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Socas LBP, Valdivia-Pérez JA, Fanani ML, Ambroggio EE. Multidimensional Spectral Phasors of LAURDAN's Excitation-Emission Matrices: The Ultimate Sensor for Lipid Phases? J Am Chem Soc 2024; 146:17230-17239. [PMID: 38874760 DOI: 10.1021/jacs.4c03443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
The impact of lipid diversity on the lateral organization of biological membranes remains a topic of debate. While the existence of domains in lamellar membranes is well-established, the nonlamellar phases occurring in biological systems are less explored due to technical constraints. Here, we present the measurement of the excitation-emission matrices (EEM) of LAURDAN in several lipid structures. LAURDAN is a fluorescence probe widely used for characterizing lipid assemblies. The EEMs were analyzed by multidimensional spectral phasors (MdSP), an approach that seizes information from both the excitation and emission spectra. We developed a computer algorithm to construct EEM data based on a model for LAURDAN's photophysics. The MdSP calculated from the simulated EEMs reveals that all feasible possibilities lie inside a universal triangle in the phasor's plot. We use this triangle to propose a ternary representation for the phasors, allowing a better assessment of LAURDAN's surroundings in terms of hydration, water mobility, and local electronic environment. Building upon this foundation, we constructed a theoretical "phase map" that can assess both lamellar and nonlamellar membranes. We thoroughly validated this theory using well-known lipid mixtures under different phase-state conditions and enzymatically generated systems. Our results confirm that the use of MdSP is a powerful tool for obtaining quantitative information on both lamellar and nonlamellar structures. This study not only advances our understanding of the impact of lipid diversity on membrane organization but also provides a robust and general framework for the assessment of fluorescence properties that can be further extended to other probes.
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Affiliation(s)
- Luis B P Socas
- Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Universidad Nacional de Córdoba, CONICET, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina
| | - Jessica A Valdivia-Pérez
- Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Universidad Nacional de Córdoba, CONICET, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina
| | - María L Fanani
- Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Universidad Nacional de Córdoba, CONICET, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina
| | - Ernesto E Ambroggio
- Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Universidad Nacional de Córdoba, CONICET, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina
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2
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Kyrychenko A, Ladokhin AS. Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions. CHEM REC 2024; 24:e202300232. [PMID: 37695081 PMCID: PMC11113672 DOI: 10.1002/tcr.202300232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.
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Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, United States
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3
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Fluorescent Probes cis- and trans-Parinaric Acids in Fluid and Gel Lipid Bilayers: A Molecular Dynamics Study. Molecules 2023; 28:molecules28052241. [PMID: 36903487 PMCID: PMC10005308 DOI: 10.3390/molecules28052241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Fluorescence probes are indispensable tools in biochemical and biophysical membrane studies. Most of them possess extrinsic fluorophores, which often constitute a source of uncertainty and potential perturbation to the host system. In this regard, the few available intrinsically fluorescent membrane probes acquire increased importance. Among them, cis- and trans-parinaric acids (c-PnA and t-PnA, respectively) stand out as probes of membrane order and dynamics. These two compounds are long-chained fatty acids, differing solely in the configurations of two double bonds of their conjugated tetraene fluorophore. In this work, we employed all-atom and coarse-grained molecular dynamics simulations to study the behavior of c-PnA and t-PnA in lipid bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), representative of the liquid disordered and solid ordered lipid phases, respectively. All-atom simulations indicate that the two probes show similar location and orientation in the simulated systems, with the carboxylate facing the water/lipid interface and the tail spanning the membrane leaflet. The two probes establish interactions with the solvent and lipids to a similar degree in POPC. However, the almost linear t-PnA molecules have tighter lipid packing around them, especially in DPPC, where they also interact more with positively charged lipid choline groups. Probably for these reasons, while both probes show similar partition (assessed from computed free energy profiles across bilayers) to POPC, t-PnA clearly partitions more extensively than c-PnA to the gel phase. t-PnA also displays more hindered fluorophore rotation, especially in DPPC. Our results agree very well with experimental fluorescence data from the literature and allow deeper understanding of the behavior of these two reporters of membrane organization.
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Membrane Interactions of Apoptotic Inhibitor Bcl-xL: What Can Be Learned using Fluorescence Spectroscopy. BBA ADVANCES 2023; 3:100076. [PMID: 37082264 PMCID: PMC10074936 DOI: 10.1016/j.bbadva.2023.100076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
Permeabilization of the mitochondrial outer membrane-a point of no return in apoptotic regulation-is tightly controlled by proteins of the Bcl-2 family. Apoptotic inhibitor Bcl-xL is an important member of this family, responsible for blocking the permeabilization, and is also a promising target for anti-cancer drugs. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (i) a soluble folded conformation, (ii) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (iii) refolded membrane-inserted conformations, for which no structural data are available. In this review, we present the summary of the application of various methods of fluorescence spectroscopy for studying membrane interaction of Bcl-xL, and specifically the formation of the refolded inserted conformation. We discuss the application of environment-sensitive probes, Förster resonance energy transfer, fluorescence correlation spectroscopy, and fluorescent quenching for structural, thermodynamic, and functional characterization of protein-lipid interactions, which can benefit studies of other members of Bcl-2 (e.g., Bax, BAK, Bid). The conformational switching between various conformations of Bcl-xL depends on the presence of divalent cations, pH and lipid composition. This insertion-refolding transition also results in the release of the BH4 regulatory domain from the folded structure of Bcl-xL, which is relevant to the lipid-regulated conversion between canonical and non-canonical modes of apoptotic inhibition.
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5
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On the temperature‐dependent isomerization of all‐
trans
‐1,6‐diphenyl‐1,3,5‐hexatriene in solution: A reappraisal. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Socas LB, Ambroggio EE. Introducing the multi-dimensional spectral phasors: a tool for the analysis of fluorescence excitation-emission matrices. Methods Appl Fluoresc 2022; 10. [PMID: 35139496 DOI: 10.1088/2050-6120/ac5389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/09/2022] [Indexed: 11/12/2022]
Abstract
The use of phasors to analyze fluorescence data was first introduced for time-resolved studies for a simpler mathematical analysis of the fluorescence-decay curves. Recently, this approach was extended to steady-state experiments with the introduction of the spectral phasors (SP), derived from the Fourier transform of the fluorescence emission spectrum. In this work, we revise key mathematical aspects that lead to an interpretation of SP as the characteristic function of a probability distribution. This formalism allows us to introduce a new tool, called multi-dimensional spectral phasor (MdSP) that seize, not only the information from the emission spectrum, but from the full excitation-emission matrix (EEM). In addition, we developed a homemade open-source Java software to facilitate the MdSP data processing. Due to this mathematical conceptualization, we settled a mechanism for the use of MdSP as a tool to tackle spectral signal unmixing problems in a more accurate way than SP. As a proof of principle, with the use of MdSP we approach two important biophysical questions: protein conformational changes and protein-ligand interactions. Specifically, we experimentally measure the EEM changes upon denaturation of human serum albumin (HSA) or during its association with the fluorescence dye 1,8-anilinonaphtalene sulphate (ANS) detected via tryptophan-ANS Förster Resonance Energy Transfer (FRET). In this sense, MdSP allows us to obtain information of the system in a simpler and finer way than the traditional SP. Specifically, understanding a protein's EEM as a molecular fingerprint opens new doors for the use of MdSP as a tool to analyze and comprehend protein conformational changes and interactions.
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Affiliation(s)
- Luis Bp Socas
- Química Biológica, Centro de Investigaciones en Química Biológica de Córdoba, Haya de la Torre y Medina Allende s/n, Cordoba, Córdoba, X5000HUA, ARGENTINA
| | - Ernesto Esteban Ambroggio
- Química Biológica, CIQUIBIC Química Biológica, Haya de la Torre y Medina Allende s/n, Cordoba, X5000HUA, ARGENTINA
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Islam MS, Gaston JP, Baker MAB. Fluorescence Approaches for Characterizing Ion Channels in Synthetic Bilayers. MEMBRANES 2021; 11:857. [PMID: 34832086 PMCID: PMC8619978 DOI: 10.3390/membranes11110857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022]
Abstract
Ion channels are membrane proteins that play important roles in a wide range of fundamental cellular processes. Studying membrane proteins at a molecular level becomes challenging in complex cellular environments. Instead, many studies focus on the isolation and reconstitution of the membrane proteins into model lipid membranes. Such simpler, in vitro, systems offer the advantage of control over the membrane and protein composition and the lipid environment. Rhodopsin and rhodopsin-like ion channels are widely studied due to their light-interacting properties and are a natural candidate for investigation with fluorescence methods. Here we review techniques for synthesizing liposomes and for reconstituting membrane proteins into lipid bilayers. We then summarize fluorescence assays which can be used to verify the functionality of reconstituted membrane proteins in synthetic liposomes.
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Affiliation(s)
- Md. Sirajul Islam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - James P. Gaston
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
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8
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Dahal D, Ojha KR, Pokhrel S, Paruchuri S, Konopka M, Liu Q, Pang Y. NIR-emitting styryl dyes with large Stokes' shifts for imaging application: From cellular plasma membrane, mitochondria to Zebrafish neuromast. DYES AND PIGMENTS : AN INTERNATIONAL JOURNAL 2021; 194:109629. [PMID: 34366501 PMCID: PMC8345024 DOI: 10.1016/j.dyepig.2021.109629] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Near-infrared (NIR) emitting probes with very large Stokes' shifts play a crucial role in bioimaging applications, as the optical signals in this region exhibit high signal to background ratio and allow deeper tissue penetration. Herein we illustrate NIR-emitting probe 2 with very large Stokes' shifts (Δλ ≈ 260 - 272 nm) by integrating the excited-state intramolecular proton transfer (ESIPT) unit 2-(2'-hydroxyphenyl)benzoxazole (HBO) into a pyridinium derived cyanine. The ESIPT not only enhances the Stokes' shifts but also improves the quantum efficiency of the probe 2 (фfl = 0.27 - 0.40 in DCM). The application of 2 in live cells imaging reveals that compound 2 stains mitochondria in eukaryotic cells, normal human lungs fibroblast (NHLF), Zebrafish's neuromast hair cells, and support cells, and inner plasma membrane in prokaryotic cells, Escherichia coli (E. coli).
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Affiliation(s)
- Dipendra Dahal
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
| | - Krishna R Ojha
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
| | - Sabita Pokhrel
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
| | - Sailaja Paruchuri
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
| | - Michael Konopka
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
| | - Qin Liu
- Department of Biology, The University of Akron, Akron, OH 44325, USA
| | - Yi Pang
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
- Maurice Morton Institute of Polymer Science, The University of Akron, Akron, OH 44325, USA
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9
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Chang Z, Deng J, Zhao W, Yang J. Exploring interactions between lipids and amyloid-forming proteins: A review on applying fluorescence and NMR techniques. Chem Phys Lipids 2021; 236:105062. [PMID: 33600803 DOI: 10.1016/j.chemphyslip.2021.105062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/27/2021] [Accepted: 02/12/2021] [Indexed: 12/13/2022]
Abstract
A hallmark of Alzheimer's, Parkinson's, and other amyloid diseases is the assembly of amyloid proteins into amyloid aggregates or fibrils. In many cases, the formation and cytotoxicity of amyloid assemblies are associated with their interaction with cell membranes. Despite studied for many years, the characterization of the interaction is challenged for reasons on the multiple aggregation states of amyloid-forming proteins, transient and weak interactions in the complex system. Although several strategies such as computation biology, spectroscopy, and imaging methods have been performed, there is an urgent need to detail the molecular mechanism in different time scales and high resolutions. This review highlighted the recent applications of fluorescence, solution and solid-state NMR in exploring the interactions between amyloid protein and membranes attributing to their advantages of high sensitivity and atomic resolution.
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Affiliation(s)
- Ziwei Chang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Jing Deng
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Weijing Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, PR China.
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10
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O’Hagan S, Kell DB. Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products. Mar Drugs 2020; 18:E582. [PMID: 33238416 PMCID: PMC7700180 DOI: 10.3390/md18110582] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
It is known that at least some fluorophores can act as 'surrogate' substrates for solute carriers (SLCs) involved in pharmaceutical drug uptake, and this promiscuity is taken to reflect at least a certain structural similarity. As part of a comprehensive study seeking the 'natural' substrates of 'orphan' transporters that also serve to take up pharmaceutical drugs into cells, we have noted that many drugs bear structural similarities to natural products. A cursory inspection of common fluorophores indicates that they too are surprisingly 'drug-like', and they also enter at least some cells. Some are also known to be substrates of efflux transporters. Consequently, we sought to assess the structural similarity of common fluorophores to marketed drugs, endogenous mammalian metabolites, and natural products. We used a set of some 150 fluorophores along with standard fingerprinting methods and the Tanimoto similarity metric. Results: The great majority of fluorophores tested exhibited significant similarity (Tanimoto similarity > 0.75) to at least one drug, as judged via descriptor properties (especially their aromaticity, for identifiable reasons that we explain), by molecular fingerprints, by visual inspection, and via the "quantitative estimate of drug likeness" technique. It is concluded that this set of fluorophores does overlap with a significant part of both the drug space and natural products space. Consequently, fluorophores do indeed offer a much wider opportunity than had possibly been realised to be used as surrogate uptake molecules in the competitive or trans-stimulation assay of membrane transporter activities.
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Affiliation(s)
- Steve O’Hagan
- Department of Chemistry, The University of Manchester, Manchester M13 9PT, UK;
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Molecular, Integrative and Systems Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
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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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Furlan AL, Laurin Y, Botcazon C, Rodríguez-Moraga N, Rippa S, Deleu M, Lins L, Sarazin C, Buchoux S. Contributions and Limitations of Biophysical Approaches to Study of the Interactions between Amphiphilic Molecules and the Plant Plasma Membrane. PLANTS 2020; 9:plants9050648. [PMID: 32443858 PMCID: PMC7285231 DOI: 10.3390/plants9050648] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 12/20/2022]
Abstract
Some amphiphilic molecules are able to interact with the lipid matrix of plant plasma membranes and trigger the immune response in plants. This original mode of perception is not yet fully understood and biophysical approaches could help to obtain molecular insights. In this review, we focus on such membrane-interacting molecules, and present biophysically grounded methods that are used and are particularly interesting in the investigation of this mode of perception. Rather than going into overly technical details, the aim of this review was to provide to readers with a plant biochemistry background a good overview of how biophysics can help to study molecular interactions between bioactive amphiphilic molecules and plant lipid membranes. In particular, we present the biomimetic membrane models typically used, solid-state nuclear magnetic resonance, molecular modeling, and fluorescence approaches, because they are especially suitable for this field of research. For each technique, we provide a brief description, a few case studies, and the inherent limitations, so non-specialists can gain a good grasp on how they could extend their toolbox and/or could apply new techniques to study amphiphilic bioactive compound and lipid interactions.
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Affiliation(s)
- Aurélien L. Furlan
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Yoann Laurin
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Camille Botcazon
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Technologie de Compiègne, 60200 Compiègne, France;
| | - Nely Rodríguez-Moraga
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Sonia Rippa
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Technologie de Compiègne, 60200 Compiègne, France;
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Sébastien Buchoux
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
- Correspondence: ; Tel.: +33-(0)3-2282-7473
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Slavgorodska M, Kyrychenko A. Structure and Dynamics of Pyrene-Labeled Poly(acrylic acid): Molecular Dynamics Simulation Study. CHEMISTRY & CHEMICAL TECHNOLOGY 2020. [DOI: 10.23939/chcht14.01.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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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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15
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Laguerre A, Schultz C. Novel lipid tools and probes for biological investigations. Curr Opin Cell Biol 2018; 53:97-104. [PMID: 30015291 DOI: 10.1016/j.ceb.2018.06.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/12/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022]
Abstract
We present the latest advances in lipid tool development for studying cellular membrane trafficking and metabolism. We focus on chemical modifications that are introduced to natural lipid structures. The new functionalities are used to follow and interfere with lipid dynamics in intact cells.
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Affiliation(s)
- Aurélien Laguerre
- Dept. of Physiology & Pharmacology, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Carsten Schultz
- Dept. of Physiology & Pharmacology, Oregon Health and Science University (OHSU), Portland, OR, USA; European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.
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16
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Sahu S, Sharma A, Mishra AK. Multiparametric Sensing of Membrane Bilayer Properties with a Highly Environment-Susceptible Fluorophore. J Phys Chem B 2018; 122:7308-7318. [DOI: 10.1021/acs.jpcb.8b02140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Saugata Sahu
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Ashutosh Sharma
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Ashok Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
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17
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Hollmann A, Martinez M, Maturana P, Semorile LC, Maffia PC. Antimicrobial Peptides: Interaction With Model and Biological Membranes and Synergism With Chemical Antibiotics. Front Chem 2018; 6:204. [PMID: 29922648 PMCID: PMC5996110 DOI: 10.3389/fchem.2018.00204] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/17/2018] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial peptides (AMPs) are promising novel antibiotics since they have shown antimicrobial activity against a wide range of bacterial species, including multiresistant bacteria; however, toxicity is the major barrier to convert antimicrobial peptides into active drugs. A profound and proper understanding of the complex interactions between these peptides and biological membranes using biophysical tools and model membranes seems to be a key factor in the race to develop a suitable antimicrobial peptide therapy for clinical use. In the search for such therapy, different combined approaches with conventional antibiotics have been evaluated in recent years and demonstrated to improve the therapeutic potential of AMPs. Some of these approaches have revealed promising additive or synergistic activity between AMPs and chemical antibiotics. This review will give an insight into the possibilities that physicochemical tools can give in the AMPs research and also address the state of the art on the current promising combined therapies between AMPs and conventional antibiotics, which appear to be a plausible future opportunity for AMPs treatment.
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Affiliation(s)
- Axel Hollmann
- Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina.,Centro de Investigación en Biofísica Aplicada y Alimentos, Consejo Nacional de Investigaciones Científicas y Técnicas and National University of Santiago del Estero, Santiago del Estero, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Melina Martinez
- Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Patricia Maturana
- Centro de Investigación en Biofísica Aplicada y Alimentos, Consejo Nacional de Investigaciones Científicas y Técnicas and National University of Santiago del Estero, Santiago del Estero, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Liliana C Semorile
- Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina
| | - Paulo C Maffia
- Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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18
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Location of fluorescent probes (2′-hydroxy derivatives of 2,5-diaryl-1,3-oxazole) in lipid membrane studied by fluorescence spectroscopy and molecular dynamics simulation. Biophys Chem 2018; 235:9-18. [DOI: 10.1016/j.bpc.2018.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 11/20/2022]
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19
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Derivatives of 2,5-Diaryl-1,3-Oxazole and 2,5-Diaryl-1,3,4-Oxadiazole as Environment-Sensitive Fluorescent Probes for Studies of Biological Membranes. REVIEWS IN FLUORESCENCE 2017 2018. [DOI: 10.1007/978-3-030-01569-5_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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20
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Buslaev P, Gushchin I. Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules. Sci Rep 2017; 7:11476. [PMID: 28904383 PMCID: PMC5597592 DOI: 10.1038/s41598-017-11761-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/25/2017] [Indexed: 12/14/2022] Open
Abstract
Molecular dynamics simulations are used extensively to study the processes on biological membranes. The simulations can be conducted at different levels of resolution: all atom (AA), where all atomistic details are provided; united atom (UA), where hydrogen atoms are treated inseparably of corresponding heavy atoms; and coarse grained (CG), where atoms are grouped into larger particles. Here, we study the behavior of model bilayers consisting of saturated and unsaturated lipids DOPC, SOPC, OSPC and DSPC in simulations performed using all atom CHARMM36 and coarse grained Martini force fields. Using principal components analysis, we show that the structural and dynamical properties of the lipids are similar, both in AA and CG simulations, although the unsaturated molecules are more dynamic and favor more extended conformations. We find that CG simulations capture 75 to 100% of the major collective motions, overestimate short range ordering, result in more flexible molecules and 5–7 fold faster sampling. We expect that the results reported here will be useful for comprehensive quantitative comparisons of simulations conducted at different resolution levels and for further development and improvement of CG force fields.
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Affiliation(s)
- Pavel Buslaev
- Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia.
| | - Ivan Gushchin
- Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia. .,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425, Jülich, Germany.
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21
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Nåbo LJ, List NH, Steinmann C, Kongsted J. Computational Approach to Evaluation of Optical Properties of Membrane Probes. J Chem Theory Comput 2017; 13:719-726. [DOI: 10.1021/acs.jctc.6b01017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lina J. Nåbo
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Nanna Holmgaard List
- Division
of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Casper Steinmann
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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22
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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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23
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Birch D, Mely Y, Wolfbeis O. A journal in ascendancy. Methods Appl Fluoresc 2015; 3:040203. [PMID: 29148502 DOI: 10.1088/2050-6120/3/4/040203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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