1
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Bacalum M, Radu M, Osella S, Knippenberg S, Ameloot M. Generalized polarization and time-resolved fluorescence provide evidence for different populations of Laurdan in lipid vesicles. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 250:112833. [PMID: 38141326 DOI: 10.1016/j.jphotobiol.2023.112833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/29/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
The solvatochromic dye Laurdan is widely used in sensing the lipid packing of both model and biological membranes. The fluorescence emission maximum shifts from about 440 nm (blue channel) in condensed membranes (So) to about 490 nm (green channel) in the liquid-crystalline phase (Lα). Although the fluorescence intensity based generalized polarization (GP) is widely used to characterize lipid membranes, the fluorescence lifetime of Laurdan, in the blue and the green channel, is less used for that purpose. Here we explore the correlation between GP and fluorescence lifetimes by spectroscopic measurements on the So and Lα phases of large unilamellar vesicles of DMPC and DPPC. A positive correlation between GP and the lifetimes is observed in each of the optical channels for the two lipid phases. Microfluorimetric determinations on giant unilamellar vesicles of DPPC and DOPC at room temperature are performed under linearly polarized two-photon excitation to disentangle possible subpopulations of Laurdan at a scale below the optical resolution. Fluorescence intensities, GP and fluorescence lifetimes depend on the angle between the orientation of the linear polarization of the excitation light and the local normal to the membrane of the optical cross-section. This angular variation depends on the lipid phase and the emission channel. GP and fluorescence intensities in the blue and green channel in So and in the blue channel in Lα exhibit a minimum near 90o. Surprisingly, the intensity in the green channel in Lα reaches a maximum near 90o. The fluorescence lifetimes in the two optical channels also reach a pronounced minimum near 90o in So and Lα, apart from the lifetime in the blue channel in Lα where the lifetime is short with minimal angular variation. To our knowledge, these experimental observations are the first to demonstrate the existence of a bent conformation of Laurdan in lipid membranes, as previously suggested by molecular dynamics calculations.
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Affiliation(s)
- Mihaela Bacalum
- Department of Life and Environmental Physics, Horia Hulubei National Institute for Physics and Nuclear Engineering, Reactorului, 30, Măgurele 077125, Romania
| | - Mihai Radu
- Department of Life and Environmental Physics, Horia Hulubei National Institute for Physics and Nuclear Engineering, Reactorului, 30, Măgurele 077125, Romania
| | - Silvio Osella
- Chemical and Biological Systems Simulation Lab, Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Stefan Knippenberg
- Biomedical Research Institute, Hasselt University, Agoralaan Bldg. C, 3590 Diepenbeek, Belgium; Theory Lab, Hasselt University, Agoralaan Bldg. D, 3590 Diepenbeek, Belgium
| | - Marcel Ameloot
- Biomedical Research Institute, Hasselt University, Agoralaan Bldg. C, 3590 Diepenbeek, Belgium.
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2
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Nieto-Garai JA, Lorizate M, Contreras FX. Shedding light on membrane rafts structure and dynamics in living cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2022; 1864:183813. [PMID: 34748743 DOI: 10.1016/j.bbamem.2021.183813] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022]
Abstract
Cellular membranes are fundamental building blocks regulating an extensive repertoire of biological functions. These structures contain lipids and membrane proteins that are known to laterally self-aggregate in the plane of the membrane, forming defined membrane nanoscale domains essential for protein activity. Membrane rafts are described as heterogeneous, dynamic, and short-lived cholesterol- and sphingolipid-enriched membrane nanodomains (10-200 nm) induced by lipid-protein and lipid-lipid interactions. Those membrane nanodomains have been extensively characterized using model membranes and in silico methods. However, despite the development of advanced fluorescence microscopy techniques, undoubted nanoscale visualization by imaging techniques of membrane rafts in the membrane of unperturbed living cells is still uncompleted, increasing the skepticism about their existence. Here, we broadly review recent biochemical and microscopy techniques used to investigate membrane rafts in living cells and we enumerate persistent open questions to answer before unlocking the mystery of membrane rafts in living cells.
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Affiliation(s)
- Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Bilbao, Spain.
| | - Maier Lorizate
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Bilbao, Spain
| | - F-Xabier Contreras
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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3
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Lee HS, Kim Y. Myricetin Disturbs the Cell Wall Integrity and Increases the Membrane Permeability of Candida albicans. J Microbiol Biotechnol 2022; 32:37-45. [PMID: 34750288 PMCID: PMC9628827 DOI: 10.4014/jmb.2110.10014] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022]
Abstract
The fungal cell wall and membrane are the principal targets of antifungals. Herein, we report that myricetin exerts antifungal activity against Candida albicans by damaging the cell wall integrity and notably enhancing the membrane permeability. In the presence of sorbitol, an osmotic protectant, the minimum inhibitory concentration (MIC) of myricetin against C. albicans increased from 20 to 40 and 80 μg/ml in 24 and 72 h, respectively, demonstrating that myricetin disturbs the cell wall integrity of C. albicans. Fluorescence microscopic images showed the presence of propidium iodidestained C. albicans cells, indicating the myricetin-induced initial damage of the cell membrane. The effects of myricetin on the membrane permeability of C. albicans cells were assessed using crystal violet-uptake and intracellular material-leakage assays. The percentage uptakes of crystal violet for myricetin-treated C. albicans cells at 1×, 2×, and 4× the MIC of myricetin were 36.5, 60.6, and 79.4%, respectively, while those for DMSO-treated C. albicans cells were 28.2, 28.9, and 29.7%, respectively. Additionally, myricetin-treated C. albicans cells showed notable DNA and protein leakage, compared with the DMSO-treated controls. Furthermore, treatment of C. albicans cells with 1× the MIC of myricetin showed a 17.2 and 28.0% reduction in the binding of the lipophilic probes diphenylhexatriene and Nile red, respectively, indicating that myricetin alters the lipid components or order in the C. albicans cell membrane, leading to increased membrane permeability. Therefore, these data will provide insights into the pharmacological worth of myricetin as a prospective antifungal for treating C. albicans infections.
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Affiliation(s)
- Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejongsi 30019, Republic of Korea
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, Jecheon 27136, Republic of Korea,Corresponding author Phone: +82-43-649-1346 Fax: +82-43-649-1341 E-mail:
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4
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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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5
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Hornum M, Kongsted J, Reinholdt P. Computational and photophysical characterization of a Laurdan malononitrile derivative. Phys Chem Chem Phys 2021; 23:9139-9146. [PMID: 33885105 DOI: 10.1039/d1cp00831e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The malononitrile group is considered one of the strongest natural electron-withdrawing groups in a chemist's arsenal. However, surprisingly little is known about how this group functions in push-pull fluorophores. In a recent computational study, we reported that replacing the ketone group of the traditional push-pull dye Laurdan with a malononitrile group significantly improves the optical properties while retaining the membrane behavior of the parent molecule Laurdan. Motivated by these results, we report here the synthesis and photophysical characterization of the said compound, 6-(1-undecyl-2,2-dicyanovinyl)-N,N-dimethyl-2-naphthylamine (CN-Laurdan). To our surprise, this new CN-Laurdan probe is found to be much less bright than the parent Laurdan due to a large drop in the fluorescence quantum yield. Using computational methods, we determine that the origin of this low quantum yield is related to the existence of a non-radiative decay pathway related to a rotation of the malononitrile moiety, suggesting that the molecule could nonetheless function very well as a molecular rotor. We confirm experimentally that CN-Laurdan functions as a molecular rotor by measuring the quantum yield in methanol/glycerol mixtures of increasing viscosity. Specifically, we found a consistent increase in the quantum yield across the entire range of tested viscosities.
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Affiliation(s)
- Mick Hornum
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M DK-5230, Denmark.
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6
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Suhaj A, Gowland D, Bonini N, Owen DM, Lorenz CD. Laurdan and Di-4-ANEPPDHQ Influence the Properties of Lipid Membranes: A Classical Molecular Dynamics and Fluorescence Study. J Phys Chem B 2020; 124:11419-11430. [PMID: 33275430 DOI: 10.1021/acs.jpcb.0c09496] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Environmentally sensitive (ES) dyes have been used for many decades to study the lipid order of cell membranes, as different lipid phases play a crucial role in a wide variety of cell processes. Yet, the understanding of how ES dyes behave, interact, and affect membranes at the atomistic scale is lacking, partially due to the lack of molecular dynamics (MD) models of these dyes. Here, we present ground- and excited-state MD models of commonly used ES dyes, Laurdan and di-4-ANEPPDHQ, and use MD simulations to study the behavior of these dyes in a disordered and an ordered membrane. We also investigate the effect that these two dyes have on the hydration and lipid order of the membranes, where we see a significant effect on the hydration of lipids proximal to the dyes. These findings are combined with experimental fluorescence experiments of ordered and disordered vesicles and live HeLa cells stained by the aforementioned dyes, where the generalized polarization (GP) values were measured at different concentrations of the dyes. We observe a small but significant decrease of GP at higher Laurdan concentrations in vesicles, while the same effect is not observed in cell membranes. The opposite effect is observed with di-4-ANEPPDHQ where no significant change in GP is seen for vesicles but a very substantial and significant decrease is seen in cell membranes. Together, our results show the profound effect that ES dyes have on membranes, and the presented MD models will be important for further understanding of these effects.
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Affiliation(s)
- Adam Suhaj
- Biological Physics and Soft Matter Group, Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Duncan Gowland
- Theory & Simulation of Condensed Matter Group, Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Nicola Bonini
- Theory & Simulation of Condensed Matter Group, Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, Department of Mathematics and Centre of Membrane Proteins and Receptors, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Christian D Lorenz
- Biological Physics and Soft Matter Group, Department of Physics, King's College London, London WC2R 2LS, United Kingdom
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7
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Zhanghao K, Liu W, Li M, Wu Z, Wang X, Chen X, Shan C, Wang H, Chen X, Dai Q, Xi P, Jin D. High-dimensional super-resolution imaging reveals heterogeneity and dynamics of subcellular lipid membranes. Nat Commun 2020; 11:5890. [PMID: 33208737 PMCID: PMC7674432 DOI: 10.1038/s41467-020-19747-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Lipid membranes are found in most intracellular organelles, and their heterogeneities play an essential role in regulating the organelles' biochemical functionalities. Here we report a Spectrum and Polarization Optical Tomography (SPOT) technique to study the subcellular lipidomics in live cells. Simply using one dye that universally stains the lipid membranes, SPOT can simultaneously resolve the membrane morphology, polarity, and phase from the three optical-dimensions of intensity, spectrum, and polarization, respectively. These high-throughput optical properties reveal lipid heterogeneities of ten subcellular compartments, at different developmental stages, and even within the same organelle. Furthermore, we obtain real-time monitoring of the multi-organelle interactive activities of cell division and successfully reveal their sophisticated lipid dynamics during the plasma membrane separation, tunneling nanotubules formation, and mitochondrial cristae dissociation. This work suggests research frontiers in correlating single-cell super-resolution lipidomics with multiplexed imaging of organelle interactome.
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Affiliation(s)
- Karl Zhanghao
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, P.R. China.
- Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China.
| | - Wenhui Liu
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Meiqi Li
- Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China
| | - Zihan Wu
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, P.R. China
| | - Xiao Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, 100871, Beijing, China
| | - Xingye Chen
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Chunyan Shan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, 100871, Beijing, China
| | - Haoqian Wang
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Xiaowei Chen
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, 100871, Beijing, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Peng Xi
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, P.R. China.
- Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China.
| | - Dayong Jin
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, P.R. China.
- Institute for Biomedical Materials & Devices (IBMD), University of Technology Sydney, Sydney, NSW 2007, Australia.
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8
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Kofod CS, Prioli S, Hornum M, Kongsted J, Reinholdt P. Computational Characterization of Novel Malononitrile Variants of Laurdan with Improved Photophysical Properties for Sensing in Membranes. J Phys Chem B 2020; 124:9526-9534. [PMID: 33074683 DOI: 10.1021/acs.jpcb.0c06011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent probes are powerful tools for improving our understanding of cellular membranes and other complex biological environments. Using simulations, we gain atomistic and electronic insights into the effectiveness of the probes. In the current work, we have used various computational approaches to comprehensively investigate the properties of the fluorescent probe Laurdan and two Laurdan-like probes: AADAL and ECL. In addition, we propose the development of their corresponding novel malononitrile variants, which are computationally characterized herein. For the candidate probes, electronic structure calculations were used to rationalize their optical properties, including their ability for two-photon activation, and molecular dynamics simulations were used to unravel atomistic details of their functioning within lipid bilayers. While Laurdan, AADAL, and ECL were found to have very similar optical and membrane partitioning profiles, their malononitrile variants were found to show significantly improved optical properties, especially in regard to two-photon cross sections, and they appear to retain the desired membrane characteristics of the parent Laurdan molecule.
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Affiliation(s)
- Cecilie Søderlund Kofod
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Salvatore Prioli
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Mick Hornum
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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9
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Filipe HAL, Moreno MJ, Loura LMS. The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations. Molecules 2020; 25:E3424. [PMID: 32731549 PMCID: PMC7435664 DOI: 10.3390/molecules25153424] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022] Open
Abstract
Fluorescent probes have been employed for more than half a century to study the structure and dynamics of model and biological membranes, using spectroscopic and/or microscopic experimental approaches. While their utilization has led to tremendous progress in our knowledge of membrane biophysics and physiology, in some respects the behavior of bilayer-inserted membrane probes has long remained inscrutable. The location, orientation and interaction of fluorophores with lipid and/or water molecules are often not well known, and they are crucial for understanding what the probe is actually reporting. Moreover, because the probe is an extraneous inclusion, it may perturb the properties of the host membrane system, altering the very properties it is supposed to measure. For these reasons, the need for independent methodologies to assess the behavior of bilayer-inserted fluorescence probes has been recognized for a long time. Because of recent improvements in computational tools, molecular dynamics (MD) simulations have become a popular means of obtaining this important information. The present review addresses MD studies of all major classes of fluorescent membrane probes, focusing in the period between 2011 and 2020, during which such work has undergone a dramatic surge in both the number of studies and the variety of probes and properties accessed.
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Affiliation(s)
- Hugo A. L. Filipe
- Chemistry Department, Coimbra Chemistry Center, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal;
| | - Maria João Moreno
- Coimbra Chemistry Center and CNC—Center for Neuroscience and Cell Biology, Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal;
| | - Luís M. S. Loura
- Coimbra Chemistry Center and CNC—Center for Neuroscience and Cell Biology, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
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10
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Licari G, Strakova K, Matile S, Tajkhorshid E. Twisting and tilting of a mechanosensitive molecular probe detects order in membranes. Chem Sci 2020; 11:5637-5649. [PMID: 32864081 PMCID: PMC7433777 DOI: 10.1039/d0sc02175j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/29/2020] [Indexed: 12/29/2022] Open
Abstract
Lateral forces in biological membranes affect a variety of dynamic cellular processes. Recent synthetic efforts have introduced fluorescent "flippers" as environment-sensitive planarizable push-pull probes that can detect lipid packing and membrane tension, and respond to lipid-induced mechanical forces by a shift in their spectroscopic properties. Herein, we investigate the molecular origin of the mechanosensitivity of the best known flipper, Flipper-TR, by an extended set of molecular dynamics (MD) simulations in membranes of increasing complexity and under different physicochemical conditions, revealing unprecedented details of the sensing process. Simulations enabled by accurate refinement of Flipper-TR force field using quantum mechanical calculations allowed us to unambiguously correlate the planarization of the two fluorescent flippers to spectroscopic response. In particular, Flipper-TR conformation exhibits bimodal distribution in disordered membranes and a unimodal distribution in highly ordered membranes. Such dramatic change was associated with a shift in Flipper-TR excitation spectra, as supported both by our simulated and experimentally-measured spectra. Flipper-TR sensitivity to phase-transition is confirmed by a temperature-jump protocol that alters the lipid phase of an ordered membrane, triggering an instantaneous mechanical twisting of the probe. Simulations show that the probe is also sensitive to surface tension, since even in a naturally disordered membrane, the unimodal distribution of coplanar flippers can be achieved if a sufficiently negative surface tension is applied to the membrane. MD simulations in ternary mixtures containing raft-like nanodomains show that the probe can discriminate lipid domains in phase-separated complex bilayers. A histogram-based approach, called DOB-phase classification, is introduced that can differentiate regions of disordered and ordered lipid phases by comparing dihedral distributions of Flipper-TR. Moreover, a new sensing mechanism involving the orientation of Flipper-TR is elucidated, corroborating experimental evidence that the probe tilt angle is strongly dependent on lipid ordering. The obtained atomic-resolution description of Flipper-TR mechanosensitivity is key to the interpretation of experimental data and to the design of novel mechanosensors with improved spectroscopic properties.
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Affiliation(s)
- Giuseppe Licari
- NIH Center for Macromolecular Modeling and Bioinformatics , Beckman Institute for Advanced Science and Technology , Department of Biochemistry , Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois , USA . ; Tel: +1-217-244-6914
| | - Karolina Strakova
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland
| | - Stefan Matile
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics , Beckman Institute for Advanced Science and Technology , Department of Biochemistry , Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois , USA . ; Tel: +1-217-244-6914
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11
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Lubart Q, Hannestad JK, Pace H, Fjällborg D, Westerlund F, Esbjörner EK, Bally M. Lipid vesicle composition influences the incorporation and fluorescence properties of the lipophilic sulphonated carbocyanine dye SP-DiO. Phys Chem Chem Phys 2020; 22:8781-8790. [DOI: 10.1039/c9cp04158c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lipid membrane composition influences insertion efficiency and photophysical properties of lipophilic membrane-inserting dyes.
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Affiliation(s)
- Quentin Lubart
- Division of Biological Physics
- Department of Physics
- Chalmers University of Technology
- 41296 Gothenburg
- Sweden
| | - Jonas K. Hannestad
- Division of Biological Physics
- Department of Physics
- Chalmers University of Technology
- 41296 Gothenburg
- Sweden
| | - Hudson Pace
- Department of Integrative Medical Biology
- Umeå University
- 90185 Umeå
- Sweden
| | - Daniel Fjällborg
- Division of Biological Physics
- Department of Physics
- Chalmers University of Technology
- 41296 Gothenburg
- Sweden
| | - Fredrik Westerlund
- Division of Chemical Biology
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- 41296 Gothenburg
- Sweden
| | - Elin K. Esbjörner
- Division of Chemical Biology
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- 41296 Gothenburg
- Sweden
| | - Marta Bally
- Department of Clinical Microbiology & Wallenberg Centre for Molecular Medicine
- Umeå University
- 90185 Umeå
- Sweden
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12
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Sulfolobus acidocaldarius Microvesicles Exhibit Unusually Tight Packing Properties as Revealed by Optical Spectroscopy. Int J Mol Sci 2019; 20:ijms20215308. [PMID: 31731418 PMCID: PMC6862217 DOI: 10.3390/ijms20215308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/23/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022] Open
Abstract
In this study, we used optical spectroscopy to characterize the physical properties of microvesicles released from the thermoacidophilic archaeon Sulfolobus acidocaldarius (Sa-MVs). The most abundant proteins in Sa-MVs are the S-layer proteins, which self-assemble on the vesicle surface forming an array of crystalline structures. Lipids in Sa-MVs are exclusively bipolar tetraethers. We found that when excited at 275 nm, intrinsic protein fluorescence of Sa-MVs at 23 °C has an emission maximum at 303 nm (or 296 nm measured at 75 °C), which is unusually low for protein samples containing multiple tryptophans and tyrosines. In the presence of 10–11 mM of the surfactant n-tetradecyl-β-d-maltoside (TDM), Sa-MVs were disintegrated, the emission maximum of intrinsic protein fluorescence was shifted to 312 nm, and the excitation maximum was changed from 288 nm to 280.5 nm, in conjunction with a significant decrease (>2 times) in excitation band sharpness. These data suggest that most of the fluorescent amino acid residues in native Sa-MVs are in a tightly packed protein matrix and that the S-layer proteins may form J-aggregates. The membranes in Sa-MVs, as well as those of unilamellar vesicles (LUVs) made of the polar lipid fraction E (PLFE) tetraether lipids isolated from S. acidocaldarius (LUVPLFE), LUVs reconstituted from the tetraether lipids extracted from Sa-MVs (LUVMV) and LUVs made of the diester lipids, were investigated using the probe 6-dodecanoyl-2-dimethylaminonaphthalene (Laurdan). The generalized polarization (GP) values of Laurdan in tightly packed Sa-MVs, LUVMV, and LUVPLFE were found to be much lower than those obtained from less tightly packed DPPC gel state, which echoes the previous finding that the GP values from tetraether lipid membranes cannot be directly compared with the GP values from diester lipid membranes, due to differences in probe disposition. Laurdan’s GP and red-edge excitation shift (REES) values in Sa-MVs and LUVMV decrease with increasing temperature monotonically with no sign for lipid phase transition. Laurdan’s REES values are high (9.3–18.9 nm) in the tetraether lipid membrane systems (i.e., Sa-MVs, LUVMV and LUVPLFE) and low (0.4–5.0 nm) in diester liposomes. The high REES and low GP values suggest that Laurdan in tetraether lipid membranes, especially in the membrane of Sa-MVs, is in a very motionally restricted environment, bound water molecules and the polar moieties in the tetraether lipid headgroups strongly interact with Laurdan’s excited state dipole moment, and “solvent” reorientation around Laurdan’s chromophore in tetraether lipid membranes occurs very slowly compared to Laurdan’s lifetime.
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Osella S, Smisdom N, Ameloot M, Knippenberg S. Conformational Changes as Driving Force for Phase Recognition: The Case of Laurdan. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11471-11481. [PMID: 31403301 DOI: 10.1021/acs.langmuir.9b01840] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The development of a universal probe to assess the phase of a lipid membrane is one of the most ambitious goals for fluorescence spectroscopy. The ability of a well-known molecule as Laurdan to reach this aim is here exploited as the behavior of the probe is fully characterized in a dipalmitoylphosphatidylcholine (DPPC) solid gel (So) phase by means of molecular dynamics simulations. Laurdan can take two conformations, depending on whether the carbonyl oxygen points toward the β-position of the naphthalene core (Conf-I) or to the α-position (Conf-II). We observe that Conf-I has an elongated form in this environment, whereas Conf-II takes an L-shape. Interestingly, our theoretical calculations show that these two conformations behave in an opposite way from what is reported in the literature for a DPPC membrane in a liquid disordered (Ld) phase, where Conf-I assumes an L-shape and Conf-II is elongated. Moreover, our results show that in DPPC (So) no intermixing between the conformations is present, whereas it has been seen in a fluid environment such as DOPC (Ld). Through a careful analysis of angle distributions and by means of the rotational autocorrelation function, we predict that the two conformers of Laurdan behave differently in different membrane environments.
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Affiliation(s)
- Silvio Osella
- Chemical and Biological Systems Simulation Lab, Centre of New Technologies , University of Warsaw , Banacha 2C , 02-097 Warsaw , Poland
| | - Nick Smisdom
- Biomedical Research Institute , Hasselt University , Agoralaan Building C , 3590 Diepenbeek , Belgium
| | - Marcel Ameloot
- Biomedical Research Institute , Hasselt University , Agoralaan Building C , 3590 Diepenbeek , Belgium
| | - Stefan Knippenberg
- Biomedical Research Institute , Hasselt University , Agoralaan Building C , 3590 Diepenbeek , Belgium
- Department of Theoretical Chemistry and Biology, School of Biotechnology , Royal Institute of Technology , SE-10691 Stockholm , Sweden
- RCPTM, Department of Physical Chemistry, Fac. Sciences , Palacký University , 771 46 Olomouc , Czech Republic
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Pederzoli M, Wasif Baig M, Kývala M, Pittner J, Cwiklik L. Photophysics of BODIPY-Based Photosensitizer for Photodynamic Therapy: Surface Hopping and Classical Molecular Dynamics. J Chem Theory Comput 2019; 15:5046-5057. [PMID: 31390517 DOI: 10.1021/acs.jctc.9b00533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Halogenated BODIPY derivatives are emerging as important candidates for photodynamic therapy of cancer cells due to their high triplet quantum yield. We probed fundamental photophysical properties and interactions with biological environments of such photosensitizers. To this end, we employed static TD-DFT quantum chemical calculations as well as TD-DFT surface hopping molecular dynamics on potential energy surfaces resulting from the eigenstates of the total electronic Hamiltonian including the spin-orbit (SO) coupling. Matrix elements of an effective one-electron spin-orbit Hamiltonian between singlet and triplet configuration interaction singles (CIS) auxiliary wave functions are calculated using a new code capable of dealing with singlets and both restricted and unrestricted triplets built up from up to three different and independent sets of (singlet, alpha, and beta) molecular orbitals. The interaction with a biological environment was addressed by using classical molecular dynamics (MD) in a scheme that implicitly accounts for electronically excited states. For the surface hopping trajectories, an accelerated MD approach was used, in which the SO couplings are scaled up, to make the calculations computationally feasible, and the lifetimes are extrapolated back to unscaled SO couplings. The lifetime of the first excited singlet state estimated by semiclassical surface hopping simulations is 139 ± 75 ps. Classical MD demonstrates that halogenated BODIPY in the ground state, in contrast to the unsubstituted one, is stable in the headgroup region of minimalistic cell membrane models, and while in the triplet state, the molecule relocates to the membrane interior ready for further steps of photodynamic therapy.
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Affiliation(s)
- Marek Pederzoli
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 2155/3 , 18223 Prague 8 , Czech Republic.,Faculty of Science, Department of Physical and Macromolecular Chemistry , Charles University in Prague , Hlavova 8 , 12840 Prague , Czech Republic
| | - Mirza Wasif Baig
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 2155/3 , 18223 Prague 8 , Czech Republic.,Faculty of Science, Department of Physical and Macromolecular Chemistry , Charles University in Prague , Hlavova 8 , 12840 Prague , Czech Republic
| | - Mojmír Kývala
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Prague 6 , Czech Republic
| | - Jiří Pittner
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 2155/3 , 18223 Prague 8 , Czech Republic
| | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 2155/3 , 18223 Prague 8 , Czech Republic.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Prague 6 , Czech Republic
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