the disease. The understanding of its damaging influence has however shifted recently from large fibrils observed in the inter-cellular environment to the small oligomers interacting with a cell membrane. We studied the effect of temperature on the latter interactions by evaluating the structural characteristics of zwitterionic phosphatidylcholine (PC) membranes with incorporated Aβ25–35 peptide. By means of small angle neutron scattering (SANS), we have observed for the first time a spontaneous reformation of extruded unilamellar vesicles (EULVs) to discoidal bicelle-like structures (BLSs) and small unilamellar vesicles (SULVs). These changes in the membrane self-organization happen during the thermodynamic phase transitions of lipids and only in the presence of the peptide. We interpret the dramatic changes in the membrane's overall shape with parallel changes in its thickness as the Aβ25–35 triggered membrane damage and a consequent reorganization of its structure. The suggested process is consistent with an action of separate peptides or small size peptide oligomers rather than the result of large Aβ fibrils.
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24
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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25
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Abstract
Cell membranes - primarily composed of lipids, sterols, and proteins - form a dynamic interface between living cells and their environment. They act as a mechanical barrier around the cell while selectively facilitating material transport, signal transduction, and various other functions necessary for the cell viability. The complex functionality of cell membranes and the hierarchical motions and responses they exhibit demand a thorough understanding of the origin of different membrane dynamics and how they are influenced by molecular additives and environmental cues. These dynamic modes include single-molecule diffusion, thermal fluctuations, and large-scale membrane deformations, to name a few. This review highlights advances in investigating structure-driven dynamics associated with model cell membranes, with a particular focus on insights gained from neutron scattering and spectroscopy experiments. We discuss the uniqueness of neutron contrast variation and its remarkable potential in probing selective membrane structure and dynamics on spatial and temporal scales over which key biological functions occur. We also present a summary of current and future opportunities in synergistic combinations of neutron scattering with molecular dynamics (MD) simulations to gain further understanding of the molecular mechanisms underlying complex membrane functions.
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Affiliation(s)
- Sudipta Gupta
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA. and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA. and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
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26
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Hayashi K, Sugimura H, Kamei T, Shimanouchi T, Nakamura H, Umakoshi H. Quantitative Determination of Relative Permittivity Based on the Fluorescence Property of Pyrene Derivatives: An Interpretation of Hydrophobicity in Self-Assembled Aggregates of Nonionic Amphiphiles. J Phys Chem B 2021; 125:6192-6200. [PMID: 34077661 DOI: 10.1021/acs.jpcb.1c00170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Aggregates in aqueous solutions can embed hydrophobic molecules, and their interactions depend on the properties of the aggregates. The electric surface potential, molecular mobility, and gradual hydrophobicity are the properties that regulate the interactions, and it is essential to understand these to quantify the properties. Electric surface potential and molecular mobility are quantified using the zeta potential and NMR measurements. In this study, the quantification of gradual hydrophobicity within the aggregate based on the relative permittivity, also called the dielectric constant, has been estimated from fluorescence spectra of pyrene-dicarboxylic acid conjugates. The localization of the pyrene moiety was modified by conjugation with succinic acid, suberic acid, or dodecanedioic acid, and the conjugates were evaluated in the shallow, middle, and deep regions of the aggregates. Span and Tween surfactants have been employed to prepare these aggregates, because they form various kinds of aggregates such as micelles and vesicles. It was realized that the hydrophobicity gradually increased from the interface to the hydrophobic core. Alternatively, a comparison of hydrophobicity within the aggregates showed no remarkable difference. Moreover, the analyses suggested that there are a few water molecules in the deep region. These results support the idea of the localization of embedded molecules in aggregates.
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Affiliation(s)
- Keita Hayashi
- Department of Chemical Engineering, National Institute of Technology, Nara College, 22 Yata-cho, Yamatokoriyama, Nara 639-1080, Japan
| | - Haruna Sugimura
- Department of Chemical Engineering, National Institute of Technology, Nara College, 22 Yata-cho, Yamatokoriyama, Nara 639-1080, Japan
| | - Toshiyuki Kamei
- Department of Chemical Engineering, National Institute of Technology, Nara College, 22 Yata-cho, Yamatokoriyama, Nara 639-1080, Japan
| | - Toshinori Shimanouchi
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hidemi Nakamura
- Department of Chemical Engineering, National Institute of Technology, Nara College, 22 Yata-cho, Yamatokoriyama, Nara 639-1080, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan
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27
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Kinnun JJ, Scott HL, Ashkar R, Katsaras J. Biomembrane Structure and Material Properties Studied With Neutron Scattering. Front Chem 2021; 9:642851. [PMID: 33987167 PMCID: PMC8110834 DOI: 10.3389/fchem.2021.642851] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cell membranes and their associated structures are dynamical supramolecular structures where different physiological processes take place. Detailed knowledge of their static and dynamic structures is therefore needed, to better understand membrane biology. The structure–function relationship is a basic tenet in biology and has been pursued using a range of different experimental approaches. In this review, we will discuss one approach, namely the use of neutron scattering techniques as applied, primarily, to model membrane systems composed of lipid bilayers. An advantage of neutron scattering, compared to other scattering techniques, is the differential sensitivity of neutrons to isotopes of hydrogen and, as a result, the relative ease of altering sample contrast by substituting protium for deuterium. This property makes neutrons an ideal probe for the study of hydrogen-rich materials, such as biomembranes. In this review article, we describe isotopic labeling studies of model and viable membranes, and discuss novel applications of neutron contrast variation in order to gain unique insights into the structure, dynamics, and molecular interactions of biological membranes. We specifically focus on how small-angle neutron scattering data is modeled using different contrast data and molecular dynamics simulations. We also briefly discuss neutron reflectometry and present a few recent advances that have taken place in neutron spin echo spectroscopy studies and the unique membrane mechanical data that can be derived from them, primarily due to new models used to fit the data.
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Affiliation(s)
- Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States
| | - Haden L Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA, United States.,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
| | - John Katsaras
- Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States.,Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, United States
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28
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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: 12] [Impact Index Per Article: 4.0] [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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29
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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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30
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Luchini A, Sebastiani F, Tidemand FG, Batchu KC, Campana M, Fragneto G, Cárdenas M, Arleth L. Peptide discs as precursors of biologically relevant supported lipid bilayers. J Colloid Interface Sci 2020; 585:376-385. [PMID: 33307306 DOI: 10.1016/j.jcis.2020.11.086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/19/2022]
Abstract
Supported lipid bilayers (SLBs) are commonly used to investigate the structure and dynamics of biological membranes. Vesicle fusion is a widely exploited method to produce SLBs. However, this process becomes less favoured when the vesicles contain complex lipid mixtures, e.g. natural lipid extracts. In these cases, it is often necessary to change experimental parameters, such as temperature, to unphysiological values to trigger the SLB formation. This may induce lipid degradation and is also not compatible with including membrane proteins or other biomolecules into the bilayers. Here, we show that the peptide discs, ~10 nm discoidal lipid bilayers stabilized in solution by a self-assembled 18A peptide belt, can be used as precursors for SLBs. The characterizations by means of neutron reflectometry and attenuated total reflectance-FTIR spectroscopy show that SLBs were successfully formed both from synthetic lipid mixtures (surface coverage 90-95%) and from natural lipid mixtures (surface coverage ~85%). Traces of 18A peptide (below 0.02 M ratio) left at the support surface after the bilayer formation do not affect the SLB structure. Altogether, we demonstrate that peptide disc formation of SLBs is much faster than the SLB formation by vesicle fusion and without the need of altering any experimental variable from physiologically relevant values.
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Affiliation(s)
- Alessandra Luchini
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
| | - Federica Sebastiani
- Biofilms Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, Per Albin Hanssons Väg 35, 21432 Malmö, Sweden
| | | | | | - Mario Campana
- ISIS-STFC, Rutherford Appleton Laboratory, Chilton, Oxon OX11 0QX, United Kingdom
| | - Giovanna Fragneto
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Marité Cárdenas
- Biofilms Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, Per Albin Hanssons Väg 35, 21432 Malmö, Sweden
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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31
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Drabik D, Gavutis M, Valiokas RN, Ulčinas AR. Determination of the Mechanical Properties of Model Lipid Bilayers Using Atomic Force Microscopy Indentation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13251-13262. [PMID: 33125251 DOI: 10.1021/acs.langmuir.0c02181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
By conducting a systematic study of model lipid membranes using the atomic force microscopy (AFM) indentation, we demonstrate the importance of an experimental protocol on the determination of their mechanical parameters. We refine the experimental approach by analyzing the influence of the contact mechanics models used to process the data, substrate preparation, and indenter geometry. We show that both bending rigidity and area compressibility can be determined from a single AFM indentation measurement.
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Affiliation(s)
- Dominik Drabik
- Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Martynas Gavutis
- Department of Nanoengineering, Center for Physical Sciences and Technology, Savanoriu̧ 231, Vilnius LT-02300, Lithuania
| | - Ramu Nas Valiokas
- Department of Nanoengineering, Center for Physical Sciences and Technology, Savanoriu̧ 231, Vilnius LT-02300, Lithuania
| | - Artu Ras Ulčinas
- Department of Nanoengineering, Center for Physical Sciences and Technology, Savanoriu̧ 231, Vilnius LT-02300, Lithuania
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32
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Kelley EG, Butler PD, Ashkar R, Bradbury R, Nagao M. Scaling relationships for the elastic moduli and viscosity of mixed lipid membranes. Proc Natl Acad Sci U S A 2020; 117:23365-23373. [PMID: 32883879 PMCID: PMC7519290 DOI: 10.1073/pnas.2008789117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The elastic and viscous properties of biological membranes play a vital role in controlling cell functions that require local reorganization of the membrane components as well as dramatic shape changes such as endocytosis, vesicular trafficking, and cell division. These properties are widely acknowledged to depend on the unique composition of lipids within the membrane, yet the effects of lipid mixing on the membrane biophysical properties remain poorly understood. Here, we present a comprehensive characterization of the structural, elastic, and viscous properties of fluid membranes composed of binary mixtures of lipids with different tail lengths. We show that the mixed lipid membrane properties are not simply additive quantities of the single-component analogs. Instead, the mixed membranes are more dynamic than either of their constituents, quantified as a decrease in their bending modulus, area compressibility modulus, and viscosity. While the enhanced dynamics are seemingly unexpected, we show that the measured moduli and viscosity for both the mixed and single-component bilayers all scale with the area per lipid and collapse onto respective master curves. This scaling links the increase in dynamics to mixing-induced changes in the lipid packing and membrane structure. More importantly, the results show that the membrane properties can be manipulated through lipid composition the same way bimodal blends of surfactants, liquid crystals, and polymers are used to engineer the mechanical properties of soft materials, with broad implications for understanding how lipid diversity relates to biomembrane function.
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Affiliation(s)
- Elizabeth G Kelley
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899;
| | - Paul D Butler
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716
- Department of Chemistry, The University of Tennessee, Knoxville, TN 37996
| | - Rana Ashkar
- Physics Department, Virginia Tech, Blacksburg, VA 20461
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 20461
| | - Robert Bradbury
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Center for Exploration of Energy and Matter, Indiana University, Bloomington, IN 47408
| | - Michihiro Nagao
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Center for Exploration of Energy and Matter, Indiana University, Bloomington, IN 47408
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716
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33
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The Equilibria in Lipid-Lipoic Acid Systems: Monolayers, Microelectrophoretic and Interfacial Tension Studies. Molecules 2020; 25:molecules25163678. [PMID: 32806764 PMCID: PMC7465766 DOI: 10.3390/molecules25163678] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/02/2020] [Accepted: 08/10/2020] [Indexed: 01/25/2023] Open
Abstract
In this examination, we investigated the effect of lipoic acid (LA) on the properties of biological membrane models (monolayers, bilayers, and liposomes) formed from phosphatidylcholine (PC) or phosphatidylserine (PS) using the Langmuir, microelectrophoresis, and interfacial tension methods. The Langmuir technique allowed us to calculate the π–A isotherms and determine the molecular surface areas of pure and mixed monolayers. Using mathematical equations, we established that LA and the lipids formed complexes at a 1:1 ratio. The interfacial tension method was based on Young and Laplace’s equation. We assumed the formation of a 1:1 complex in the PC–LA system. Using the mathematical relationships, we derived the parameters characterizing the resulting complex, i.e., the surface occupied by the complex and the interfacial tension and stability constant of the formed complex. The microelectrophoretic method was used to determine the dependence of the zeta potential of the lipid membranes as a function of the pH (pH 2 to 10) of the electrolyte solution. The results indicate that modification of PC or PS membranes with LA affects changes in the zeta potential and the isoelectric point values.
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34
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Identification of N-acyl amino acids that are positive allosteric modulators of glycine receptors. Biochem Pharmacol 2020; 180:114117. [PMID: 32579961 DOI: 10.1016/j.bcp.2020.114117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 01/31/2023]
Abstract
Glycine receptors (GlyRs) mediate inhibitory neurotransmission within the spinal cord and play a crucial role in nociceptive signalling. This makes them primary targets for the development of novel chronic pain therapies. Endogenous lipids have previously been shown to modulate glycine receptors and produce analgesia in pain models, however little is known about what chemical features mediate these effects. In this study, we characterised lipid modulation of GlyRs by screening a library of N-acyl amino acids across all receptor subtypes and determined chemical features crucial for their activity. Acyl-glycine's with a C18 carbon tail were found to produce the greatest potentiation, and require a cis double bond within the central region of the carbon tail (ω6 - ω9) to be active. At 1 µM, C18 ω6,9 glycine potentiated glycine induced currents in α3 and α3β receptors by over 50%, and α1, α2, α1β and α2β receptors by over 100%. C18 ω9 glycine (N-oleoyl glycine) significantly enhance glycine induced peak currents and cause a dose-dependent shift in the glycine concentration response. In the presence of 3 µM C18 ω9 glycine, the EC5o of glycine at the α1 receptor was reduced from 17 µM to 10 µM. This study has identified several acyl-amino acids which are positive allosteric modulators of GlyRs and make promising lead compounds for the development of novel chronic pain therapies.
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35
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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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36
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Varadarajan V, Desikan R, Ayappa KG. Assessing the extent of the structural and dynamic modulation of membrane lipids due to pore forming toxins: insights from molecular dynamics simulations. SOFT MATTER 2020; 16:4840-4857. [PMID: 32421131 DOI: 10.1039/d0sm00086h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Infections caused by many virulent bacterial strains are triggered by the release of pore forming toxins (PFTs), which form oligomeric transmembrane pore complexes on the target plasma membrane. The spatial extent of the perturbation to the surrounding lipids during pore formation is relatively unexplored. Using all-atom molecular dynamics simulations, we investigate the changes in the structure and dynamics of lipids in a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer in the presence of contrasting PFTs. Cytolysin A (ClyA), an α toxin with its inserted wedge shaped bundle of inserted α helices, induces significant asymmetry across the membrane leaflets in comparison with α hemolysin (AHL), a β toxin. Despite the differences in hydrophobic mismatch and uniquely different topologies of the two oligomers, perturbations to lipid order as reflected in the tilt angle and order parameters and membrane thinning are short ranged, lying within ∼2.5 nm from the periphery of either pore complex, and commensurate with distances typically associated with van der Waals forces. In contrast, the spatial extent of perturbations to the lipid dynamics extends outward to at least 4 nm for both proteins, and the continuous survival probabilities reveal the presence of a tightly bound shell of lipids in this region. Displacement probability distributions show long tails and the distinctly non-Gaussian features reflect the induced dynamic heterogeneity. A detailed profiling of the protein-lipid contacts with tyrosine, tryptophan, lysine and arginine residues shows increased non-polar contacts in the cytoplasmic leaflet for both PFTs, with a higher number of atomic contacts in the case of AHL in the extracellular leaflet due to the mushroom-like topology of the pore complex. The short ranged nature of the perturbations observed in this simple one component membrane suggests inherent plasticity of membrane lipids enabling the recovery of the structure and membrane fluidity even in the presence of these large oligomeric transmembrane protein assemblies. This observation has implications in membrane repair processes such as budding or vesicle fusion events used to mitigate PFT virulence, where the underlying lipid dynamics and fluidity in the vicinity of the pore complex are expected to play an important role.
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Affiliation(s)
- Vadhana Varadarajan
- Department of Chemical Engineering, Indian Institute of Science, Bangalore-560012, India.
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37
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Bozelli JC, Yune J, Dang X, Narayana JL, Wang G, Epand RM. Membrane activity of two short Trp-rich amphipathic peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183280. [PMID: 32220553 DOI: 10.1016/j.bbamem.2020.183280] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/09/2020] [Accepted: 03/18/2020] [Indexed: 12/13/2022]
Abstract
Short linear antimicrobial peptides are attractive templates for developing new antibiotics. Here, it is described a study of the interaction between two short Trp-rich peptides, horine and verine-L, and model membranes. Isothermal titration calorimetry studies showed that the affinity of these peptides towards large unilamellar vesicles (LUV) having a lipid composition mimicking the lipid composition of S. aureus membranes is ca. 30-fold higher than that towards E. coli mimetics. The former interaction is driven by enthalpy and entropy, while the latter case is driven by entropy, suggesting differences in the forces that play a role in the binding to the two types of model membranes. Upon membrane binding the peptides acquired different conformations according to circular dichroism (CD) studies; however, in both cases CD studies indicated stacked W-residues. Peptide-induced membrane permeabilization, lipid flip-flop, molecular packing at the membrane-water interface, and lateral lipid segregation were observed in all cases. However, the extent of these peptide-induced changes on membrane properties was always higher in S. aureus than E. coli mimetics. Both peptides seem to act via a similar mechanism of membrane permeabilization of S. aureus membrane mimetics, while their mechanisms seem to differ in the case of E. coli. This may be the result of differences in both the peptides´ structure and the membrane lipid composition between both types of bacteria.
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Affiliation(s)
- José C Bozelli
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 4K1, Canada
| | - Jenny Yune
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 4K1, Canada
| | - Xiangli Dang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE 68198-5990, USA
| | - Jayaram Lakshmaiah Narayana
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE 68198-5990, USA
| | - Guangshun Wang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE 68198-5990, USA
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 4K1, Canada.
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38
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Wlodek M, Slastanova A, Fox LJ, Taylor N, Bikondoa O, Szuwarzynski M, Kolasinska-Sojka M, Warszynski P, Briscoe WH. Structural evolution of supported lipid bilayers intercalated with quantum dots. J Colloid Interface Sci 2020; 562:409-417. [PMID: 31806357 DOI: 10.1016/j.jcis.2019.11.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 10/25/2022]
Abstract
HYPOTHESIS Supported lipid bilayers (SLBs) embedded with hydrophobic quantum dots (QDs) undergo temporal structural rearrangement. EXPERIMENTS Synchrotron X-ray reflectivity (XRR) was applied to monitor the temporal structural changes over a period of 24 h of mixed SLBs of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) / 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-ethanolamine (POPE) intercalated with 4.9 nm hydrophobic cadmium sulphide quantum dots (CdS QDs). The QD-embedded SLBs (QD-SLBs) were formed via rupture of the mixed liposomes on a positively charged polyethylene imine (PEI) monolayer. Atomic force microscopy (AFM) imaging provided complementary characterization of the bilayer morphology. FINDINGS Our results show time-dependent perturbations in the SLB structure due to the interaction upon QD incorporation. Compared to the SLB without QDs, at 3 h incubation time, there was a measurable decrease in the bilayer thickness and a concurrent increase in the scattering length density (SLD) of the QD-SLB. The QD-SLB then became progressively thicker with increasing incubation time, which - along with the fitted SLD profile - was attributed to the structural rearrangement due to the QDs being expelled from the inner leaflet to the outer leaflet of the bilayer. Our results give unprecedented mechanistic insights into the structural evolution of QD-SLBs on a polymer cushion, important to their potential biomedical and biosensing applications.
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Affiliation(s)
- Magdalena Wlodek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
| | - Anna Slastanova
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Laura J Fox
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Nicholas Taylor
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Oier Bikondoa
- XMaS, The UK-CRG Beamline, The European Synchrotron (ESRF), 71 Avenue des Martyrs, 38043 Grenoble, France; Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Michal Szuwarzynski
- AGH University of Science and Technology, Academic Centre for Materials and Nanotechnology, al. A. Mickiewicza 30, PL-30059 Krakow, Poland
| | - Marta Kolasinska-Sojka
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Piotr Warszynski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Wuge H Briscoe
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.
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39
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Srivastava A, Malik S, Karmakar S, Debnath A. Dynamic coupling of a hydration layer to a fluid phospholipid membrane: intermittency and multiple time-scale relaxations. Phys Chem Chem Phys 2020; 22:21158-21168. [DOI: 10.1039/d0cp02803g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the coupling of a hydration layer and a lipid membrane is crucial to gaining access to membrane dynamics and understanding its functionality towards various biological processes.
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Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
| | - Sheeba Malik
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences
- Tata Institute of Fundamental Research
- Hyderabad 500107
- India
| | - Ananya Debnath
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
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40
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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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41
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Kučerka N, Gallová J, Uhríková D. The membrane structure and function affected by water. Chem Phys Lipids 2019; 221:140-144. [DOI: 10.1016/j.chemphyslip.2019.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 01/24/2023]
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42
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Lind TK, Skoda MWA, Cárdenas M. Formation and Characterization of Supported Lipid Bilayers Composed of Phosphatidylethanolamine and Phosphatidylglycerol by Vesicle Fusion, a Simple but Relevant Model for Bacterial Membranes. ACS OMEGA 2019; 4:10687-10694. [PMID: 31460166 PMCID: PMC6648305 DOI: 10.1021/acsomega.9b01075] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/06/2019] [Indexed: 05/06/2023]
Abstract
Supported lipid bilayers (SLBs) are simple and robust biomimics with controlled lipid composition that are widely used as models of both mammalian and bacterial membranes. However, the lipids typically used for SLB formation poorly resemble those of bacterial cell membranes due to the lack of available protocols to form SLBs using mixtures of lipids relevant for bacteria such as phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). Although a few reports have been published recently on the formation of SLBs from Escherichia coli lipid extracts, a detailed understanding of these systems is challenging due to the complexity of the lipid composition in such natural extracts. Here, we present for the first time a simple and reliable protocol optimized to form high-quality SLBs using mixtures of PE and PG at compositions relevant for Gram-negative membranes. We show using neutron reflection and quartz microbalance not only that Ca2+ ions and temperature are key parameters for successful bilayer deposition but also that mass transfer to the surface is a limiting factor. Continuous flow of the lipid suspension is thus crucial for obtaining full SLB coverage. We furthermore characterize the resulting bilayers and report structural parameters, for the first time for PE and PG mixtures, which are in good agreement with those reported earlier for pure POPE vesicles. With this protocol in place, more suitable and reproducible studies can be conducted to understand biomolecular processes occurring at cell membranes, for example, for testing specificities and to unravel the mechanism of interaction of antimicrobial peptides.
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Affiliation(s)
- Tania Kjellerup Lind
- Biofilms Research
Centre for Biointerfaces and Biomedical Science Department, Faculty
of Health and Society, Malmo University, Malmo 20506, Sweden
| | | | - Marité Cárdenas
- Biofilms Research
Centre for Biointerfaces and Biomedical Science Department, Faculty
of Health and Society, Malmo University, Malmo 20506, Sweden
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43
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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44
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Abstract
Spontaneous solute and solvent permeation through membranes is of vital importance to human life, be it gas exchange in red blood cells, metabolite excretion, drug/toxin uptake, or water homeostasis. Knowledge of the underlying molecular mechanisms is the sine qua non of every functional assignment to membrane transporters. The basis of our current solubility diffusion model was laid by Meyer and Overton. It correlates the solubility of a substance in an organic phase with its membrane permeability. Since then, a wide range of studies challenging this rule have appeared. Commonly, the discrepancies have their origin in ill-used measurement approaches, as we demonstrate on the example of membrane CO2 transport. On the basis of the insight that scanning electrochemical microscopy offered into solute concentration distributions in immediate membrane vicinity of planar membranes, we analyzed the interplay between chemical reactions and diffusion for solvent transport, weak acid permeation, and enzymatic reactions adjacent to membranes. We conclude that buffer reactions must also be considered in spectroscopic investigations of weak acid transport in vesicular suspensions. The evaluation of energetic contributions to membrane translocation of charged species demonstrates the compatibility of the resulting membrane current with the solubility diffusion model. A local partition coefficient that depends on membrane penetration depth governs spontaneous membrane translocation of both charged and uncharged molecules. It is determined not only by the solubility in an organic phase but also by other factors like cholesterol concentration and intrinsic electric membrane potentials.
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Affiliation(s)
- Christof Hannesschlaeger
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
| | - Andreas Horner
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
| | - Peter Pohl
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
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45
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Effects of oxidation on the physicochemical properties of polyunsaturated lipid membranes. J Colloid Interface Sci 2019; 538:404-419. [DOI: 10.1016/j.jcis.2018.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/29/2018] [Accepted: 12/02/2018] [Indexed: 12/13/2022]
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46
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Mallikarjunaiah KJ, Kinnun JJ, Petrache HI, Brown MF. Flexible lipid nanomaterials studied by NMR spectroscopy. Phys Chem Chem Phys 2019; 21:18422-18457. [DOI: 10.1039/c8cp06179c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in solid-state nuclear magnetic resonance spectroscopy inform the emergence of material properties from atomistic-level interactions in membrane lipid nanostructures.
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Affiliation(s)
- K. J. Mallikarjunaiah
- Department of Chemistry and Biochemistry
- University of Arizona
- Tucson
- USA
- Department of Physics
| | - Jacob J. Kinnun
- Department of Physics
- Indiana University-Purdue University
- Indianapolis
- USA
| | - Horia I. Petrache
- Department of Physics
- Indiana University-Purdue University
- Indianapolis
- USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry
- University of Arizona
- Tucson
- USA
- Department of Physics
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47
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Otto F, Brezesinski G, van Hoogevest P, Neubert R. Physicochemical characterization of natural phospholipid excipients with varying PC content. Colloids Surf A Physicochem Eng Asp 2018. [DOI: 10.1016/j.colsurfa.2018.08.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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48
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Thermodynamic Characterization of Mixed Monolayers of a Novel Oxazolidine Derivative and Phospholipids. J Membr Biol 2018; 251:723-733. [PMID: 30283978 DOI: 10.1007/s00232-018-0049-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/27/2018] [Indexed: 10/28/2022]
Abstract
Oxazolidine derivatives (OxD) are five ring-membered compounds that contain at least one oxygen and nitrogen in their molecular structure. OxD are known due to several therapeutic activities such as anticancer and antibiotic properties. In this paper, we performed a thermodynamic analysis of the mixed films composed by dipalmitoylphosphatidylglycerol (DPPG), dipalmitoylphosphoethanolamine (DPPE), dipalmitoyl phosphatidylcholine (DPPC) or L-α phosphatidylcholine (PC) with a novel oxazolidine derivate (OxD). Relevant thermodynamic parameters such as excess areas (ΔAE), excess free energies (ΔG), and Gibbs free energy of mixing (AGmix) were derived from the surface pressure data. The topographical analysis was performed using atomic force microscopy. Based on the calculated values of the thermodynamic parameters, we observed that the miscibility of the mixed films was directly dependent on their composition. DPPG/OxD and DPPE/OxD systems present the best-mixed character at low pressures at OxD molar fraction equivalent to 0.25.
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49
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Wlodek M, Kolasinska-Sojka M, Szuwarzynski M, Kereïche S, Kovacik L, Zhou L, Islas L, Warszynski P, Briscoe WH. Supported lipid bilayers with encapsulated quantum dots (QDs) via liposome fusion: effect of QD size on bilayer formation and structure. NANOSCALE 2018; 10:17965-17974. [PMID: 30226255 DOI: 10.1039/c8nr05877f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding interactions between functional nanoparticles and lipid bilayers is important to many emerging biomedical and bioanalytical applications. In this paper, we report incorporation of hydrophobic cadmium sulphide quantum dots (CdS QDs) into mixed 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) liposomes, and into their supported bilayers (SLBs). The QDs were found embedded in the hydrophobic regions of the liposomes and the supported bilayers, which retained the QD fluorescent properties. In particular, we studied the effect of the QD size (2.7-5.4 nm in diameter) on the formation kinetics and structure of the supported POPC/POPE bilayers, monitored in situ using quartz crystal microbalance with dissipation monitoring (QCM-D), as the liposomes ruptured onto the substrate. The morphology of the obtained QD-lipid hybrid bilayers was studied using atomic force microscopy (AFM), and their structure by synchrotron X-ray reflectivity (XRR). It was shown that the incorporation of hydrophobic QDs promoted bilayer formation on the PEI cushion, evident from the rupture and fusion of the QD-endowed liposomes at a lower surface coverage compared to the liposomes without QDs. Furthermore, the degree of disruption in the supported bilayer structure caused by the QDs was found to be correlated with the QD size. Our results provide mechanistic insights into the kinetics of the rupturing and formation process of QD-endowed supported lipid bilayers via liposome fusion on polymer cushions.
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Affiliation(s)
- Magdalena Wlodek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
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50
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Parkkila P, Elderdfi M, Bunker A, Viitala T. Biophysical Characterization of Supported Lipid Bilayers Using Parallel Dual-Wavelength Surface Plasmon Resonance and Quartz Crystal Microbalance Measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8081-8091. [PMID: 29894192 PMCID: PMC6203186 DOI: 10.1021/acs.langmuir.8b01259] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/29/2018] [Indexed: 05/30/2023]
Abstract
Supported lipid bilayers (SLBs) have been used extensively as an effective model of biological membranes, in the context of in vitro biophysics research, and the membranes of liposomes, in the context of the development of nanoscale drug delivery devices. Despite numerous surface-sensitive techniques having been applied to their study, the comprehensive optical characterization of SLBs using surface plasmon resonance (SPR) has not been conducted. In this study, Fresnel multilayer analysis is utilized to effectively calculate layer parameters (thickness and refractive indices) with the aid of dual-wavelength and dispersion coefficient analysis, in which the linear change in the refractive index as a function of wavelength is assumed. Using complementary information from impedance-based quartz crystal microbalance experiments, biophysical properties, for example, area-per-lipid-molecule and the quantity of lipid-associated water molecules, are calculated for different lipid types and mixtures, one of which is representative of a raft-forming lipid mixture. It is proposed that the hydration layer beneath the bilayer is, in fact, an integral part of the measured optical signal. Also, the traditional Jung model analysis and the ratio of SPR responses are investigated in terms of assessing the structure of the lipid layer that is formed.
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Affiliation(s)
- Petteri Parkkila
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Mohamed Elderdfi
- Department
of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | - Alex Bunker
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Tapani Viitala
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
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