{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T08:08:30Z","timestamp":1774598910337,"version":"3.50.1"},"reference-count":164,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2020,7,28]],"date-time":"2020-07-28T00:00:00Z","timestamp":1595894400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/00313\/2020"],"award-info":[{"award-number":["UIDB\/00313\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["PT2020-PTDC\/DTP-FTO\/2784\/2014"],"award-info":[{"award-number":["PT2020-PTDC\/DTP-FTO\/2784\/2014"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["POCI-01-0247-FEDER-033368"],"award-info":[{"award-number":["POCI-01-0247-FEDER-033368"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["CENTRO-01-0247-FEDER-033838"],"award-info":[{"award-number":["CENTRO-01-0247-FEDER-033838"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/molecules25153424","type":"journal-article","created":{"date-parts":[[2020,7,30]],"date-time":"2020-07-30T12:15:38Z","timestamp":1596111338000},"page":"3424","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations"],"prefix":"10.3390","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6935-4307","authenticated-orcid":false,"given":"Hugo A. L.","family":"Filipe","sequence":"first","affiliation":[{"name":"Chemistry Department, Coimbra Chemistry Center, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3076-9905","authenticated-orcid":false,"given":"Maria Jo\u00e3o","family":"Moreno","sequence":"additional","affiliation":[{"name":"Coimbra Chemistry Center and CNC\u2014Center for Neuroscience and Cell Biology, Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1051-2312","authenticated-orcid":false,"given":"Lu\u00eds M. S.","family":"Loura","sequence":"additional","affiliation":[{"name":"Coimbra Chemistry Center and CNC\u2014Center for Neuroscience and Cell Biology, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2020,7,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1073\/pnas.67.2.579","article-title":"Fluorescent probes of biological membranes","volume":"67","author":"Waggoner","year":"1970","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Korn, E.D. (1975). Fluorescent probes in membrane studies. Biophysical Approaches, Springer.","DOI":"10.1007\/978-1-4684-2907-7"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"3461","DOI":"10.1016\/j.bpj.2009.02.012","article-title":"Monitoring biophysical properties of lipid membranes by environment-sensitive fluorescent probes","volume":"96","author":"Demchenko","year":"2009","journal-title":"Biophys. J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/978-1-4939-1752-5_3","article-title":"Introduction to fluorescence probing of biological membranes","volume":"1232","author":"Demchenko","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"042003","DOI":"10.1088\/2050-6120\/3\/4\/042003","article-title":"Using fluorescence for studies of biological membranes: A review","volume":"3","author":"Kyrychenko","year":"2015","journal-title":"Methods Appl. Fluoresc."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1021\/acs.accounts.6b00517","article-title":"Solvatochromic and fluorogenic dyes as environment-sensitive probes: Design and biological applications","volume":"50","author":"Klymchenko","year":"2017","journal-title":"Acc. Chem. Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.bbamem.2008.10.012","article-title":"FRET analysis of domain formation and properties in complex membrane systems","volume":"1788","author":"Loura","year":"2009","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1073\/pnas.69.6.1499","article-title":"X-ray diffraction studies of lecithin bimolecular leaflets with incorporated fluorescent probes","volume":"69","author":"Lesslauer","year":"1972","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1134\/S1811238213070060","article-title":"Computer simulation of lipid membranes: Methodology and achievements","volume":"55","author":"Rabinovich","year":"2013","journal-title":"Polym. Sci. Ser. C"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"5607","DOI":"10.1021\/acs.chemrev.8b00538","article-title":"Multiscale simulations of biological membranes: The challenge to understand biological phenomena in a living substance","volume":"119","author":"Enkavi","year":"2019","journal-title":"Chem. Rev."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"393","DOI":"10.3389\/fphys.2019.00393","article-title":"Interaction of bile salts with lipid bilayers: An atomistic molecular dynamics study","volume":"10","author":"Neves","year":"2019","journal-title":"Front. Physiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1007\/s12551-009-0016-5","article-title":"Fluorescent membrane probes\u2019 behavior in lipid bilayers: Insights from molecular dynamics simulations","volume":"1","author":"Loura","year":"2009","journal-title":"Biophys. Rev."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"5437","DOI":"10.3390\/molecules16075437","article-title":"Recent developments in molecular dynamics simulations of fluorescent membrane probes","volume":"16","author":"Loura","year":"2011","journal-title":"Molecules"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2353","DOI":"10.1016\/j.bbamem.2016.02.014","article-title":"Molecular modeling of lipid probes and their influence on the membrane","volume":"1858","author":"Faller","year":"2016","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"13438","DOI":"10.1021\/jp048381g","article-title":"Distribution, orientation, and dynamics of DPH probes in DPPC bilayer","volume":"108","author":"Holopainen","year":"2004","journal-title":"J. Phys. Chem. B"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"15403","DOI":"10.1021\/jp061300r","article-title":"Influence of pyrene-labeling on fluid lipid membranes","volume":"110","author":"Holopainen","year":"2006","journal-title":"J. Phys. Chem. B"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"4026","DOI":"10.1021\/ct200196m","article-title":"An automated force field topology builder (ATB) and repository: Version 1.0","volume":"7","author":"Malde","year":"2011","journal-title":"J. Chem. Theory Comput."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s10822-014-9713-7","article-title":"Testing and validation of the automated topology builder (ATB) version 2.0: Prediction of hydration free enthalpies","volume":"28","author":"Koziara","year":"2014","journal-title":"J. Comput. Aided. Mol. Des."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1002\/jcc.20945","article-title":"CHARMM-GUI: A web-based graphical user interface for CHARMM","volume":"29","author":"Jo","year":"2008","journal-title":"J. Comput. Chem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1002\/jcc.24829","article-title":"CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules","volume":"38","author":"Kim","year":"2017","journal-title":"J. Comput. Chem."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.jmgm.2005.12.005","article-title":"Automatic atom type and bond type perception in molecular mechanical calculations","volume":"25","author":"Wang","year":"2006","journal-title":"J. Mol. Graph. Model."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"W331","DOI":"10.1093\/nar\/gkx312","article-title":"LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands","volume":"45","author":"Dodda","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3840","DOI":"10.1021\/acs.jctc.8b00150","article-title":"Quantitative assessment of methods used to obtain rate constants from molecular dynamics simulations\u2013Translocation of cholesterol across lipid bilayers","volume":"14","author":"Filipe","year":"2018","journal-title":"J. Chem. Theory Comput."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Jura\u010dka, J., \u0160rejber, M., Mel\u00edkov\u00e1, M., Bazgier, V., and Berka, K. (2019). MolMeDB: Molecules on membranes database. Database, 2019.","DOI":"10.1093\/database\/baz078"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1021\/acs.jcim.9b00225","article-title":"PerMM: A web tool and database for analysis of passive membrane permeability and translocation pathways of bioactive molecules","volume":"59","author":"Lomize","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/0009-3084(89)90049-2","article-title":"Membrane \u201cfluidity\u201d as detected by diphenylhexatriene probes","volume":"50","author":"Lentz","year":"1989","journal-title":"Chem. Phys. Lipids"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1016\/S0006-3495(98)74011-1","article-title":"Molecular order and dynamics in bilayers consisting of highly polyunsaturated phospholipids","volume":"74","author":"Mitchell","year":"1998","journal-title":"Biophys. J."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0301-4622(96)02267-3","article-title":"Molecular dynamics simulation of a dye molecule in the interior of a bilayer: 1,6-diphenyl-1,3,5-hexatriene in dipalmitoylphosphatidylcholine","volume":"69","author":"Huertas","year":"1997","journal-title":"Biophys. Chem."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"3398","DOI":"10.1529\/biophysj.104.055533","article-title":"Influence of DPH on the structure and dynamics of a DPPC bilayer","volume":"88","author":"Holopainen","year":"2005","journal-title":"Biophys. J."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2704","DOI":"10.1021\/jp908533x","article-title":"Effects of DPH on DPPC-cholesterol membranes with varying concentrations of cholesterol: From local perturbations to limitations in fluorescence anisotropy experiments","volume":"114","author":"Holopainen","year":"2010","journal-title":"J. Phys. Chem. B"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.molstruc.2012.12.015","article-title":"The interaction of fluorescent DPH probes with unsaturated phospholipid membranes: A molecular dynamics study","volume":"1044","author":"Hurjui","year":"2013","journal-title":"J. Mol. Struct."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2647","DOI":"10.1016\/j.bbamem.2016.07.013","article-title":"Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study","volume":"1858","author":"Robalo","year":"2016","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"7594","DOI":"10.1039\/C8CP07754A","article-title":"Orientational distribution of DPH in lipid membranes: A comparison of molecular dynamics calculations and experimental time-resolved anisotropy experiments","volume":"21","author":"Ameloot","year":"2019","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/S0006-3495(84)84049-7","article-title":"Effect of orientational order on the decay of the fluorescence anisotropy in membrane suspensions. A new approximate solution of the rotational diffusion equation","volume":"46","author":"Pottel","year":"1984","journal-title":"Biophys. J."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"104784","DOI":"10.1016\/j.chemphyslip.2019.104784","article-title":"Behavior of the DPH fluorescence probe in membranes perturbed by drugs","volume":"223","author":"Poojari","year":"2019","journal-title":"Chem. Phys. Lipids"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Nelson, S.C., Neeley, S.K., Melonakos, E.D., Bell, J.D., and Busath, D.D. (2012). Fluorescence anisotropy of diphenylhexatriene and its cationic Trimethylamino derivative in liquid dipalmitoylphosphatidylcholine liposomes: Opposing responses to isoflurane. BMC Biophys., 5.","DOI":"10.1186\/2046-1682-5-5"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S0009-3084(02)00020-8","article-title":"Pyrene-labeled lipids as tools in membrane biophysics and cell biology","volume":"116","author":"Somerharju","year":"2002","journal-title":"Chem. Phys. Lipids"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1818","DOI":"10.1529\/biophysj.104.052399","article-title":"2H-NMR study and molecular dynamics simulation of the location, alignment, and mobility of pyrene in POPC bilayers","volume":"88","author":"Hoff","year":"2005","journal-title":"Biophys. J."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3640","DOI":"10.1021\/jp065956w","article-title":"Free pyrene probes in gel and fluid membranes: Perspective through atomistic simulations","volume":"111","author":"Vattulainen","year":"2007","journal-title":"J. Phys. Chem. B"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1016\/j.bbamem.2012.12.014","article-title":"Sensing hydration and behavior of pyrene in POPC and POPC\/cholesterol bilayers: A molecular dynamics study","volume":"1828","author":"Loura","year":"2013","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"2914","DOI":"10.1016\/j.bbamem.2007.08.012","article-title":"Bilayer polarity and its thermal dependency in the \u2113o and \u2113d phases of binary phosphatidylcholine\/cholesterol mixtures","volume":"1768","author":"Arrais","year":"2007","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1016\/j.colsurfa.2014.12.012","article-title":"Behavior of pyrene as a polarity probe in palmitoylsphingomyelin and palmitoylsphingomyelin\/cholesterol bilayers: A molecular dynamics simulation study","volume":"480","author":"Santos","year":"2015","journal-title":"Colloids Surf. Physicochem. Eng. Asp."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.chemphyslip.2013.10.004","article-title":"How to link pyrene to its host lipid to minimize the extent of membrane perturbations and to optimize pyrene dimer formation","volume":"177","author":"Holopainen","year":"2014","journal-title":"Chem. Phys. Lipids"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1021\/jp951577j","article-title":"Long-range diffusion coefficients in two-dimensional fluid media measured by the pyrene excimer reaction","volume":"100","author":"Martins","year":"1996","journal-title":"J. Phys. Chem."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1039\/a806472e","article-title":"Sensing isothermal changes in the lateral pressure in model membranes using di-pyrenyl phosphatidylcholine","volume":"111","author":"Templer","year":"1999","journal-title":"Faraday Discuss."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1016\/j.bbamem.2014.01.030","article-title":"Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations","volume":"1838","author":"Vattulainen","year":"2014","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"4418","DOI":"10.1021\/jacs.6b13024","article-title":"Triggering on\/off states of photoswitchable probes in biological environments","volume":"139","author":"Osella","year":"2017","journal-title":"J. Am. Chem. Soc."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0009-3084(90)90128-E","article-title":"Chemistry and biology of N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-labeled lipids: Fluorescent probes of biological and model membranes","volume":"53","author":"Chattopadhyay","year":"1990","journal-title":"Chem. Phys. Lipids"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.chemphyslip.2003.09.004","article-title":"Organization and dynamics of N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-labeled lipids: A fluorescence approach","volume":"127","author":"Mukherjee","year":"2004","journal-title":"Chem. Phys. Lipids"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1016\/j.bbamem.2006.10.011","article-title":"Location and dynamics of acyl chain NBD-labeled phosphatidylcholine (NBD-PC) in DPPC bilayers. A molecular dynamics and time-resolved fluorescence anisotropy study","volume":"1768","author":"Loura","year":"2007","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/j.bbamem.2007.10.022","article-title":"Effects of fluorescent probe NBD-PC on the structure, dynamics and phase transition of DPPC. A molecular dynamics and differential scanning calorimetry study","volume":"1778","author":"Loura","year":"2008","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.theochem.2010.01.027","article-title":"Direct calculation of F\u00f6rster orientation factor of membrane probes by molecular simulation","volume":"946","author":"Loura","year":"2010","journal-title":"J. Mol. Struct. Theochem."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"15252","DOI":"10.3390\/ijms131115252","article-title":"Simple estimation of f\u00f6rster resonance energy transfer (FRET) orientation factor distribution in membranes","volume":"13","author":"Loura","year":"2012","journal-title":"Int. J. Mol. Sci."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"14545","DOI":"10.3390\/ijms131114545","article-title":"Lateral distribution of NBD-PC fluorescent lipid analogs in membranes probed by molecular dynamics-assisted analysis of f\u00f6rster resonance energy transfer (FRET) and fluorescence quenching","volume":"13","author":"Loura","year":"2012","journal-title":"Int. J. Mol. Sci."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"16337","DOI":"10.1021\/jp105163k","article-title":"Chain length effect on the binding of amphiphiles to serum albumin and to POPC bilayers","volume":"114","author":"Cardoso","year":"2010","journal-title":"J. Phys. Chem. B"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"10098","DOI":"10.1021\/jp203429s","article-title":"Chain-length dependence of insertion, desorption, and translocation of a homologous series of 7-nitrobenz-2-oxa-1,3-diazol-4-yl-labeled aliphatic amines in membranes","volume":"115","author":"Cardoso","year":"2011","journal-title":"J. Phys. Chem. B"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"10109","DOI":"10.1021\/jp203532c","article-title":"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","volume":"115","author":"Filipe","year":"2011","journal-title":"J. Phys. Chem. B"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"3572","DOI":"10.1021\/jp501622d","article-title":"How to tackle the issues in free energy simulations of long amphiphiles interacting with lipid membranes: Convergence and local membrane deformations","volume":"118","author":"Filipe","year":"2014","journal-title":"J. Phys. Chem. B"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"27534","DOI":"10.1039\/C5CP04191K","article-title":"Interaction of NBD-labelled fatty amines with liquid-ordered membranes: A combined molecular dynamics simulation and fluorescence spectroscopy study","volume":"17","author":"Filipe","year":"2015","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"15807","DOI":"10.1021\/jp907981y","article-title":"Location, tilt, and binding: A molecular dynamics study of voltage-sensitive dyes in biomembranes","volume":"113","author":"Hinner","year":"2009","journal-title":"J. Phys. Chem. B"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1007\/s00232-014-9709-1","article-title":"Calibration of distribution analysis of the depth of membrane penetration using simulations and depth-dependent fluorescence quenching","volume":"248","author":"Kyrychenko","year":"2015","journal-title":"J. Membr. Biol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"20066","DOI":"10.1039\/C5CP01596K","article-title":"Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: A molecular dynamics study","volume":"17","author":"Filipe","year":"2015","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1021\/bi00375a006","article-title":"Parallax method for direct measurement of membrane penetration depth utilizing fluorescence quenching by spin-labeled phospholipids","volume":"26","author":"London","year":"1987","journal-title":"Biochemistry"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"7042","DOI":"10.1039\/C5CP05238F","article-title":"Fluorescence of nitrobenzoxadiazole (NBD)-labeled lipids in model membranes is connected not to lipid mobility but to probe location","volume":"18","author":"Amaro","year":"2016","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"M\u00e9ly, Y., and Duportail, G. (2013). Application of NBD-labeled lipids in membrane and cell biology. Fluorescent Methods to Study Biological Membranes, Springer.","DOI":"10.1007\/978-3-642-33128-2"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/1010-6030(93)85048-D","article-title":"Drastic changes in the fluorescence properties of NBD probes with the polarity of the medium: Involvement of a TICT state?","volume":"70","author":"Fayet","year":"1993","journal-title":"J. Photochem. Photobiol. A Chem."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/1010-6030(93)80008-W","article-title":"Theoretical and experimental analyses of optical transitions of nitrobenzoxadiazole (NBD) derivatives","volume":"70","author":"Paprica","year":"1993","journal-title":"J. Photochem. Photobiol. A Chem."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2809","DOI":"10.1021\/j100062a014","article-title":"Dipole moment change of NBD group upon excitation studied using solvatochromic and quantum chemical approaches: Implications in membrane research","volume":"98","author":"Mukherjee","year":"1994","journal-title":"J. Phys. Chem."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1039\/C8CP06064A","article-title":"Orientation of nitro-group governs the fluorescence lifetime of nitrobenzoxadiazole (NBD)-labeled lipids in lipid bilayers","volume":"21","author":"Filipe","year":"2019","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1541","DOI":"10.1016\/j.bbamem.2006.05.019","article-title":"To see or not to see: Lateral organization of biological membranes and fluorescence microscopy","volume":"1758","author":"Bagatolli","year":"2006","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/S0006-3495(91)82041-0","article-title":"Quantitation of lipid phases in phospholipid vesicles by the generalized polarization of Laurdan fluorescence","volume":"60","author":"Parasassi","year":"1991","journal-title":"Biophys. J."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1724","DOI":"10.1016\/j.bbamem.2010.05.020","article-title":"Numerical studies of the membrane fluorescent dyes dynamics in ground and excited states","volume":"1798","author":"Kraszewski","year":"2010","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"11428","DOI":"10.1021\/jp205966b","article-title":"Absorption and fluorescence of PRODAN in phospholipid bilayers: A combined quantum mechanics and classical molecular dynamics study","volume":"115","author":"Cwiklik","year":"2011","journal-title":"J. Phys. Chem. A"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1021\/la304235r","article-title":"Will C-Laurdan dethrone Laurdan in fluorescent solvent relaxation techniques for lipid membrane studies?","volume":"29","author":"Kraszewski","year":"2013","journal-title":"Langmuir"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"6169","DOI":"10.1021\/acs.jctc.6b00906","article-title":"Investigation into biological environments through (non)linear optics: A multiscale study of laurdan derivatives","volume":"12","author":"Osella","year":"2016","journal-title":"J. Chem. Theory Comput."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Baig, M.W., Pederzoli, M., Jurkiewicz, P., Cwiklik, L., and Pittner, J. (2018). Orientation of Laurdan in phospholipid bilayers influences its fluorescence: Quantum mechanics and classical molecular dynamics study. Molecules, 23.","DOI":"10.3390\/molecules23071707"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"11471","DOI":"10.1021\/acs.langmuir.9b01840","article-title":"Conformational changes as driving force for phase recognition: The case of Laurdan","volume":"35","author":"Osella","year":"2019","journal-title":"Langmuir"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"5769","DOI":"10.1021\/acsabm.9b00789","article-title":"Laurdan as a molecular rotor in biological environments","volume":"2","author":"Osella","year":"2019","journal-title":"ACS Appl. Bio Mater."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"16060","DOI":"10.1039\/C8CP00543E","article-title":"PRODAN differentially influences its local environment","volume":"20","author":"Suhaj","year":"2018","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1021\/cr00032a005","article-title":"Solvatochromic dyes as solvent polarity indicators","volume":"94","author":"Reichardt","year":"1994","journal-title":"Chem. Rev."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1083\/jcb.100.3.965","article-title":"Nile red: A selective fluorescent stain for intracellular lipid droplets","volume":"100","author":"Greenspan","year":"1985","journal-title":"J. Cell Biol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"13764","DOI":"10.1002\/chem.201601570","article-title":"Nile red and Nile blue: Applications and syntheses of structural analogues","volume":"22","author":"Martinez","year":"2016","journal-title":"Chem. A Eur. J."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1021\/acs.jctc.5b00520","article-title":"Two-dimensional potentials of mean force of Nile red in intact and damaged model bilayers. Application to calculations of fluorescence spectra","volume":"12","author":"Singh","year":"2016","journal-title":"J. Chem. Theory Comput."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1021\/acsomega.8b02503","article-title":"Aggregation of Nile red in water: Prevention through encapsulation in \u03b2-cyclodextrin","volume":"4","author":"Ray","year":"2019","journal-title":"ACS Omega"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"2123","DOI":"10.1016\/j.bbamem.2017.08.002","article-title":"Caspase-3 activation decreases lipid order in the outer plasma membrane leaflet during apoptosis: A fluorescent probe study","volume":"1859","author":"Pyrshev","year":"2017","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"10424","DOI":"10.1021\/acs.jpcb.9b09691","article-title":"Rational design of Nile red analogs for sensing in membranes","volume":"123","author":"Prioli","year":"2019","journal-title":"J. Phys. Chem. B"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1146\/annurev-biochem-070110-123033","article-title":"Measurements and implications of the membrane dipole potential","volume":"81","author":"Wang","year":"2012","journal-title":"Annu. Rev. Biochem."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/978-3-319-17641-3_2","article-title":"Design and use of organic voltage sensitive dyes","volume":"859","author":"Loew","year":"2015","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"2608","DOI":"10.1016\/j.bbamem.2011.06.010","article-title":"Effect of membrane tension on the electric field and dipole potential of lipid bilayer membrane","volume":"1808","author":"Warshaviak","year":"2011","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Bouquiaux, C., Tonnel\u00e9, C., Castet, F., and Champagne, B. (2020). Second-order nonlinear optical properties of an amphiphilic dye embedded in a lipid bilayer. A combined molecular dynamics-quantum chemistry study. J. Phys. Chem. B.","DOI":"10.1021\/acs.jpcb.9b10988"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1021\/acschembio.6b00981","article-title":"A rationally designed, general strategy for membrane orientation of photoinduced electron transfer-based voltage-sensitive dyes","volume":"12","author":"Kulkarni","year":"2017","journal-title":"ACS Chem. Biol."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1039\/C6AN01942K","article-title":"A review: The trend of progress about pH probes in cell application in recent years","volume":"142","author":"Yue","year":"2017","journal-title":"Analyst"},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Diana, R., Panunzi, B., Tuzi, A., Piotto, S., Concilio, S., and Caruso, U. (2019). An amphiphilic pyridinoyl-hydrazone probe for colorimetric and fluorescence pH sensing. Molecules, 24.","DOI":"10.3390\/molecules24213833"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1529\/biophysj.106.095026","article-title":"FRET study of membrane proteins: Determination of the tilt and orientation of the N-terminal domain of M13 major coat protein","volume":"92","author":"Nazarov","year":"2007","journal-title":"Biophys. J."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1007\/s00249-009-0527-9","article-title":"Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins","volume":"39","author":"Vos","year":"2010","journal-title":"Eur. Biophys. J."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.ejmech.2013.06.022","article-title":"Design, synthesis and cellular dynamics studies in membranes of a new coumarin-based \u201cturn-off\u201d fluorescent probe selective for Fe2+","volume":"67","author":"Mena","year":"2013","journal-title":"Eur. J. Med. Chem."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1016\/j.tetlet.2013.12.033","article-title":"A coumarinylaldoxime as a specific sensor for Cu2+ and its biological application","volume":"55","author":"Cassels","year":"2014","journal-title":"Tetrahedron Lett."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.ejmech.2014.02.016","article-title":"Synthesis of coumarin derivatives as fluorescent probes for membrane and cell dynamics studies","volume":"76","author":"Caballero","year":"2014","journal-title":"Eur. J. Med. Chem."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1021\/ct2009208","article-title":"Convergence of free energy profile of coumarin in lipid bilayer","volume":"8","author":"Berka","year":"2012","journal-title":"J. Chem. Theory Comput."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"13574","DOI":"10.1021\/jp106981c","article-title":"Partitioning and localization of environment-sensitive 2-(2\u2032-pyridyl)- and 2-(2\u2032-pyrimidyl)-indoles in lipid membranes: A joint refinement using fluorescence measurements and molecular dynamics simulations","volume":"114","author":"Kyrychenko","year":"2010","journal-title":"J. Phys. Chem. B"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.bpc.2010.12.001","article-title":"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","volume":"154","author":"Kyrychenko","year":"2011","journal-title":"Biophys. Chem."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.bpc.2018.01.005","article-title":"Location of fluorescent probes (2\u2032-hydroxy derivatives of 2,5-diaryl-1,3-oxazole) in lipid membrane studied by fluorescence spectroscopy and molecular dynamics simulation","volume":"235","author":"Posokhov","year":"2018","journal-title":"Biophys. Chem."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"21059","DOI":"10.1021\/jp3060813","article-title":"Fluorescence probing of thiol-functionalized gold nanoparticles: Is alkylthiol coating of a nanoparticle as hydrophobic as expected?","volume":"116","author":"Kyrychenko","year":"2012","journal-title":"J. Phys. Chem. C"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/S0076-6879(97)78024-8","article-title":"Distribution analysis of depth-dependent fluorescence quenching in membranes: A practical guide","volume":"278","author":"Ladokhin","year":"1997","journal-title":"Methods Enzymol."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"4770","DOI":"10.1021\/jp310638f","article-title":"Validation of depth-dependent fluorescence quenching in membranes by molecular dynamics simulation of tryptophan octyl ester in POPC bilayer","volume":"117","author":"Kyrychenko","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1016\/S0006-3495(95)79924-6","article-title":"Fluorescence of membrane-bound tryptophan octyl ester: A model for studying intrinsic fluorescence of protein-membrane interactions","volume":"69","author":"Ladokhin","year":"1995","journal-title":"Biophys. J."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"5875","DOI":"10.1021\/jp4026706","article-title":"Molecular dynamics simulations of depth distribution of spin-labeled phospholipids within lipid bilayer","volume":"117","author":"Kyrychenko","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1007\/s00232-019-00094-1","article-title":"Location of TEMPO-PC in lipid bilayers: Implications for fluorescence quenching","volume":"253","author":"Kyrychenko","year":"2020","journal-title":"J. Membr. Biol."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1007\/s00232-018-0030-2","article-title":"Refining protein penetration into the lipid bilayer using fluorescence quenching and molecular dynamics simulations: The case of diphtheria toxin translocation domain","volume":"251","author":"Kyrychenko","year":"2018","journal-title":"J. Membr. Biol."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1021\/jp4067026","article-title":"Accurate determination of the orientational distribution of a fluorescent molecule in a phospholipid membrane","volume":"118","author":"Timr","year":"2014","journal-title":"J. Phys. Chem. B"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"9706","DOI":"10.1021\/acs.jpcb.5b05123","article-title":"Nonlinear optical properties of fluorescent dyes allow for accurate determination of their molecular orientations in phospholipid membranes","volume":"119","author":"Timr","year":"2015","journal-title":"J. Phys. Chem. B"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"24185","DOI":"10.1039\/C6CP01201A","article-title":"New insight into probe-location dependent polarity and hydration at lipid\/water interfaces: Comparison between gel- and fluid-phases of lipid bilayers","volume":"18","author":"Singh","year":"2016","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"25870","DOI":"10.1039\/C7CP03108D","article-title":"Probe-location dependent resonance energy transfer at lipid\/water interfaces: Comparison between the gel- and fluid-phase of lipid bilayer","volume":"19","author":"Singh","year":"2017","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"2502","DOI":"10.1039\/c3sc50290b","article-title":"Unraveling the peculiar modus operandi of a new class of solvatochromic fluorescent molecular rotors by spectroscopic and quantum mechanical methods","volume":"4","author":"Koenig","year":"2013","journal-title":"Chem. Sci."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"3018","DOI":"10.1039\/C5TC03541D","article-title":"A fluorescent molecular rotor showing vapochromism, aggregation-induced emission, and environmental sensing in living cells","volume":"4","author":"Koenig","year":"2016","journal-title":"J. Mater. Chem. C"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"30590","DOI":"10.1039\/C7CP04688J","article-title":"Computational study of the DPAP molecular rotor in various environments: From force field development to molecular dynamics simulations and spectroscopic calculations","volume":"19","author":"Macchiagodena","year":"2017","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"e1802105","DOI":"10.1002\/adma.201802105","article-title":"Highly efficient photosensitizers with far-red\/near-infrared aggregation-induced emission for in vitro and in vivo cancer theranostics","volume":"30","author":"Wang","year":"2018","journal-title":"Adv. Mater."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"3685","DOI":"10.1039\/C7SC04963C","article-title":"Rational design of a water-soluble NIR AIEgen, and its application in ultrafast wash-free cellular imaging and photodynamic cancer cell ablation","volume":"9","author":"Wang","year":"2018","journal-title":"Chem. Sci."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"2016","DOI":"10.1039\/C9MH00906J","article-title":"Charge control of fluorescent probes to selectively target the cell membrane or mitochondria: Theoretical prediction and experimental validation","volume":"6","author":"Zheng","year":"2019","journal-title":"Mater. Horiz."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"4155","DOI":"10.1021\/j100066a040","article-title":"Simulation of water transport through a lipid membrane","volume":"98","author":"Marrink","year":"1994","journal-title":"J. Phys. Chem."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"4953","DOI":"10.1039\/C5CS00030K","article-title":"BODIPY-based probes for the fluorescence imaging of biomolecules in living cells","volume":"44","author":"Kowada","year":"2015","journal-title":"Chem. Soc. Rev."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"1839","DOI":"10.1111\/j.1600-0854.2008.00801.x","article-title":"BODIPY-cholesterol: A new tool to visualize sterol trafficking in living cells and organisms","volume":"9","author":"Uronen","year":"2008","journal-title":"Traffic"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"6157","DOI":"10.1021\/jp109629v","article-title":"Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: Insights from molecular dynamics simulations","volume":"115","author":"Song","year":"2011","journal-title":"J. Phys. Chem. B"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"18393","DOI":"10.1039\/C5CP01937K","article-title":"Imaging phase separation in model lipid membranes through the use of BODIPY based molecular rotors","volume":"17","author":"Dent","year":"2015","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Steinmark, I.E., James, A.L., Chung, P.-H., Morton, P.E., Parsons, M., Dreiss, C.A., Lorenz, C.D., Yahioglu, G., and Suhling, K. (2019). Targeted fluorescence lifetime probes reveal responsive organelle viscosity and membrane fluidity. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0211165"},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"e1907139","DOI":"10.1002\/smll.201907139","article-title":"Time-resolved fluorescence anisotropy of a molecular rotor resolves microscopic viscosity parameters in complex environments","volume":"16","author":"Steinmark","year":"2020","journal-title":"Small"},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"252","DOI":"10.3389\/fphys.2017.00252","article-title":"Phase partitioning of GM1 and its bodipy-labeled analog determine their different binding to cholera toxin","volume":"8","author":"Rissanen","year":"2017","journal-title":"Front. Physiol."},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"3495","DOI":"10.1021\/acs.langmuir.6b00478","article-title":"A blue-light-emitting BODIPY probe for lipid membranes","volume":"32","author":"Bacalum","year":"2016","journal-title":"Langmuir"},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"9072","DOI":"10.1021\/acs.langmuir.8b01164","article-title":"Atomistic picture of fluorescent probes with hydrocarbon tails in lipid bilayer membranes: An investigation of selective affinities and fluorescent anisotropies in different environmental phases","volume":"34","author":"Knippenberg","year":"2018","journal-title":"Langmuir"},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"3548","DOI":"10.1039\/b716979e","article-title":"Molecular dynamics simulations of DiI-C18(3) in a DPPC lipid bilayer","volume":"10","author":"Gullapalli","year":"2008","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"1368","DOI":"10.1039\/C0CP00430H","article-title":"Atomistic simulation of lipid and DiI dynamics in membrane bilayers under tension","volume":"13","author":"Muddana","year":"2011","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"4844","DOI":"10.1021\/jp400289d","article-title":"Limited perturbation of a DPPC bilayer by fluorescent lipid probes: A molecular dynamics study","volume":"117","author":"Ackerman","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"5350","DOI":"10.1021\/acs.jctc.8b00553","article-title":"Combining (non)linear optical and fluorescence analysis of DiD to enhance lipid phase recognition","volume":"14","author":"Osella","year":"2018","journal-title":"J. Chem. Theory Comput."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"117329","DOI":"10.1016\/j.saa.2019.117329","article-title":"Cyanine dyes with tail length asymmetry enhance photoselection: A multiscale study on DiD probes in a liquid disordered membrane","volume":"224","author":"Aniander","year":"2020","journal-title":"Spectrochim. Acta Part. A Mol. Biomol. Spectrosc."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"e1703851","DOI":"10.1002\/smll.201703851","article-title":"Nanostructuring lipophilic dyes in water using stable vesicles, quatsomes, as scaffolds and their use as probes for bioimaging","volume":"14","author":"Ardizzone","year":"2018","journal-title":"Small"},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"2410","DOI":"10.1039\/b901612k","article-title":"Synthesis and applications of rhodamine derivatives as fluorescent probes","volume":"38","author":"Beija","year":"2009","journal-title":"Chem. Soc. Rev."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.trac.2017.08.013","article-title":"Fluorescein applications as fluorescent probes for the detection of analytes","volume":"97","author":"Yan","year":"2017","journal-title":"Trends Anal. Chem."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"8758","DOI":"10.1021\/jp902877y","article-title":"Computational studies of Texas Red-1,2-dihexadecanoyl-sn-glycero-3- phosphoethanolamine-model building and applications","volume":"113","author":"Skaug","year":"2009","journal-title":"J. Phys. Chem. B"},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cplett.2009.12.015","article-title":"A molecular dynamics model of rhodamine-labeled phospholipid incorporated into a lipid bilayer","volume":"485","author":"Kyrychenko","year":"2010","journal-title":"Chem. Phys. Lett."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"8500","DOI":"10.1021\/jp203738m","article-title":"The impact of texas red on lipid bilayer properties","volume":"115","author":"Skaug","year":"2011","journal-title":"J. Phys. Chem. B"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"4935","DOI":"10.1016\/j.bpj.2009.04.019","article-title":"Theory of raft formation by the cross-linking of saturated or unsaturated lipids in model lipid bilayers","volume":"96","author":"Putzel","year":"2009","journal-title":"Biophys. J."},{"key":"ref_142","first-page":"1","article-title":"Interplay between lipid lateral diffusion, dye concentration and membrane permeability unveiled by a combined spectroscopic and computational study of a model lipid bilayer","volume":"9","author":"Chandramouli","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/s00232-019-00081-6","article-title":"Temperature dependence of the structure and dynamics of a dye-labeled lipid in a planar phospholipid bilayer: A computational study","volume":"252","author":"Akhunzada","year":"2019","journal-title":"J. Membr. Biol."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"2436","DOI":"10.1016\/j.bbamem.2018.07.003","article-title":"How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative","volume":"1860","author":"Mobarak","year":"2018","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1194\/jlr.M700543-JLR200","article-title":"A fluorescent sphingolipid binding domain peptide probe interacts with sphingolipids and cholesterol-dependent raft domains[s]","volume":"49","author":"Hebbar","year":"2008","journal-title":"J. Lipid Res."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"26318","DOI":"10.3390\/ijms161125955","article-title":"A\u03b21-25-derived sphingolipid-domain tracer peptide sbd interacts with membrane ganglioside clusters via a coil-helix-coil motif","volume":"16","author":"Wang","year":"2015","journal-title":"Int. J. Mol. Sci."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1016\/j.steroids.2010.11.001","article-title":"Probes for studying cholesterol binding and cell biology","volume":"76","author":"Gimpl","year":"2011","journal-title":"Steroids"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.chemphyslip.2016.03.003","article-title":"Imaging approaches for analysis of cholesterol distribution and dynamics in the plasma membrane","volume":"199","author":"Modzel","year":"2016","journal-title":"Chem. Phys. Lipids"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"5806","DOI":"10.1021\/jp312026u","article-title":"Behavior of fluorescent cholesterol analogues dehydroergosterol and cholestatrienol in lipid bilayers: A molecular dynamics study","volume":"117","author":"Robalo","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"45563","DOI":"10.1074\/jbc.M303567200","article-title":"The potential of fluorescent and spin-labeled steroid analogs to mimic natural cholesterol","volume":"278","author":"Scheidt","year":"2003","journal-title":"J. Biol. Chem."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"7345","DOI":"10.1021\/jp406883k","article-title":"Dehydroergosterol as an analogue for cholesterol: Why it mimics cholesterol so well-or does it?","volume":"118","author":"Pourmousa","year":"2014","journal-title":"J. Phys. Chem. B"},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"2188","DOI":"10.1016\/j.bbamem.2015.04.018","article-title":"Design of new fluorescent cholesterol and ergosterol analogs: Insights from theory","volume":"1848","author":"List","year":"2015","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1021\/acs.jctc.6b01017","article-title":"Computational approach to evaluation of optical properties of membrane probes","volume":"13","author":"List","year":"2017","journal-title":"J. Chem. Theory Comput."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"15487","DOI":"10.1039\/C9CP01902B","article-title":"Rational design of novel fluorescent analogues of cholesterol: A \u201cstep-by-step\u201d computational study","volume":"21","author":"Bonvicini","year":"2019","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1111\/jmi.12691","article-title":"Live-cell imaging of new polyene sterols for improved analysis of intracellular cholesterol transport","volume":"271","author":"Modzel","year":"2018","journal-title":"J. Microsc."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.chemphyslip.2017.12.005","article-title":"Structural design of intrinsically fluorescent oxysterols","volume":"212","author":"Modzel","year":"2018","journal-title":"Chem. Phys. Lipids"},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"2087","DOI":"10.1002\/cbic.201402042","article-title":"Synthesis of cholesterol analogues bearing BODIPY fluorophores by suzuki or liebeskind-srogl cross-coupling and evaluation of their potential for visualization of cholesterol pools","volume":"15","author":"Liu","year":"2014","journal-title":"ChemBioChem"},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"7313","DOI":"10.1021\/acs.jpcb.9b04967","article-title":"Computational characterization of a cholesterol-based molecular rotor in lipid membranes","volume":"123","author":"Reinholdt","year":"2019","journal-title":"J. Phys. Chem. B"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1016\/j.bpj.2013.09.031","article-title":"Membrane orientation and lateral diffusion of BODIPY-cholesterol as a function of probe structure","volume":"105","author":"Solanko","year":"2013","journal-title":"Biophys. J."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"15848","DOI":"10.1021\/acs.jpcb.5b10188","article-title":"How well does BODIPY-cholesteryl ester mimic unlabeled cholesteryl esters in high density lipoprotein particles?","volume":"119","author":"Karilainen","year":"2015","journal-title":"J. Phys. Chem. B"},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"13731","DOI":"10.1021\/jp406135a","article-title":"NBD-labeled cholesterol analogues in phospholipid bilayers: Insights from molecular dynamics","volume":"117","author":"Robalo","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/S0005-2736(01)00269-3","article-title":"Exclusion of a cholesterol analog from the cholesterol-rich phase in model membranes","volume":"1511","author":"Loura","year":"2001","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1021\/bi951953q","article-title":"Membrane organization at low cholesterol concentrations: A study using 7-nitrobenz-2-oxa-1,3-diazol-4-yl-labeled cholesterol","volume":"35","author":"Mukherjee","year":"1996","journal-title":"Biochemistry"},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"2226","DOI":"10.1016\/S0006-3495(97)78866-0","article-title":"Dehydroergosterol structural organization in aqueous medium and in a model system of membranes","volume":"72","author":"Loura","year":"1997","journal-title":"Biophys. J."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/25\/15\/3424\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:52:22Z","timestamp":1760176342000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/25\/15\/3424"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,28]]},"references-count":164,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2020,8]]}},"alternative-id":["molecules25153424"],"URL":"https:\/\/doi.org\/10.3390\/molecules25153424","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,28]]}}}