Calibration of the parallax fluorescence quenching method for determination of membrane penetration depth: refinement and comparison of quenching by spin-labeled and brominated lipids.

We previously introduced the "parallax" method, which uses fluorescence quenching by spin-labeled lipids in order to measure the depth of molecules within a membrane [Chattopadhyay, A., & London, E. (1987) Biochemistry 26, 39-45]. In this report the accuracy of this method is established by comparison of spin-label quenching to that obtained using brominated lipids. To accomplish this, the fluorescent molecules used were a fatty acid labeled with a carbazole buried deeply within the acyl chain region of the membrane, an acyl-Trp with the Trp residue residing near the polar membrane region, and cytochrome b5, which has Trp residues in its membrane-inserted region. The depths calculated from the amount of bromine quenching agreed with those determined using parallax analysis. This indicates that the depth reported by parallax analysis is accurate and that the spin labels residue very close to their predicted locations in the membrane. Furthermore, there was good agreement when parallax analysis was applied both to quenching by brominated and spin-labeled molecules, suggesting that the analysis is valid in both cases. The effect that different distributions and motions of fluorophores and quenchers would have on parallax analysis was also examined. For uniform distributions of quenchers or fluorophores over a range of depths, it was found that the analysis reports the average fluorophore depth. In addition, experimental data suggest that motional effects do not significantly alter the measured depths. This is consistent with the motions during the short excited state lifetime of the fluorophores being relatively small and/or relatively isotropic.     

Average membrane penetration depth of tryptophan residues of the nicotinic acetylcholine receptor by the parallax method.

The membrane penetration depths of tryptophan residues in the nicotinic acetylcholine receptor from Torpedo californica have been analyzed in reconstituted membranes containing purified receptor and defined lipids. Dioleoylphosphatidylcholine and three spin-labeled phosphatidylcholines with the nitroxide group at three different positions on the fatty acyl chain were used for reconstitution of the receptor. The spin-labeled phospholipids serve as quenchers of tryptophan fluorescence. Differential quenching of the intrinsic fluorescence of the acetylcholine receptor by the spin-labeled phospholipids has been utilized to analyze the average membrane penetration depth of tryptophans by the parallax method [Chattopadhyay, A., & London, E. (1987) Biochemistry 26, 39-45]. Analyses of the quenching data indicate that the tryptophan residues on the average are at a shallow location (10.1 A from the center of the bilayer) in the membrane. In addition, the generally low levels of quenching imply that the majority of tryptophan residues are located in the putative extramembranous region of the receptor. These results are consistent with several proposed models for the tertiary structure of the acetylcholine receptor and are relevant to ongoing analyses of the overall conformation and orientation of the acetylcholine receptor in the membrane.     

Localization of bilirubin in phospholipid bilayers by parallax analysis of fluorescence quenching

It has been proposed that the neurotoxicity observed in severely jaundiced infants results from the binding of unconjugated bilirubin to nerve cell membranes. However, despite potentially important clinical ramifications, there remains significant controversy regarding the physical nature of bilirubin-membrane interactions. We used the technique of parallax analysis of fluorescence quenching (Chattopadhyay, A., and E. London. 1987. Biochemistry. 26: 39;-45) to measure the depth of penetration of bilirubin in model phospholipid bilayers. The localization of unconjugated bilirubin and ditaurobilirubin within small unilamellar vesicles composed of dioleoylphosphatidylcholine was determined through an analysis of the quenching of bilirubin fluorescence by spin-labeled phospholipids, and by bilirubin-mediated quenching of a series of anthroyloxy fatty acid probes at various depths within the membrane bilayer. Findings were further verified with potassium iodide as an aqueous quencher. Our results indicate that, at pH 10, unconjugated bilirubin localizes approximately 20 A from the bilayer center, in the region of the polar head groups. Further analyses suggest a modest influence of pH, membrane cholesterol content, and vesicle diameter on the bilirubin penetration depth. Taken together, these data support that, under physiologic conditions, bilirubin localizes to the polar region of phospholipid bilayers, near the membrane-water interface.     

Measuring membrane penetration with depth-dependent fluorescence quenching: Distribution analysis is coming of age

Depth-dependent fluorescence quenching by lipid-attached quenchers (e.g., bromine atoms and doxyl groups) is an important tool for determining the penetration of proteins and peptides into lipid bilayers. Extracting quantitative information and accurate calculations of the depth of the fluorophore are complicated by thermal disorder, resulting in broad distributions of the transverse positions of both quenchers and fluorophores. Twenty-one years ago a methodology called distribution analysis (DA) was introduced, based on the emerging view of the complexity of the transverse organization of lipid bilayer structure. The method is aimed at extracting quantitative information on membrane penetration, such as position and width of fluorophore's distribution along the depth coordinate and its exposure to the lipid phase. Here we review recent progress in refining the DA method and illustrate its applications to protein–membrane interactions. We demonstrate how basic assumptions of the DA approach can be validated using molecular dynamics simulations and how the precision of depth determination is improved by applying a new protocol based on a combination of steady-state and time-resolved fluorescence quenching. Using the example of the MPER fragment of the membrane-spanning domain of the HIV-1 gp41 fusion protein, we illustrate how DA applications and computer simulations can be used together to reveal the molecular organization of a protein–membrane complex. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.     

Use of pyrene as a luminescence indicator of the viscosity of model and biological membranes

The pyrene movement in a lipid bilayer has been shown to occur not only in the lateral but also transmembrane direction. Within the excited state lifetime the pyrene monomer elevates from the depth to the polar regions of the membrane and emits a luminescence photon. The excimer does not exhibit any marked transmembrane movement while luminescing from the hydrophobic regions. The luminescence quenching efficiency of monomers and excimers depends on the depth of quencher penetration into the membrane. In the lipid bilayer the pyrene luminescence is strongly quenched by molecular oxygen. The pyrene binding to membrane proteins protects it from quenching. A conclusion has been made that the carrying out estimations of membrane viscosity from pyrene luminescence require considerable correction.     

Chlorinated hydrocarbon-cell membrane interactions studied by the fluorescence quenching of carbazole-labeled phospholipids: Probe synthesis and characterization of the quenching methodology

In recognition of the need to understand better the interactions of the chlorinated hydrocarbon insecticides with cell membranes we investigated the use of fluorescence quenching of membrane-bound fluorophores by these chlorinated hydrocarbons. An extensive survey of potential fluorophores identified the N-alkyl derivatives of carbazole as being especially suitable fluorophores. The fluorescence emission of these derivatives is quenched by a wide variety of commonly-used chlorinated hydrocarbons. This quenching is collisional and does not result in significant photodecomposition.Four structurally distinct carbazole-labeled phospholipids were synthesized, and their structures were confirmed by 270 MHz proton NMR and by chromatographic and chemical means. The carbazole moiety of each labeled phospholipid should be localized at a different depth in lipid bilayer. However, water soluble quenchers indicate that the fluorophores are inaccessible to the aqueous phase, irrespective of their point of attachment to the phospholipids.When incorporated into lipid bilayers, the fluorescence lifetime of these carbazole-labeled phospholipids reveals the collisional frequency between the fluorophore and the chlorinated hydrocarbon. As a result quenching of membrane-bound fluorophores may be used to measure: (1) the diffusional rate of the chlorinated hydrocarbon in the bilayer; (2) the lipid-water partition coefficient; (3) the maximum binding capacity of the membrane for the chlorinated hydrocarbon. Examples of all these measurements are given, and the fluorometric results are confirmed by direct chemical analysis.     

On measuring biomembrane microviscosity using pyrene luminescence in aerobic conditions

The movement of pyrene in a lipid bilayer is shown to occur not only in the lateral but also transmembrane direction. Within the excited state lifetime, the pyrene monomer elevates from the depth to the polar region of the membrane and emits a luminescence photon. The excimer does not exhibit any marked transmembrane movement. The luminescence quenching efficiency of monomers and excimers depends on the depth of penetration of the quencher into the membrane. In the lipid bilayer, pyrene luminescence is strongly quenched by oxygen. The binding of pyrene to membrane proteins protects it from quenching. It has been concluded that the widely used estimations of membrane viscosity from pyrene luminescence intensity are incorrect.     

Joint determination by Brownian dynamics and fluorescence quenching of the in-depth location profile of biomolecules in membranes

The in-depth molar distribution function of fluorophores is revealed by a new methodology for fluorescence quenching data analysis in membranes. Brownian dynamics simulation was used to study the in-depth location profile of quenchers. A Lorentzian profile was reached. Since the Stern-Volmer equation is valid at every depth in the membrane for low quencher concentrations, the molar distribution of the fluorophore (also regarded as a Lorentzian) can be achieved. The average location and the broadness of the fluorophore distribution can be calculated. The importance of the knowledge of the location width is demonstrated and discussed, since this parameter reveals important conclusions on structural features of the interaction of membranes with probes and biomolecules (e.g., conformational freedom in proteins), as well as photophysical properties (e.g., differential fluorophore quantum yields). Subsequent use of this methodology by the reader does not, necessarily, involve the performance of simulations and is not limited to the use of Lorentzian function distributions.     

Fluorescence quenching of a series of membrane probes measured in living cells by flow cytometry

The transverse location normal to the bilayer surface of a series of n-(9-anthroyloxy) fatty acid probes, where n = 2, 3, 6, 7, 9, 12, and 16, was determined by fluorescence quenching measurements with a flow cytometer. We show that the anthroyloxy moieties of the probes locate at a graded series of depths in the outer leaflet of the plasma membrane of living HeLa cells, in a manner similar to that previously observed for model membrane systems, and mitochondria. For different n, the efficiency of quenching with an aqueous phase quencher, Cu+2, was 2 greater than or equal to 3 greater than 6 greater than or equal to 7 greater than 9 greater than 12 greater than 16. Therefore, flow cytometry permits use of these probes for measurements of dynamic parameters related to membrane fluidity at different depths in the plasma membranes of living cells.     

Effect of taper geometries and launch angle on evanescent wave penetration depth in optical fibers

A large penetration depth of an evanescent wave is the key to success for developing an ultra high-resolution fiber-based evanescent wave biosensor. Tapering the fiber and launching light at an angle has the potential of increasing the penetration depth of evanescent wave manifolds. The effects of tapering, launch angle and taper length of the fiber have been explored in detail using a ray-tracing model to calculate the highest possible penetration depth of the evanescent field. Evanescent wave penetration depths of the order of the size of living cells have been achieved by optimizing the parameters relating geometry of tapered fibers.     

Dual-wavelength phosphorimetry for determination of cortical and subcortical microvascular oxygenation in rat kidney.

This study presents a dual-wavelength phosphorimeter developed to measure microvascular PO2 (microPO2) in different depths in tissue and demonstrates its use in rat kidney. The used phosphorescent dye is Oxyphor G2 with excitation bands at 440 and 632 nm. The broad spectral gap between the excitation bands combined with a relatively low light absorption of 632 nm light by tissue results in a marked difference in penetration depths of both excitation wavelengths. In rat kidney, we determine the catchments depth of the 440-nm excitation to be 700 microm, whereas the catchments depth of 632 nm is as much as 4 mm. Therefore, the measurements differentiate between cortex and outer medulla, respectively. In vitro, no difference in PO2 readings between both channels was found. On the rat kidney in vivo, the measured cortical microPO2 was on average 20 Torr higher than the medullary microPO2 over a wide PO2 range induced by variations in inspired oxygen fraction. Examples provided from endotoxemia and resuscitation show differences in responses of mean cortical and medullary PO2 readings as well as in the shape of the PO2 histograms. It can be concluded that oxygen-dependent quenching of phosphorescence of Oxyphor G2 allows quantitative measurement of microPO2 noninvasively in two different depths in vivo. Oxygen levels measured by this technique in the rat renal cortex and outer medulla are consistent with previously published values detected by Clark-type oxygen electrodes. Dual-wavelength phosphorimetry is excellently suited for monitoring microPO2 changes in two different anatomical layers under pathophysiological conditions with the characteristics of providing oxygen histograms from two depths and having a penetration depth of several millimeters.     

New BODIPY lipid probes for fluorescence studies of membranes

Many fluorescent lipid probes tend to loop back to the membrane interface when attached to a lipid acyl chain rather than embedding deeply into the bilayer. To achieve maximum embedding of BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) fluorophore into the bilayer apolar region, a series of sn-2 acyl-labeled phosphatidylcholines was synthesized bearing 4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene-8-yl (Me(4)-BODIPY-8) at the end of C(3)-, C(5)-, C(7)-, or C(9)-acyl. A strategy was used of symmetrically dispersing the methyl groups at BODIPY ring positions 1, 3, 5, and 7 to decrease fluorophore polarity. Iodide quenching of the phosphatidylcholine probes in bilayer vesicles confirmed that the Me(4)-BODIPY-8 fluorophore was embedded in the bilayer. Parallax analysis of Me(4)-BODIPY-8 fluorescence quenching by phosphatidylcholines containing iodide at different positions along the sn-2 acyl chain indicated that the penetration depth of Me(4)-BODIPY-8 into the bilayer was determined by the length of the linking acyl chain. Evaluation using monolayers showed minimal perturbation of <10 mol% probe in fluid-phase and cholesterol-enriched phosphatidylcholine. Spectral characterization in monolayers and bilayers confirmed the retention of many features of other BODIPY derivatives (i.e., absorption and emission wavelength maxima near 498 nm and approximately 506-515 nm) but also showed the absence of the 620-630 nm peak associated with BODIPY dimer fluorescence and the presence of a 570 nm emission shoulder at high Me(4)-BODIPY-8 surface concentrations. We conclude that the new probes should have versatile utility in membrane studies, especially when precise location of the reporter group is needed.     

The location of protein in serum lipoproteins: a fluorescence quenching study.

Quenching of the tryptophan fluorescence of pig serum HDL3 and LDL2 lipoproteins by iodide and succinimide has been used to estimate the accessibility of the fluorophores to the solvent and, by inference, the location of the protein in the macromolecular complexes. At least 80% of the protein is thought to be located at or near the surface in both lipoproteins but its accessibility is hindered especially in LDL2. A difference in surface topography in the two lipoproteins is suggested with the protein in LDL2 more buried in lipid and further away from the charged phospholipid polar groups than in HDL3. A refined treatment of the quenching data has been developed to take account of the heterogeneity of quenching sites found in the lipoproteins.     

Two-color STED microscopy of living synapses using a single laser-beam pair

The advent of superresolution microscopy has opened up new research opportunities into dynamic processes at the nanoscale inside living biological specimens. This is particularly true for synapses, which are very small, highly dynamic, and embedded in brain tissue. Stimulated emission depletion (STED) microscopy, a recently developed laser-scanning technique, has been shown to be well suited for imaging living synapses in brain slices using yellow fluorescent protein as a single label. However, it would be highly desirable to be able to image presynaptic boutons and postsynaptic spines, which together form synapses, using two different fluorophores. As STED microscopy uses separate laser beams for fluorescence excitation and quenching, incorporation of multicolor imaging for STED is more difficult than for conventional light microscopy. Although two-color schemes exist for STED microscopy, these approaches have several drawbacks due to their complexity, cost, and incompatibility with common labeling strategies and fluorophores. Therefore, we set out to develop a straightforward method for two-color STED microscopy that permits the use of popular green-yellow fluorescent labels such as green fluorescent protein, yellow fluorescent protein, Alexa Fluor 488, and calcein green. Our new (to our knowledge) method is based on a single-excitation/STED laser-beam pair to simultaneously excite and quench pairs of these fluorophores, whose signals can be separated by spectral detection and linear unmixing. We illustrate the potential of this approach by two-color superresolution time-lapse imaging of axonal boutons and dendritic spines in living organotypic brain slices.     

Surface plasmon resonance imaging on a microchip for detection of DNA-modified gold nanoparticles deposited onto the surface in a non-cross-linking configuration

We report theoretical predictions and experimental observations of the reduced detection volume with the use of surface-plasmon-coupled emission (SPCE). The effective fluorescence volume (detection volume) in SPCE experiments depends on two near-field factors: the depth of evanescent wave excitation and a distance-dependent coupling of excited fluorophores to the surface plasmons. With direct excitation of the sample (reverse Kretschmann excitation) the detection volume is restricted only by the distance-dependent coupling of the excitation to the surface plasmons. However, with the excitation through the glass prism at surface plasmon resonance angle (Kretschmann configuration), the detection volume is a product of evanescent wave penetration depth and distance-dependent coupling. In addition, the detection volume is further reduced by a metal quenching of excited fluorophores at a close proximity (below 10nm). The height of the detected volume size is 40-70nm, depending on the orientation of the excited dipoles. We show that, by using the Kretschmann configuration in a microscope with a high-numerical-aperture objective (1.45) together with confocal detection, the detection volume can be reduced to 1-2attoL. The strong dependence of the coupling to the surface plasmons on the orientation of excited dipoles can be used to study the small conformational changes of macromolecules.     

Analysis of protein and peptide penetration into membranes by depth-dependent fluorescence quenching: theoretical considerations.

Depth-dependent fluorescence quenching in membranes is playing an increasingly important role in the determination of the low resolution structure of membrane proteins. This paper presents a graphical way of visualizing membrane quenching caused by lipid-attached bromines or spin labels with the help of a depth-dependent fluorescence quenching profile. Two methods are presently available to extract information on membrane penetration from quenching: the parallax method (PM; ) and distribution analysis (DA; A. S. Biophys. J. 64:290a (Abstr.); A. S. Methods Enzymol. 278:462-473). Analysis of various experimental and simulated data by these two methods is presented. The effects of uncertainty in the local concentration of quenching lipids (due to protein shielding or nonideality in lipid mixing), the existence of multiple conformations of membrane-bound protein, incomplete binding, and uncertainty in the fluorescence in nonquenching lipid are described. Regardless of the analytical form of the quenching profile (Gaussian function for DA or truncated parabola for PM), it has three primary characteristics: position on the depth scale, area, and width. The most important result, not surprisingly, is that one needs three fitting parameters to describe the quenching. This will keep the measures of the quenching profile independent of each other resulting in the reduction of systematic errors in depth determination. This can be achieved by using either DA or a suggested modification of the PM that introduces a third parameter related to quenching efficiency. Because DA utilizes a smooth fitting function, it offers an advantage for the analysis of deeply penetrating probes, where the effects of transleaflet quenching should be considered.     

Observing secretory granules with a multiangle evanescent wave microscope

In total internal reflection fluorescence microscopy (TIRFM), fluorophores near a surface can be excited with evanescent waves, which decay exponentially with distance from the interface. Penetration depths of evanescent waves from 60 nm to 300 nm were generated by varying the angle of incidence of a laser beam. With a novel telecentric multiangle evanescent wave microscope, we monitored and investigated both single secretory granules and pools of granules in bovine chromaffin cells. By measuring the fluorescence intensity as a function of penetration depth, it is possible through a Laplace transform to obtain the fluorophore distribution as a function of axial position. We discuss the extent to which it is possible to determine distances and diameters of granules with this microscopy technique by modeling the fluorescent volumes of spheres in evanescent fields. The anisotropic near-field detection of fluorophores and the influence of the detection point-spread function are considered. The diameters of isolated granules between 70 nm and 300 nm have been reconstructed, which is clearly beyond the resolution limit of a confocal microscope. Furthermore, the paper demonstrates how evanescent waves propagate along surfaces and scatter at objects with a higher refractive index. TIRFM will have a limited applicability for quantitative measurements when the parameters used to define evanescent waves are not optimally selected.     

Association of daunomycin to membrane domains studied by fluorescence resonance energy transfer

1,6-Diphenyl-1,3,5-hexatriene and 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene are fluorophores used to explore different hydrophobic domains of membrane bilayers (Andrich, M.P. and Vanderkooi, J.M. (1976) Biochemistry 15, 1257-1265; Prendergast, F.G., Haugland, R.P. and Callahan, P.J. (1981) Biochemistry 20, 7333-7338). Fluorescence resonance energy transfer between these fluorophores, acting as energy donors, and the anthracycline, daunomycin, as the acceptor, was used to analyze the interaction of the drug with natural membranes, and its relative location within the membrane bilayer. The transfer process was demonstrated by: (1) emission fluorescence of the acceptor when the samples were excited at the excitation maximum of the donor (360 nm); and (2) progressive quenching of the energy donor (at 428 nm) when in the presence of increasing acceptor concentration. Also, the disruption of the energy transfer by solubilization of the membrane with Triton X-100 evidences a role for the membrane in providing the appropriate site(s) for energy transfer to occur. At moderately low daunomycin/membrane lipid ratios, the different efficiencies of resonance energy transfer between the two donors and daunomycin predicts a preferential, but not exclusive, location of the drug at membrane 'surface' domains, i.e., those regions of the bilayer explored by the 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene probe. In support of this observation, a large fraction (approx. 75%) of membrane-associated daunomycin was rapidly sequestered away from the membrane upon addition of excess DNA, which forms high-affinity complexes with daunomycin (Chaires, J.B., Dattagupta, n. and Crothers, D.M. (1982) Biochemistry 21, 3927-3932), thus acting as a drug 'sink'. Also, a large fraction of drug was accessible to fluorescence quenching by iodide, a collisional water-soluble quencher. On the other hand, a smaller population of the membrane-associated daunomycin was characterized by slow sequestering by the added DNA and inaccessibility to quenching by iodide. We conclude that the daunomycin, which is only slowly sequestered, is located deep within the hydrophobic domains of the bilayer, likely to be those probed by 1,6-diphenyl-1,3,5-hexatriene.     

Refining membrane penetration by a combination of steady-state and time-resolved depth-dependent fluorescence quenching

Accurate determination of the depth of membrane penetration of a fluorescent probe, attached to a lipid, protein, or other macromolecule of interest, using depth-dependent quenching methodology is complicated by thermal motion in the lipid bilayer. Here, we suggest that a combination of steady-state and time-resolved measurements can be used to generate a static quenching profile that reduces the contribution from transverse diffusion occurring during the excited-state lifetime. This procedure results in narrower quenching profiles, compared with those obtained by traditional measurements, and thus improves precision in determination of the underlying depth distribution of the probe.     

Comparison of fluorescence energy transfer and quenching methods to establish the position and orientation of components within the transverse plane of the lipid bilayer. Application to the gramicidin A--bilayer interaction.

Fluorescence quenching and resonance energy transfer methods have been used to investigate the position of fluorophores in the lateral and transverse planes of the lipid bilayer. A series of n-(9-anthroyloxy) fatty acids (n = 2, 6, 9, and 12) have been used as energy-transfer acceptors so that apparent transfer distances from a membrane-bound donor (N-stearoyltryptophan) have a transverse as well as a lateral component. Both theory and experiment show that the energy-transfer method is not precise enough to discriminate between the positions of the fluorophores in the transverse plane of the bilayer. The n-(9-anthroyloxy) fatty acids are also susceptible to quenching by the indole moiety of tryptophan. The relative quenching efficiency can provide a semiquantitative measure of the position of quenching molecules in the lipid bilayer. The quenching techniques are applied to the determination of the orientation of gramicidin A in lipid bilayers. The tryptophan residues of gramicidin appear to be located near the membrane surface in agreement with the head-to-head dimeric structure proposed by D. W. Urry et al. [(1971) Proc. Natl. Acad. Sci. U.S.A. 68, 672--676].