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Bujor A, Hanganu A, Baratoiu R, Hristea EN, Tudose M, Tecuceanu V, Madalan AM, Ionita P. Novel Derivatives of Nitrobenzofurazan with Chromogenic and Fluorogenic Properties. Molecules 2023; 28:6146. [PMID: 37630398 PMCID: PMC10459551 DOI: 10.3390/molecules28166146] [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: 08/04/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Five new derivatives were obtained utilizing 4-chloro-7-nitrobenzofurazan (NBD-chloride) in combination with furfurylamine, adamantylamine, aminohippuric acid, phenylalanine, and dehydroabietylamine. These derivatives were then subjected to a comparative analysis of their physical, chemical, and certain biological properties alongside two analogous and known compounds derived from the glycine and 4-amino-TEMPO free radical.
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Affiliation(s)
- Alexandru Bujor
- Department of Inorganic, Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 90 Panduri, 050663 Bucharest, Romania; (A.B.); (A.H.); (A.M.M.)
| | - Anamaria Hanganu
- Department of Inorganic, Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 90 Panduri, 050663 Bucharest, Romania; (A.B.); (A.H.); (A.M.M.)
- Institute of Organic and Supramolecular Chemistry, Spl. Independentei 202B, 060023 Bucharest, Romania;
| | - Rodica Baratoiu
- Institute of Physical Chemistry, Spl. Independentei 202, 060023 Bucharest, Romania; (R.B.); (E.N.H.); (M.T.)
| | - Elena N. Hristea
- Institute of Physical Chemistry, Spl. Independentei 202, 060023 Bucharest, Romania; (R.B.); (E.N.H.); (M.T.)
| | - Madalina Tudose
- Institute of Physical Chemistry, Spl. Independentei 202, 060023 Bucharest, Romania; (R.B.); (E.N.H.); (M.T.)
| | - Victorita Tecuceanu
- Institute of Organic and Supramolecular Chemistry, Spl. Independentei 202B, 060023 Bucharest, Romania;
| | - Augustin M. Madalan
- Department of Inorganic, Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 90 Panduri, 050663 Bucharest, Romania; (A.B.); (A.H.); (A.M.M.)
| | - Petre Ionita
- Department of Inorganic, Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 90 Panduri, 050663 Bucharest, Romania; (A.B.); (A.H.); (A.M.M.)
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Marquezin CA, Lamy MT, de Souza ES. Molecular collisions or resonance energy transfer in lipid vesicles? A methodology to tackle this question. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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The interaction of a thiosemicarbazone derived from R - (+) - limonene with lipid membranes. Chem Phys Lipids 2020; 234:105018. [PMID: 33232725 DOI: 10.1016/j.chemphyslip.2020.105018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/21/2022]
Abstract
As a potential drug, 2-nitrobenzaldehyde-thiosemicarbazone (2-TSC), a thiosemicarbazone derived from the terpene R-(+)-limonene, was studied through calorimetric and spectroscopic techniques. Differential Scanning Calorimetry (DSC) data showed that 2-TSC causes structural changes in a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DMPC) membrane, strongly decreasing the cooperativity of the bilayer gel-fluid thermal transition. Optical absorption spectroscopy showed that 2-TSC is more soluble in ethanol and lipids than in water medium, and that the drug displays different structures in the different environments. Though 2-TSC displays no fluorescence, time resolved fluorescence showed that the drug is an effective quencher of the fluorescent probe 6-dodecanoyl-2-dimethylaminonaphthalene (Laurdan). As it is well accepted that Laurdan is positioned into the bilayer close to the membrane surface, that is possibly the localization of 2-TSC in a bilayer. Electron spin resonance (ESR) of the probe 1-palmitoyl-2-stearoyl-(14-doxyl)-sn-glycero-3-phosphocholine (14-PCSL) revealed that 2-TSC is inserted into the hydrocarbon part of the bilayer, fluidizing the lipid bilayer gel phase and rigidifying or organizing the bilayer fluid phase. Similar effects are found for other lipophilic molecules, including cholesterol. These results are useful to improve the understanding of the processes that govern the interaction of thiosemicarbazones with cell membranes, related to the activity of the drugs and their cytotoxicity.
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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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Marquezin CA, Ito AS, de Souza ES. Organization and dynamics of NBD-labeled lipids in lipid bilayer analyzed by FRET using the small membrane fluorescent probe AHBA as donor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:182995. [DOI: 10.1016/j.bbamem.2019.05.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/13/2019] [Accepted: 05/23/2019] [Indexed: 01/22/2023]
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6
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Nonspecific nanocarriers for doxorubicin and cytarabine in the presence of fatted and defatted human albumin. Part I. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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7
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Subramanian V, Zurek NA, Evans DG, Shreve AP. Predictive modeling of broad wavelength light-harvesting performance in assemblies of multiple chromophores. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Determination of the fluorescence labels location in lipid bilayer based on fluorescence quenching. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.02.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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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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Kyrychenko A, Rodnin MV, Ghatak C, Ladokhin AS. Joint refinement of FRET measurements using spectroscopic and computational tools. Anal Biochem 2017; 522:1-9. [PMID: 28108168 DOI: 10.1016/j.ab.2017.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 01/12/2017] [Accepted: 01/16/2017] [Indexed: 12/28/2022]
Abstract
The variability of the orientation factor is a long-standing challenge in converting FRET efficiency measurements into donor-acceptor distances. We propose the use of molecular dynamics (MD) simulations to characterize orientation distributions and thus improve the accuracy of distance measurements. Here, we test this approach by comparing experimental and simulated FRET efficiencies for a model donor-acceptor pair of enhanced cyan and enhanced yellow FPs connected by a flexible linker. Several spectroscopic techniques were used to characterize FRET in solution. In addition, a series of atomistic MD simulations of a total length of 1.5 μs were carried out to calculate the distances and the orientation factor in the FRET-pair. The resulting MD-based and experimentally measured FRET efficiency histograms coincided with each other, allowing for direct comparison of distance distributions. Despite the fact that the calculated average orientation factor was close to 2/3, the application of the average κ2 to the entire histogram of FRET efficiencies resulted in a substantial artificial broadening of the calculated distribution of apparent donor-acceptor distances. By combining single pair-FRET measurements with computational tools, we demonstrate that accounting for the donor and acceptor orientation heterogeneity is critical for accurate representation of the donor-acceptor distance distribution from FRET measurements.
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Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine; Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160-7421, USA.
| | - Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160-7421, USA
| | - Chiranjib Ghatak
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160-7421, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160-7421, USA.
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Filipe HAL, Bowman D, Palmeira T, Cardoso RMS, Loura LMS, Moreno MJ. Interaction of NBD-labelled fatty amines with liquid-ordered membranes: a combined molecular dynamics simulation and fluorescence spectroscopy study. Phys Chem Chem Phys 2016; 17:27534-47. [PMID: 26426766 DOI: 10.1039/c5cp04191k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A complete homologous series of fluorescent 7-nitrobenz-2-oxa-1,3-diazol-4-yl-(NBD) labelled fatty amines of varying alkyl chain lengths, NBD-Cn, inserted in 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphocholine (POPC) or N-palmitoyl sphingomyelin (SpM) bilayers, with 50 mol% and 40 mol% cholesterol (Chol), respectively, was studied using atomistic molecular dynamics simulations. For all amphiphiles in both bilayers, the NBD fluorophore locates at the interface, in a more external position than that previously observed for pure POPC bilayers. This shallower location of the NBD group agrees with the lower fluorescent quantum yield, shorter fluorescence lifetime, and higher ionisation constants (smaller pKa) determined experimentally. The more external location is also consistent with the changes measured in steady-state fluorescence anisotropy from POPC to POPC/Chol (1 : 1) vesicles. Accordingly, the equilibrium location of the NBD group within the various bilayers is mainly dictated by bilayer compositions, and is mostly unaffected by the length of the attached alkyl chain. Similarly to the behaviour observed in POPC bilayers, the longer-chained NBD-Cn amphiphiles show significant mass density near the mixed bilayers' midplanes, and the alkyl chains of the longer derivatives, mainly NBD-C16, penetrate the opposite bilayer leaflet to some extent. However, this effect is quantitatively less pronounced in these ordered bilayers than in POPC. Similarly to POPC bilayers, the effects of these amphiphiles on the structure and dynamics of the host lipid were found to be relatively mild, in comparison with acyl-chain phospholipid analogues.
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Affiliation(s)
- Hugo A L Filipe
- Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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12
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Kyrychenko A. Using fluorescence for studies of biological membranes: a review. Methods Appl Fluoresc 2015; 3:042003. [DOI: 10.1088/2050-6120/3/4/042003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Filipe HAL, Santos LS, Prates Ramalho JP, Moreno MJ, Loura LMS. Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: a molecular dynamics study. Phys Chem Chem Phys 2015; 17:20066-79. [DOI: 10.1039/c5cp01596k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An NBD-diC16PE/POPC bilayer with typical fluorophore inverted-snorkelling configurations, and mass density profiles across the membrane. The wide distribution of the NBD fluorophore lies at the origin of its complex emission kinetics.
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Affiliation(s)
- Hugo A. L. Filipe
- Departamento de Química
- Faculty of Science and Technnology
- University of Coimbra
- Rua Larga
- Portugal
| | - Lennon S. Santos
- Departamento de Química
- Faculty of Science and Technnology
- University of Coimbra
- Rua Larga
- Portugal
| | - J. P. Prates Ramalho
- Departamento de Química
- Escola de Ciências e Tecnologia
- Universidade de Évora
- Rua Romão Ramalho
- Portugal
| | - Maria João Moreno
- Departamento de Química
- Faculty of Science and Technnology
- University of Coimbra
- Rua Larga
- Portugal
| | - Luís M. S. Loura
- Centro de Química de Coimbra
- Rua Larga
- Portugal
- Centro de Neurociências e Biologia Celular
- Universidade de Coimbra
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Calibration of Distribution Analysis of the Depth of Membrane Penetration Using Simulations and Depth-Dependent Fluorescence Quenching. J Membr Biol 2014; 248:583-94. [PMID: 25107303 DOI: 10.1007/s00232-014-9709-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/15/2014] [Indexed: 10/24/2022]
Abstract
Determination of the depth of membrane penetration provides important information for studies of membrane protein folding and protein-lipid interactions. Here, we use a combination of molecular dynamics (MD) simulations and depth-dependent fluorescence quenching to calibrate the methodology for extracting quantitative information on membrane penetration. In order to investigate the immersion depth of the fluorescent label in lipid bilayer, we studied 7-nitrobenz-2-oxa-1,3-diazole (NBD) attached to the lipid headgroup in NBD-PE incorporated into POPC bilayer. The immersion depth of NBD was estimated by measuring steady-state and time-resolved fluorescence quenching with spin-labeled lipids co-incorporated into lipid vesicles. Six different spin-labeled lipids were utilized: one with headgroup-attached Tempo probe (Tempo-PC) and five with acyl chain-labeled n-Doxyl moieties (n-Doxyl-PC where n is a chain labeling position equal to 5, 7, 10, 12, and 14, respectively). The Stern-Volmer analysis revealed that NBD quenching in membranes occurs by both static and dynamic collisional quenching processes. Using the methodology of Distribution Analysis, the immersion depth and the apparent half-width of the transversal distributions of the NBD moiety were estimated to be 14.7 and 6.7 Å, respectively, from the bilayer center. This position is independently validated by atomistic MD simulations of NBD-PE lipids in a POPC bilayer (14.4 Å). In addition, we demonstrate that MD simulations of the transverse overlap integrals between dye and quencher distributions can be used for proper analysis of the depth-dependent quenching profile. Finally, we illustrate the application of this methodology by determining membrane penetration of site selectively labeled mutants of diphtheria toxin T-domain.
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Urbančič I, Ljubetič A, Arsov Z, Strancar J. Coexistence of probe conformations in lipid phases-a polarized fluorescence microspectroscopy study. Biophys J 2014; 105:919-27. [PMID: 23972844 DOI: 10.1016/j.bpj.2013.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 01/14/2023] Open
Abstract
Several well-established fluorescence methods depend on environment-sensitive probes that report about molecular properties of their local environment. For reliable interpretation of experiments, careful characterization of probes' behavior is required. In this study, bleaching-corrected polarized fluorescence microspectroscopy with nanometer spectral peak position resolution was applied to characterize conformations of two alkyl chain-labeled 7-nitro-2-1,3-benzoxadiazol-4-yl phospholipids in three model membranes, representing the three main lipid phases. The combination of polarized and spectral detection revealed two main probe conformations with their preferential fluorophore dipole orientations roughly parallel and perpendicular to membrane normal. Their peak positions were separated by 2-6 nm because of different local polarities and depended on lipid environment. The relative populations of conformations, estimated by a numerical model, indicated a specific sensitivity of the two probes to molecular packing with cholesterol. The coexistence of probe conformations could be further exploited to investigate membrane organization below microscopy spatial resolution, such as lipid rafts. With the addition of polarized excitation or detection to any environment-sensitive fluorescence imaging technique, the conformational analysis can be directly applied to explore local membrane complexity.
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Affiliation(s)
- Iztok Urbančič
- Laboratory of Biophysics, Condensed Matter Physics Department, Jožef Stefan Institute, Ljubljana, Slovenia
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Simple estimation of Förster Resonance Energy Transfer (FRET) orientation factor distribution in membranes. Int J Mol Sci 2012. [PMID: 23203123 PMCID: PMC3509639 DOI: 10.3390/ijms131115252] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Because of its acute sensitivity to distance in the nanometer scale, Förster resonance energy transfer (FRET) has found a large variety of applications in many fields of chemistry, physics, and biology. One important issue regarding the correct usage of FRET is its dependence on the donor-acceptor relative orientation, expressed as the orientation factor κ2. Different donor/acceptor conformations can lead to κ2 values in the 0 ≤ κ2 ≤ 4 range. Because the characteristic distance for FRET, R0, is proportional to (κ2)1/6, uncertainties in the orientation factor are reflected in the quality of information that can be retrieved from a FRET experiment. In most cases, the average value of κ2 corresponding to the dynamic isotropic limit (<κ2> = 2/3) is used for computation of R0 and hence donor-acceptor distances and acceptor concentrations. However, this can lead to significant error in unfavorable cases. This issue is more critical in membrane systems, because of their intrinsically anisotropic nature and their reduced fluidity in comparison to most common solvents. Here, a simple numerical simulation method for estimation of the probability density function of κ2 for membrane-embedded donor and acceptor fluorophores in the dynamic regime is presented. In the simplest form, the proposed procedure uses as input the most probable orientations of the donor and acceptor transition dipoles, obtained by experimental (including linear dichroism) or theoretical (such as molecular dynamics simulation) techniques. Optionally, information about the widths of the donor and/or acceptor angular distributions may be incorporated. The methodology is illustrated for special limiting cases and common membrane FRET pairs.
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