1
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Ragaller F, Andronico L, Sykora J, Kulig W, Rog T, Urem YB, Abhinav, Danylchuk DI, Hof M, Klymchenko A, Amaro M, Vattulainen I, Sezgin E. Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties. Open Biol 2022; 12:220175. [PMID: 36099931 PMCID: PMC9470265 DOI: 10.1098/rsob.220175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades, several environment-sensitive probes have been developed and become popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we characterized the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration (cis versus trans), phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question.
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Affiliation(s)
- Franziska Ragaller
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Luca Andronico
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Jan Sykora
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Rog
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Yagmur Balim Urem
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Abhinav
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Andrey Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Mariana Amaro
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
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2
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Kowalska M, Broniatowski M, Mach M, Płachta Ł, Wydro P. The effect of the polyethylene glycol chain length of a lipopolymer (DSPE-PEGn) on the properties of DPPC monolayers and bilayers. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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3
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Osella S, Knippenberg S. The influence of lipid membranes on fluorescent probes' optical properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183494. [PMID: 33129783 DOI: 10.1016/j.bbamem.2020.183494] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND Organic fluorophores embedded in lipid bilayers can nowadays be described by a multiscale computational approach. Combining different length and time scales, a full characterization of the probe localization and optical properties led to novel insight into the effect of the environments. SCOPE OF REVIEW Following an introduction on computational advancements, three relevant probes are reviewed that delineate how a multiscale approach can lead to novel insight into the probes' (non) linear optical properties. Attention is paid to the quality of the theoretical description of the optical techniques. MAJOR CONCLUSIONS Computation can assess a priori novel probes' optical properties and guide the analysis and interpretation of experimental data in novel studies. The properties can be used to gain information on the phase and condition of the surrounding biological environment. GENERAL SIGNIFICANCE Computation showed that a canonical view on some of the probes should be revisited and adapted.
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Affiliation(s)
- Silvio Osella
- Biological Systems Simulation Lab, Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland.
| | - Stefan Knippenberg
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic; Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden; Theoretical Physics, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
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4
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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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5
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Modulation effect of core-wall ratio on the stability and antibacterial activity of cinnamaldehyde liposomes. Chem Phys Lipids 2019; 223:104790. [DOI: 10.1016/j.chemphyslip.2019.104790] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/30/2019] [Accepted: 06/26/2019] [Indexed: 11/19/2022]
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6
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Poojari C, Wilkosz N, Lira RB, Dimova R, Jurkiewicz P, Petka R, Kepczynski M, Róg T. Behavior of the DPH fluorescence probe in membranes perturbed by drugs. Chem Phys Lipids 2019; 223:104784. [PMID: 31199906 DOI: 10.1016/j.chemphyslip.2019.104784] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/09/2019] [Accepted: 06/08/2019] [Indexed: 12/22/2022]
Abstract
1,6-Diphenyl-1,3,5-hexatriene (DPH) is one of the most commonly used fluorescent probes to study dynamical and structural properties of lipid bilayers and cellular membranes via measuring steady-state or time-resolved fluorescence anisotropy. In this study, we present a limitation in the use of DPH to predict the order of lipid acyl chains when the lipid bilayer is doped with itraconazole (ITZ), an antifungal drug. Our steady-state fluorescence anisotropy measurements showed a significant decrease in fluorescence anisotropy of DPH embedded in the ITZ-containing membrane, suggesting a substantial increase in membrane fluidity, which indirectly indicates a decrease in the order of the hydrocarbon chains. This result or its interpretation is in disagreement with the fluorescence recovery after photobleaching measurements and molecular dynamics (MD) simulation data. The results of these experiments and calculations indicate an increase in the hydrocarbon chain order. The MD simulations of the bilayer containing both ITZ and DPH provide explanations for these observations. Apparently, in the presence of the drug, the DPH molecules are pushed deeper into the hydrophobic membrane core below the lipid double bonds, and the probe predominately adopts the orientation of the ITZ molecules that is parallel to the membrane surface, instead of orienting parallel to the lipid acyl chains. For this reason, DPH anisotropy provides information related to the less ordered central region of the membrane rather than reporting the properties of the upper segments of the lipid acyl chains.
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Affiliation(s)
- Chetan Poojari
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101 Tampere, Finland
| | - Natalia Wilkosz
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Rafael B Lira
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry AS CR, v.v.i, Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Rafał Petka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland.
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, PO Box 64, FI-00014, Helsinki, Finland.
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7
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Paloncýová M, Ameloot M, Knippenberg S. Orientational distribution of DPH in lipid membranes: a comparison of molecular dynamics calculations and experimental time-resolved anisotropy experiments. Phys Chem Chem Phys 2019; 21:7594-7604. [DOI: 10.1039/c8cp07754a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The behavior of the fluorescent probe diphenylhexatriene (DPH) in different lipid phases is investigated. The rotational autocorrelation functions are calculated in order to model the time-resolved fluorescence anisotropy decay. The role of the order parameters is discussed.
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Affiliation(s)
- Markéta Paloncýová
- Department of Theoretical Chemistry and Biology
- School of Engineering Sciences in Chemistry
- Biotechnology and Health
- Royal Institute of Technology
- Stockholm
| | - Marcel Ameloot
- Biomedical Research Institute, Hasselt University
- 3590 Diepenbeek
- Belgium
| | - Stefan Knippenberg
- Department of Theoretical Chemistry and Biology
- School of Engineering Sciences in Chemistry
- Biotechnology and Health
- Royal Institute of Technology
- Stockholm
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8
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Tretiakova D, Alekseeva A, Galimzyanov T, Boldyrev A, Chernyadyev A, Ermakov Y, Batishchev O, Vodovozova E, Boldyrev I. Lateral stress profile and fluorescent lipid probes. FRET pair of probes that introduces minimal distortions into lipid packing. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2337-2347. [DOI: 10.1016/j.bbamem.2018.05.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/17/2018] [Accepted: 05/30/2018] [Indexed: 12/31/2022]
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9
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Mobarak E, Javanainen M, Kulig W, Honigmann A, Sezgin E, Aho N, Eggeling C, Rog T, Vattulainen I. How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:2436-2445. [PMID: 30028957 DOI: 10.1016/j.bbamem.2018.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 11/28/2022]
Abstract
Organic dye-tagged lipid analogs are essential for many fluorescence-based investigations of complex membrane structures, especially when using advanced microscopy approaches. However, lipid analogs may interfere with membrane structure and dynamics, and it is not obvious that the properties of lipid analogs would match those of non-labeled host lipids. In this work, we bridged atomistic simulations with super-resolution imaging experiments and biomimetic membranes to assess the performance of commonly used sphingomyelin-based lipid analogs. The objective was to compare, on equal footing, the relative strengths and weaknesses of acyl chain labeling, headgroup labeling, and labeling based on poly-ethyl-glycol (PEG) linkers in determining biomembrane properties. We observed that the most appropriate strategy to minimize dye-induced membrane perturbations and to allow consideration of Brownian-like diffusion in liquid-ordered membrane environments is to decouple the dye from a membrane by a PEG linker attached to a lipid headgroup. Yet, while the use of PEG linkers may sound a rational and even an obvious approach to explore membrane dynamics, the results also suggest that the dyes exploiting PEG linkers interfere with molecular interactions and their dynamics. Overall, the results highlight the great care needed when using fluorescent lipid analogs, in particular accurate controls.
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Affiliation(s)
- Edouard Mobarak
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland; Laboratory of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland
| | - Matti Javanainen
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland; Laboratory of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland; Laboratory of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
| | - Noora Aho
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom; Institute of Applied Optics Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany; Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Tomasz Rog
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland; Laboratory of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland; Laboratory of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; MEMPHYS - Center for Biomembrane Physics (www.memphys.dk).
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10
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Hu D, Yan L, Liu T, Xu Z, Zhao L. Solubility and diffusion behavior of compressed CO
2
in polyurethane oligomer. J Appl Polym Sci 2018. [DOI: 10.1002/app.47100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- D. Hu
- Shanghai Key Laboratory of Multiphase Materials Chemical EngineeringEast China University of Science and Technology Shanghai 200237 People's Republic of China
| | - L. Yan
- Shanghai Key Laboratory of Multiphase Materials Chemical EngineeringEast China University of Science and Technology Shanghai 200237 People's Republic of China
| | - T. Liu
- Shanghai Key Laboratory of Multiphase Materials Chemical EngineeringEast China University of Science and Technology Shanghai 200237 People's Republic of China
| | - Z. Xu
- Shanghai Key Laboratory of Multiphase Materials Chemical EngineeringEast China University of Science and Technology Shanghai 200237 People's Republic of China
| | - L. Zhao
- Shanghai Key Laboratory of Multiphase Materials Chemical EngineeringEast China University of Science and Technology Shanghai 200237 People's Republic of China
- College of Chemistry and Chemical EngineeringXinjiang University Urumqi 830046 China
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11
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Cholesterol modulates the liposome membrane fluidity and permeability for a hydrophilic molecule. Food Chem Toxicol 2018; 113:40-48. [PMID: 29337230 DOI: 10.1016/j.fct.2018.01.017] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 01/27/2023]
Abstract
The effect of cholesterol (CHOL) content on the permeability and fluidity of dipalmitoylphosphatidylcholine (DPPC) liposome membrane was investigated. Liposomes encapsulating sulforhodamine B (SRB), a fluorescent dye, were prepared by reverse phase evaporation technique (REV) at various DPPC:CHOL molar ratios (from 100:0 to 100:100). The release kinetics of SRB was studied during 48 h in buffer (pH 7.4) containing NaCl at 37 °C. The DPPC:CHOL formulations were also characterized for their size, polydispersity index and morphology. Increasing CHOL concentration induced an increase in the mean liposomes size accompanying with a shape transition from irregular to nanosized, regular and spherical vesicles. The release kinetics of SRB showed a biphasic pattern; the release data was then analyzed using different mathematical models. On the overall, the SRB release was governed by a non-Fickian diffusion during the first period (0-10 h) while it followed a Fickian diffusion between 10 and 48 h. Changes in DPPC liposome membrane fluidity of various batches (CHOL% 0, 10, 20, 30 and 100) were monitored by using 5- and 16 doxyl stearic acids (DSA) as spin labels. CHOL induced a decrease in the bilayer fluidity. Concisely, CHOL represents a critical component in modulating the release of hydrophilic molecules from lipid vesicles.
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12
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A study of zwitterionic/cationic vesicle formation and the influence of hyaluronan on this formation. Colloid Polym Sci 2017. [DOI: 10.1007/s00396-017-4103-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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do Canto AMTM, Robalo JR, Santos PD, Carvalho AJP, Ramalho JPP, Loura LMS. Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2647-2661. [PMID: 27475296 DOI: 10.1016/j.bbamem.2016.07.013] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/05/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Fluorescence spectroscopy and microscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in these membranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3-4Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using them as membrane reporters.
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Affiliation(s)
- António M T M do Canto
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - João R Robalo
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal; Theory and Bio-Systems Department, Max Planck Institute of Colloids and Interfaces, Wissenschaftspark Golm, D-14424 Potsdam, Germany
| | - Patrícia D Santos
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - Alfredo J Palace Carvalho
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - J P Prates Ramalho
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - Luís M S Loura
- Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, P-3000-548 Coimbra, Portugal; Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, P-3004-535 Coimbra, Portugal.
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14
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Filipe HAL, Bowman D, Palmeira T, Cardoso RMS, Loura LMS, Moreno MJ. Interaction of NBD-labelled fatty amines with liquid-ordered membranes: a combined molecular dynamics simulation and fluorescence spectroscopy study. Phys Chem Chem Phys 2016; 17:27534-47. [PMID: 26426766 DOI: 10.1039/c5cp04191k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A complete homologous series of fluorescent 7-nitrobenz-2-oxa-1,3-diazol-4-yl-(NBD) labelled fatty amines of varying alkyl chain lengths, NBD-Cn, inserted in 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphocholine (POPC) or N-palmitoyl sphingomyelin (SpM) bilayers, with 50 mol% and 40 mol% cholesterol (Chol), respectively, was studied using atomistic molecular dynamics simulations. For all amphiphiles in both bilayers, the NBD fluorophore locates at the interface, in a more external position than that previously observed for pure POPC bilayers. This shallower location of the NBD group agrees with the lower fluorescent quantum yield, shorter fluorescence lifetime, and higher ionisation constants (smaller pKa) determined experimentally. The more external location is also consistent with the changes measured in steady-state fluorescence anisotropy from POPC to POPC/Chol (1 : 1) vesicles. Accordingly, the equilibrium location of the NBD group within the various bilayers is mainly dictated by bilayer compositions, and is mostly unaffected by the length of the attached alkyl chain. Similarly to the behaviour observed in POPC bilayers, the longer-chained NBD-Cn amphiphiles show significant mass density near the mixed bilayers' midplanes, and the alkyl chains of the longer derivatives, mainly NBD-C16, penetrate the opposite bilayer leaflet to some extent. However, this effect is quantitatively less pronounced in these ordered bilayers than in POPC. Similarly to POPC bilayers, the effects of these amphiphiles on the structure and dynamics of the host lipid were found to be relatively mild, in comparison with acyl-chain phospholipid analogues.
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Affiliation(s)
- Hugo A L Filipe
- Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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15
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Karilainen T, Vuorela T, Vattulainen I. How Well Does BODIPY-Cholesteryl Ester Mimic Unlabeled Cholesteryl Esters in High Density Lipoprotein Particles? J Phys Chem B 2015; 119:15848-56. [DOI: 10.1021/acs.jpcb.5b10188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Topi Karilainen
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Timo Vuorela
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
- Department
of Physics, University of Helsinki, P.O. Box 43, FI-00014 Helsinki, Finland
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16
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Singh M, Bajaj A. Unraveling the impact of hydroxylation on interactions of bile acid cationic lipids with model membranes by in-depth calorimetry studies. Phys Chem Chem Phys 2015; 16:19266-74. [PMID: 25098317 DOI: 10.1039/c4cp02283a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We used eight bile acid cationic lipids differing in the number of hydroxyl groups and performed in-depth differential scanning calorimetry studies on model membranes doped with different percentages of these cationic bile acids. These studies revealed that the number and positioning of free hydroxyl groups on bile acids modulate the phase transition and co-operativity of membranes. Lithocholic acid based cationic lipids having no free hydroxyl groups gel well with dipalmitoylphosphatidylcholine (DPPC) membranes. Chenodeoxycholic acid lipids having one free hydroxyl group at the 7'-carbon position disrupt the membranes and lower their co-operativity. Deoxycholic acid and cholic acid based cationic lipids have free hydroxyl groups at the 12'-carbon position, and at 7'- and 12'-carbon positions respectively. Doping of these lipids at high concentrations increases the co-operativity of membranes suggesting that these lipids might induce self-assembly in DPPC membranes. These different modes of interactions between cationic lipids and model membranes would help in future for exploring their use in DNA/drug delivery.
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Affiliation(s)
- Manish Singh
- The Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 180 UdyogVihar, Phase I, Gurgaon-122016, Haryana, India.
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17
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Kulig W, Jurkiewicz P, Olżyńska A, Tynkkynen J, Javanainen M, Manna M, Rog T, Hof M, Vattulainen I, Jungwirth P. Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:422-32. [DOI: 10.1016/j.bbamem.2014.10.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/06/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
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18
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Robalo JR, Ramalho JPP, Huster D, Loura LMS. Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study. Phys Chem Chem Phys 2015; 17:22736-48. [DOI: 10.1039/c5cp03097h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cholesterol provides best hydrophobic matching, induces maximal membrane ordering, and displays highest preference for saturated phospholipid acyl chains, among a homologous ser ies of sterols with side chains of varying lengths.
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Affiliation(s)
- João R. Robalo
- Centro de Química de Évora and Departamento de Química
- Escola de Ciências e Tecnologia
- Universidade de Évora
- P-7000-671 Évora
- Portugal
| | - J. P. Prates Ramalho
- Centro de Química de Évora and Departamento de Química
- Escola de Ciências e Tecnologia
- Universidade de Évora
- P-7000-671 Évora
- Portugal
| | - Daniel Huster
- Institute of Medical Physics and Biophysics
- University of Leipzig
- D-04107 Leipzig
- Germany
| | - Luís M. S. Loura
- Centro de Química de Coimbra
- P-3004-535 Coimbra
- Portugal
- Faculdade de Farmácia
- Universidade de Coimbra
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19
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Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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20
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Fraenza CC, Meledandri CJ, Anoardo E, Brougham DF. The effect of cholesterol on membrane dynamics on different timescales in lipid bilayers from fast field-cycling NMR relaxometry studies of unilamellar vesicles. Chemphyschem 2014; 15:425-35. [PMID: 24482248 DOI: 10.1002/cphc.201301051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Indexed: 01/16/2023]
Abstract
The general applicability of fast field-cycling nuclear magnetic resonance relaxometry in the study of dynamics in lipid bilayers is demonstrated through analysis of binary unilamellar liposomes composed of 1,2-dioleoyl-sn-glycero-3-posphocholine (DOPC) and cholesterol. We extend an evidence-based method to simulating the NMR relaxation response, previously validated for single-component membranes, to evaluate the effect of the sterol molecule on local ordering and dynamics over multiple timescales. The relaxometric results are found to be most consistent with the partitioning of the lipid molecules into affected and unaffected portions, rather than a single averaged phase. Our analysis suggests that up to 25 mol%, each cholesterol molecule orders three DOPC molecules, providing experimental backup to the findings of many molecular dynamics studies. A methodology is established for studying dynamics on multiple timescales in unilamellar membranes of more complex compositions.
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Affiliation(s)
- Carla C Fraenza
- Laboratorio de Relaxometría y Técnicas Especiales, Grupo de Resonancia Magnética Nuclear, Facultad de Matemática, Astronomía y Física, Universidad Nacional de Córdoba and IFEG (CONICET), Córdoba (Argentina)
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21
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Fraňová MD, Repáková J, Holopainen JM, Vattulainen I. How to link pyrene to its host lipid to minimize the extent of membrane perturbations and to optimize pyrene dimer formation. Chem Phys Lipids 2014; 177:19-25. [DOI: 10.1016/j.chemphyslip.2013.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 11/30/2022]
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22
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Timr Š, Bondar A, Cwiklik L, Štefl M, Hof M, Vazdar M, Lazar J, Jungwirth P. Accurate Determination of the Orientational Distribution of a Fluorescent Molecule in a Phospholipid Membrane. J Phys Chem B 2013; 118:855-63. [DOI: 10.1021/jp4067026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Štěpán Timr
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Alexey Bondar
- Institute of Nanobiology and Structural
Biology GCRC, Academy of Sciences of the Czech Republic, v.v.i.,
Zámek 136, 37333 Nové Hrady, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská
31, 37005 České
Budějovice, Czech Republic
| | - Lukasz Cwiklik
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Martin Štefl
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Martin Hof
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Mario Vazdar
- Rudjer Bošković Institute, Division
of Organic Chemistry and Biochemistry,
POB 180, HR-10002 Zagreb, Croatia
| | - Josef Lazar
- Institute of Nanobiology and Structural
Biology GCRC, Academy of Sciences of the Czech Republic, v.v.i.,
Zámek 136, 37333 Nové Hrady, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská
31, 37005 České
Budějovice, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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23
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Hurjui I, Neamtu A, Dorohoi DO. Computational and spectral studies of 1,6-diphenyl-1,3,5-hexatriene (DPH) multicomponent solutions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 115:382-387. [PMID: 23867641 DOI: 10.1016/j.saa.2013.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 06/03/2013] [Accepted: 06/05/2013] [Indexed: 06/02/2023]
Abstract
The multicomponent 1,6-diphenyl-1,3,5-hexatriene+tetrahydrofuran+water+ethanol (DPH+THF+W+E) solutions with variable content in water were studied by computational and spectral means. The computational results that indicate micelle formation in multicomponent solutions at high water content were correlated by the independence of the wavenumber in the maximum of the fluorescence on the solvent composition.
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Affiliation(s)
- Ion Hurjui
- Biophysical and Medical Physics Dept., Faculty of Medicine, Gr. T. Popa University, 16 University Street, Iasi 700115, Romania
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24
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Robalo JR, Ramalho JPP, Loura LMS. NBD-Labeled Cholesterol Analogues in Phospholipid Bilayers: Insights from Molecular Dynamics. J Phys Chem B 2013; 117:13731-42. [DOI: 10.1021/jp406135a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- João R. Robalo
- Departamento
de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
- Centro
de Química de Évora, Universidade de Évora, Rua
Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - J. P. Prates Ramalho
- Departamento
de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
- Centro
de Química de Évora, Universidade de Évora, Rua
Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - Luís M. S. Loura
- Faculdade
de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Centro
de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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25
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Rabinovich AL, Lyubartsev AP. Computer simulation of lipid membranes: Methodology and achievements. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213070060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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26
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Hurjui I, Neamtu A, Dorohoi DO. The interaction of fluorescent DPH probes with unsaturated phospholipid membranes: A molecular dynamics study. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Wydro P. The influence of cholesterol on multicomponent Langmuir monolayers imitating outer and inner leaflet of human erythrocyte membrane. Colloids Surf B Biointerfaces 2013. [DOI: 10.1016/j.colsurfb.2012.10.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Yamamoto Y, Hori H, Kai S, Ishikawa T, Ohnishi A, Tsumura N, Morita N. Quality control of Photosystem II: reversible and irreversible protein aggregation decides the fate of Photosystem II under excessive illumination. FRONTIERS IN PLANT SCIENCE 2013; 4:433. [PMID: 24194743 PMCID: PMC3810940 DOI: 10.3389/fpls.2013.00433] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 10/11/2013] [Indexed: 05/20/2023]
Abstract
In response to excessive light, the thylakoid membranes of higher plant chloroplasts show dynamic changes including the degradation and reassembly of proteins, a change in the distribution of proteins, and large-scale structural changes such as unstacking of the grana. Here, we examined the aggregation of light-harvesting chlorophyll-protein complexes and Photosystem II core subunits of spinach thylakoid membranes under light stress with 77K chlorophyll fluorescence; aggregation of these proteins was found to proceed with increasing light intensity. Measurement of changes in the fluidity of thylakoid membranes with fluorescence polarization of diphenylhexatriene showed that membrane fluidity increased at a light intensity of 500-1,000 μmol photons m(-) (2) s(-) (1), and decreased at very high light intensity (1,500 μmol photons m(-) (2) s(-) (1)). The aggregation of light-harvesting complexes at moderately high light intensity is known to be reversible, while that of Photosystem II core subunits at extremely high light intensity is irreversible. It is likely that the reversibility of protein aggregation is closely related to membrane fluidity: increases in fluidity should stimulate reversible protein aggregation, whereas irreversible protein aggregation might decrease membrane fluidity. When spinach leaves were pre-illuminated with moderately high light intensity, the qE component of non-photochemical quenching and the optimum quantum yield of Photosystem II increased, indicating that Photosystem II/light-harvesting complexes rearranged in the thylakoid membranes to optimize Photosystem II activity. Transmission electron microscopy revealed that the thylakoids underwent partial unstacking under these light stress conditions. Thus, protein aggregation is involved in thylakoid dynamics and regulates photochemical reactions, thereby deciding the fate of Photosystem II.
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Affiliation(s)
- Yasusi Yamamoto
- *Correspondence: Yasusi Yamamoto, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan e-mail:
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29
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Krol S, Macrez R, Docagne F, Defer G, Laurent S, Rahman M, Hajipour MJ, Kehoe PG, Mahmoudi M. Therapeutic Benefits from Nanoparticles: The Potential Significance of Nanoscience in Diseases with Compromise to the Blood Brain Barrier. Chem Rev 2012; 113:1877-903. [DOI: 10.1021/cr200472g] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Silke Krol
- Fondazione IRCCS Institute of Neurology “Carlo Besta”, Milan, Italy
| | - Richard Macrez
- Inserm U919, University Caen Basse Normandie, Serine Proteases and Pathophysiology of the Neurovascular Unit, GIP CYCERON, F-14074 Caen, France
- Department of Neurology, University Hospital of Caen, Caen, France
| | - Fabian Docagne
- Inserm U919, University Caen Basse Normandie, Serine Proteases and Pathophysiology of the Neurovascular Unit, GIP CYCERON, F-14074 Caen, France
| | - Gilles Defer
- Inserm U919, University Caen Basse Normandie, Serine Proteases and Pathophysiology of the Neurovascular Unit, GIP CYCERON, F-14074 Caen, France
- Department of Neurology, University Hospital of Caen, Caen, France
| | - Sophie Laurent
- Department of General, Organic, and Biomedical Chemistry, NMR and Molecular Imaging Laboratory, University of Mons, Avenue Maistriau, 19, B-7000 Mons, Belgium
| | - Masoud Rahman
- Laboratory of NanoBio Interactions , Department of Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad J. Hajipour
- Laboratory of NanoBio Interactions , Department of Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Patrick G. Kehoe
- Dementia Research Group, School of Clinical Sciences, Faculty of Medicine and Dentistry, University of Bristol, John James Laboratories, Frenchay Hospital, Bristol, U.K
| | - Morteza Mahmoudi
- Laboratory of NanoBio Interactions , Department of Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Current address: School of Chemical Sciences, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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30
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Filipe HAL, Moreno MJ, Loura LMS. Interaction of 7-nitrobenz-2-oxa-1,3-diazol-4-yl-labeled fatty amines with 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphocholine bilayers: a molecular dynamics study. J Phys Chem B 2011; 115:10109-19. [PMID: 21749140 DOI: 10.1021/jp203532c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A complete homologous series of fluorescent 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD)-labeled fatty amines of varying alkyl chain length, NBD-C(n), inserted in 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers, was studied using atomistic molecular dynamics (MD) simulations. For all amphiphiles, the NBD fluorophore locates near the glycerol backbone/carbonyl region of POPC and establishes stable hydrogen bonding with POPC ester oxygen atoms. Small differences observed in the transverse location of the fluorophore correlate with other calculated parameters and with small discrepancies recently measured in the photophysical properties of the molecules. The longer-chained NBD-C(n) amphiphiles show significant mass density near the bilayer midplane, and the chains of these derivatives interdigitate to some extent the opposite bilayer leaflet. This phenomenon leads to a slower lateral diffusion for the longer-chained derivatives (n > 12). Effects of these amphiphiles on the structure and dynamics of the host lipid were found to be relatively mild, in comparison with acyl-chain-labeled NBD probes. The molecular details obtained by this work allow the rationalization of the nonmonotonic behavior, recently obtained experimentally, for the photophysical parameters of the amphiphiles and the kinetic and thermodynamic parameters for their interaction with the POPC membranes.
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Affiliation(s)
- Hugo A L Filipe
- Centro de Química de Coimbra, Universidade de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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31
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Loura LMS, Ramalho JPP. Recent developments in molecular dynamics simulations of fluorescent membrane probes. Molecules 2011; 16:5437-52. [PMID: 21709624 PMCID: PMC6264736 DOI: 10.3390/molecules16075437] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 06/21/2011] [Accepted: 06/22/2011] [Indexed: 01/25/2023] Open
Abstract
Due to their sensitivity and versatility, the use of fluorescence techniques in membrane biophysics is widespread. Because membrane lipids are non-fluorescent, extrinsic membrane probes are widely used. However, the behaviour of these probes when inserted in the bilayer is often poorly understood, and it can be hard to distinguish between legitimate membrane properties and perturbation resulting from probe incorporation. Atomistic molecular dynamics simulations present a convenient way to address these issues and have been increasingly used in recent years in this context. This article reviews the application of molecular dynamics to the study of fluorescent membrane probes, focusing on recent work with complex design fluorophores and ordered bilayer systems.
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Affiliation(s)
- Luís M. S. Loura
- Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal;
- Centro de Química de Coimbra, Universidade de Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - J. P. Prates Ramalho
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, 7002-554 Évora, Portugal
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32
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Kyrychenko A, Sevriukov IY, Syzova ZA, Ladokhin AS, Doroshenko AO. Partitioning of 2,6-Bis(1H-Benzimidazol-2-yl)pyridine fluorophore into a phospholipid bilayer: complementary use of fluorescence quenching studies and molecular dynamics simulations. Biophys Chem 2011; 154:8-17. [PMID: 21211898 PMCID: PMC4167733 DOI: 10.1016/j.bpc.2010.12.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/04/2010] [Accepted: 12/05/2010] [Indexed: 10/18/2022]
Abstract
Successful use of fluorescence sensing in elucidating the biophysical properties of lipid membranes requires knowledge of the distribution and location of an emitting molecule in the bilayer. We report here that 2,6-bis(1H-benzimidazol-2-yl)pyridine (BBP), which is almost non-fluorescent in aqueous solutions, reveals a strong emission enhancement in a hydrophobic environment of a phospholipid bilayer, making it interesting for fluorescence probing of water content in a lipid membrane. Comparing the fluorescence behavior of BBP in a wide variety of solvents with those in phospholipid vesicles, we suggest that the hydrogen bonding interactions between a BBP fluorophore and water molecules play a crucial role in the observed "light switch effect". Therefore, the loss of water-induced fluorescence quenching inside a membrane are thought to be due to deep penetration of BBP into the hydrophobic, water-free region of a bilayer. Characterized by strong quenching by transition metal ions in solution, BBP also demonstrated significant shielding from the action of the quencher in the presence of phospholipid vesicles. We used the increase in fluorescence intensity, measured upon titration of probe molecules with lipid vesicles, to estimate the partition constant and the Gibbs free energy (ΔG) of transfer of BBP from aqueous buffer into a membrane. Partitioning BBP revealed strongly favorable ΔG, which depends only slightly on the lipid composition of a bilayer, varying in a range from -6.5 to -7.0kcal/mol. To elucidate the binding interactions of the probe with a membrane on the molecular level, a distribution and favorable location of BBP in a POPC bilayer were modeled via atomistic molecular dynamics (MD) simulations using two different approaches: (i) free, diffusion-driven partitioning of the probe molecules into a bilayer and (ii) constrained umbrella sampling of a penetration profile of the dye molecule across a bilayer. Both of these MD approaches agreed with regard to the preferred location of a BBP fluorophore within the interfacial region of a bilayer, located between the hydrocarbon acyl tails and the initial portion of the lipid headgroups. MD simulations also revealed restricted permeability of water molecules into this region of a POPC bilayer, determining the strong fluorescence enhancement observed experimentally for the membrane-partitioned form of BBP.
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Affiliation(s)
- Alexander Kyrychenko
- Institute for Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61077, Ukraine
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160-7421, United States
- Ukrainian-American Laboratory of Computational Chemistry, Kharkiv, Ukraine and Jackson, Mississippi, United States
| | - Igor Yu. Sevriukov
- Institute for Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61077, Ukraine
| | - Zoya A. Syzova
- Institute for Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61077, Ukraine
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160-7421, United States
| | - Andrey O. Doroshenko
- Institute for Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61077, Ukraine
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Biswas J, Bajaj A, Bhattacharya S. Membranes of Cationic Gemini Lipids based on Cholesterol with Hydroxyl Headgroups and their Interactions with DNA and Phospholipid. J Phys Chem B 2010; 115:478-86. [DOI: 10.1021/jp108372z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joydeep Biswas
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India, Chemical Biology Unit of JNCASR, Bangalore 560 064, India, and J. C. Bose Fellow, DST, New Delhi, India
| | - Avinash Bajaj
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India, Chemical Biology Unit of JNCASR, Bangalore 560 064, India, and J. C. Bose Fellow, DST, New Delhi, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India, Chemical Biology Unit of JNCASR, Bangalore 560 064, India, and J. C. Bose Fellow, DST, New Delhi, India
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Lokajová J, Pukkila J, Holopainen JM, Wiedmer SK. In vitro capturing of various lipophilic illicit drugs by lipid dispersions. An electrokinetic capillary chromatography and fluorescence polarization study. Eur J Pharm Sci 2010; 41:515-22. [DOI: 10.1016/j.ejps.2010.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 08/17/2010] [Accepted: 08/18/2010] [Indexed: 01/22/2023]
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35
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Kyrychenko A, Wu F, Thummel RP, Waluk J, Ladokhin AS. Partitioning and localization of environment-sensitive 2-(2'-pyridyl)- and 2-(2'-pyrimidyl)-indoles in lipid membranes: a joint refinement using fluorescence measurements and molecular dynamics simulations. J Phys Chem B 2010; 114:13574-84. [PMID: 20925327 PMCID: PMC4470561 DOI: 10.1021/jp106981c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence of environment-sensitive dyes is widely applied to monitor local structure and solvation dynamics of biomolecules. It has been shown that, in comparison with a parent indole fluorophore, fluorescence of 2-(2'-pyridyl)-5-methylindole (5M-PyIn-0) and 2-[2'-(4',6'-dimethylpyrimidyl)]-indole (DMPmIn-0) is remarkably sensitive to hydrogen bonding with protic partners. Strong fluorescence, observed for these compounds in nonpolar and polar aprotic solvents, is efficiently quenched in aqueous solution. This study demonstrates that 5M-PyIn-0 and DMPmIn-0, which are almost nonemitting in aqueous solution, become highly fluorescent upon titrating with phospholipid vesicles. The fluorescence enhancement is accompanied by a significant blue shift of emission maximum. The Gibbs free energy of membrane partitioning, measured by the increase in the steady-state fluorescence intensities during transfer from an aqueous environment to a lipid bilayer, is very favorable for both compounds, being in a range from -7.1 to -8.0 kcal/mol and depending only slightly on lipid composition of the membrane. The fluorescence enhancement upon membrane partitioning is indicative of the loss of the specific hydrogen-bonding interactions between the excited fluorophore and water molecules, causing efficient fluorescence quenching in bulk water. This conclusion is supported by atomistic molecular dynamics (MD) simulations, demonstrating that both 5M-PyIn-0 and DMPmIn-0 bind rapidly and partition deeply into a lipid bilayer. MD simulations also show a rapid, nanosecond-scale decrease in the probability of solute-solvent hydrogen bonding during passive diffusion of the probe molecules from bulk water into a lipid bilayer. At equilibrium conditions, both 5M-PyIn-0 and DMPmIn-0 prefer deep localization within the hydrophobic, water-free region of the bilayer. A free energy profile of penetration across a bilayer estimated using MD umbrella sampling shows that both indole derivatives favor residence in a rather wide potential energy well located 10-15 Å from the bilayer center.
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Affiliation(s)
- Alexander Kyrychenko
- Corresponding authors. (A.K.) Phone: (+38)-057-707-5335. . (J.W.) Fax: (+48)-22-343-3333. . (A.S.L.) Fax: (+1)-913-588-7440.
| | | | | | - Jacek Waluk
- Corresponding authors. (A.K.) Phone: (+38)-057-707-5335. . (J.W.) Fax: (+48)-22-343-3333. . (A.S.L.) Fax: (+1)-913-588-7440.
| | - Alexey S. Ladokhin
- Corresponding authors. (A.K.) Phone: (+38)-057-707-5335. . (J.W.) Fax: (+48)-22-343-3333. . (A.S.L.) Fax: (+1)-913-588-7440.
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