Analysis of Simulated Fluorescence Intensities Decays by a New Maximum Entropy Method Algorithm

A new algorithm for the Maximum Entropy Method (MEM) is proposed for recovering the lifetime distribution in time-resolved fluorescence decays. The procedure is based on seeking the distribution that maximizes the Skilling entropy function subjected to the chi-squared constraint χ ²?~?1 through iterative linear approximations, LU decomposition of the Hessian matrix of the lagrangian problem and the Golden Section Search for backtracking. The accuracy of this algorithm has been investigated through comparisons with simulated fluorescence decays both of narrow and broad lifetime distributions. The proposed approach is capable to analyse datasets of up to 4,096 points with a discretization ranging from 100 to 1,000 lifetimes. A good agreement with non linear fitting estimates has been observed when the method has been applied to multi-exponential decays. Remarkable results have been also obtained for the broad lifetime distributions where the position is recovered with high accuracy and the distribution width is estimated within 3 %. These results indicate that the procedure proposed generates MEM lifetime distributions that can be used to quantify the real heterogeneity of lifetimes in a sample.     

Analysis of fluorescence decay kinetics of thioflavin t by a maximum entropy method

The application of a maximum entropy method (MEM) for analysis of time-resolved fluorescence data is discussed. A developed version of MEM has been tested using simulated kinetic data. Based on computed results, practical criteria have been established to determine whether the lifetime distribution of emitting centers is described by a discrete spectrum (a set of two or three exponentials) or by a continuous one (mono- or bimodal distribution of exponentials). The proposed method has been used to analyze the fluorescence decay kinetics of thioflavin T (ThT) intercalated into amyloid fibrils. The presence of two peaks in the lifetime distribution of emitting centers has been explained by the existence in fibrils of two types of binding centers substantially differing in microenvironment rigidity. This suggestion is supported by the results of fluorescence quenching of intercalated ThT with the quencher KI.     

Fluorescence lifetime distributions in membrane systems

Membranes are complex biological systems that display heterogeneity at all spatial scales. At a molecular level, the heterogeneity arises from lipid and protein composition. At the cellular level, heterogeneity is due to membrane organization and large scale morphology. A quantitative evaluation of membrane heterogeneity at a microscopic level is very important for several fields of membrane studies. We have developed a method for the analysis of the decay of fluorescent membrane probes that can provide a quantity sensitive to membrane heterogeneity. This method is based on the analysis of the fluorescence decay using continuous lifetime distributions. The major challenge in the interpretation of the analysis results is in the identification, at a molecular level, of the mechanisms that influence the fluorescence decay. In this review we illustrate the principles of data analysis and we show examples of identification of the measured parameters with specific variables that affect membrane heterogeneity.     

Fluorescence of organic dyes in lipid membranes: Site of solubilization and effects of viscosity and refractive index on lifetimes

The fluorescence decay of several organic dye molecules intercalated in egg phosphatidylcholine lipid membrane vesicles is consistent with the existence of two or three prominent lifetime components rather than a single continuous distribution of lifetimes. The major lifetime components are identified with different sites of solubilization in the membrane. The variation of the lifetime of the membrane-bound dye was studied as a function of the sucrose concentration, which varied the viscosity and refractive index of the aqueous solution. The combined effect of viscosity and refractive index on the lifetime of the dye was used to identify the site of solubilization of the dye in the membrane. The study was useful to identify dye molecules on the surface which are exposed to the aqueous phase, for which the fluorescence lifetime increased systematically with sucrose (viscosity effect). More importantly, it was possible in a few cases to identify the dye molecules which are oriented in the membrane phase, and the fluorescence lifetime decreased systematically with sucrose (refractive index effect). Anomalous values of order parameters determined from the refractive index effect are explained in terms of an orientational distribution of the linear dye molecule weighted in favor of mutually orthogonal orientations.     

Time-Resolved Flavin Adenine Dinucleotide Fluorescence Study of the Interaction Between Immobilized Glucose Oxidase and Glucose

Time-resolved fluorescence experiments have shown that flavin adenine dinucleotide (FAD) fluorescence emission of sol–gel immobilized glucose oxidase (GOD) exhibits a three-exponential decaying behaviour characterized by long- (about 2.0–3.0 ns), intermediate- (about 300 ps) and short- (less than 10 ps) lifetime, each one being characteristic of a peculiar conformational state of the FAD structure. In the present work time-resolved fluorescence is used to monitor FAD signals in the time interval immediately following the addition of glucose at various concentrations in order to detect the conformational changes occurring during the interaction between sol–gel immobilized GOD and glucose. The analysis of time-dependent fluorescence emission signal has shown that the FAD conformational state changes during the process from a configuration with a prevalence of the state characterized by the long lifetime to a configuration with increased contribution from the process with the intermediate lifetime. The time needed to complete this configuration change decreases with the concentration of added glucose. The results here reported indicate that time-resoled fluorescence can be extremely useful for a better understanding of solid phase biocatalysis that is particularly important in light of their clinical and biotechnological applications.     

Probing the Conformational Stability of Two Different Copper Proteins: A Dynamic Fluorescence Study on Azurin and Ascorbate Oxidase

Tryptophan fluorescence is extremely useful to monitor structural conformational transitions in proteins. Denaturant-induced unfolding of azurin and ascorbate oxidase has been studied by dynamic fluorescence measurements in the frequency domain and the results have been interpreted in terms of continuous distribution of lifetimes. The data add new information on the unfolding mechanism that was previously analyzed by steady-state emission spectroscopy. In particular, the existence of multiple, parallel unfolding pathways may be envisaged and correlated, in both cases, to the two protein structures. The effect of metal depletion has been also characterized by fluorescence lifetime measurements. In the case of azurin, a monomeric protein, the data demonstrate that copper removal yields a totally different unfolding pathways with respect to the holo protein, indicating that metal ion plays a fundamental structural role in the wild type, native protein. In the case of ascorbate oxidase a dimer of 140 kDa, only minor effects have been detected by copper removal. However, the analysis of the fluorescence decay in presence of different amounts of guanidinium hydrochloride gives new important insights on the unfolding intermediates. In particular the data support the hypothesis of a partial exposure of an outer layer of dimer at intermediate denaturant concentration. This ability of dynamic fluorescence to pinpoint the presence of structural micro-heterogeneity in the unfolding pathways of proteins demonstrates the greater power of this technique compared to the most commonly used steady-state measurements.     

Analysis of the local conformation of proteins with two-dimensional fluorescence techniques

Two 2D fluorescence techniques are described which allow the study of conformational changes in proteins in their native form in μM solutions using aromatic amino acids (tryptophan, tyrosine) as intrinsic fluorescence markers. Simultaneous time- and wavelength-resolved fluorescence spectra are measured using a 80 ps laser source in conjunction with streak detection in the exit plane of an astigmatism-corrected spectrometer. This approach allows identification of different photophysical processes by their associated lifetime and spectral intensity distribution; errors due to the more common integration over a wider spectral range are avoided. Time-resolved spectra are sensitive to changes in the collisional environment (dynamic quenching) and can thus be used to monitor local conformation changes close to the respective fluorophors. This is demonstrated for the Ras protein which undergoes a drastic conformation change while binding to different nucleotides. Excitation-emission spectra are two-dimensional fluorescence images with one axis corresponding to the excitation and the other to the emission wavelength. Thus, they contain all conventional excitation and fluorescence spectra of a given substance. The 2D structure facilitates the interpretation of these spectra and allows the direct identification of resonance effects, scattering and the isolation of the contribution of different fluorophors to the complete spectrum. This is demonstrated for mixtures of tyrosine and tryptophan. In this case, both wavelength-resolved spectra and temporal decays are affected by energy transfer processes between the two amino acids. In a last example, both static and time-resolved spectral methods are combined to determine the respective contribution of static and dynamic quenching in calsequestrin. Evaluation of the fluorescence data is in good agreement with a recent crystallographic analysis which shows that all tryptophans are located in a conserved domain of the protein. Addition of Ca²⁺ ions leads to a more compact form of calsequestrin and to polymers. This information would not be obtainable from either of the two techniques alone. Received: 10 February 2000 / Published online: 13 September 2000     

Characterization of human immunodeficiency virus-1 (HIV-1) rev by (time-resolved) fluorescence spectroscopy

Fluorescence spectroscopy has been applied to the single tryptophan-containing regulatory protein Rev of human immunodeficiency virus (HIV-1). The fluorescence emission was found to have a maximum at 336 nm which refers to a surrounding of the chromophore of intermediate polarity. Fluorescence transients recorded at the maximum of fluorescence were found to decay nonexponentially. A bimodal lifetime distribution is obtained from exponential series analysis (ESM) with centers at 1.7 and 4.5 ns. Two microenvironments for tryptophan are suggested to be responsible for the two lifetime distributions. No innerfilter effect occurred in a Rev solution up to a concentration of 40 μM. A data quality study of ESM analysis as function of collected counts in the peak channel maximum (CIM) showed that, for reliable reconvolution, at least 15,000 CIM are necessary. The widths of the two distributions are shown to be temperature dependent. The broadening of the lifetime distributions when the temperature is raised to 50°C is interpreted as extension of the number of conformational substates which do not interconvert on the fluorescence time scale. The thermal deactivation (temperature quenching) is reflected in a constant decrease in the center of the short-lived lifetime distribution.     

Diphenylhexatriene-phosphatidylcholine fluorescence in POPC vesicles: Comparison of the exponential-series and the maximum-entropy methods

We have investigated the time-resolved fluorescence of diphenylhexatriene (DPH) covalently linked to phosphatidylcholine (PC) in palmitoyloleoylglycerophosphocholine (POPC) vesicles with special consideration of the comparison of two methods for distributional lifetime analysis: the exponential-series method (ESM) and the maximum-entropy method (MEM). Generally, both methods were found to reveal equivalent results on high-quality data. Different are the shapes of the recovered distributions (symmetry and width) as well as the time effort for the numerical analysis.     

Distribution analysis of membrane penetration of proteins by depth-dependent fluorescence quenching

A new approach is presented to evaluate the depth-dependent quenching of the fluorescence of membrane-bound probes and integral proteins. By utilizing at least three quenchers of known and distinctly different depths, the following parameters can be recovered: most probable depth of the probe; dispersion of the depth distribution, which will depend on the size of probe and fluctuations in its position; and quenching efficiency, which is related to the exposure of a particular fluorophore to the lipid phase. The exposure of tryptophan residues in integral proteins can be quantitatively determined with respect to the model compound (tryptophan octyl ester). The proposed method was applied to the investigation of membrane complexes of the bee venom melittin and cytochrome b₅.     

Quenchers Induce Wavelength Dependence on Protein Fluorescence Lifetimes

We have analysed the picosecond resolved fluorescence emission decay of horseradish peroxidase A2 and of HEW lysozyme acquired with a streak camera. Analyses of the fluorescence decay data of both proteins revealed that the dynamics of the decay is dependent on the emission wavelength. Our data strongly indicates that resonance energy transfer occurring between aromatic residues and different protein fluorescence quencher groups, and the nature of the quencher groups, are the causes of the observed wavelength dependent mean lifetime distribution. Using the global analysis data to calculate the fluorescence mean lifetime at each wavelength revealed that for lysozyme, the mean fluorescence lifetime increased with observation wavelength, whereas the opposite was the case for peroxidase. Both proteins contain strong fluorescence quencher groups located in close spatial proximity to the protein’s aromatic residues. Lysozyme contains disulfide bridges as the main fluorescence quencher whereas peroxidase contains a heme group. Both for lysozyme and horseradish peroxidase there is a clear correlation between the observed fluorescence mean lifetime of the protein at a particular emission wavelength and the respective quencher’s extinction coefficient at the respective wavelength. Furthermore, our study also reports a comparison of the analyses of the fluorescence data done with three different methods. Analyses of the fluorescence decay at 10 different fluorescence emission wavelengths revealed significant differences in both fluorescence lifetimes and the pre-exponential factor distributions. Such values differed from the values recovered from the integrated decay curves and from global analyse.     

Analysis of cell surface molecular distributions and cellular signaling by flow cytometry

Flow cytometry is a fast analysis and separation method for large cell populations, based on collection and processing of optical signals gained on a cell-by-cell basis. These optical signals are scattered light and fluorescence. Owing to its unique potential ofStatistical data analysis and sensitive monitoring of (micro)heterogeneities in large cell populations, flow cytometry—in combination with microscopic imaging techniques—is a powerful tool to study molecular details of cellular signal transduction processes as well. The method also has a widespread clinical application, mostly in analysis of lymphocyte subpopulations for diagnostic (or research) purposes in diseases related to the immune system. A special application of flow cytometry is the mapping of molecular interactions (proximity relationships between membrane proteins) at the cell surface, on a cell-by-cell basis. We developed two approaches to study such questions; both are based ondistance-dependent quenching of excited state fluorophores (donors) by fluorescent or dark (nitroxide radical) acceptors via Förstertype dipole-dipole resonance energy transfer (FRET) and long-range electron transfer (LRET) mechanisms, respectively. A critical evaluation of these methods using donor- or acceptor-conjugated monoclonal antibodies (or their Fab fragments) to select the appropriate cell surface receptor or antigen will be presented in comparison with other approaches for similar purposes. The applicability of FRET and LRET for two-dimensional antigen mapping as well as for detection of conformational changes in extracellular domains of membrane-bound proteins is discussed and illustrated by examples of several lymphoma cell lines. Another special application area of flow cytometry is the analysis of different aspects of cellular signal transduction, e.g., changes of intracellular ion (Ca²⁺, H⁺, Na⁺) concentrations, regulation of ion channel activities, or more complex physiological responses of cell to external stimuli via correlated fluorescence and scatter signal analysis, on a cell-by-cell basis. This way different signaling events such as changes in membrane permeability, membrane potential, cell size and shape, ion distribution, cell density, chromatin structure, etc., can be easily and quickly monitored over large cell populations with the advantage of revealing microheterogeneities in the cellular responses. Flow cytometry also offers the possibility to follow the kinetics of slow (minute- and hour-scale) biological processes in cell populations. These applications are illustrated by the example of complex flow cytometric analysis of signaling in extracellular ATP-triggered apoptosis (programmed cell death) of murine thymic lymphocytes.     

激光诱导植物荧光寿命校正技术及其特性分析

激光诱导植物荧光寿命测量法是在植物荧光光谱分析法基础上开发的一种评估植物生长状况及环境监测的新技术。根据植物叶绿素荧光信号的物理特性,利用信息仿真技术开发了一种叶绿素荧光寿命校正方法,可提高植物叶绿素荧光寿命的测量精度。利用激光诱导叶绿素荧光寿命测量系统分别测得叶绿素荧光及其背景信号,先用解卷积法叶绿素荧光信号中分离出荧光衰减函数,可获取荧光寿命估计值。再结合叶绿素荧光寿命校正技术就能反演得到高精度的植物荧光寿命。仿真与实验结果表明：该方法可实现高精度的植物荧光寿命实时监测;并对不同含量的叶绿素提取液进行了测试,构建了植物荧光寿命与叶绿素含量的对应关系模型。未来该技术可用于遥感监测海洋、湖泊、河流中藻类植物的生物含量。     

Modulation of Fluorophore Environment in Host Membranes of Varying Charge

The net electrical charge of the biological membrane represents an important parameter in the organization, dynamics and function of the membrane. In this paper, we have characterized the change in the microenvironment experienced by a membrane-bound fluorescent probe when the charge of the phospholipids constituting the host membrane is changed from zwitterionic to cationic with minimal change in the chemical structure of the host lipid. In particular, we have explored the difference in the microenvironment experienced by the fluorescent probe 2-(9-anthroyloxy)stearic acid (2-AS) in model membranes of zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and cationic 1-palmitoyl-2-oleoyl-sn-glycero-3-ethylphosphocholine (EPOPC) which are otherwise chemically similar, using the wavelength-selective fluorescence approach and other fluorescence parameters. Our results show that the microenvironment experienced by a membrane probe such as 2-AS is different in POPC and EPOPC membranes, as reported by red edge excitation shift (REES) and other fluorescence parameters. The difference in environment encountered by the probe in the two cases could possibly be due to variation in hydration in the two membranes owing to different charges.     

A method for quantitative interpretation of fluorescence detection of poly(ethylene glycol)-mediated 1-palmitoyl-2-[[[2-[4-(phenyl-trans-1,3,5-hexatrienyl) phenyl]ethyl]oxyl]carbonyl]3-sn-phosphatidylcholine (DPHpPC) transfer and fusion between phospholipid vesicles in the dehydrated state

A method has been developed for calculating the expected fluorescence lifetime of the DPH _p PC probe distributed between different membrane environments. We show how this method can be used to distinguish between lipid transfer and fusion between large unilamellar vesicles occurring in the presence of poly(ethylene glycol) (PEG). This application of the calculation took into consideration the heterogeneity of microenvironments experienced by the probe in a sample containing vesicle aggregates of different sizes. Assuming that the aggregate size distribution was a delta function of the aggregate size, comparison of the calculated and observed lifetimes yielded an estimate of the vesicle aggregate size. For vesicles of varying compositions in the presence of dehydrating concentrations of PEG, this method suggested that only small aggreggates formed. For vesicles that could be demonstrated by other means not to have fused, the data were consistent with lipid transfer occurring only between the outer leaflets of two to four vesicles, even at high PEG concentrations. For vesicles that could be demonstrated to fuse by contents mixing and size changes, the fluorescence lifetime data were consistent with lipid transfer between both the inner and the outer leaflets of two to four fused vesicles. At very high PEG concentrations, where extensive rupture and large, multilamellar products were previously observed, the lifetime data were consistent with much more extensive lipid transfer within larger aggregates. The agreement of predictions made on the basis of lifetime measurements with other observations attests to the validity of the fluorescence lifetime method. In addition, the model and data presented here provide evidence that fusion occurs between small numbers of PEG-aggregated vesicles before the removal of PEG.     

pH-induced Conformational Isomerization of Bovine Serum Albumin Studied by Extrinsic and Intrinsic Protein Fluorescence

Serum albumins are multi-domain all α-helical proteins that are present in the circulatory system and aid in the transport of a variety of metabolites, endogenous ligands, drugs etc. Earlier observations have indicated that serum albumins adopt a range of reversible conformational isomers depending on the pH of the solution. Herein, we report the concurrent changes in the protein conformation and size that are inherent to the pH-induced conformational isomers of bovine serum albumin (BSA). We have investigated the fluorescence properties of both intrinsic (tryptophan) and extrinsic (ANS, pyrene) fluorophores to shed light into the structural features of the pH-dependent conformers. We have been able to identify a number of conformational isomers using multiple fluorescence observables as a function of pH titration. Our results indicate that at pH 3, a partially-folded, ‘molten-globule-like’ state is populated. Moreover, equilibrium unfolding studies indicated that the ‘molten-globule-like’ state unfolds in a non-cooperative fashion and is thermodynamically less stable than the native state. The fluorescence-based approach described in the present work has implications in the study of pH-induced conformational plasticity of other physiologically relevant proteins.     

Fluorescence evidence for cholesterol regular distribution in phosphatidylcholine and in sphingomyelin lipid bilayers

Our previous studies indicated that sterols (including cholesterol and dehydroergosterol) can be regularly distributed into hexagonal superlattices in the plane of liquid-crystalline phosphatidylcholine bilayers. It was suggested that regular and irregular regions coexist in the membrane. In the present study, we report supporting evidence for our sterol regular distribution model. We have examined the fractional concentration dependencies of dehydroergosterol (a naturally occurring cholesterol analogue) fluorescence intensity and lifetime in various phosphatidylcholine and sphingomyelin bilayers. Fluorescence intensity and lifetime dips have been observed at specific sterol mole fractions. At those mole fractions, the acrylamide quenching rate constant of dehydroergosterol fluorescence reaches a local maximum. Those mole fractions match the critical sterol mole fractions at which sterol molecules are expected to be regularly distributed into hexagonal superlattices. The results support the idea that the sterols in the regular region are embedded in the bilayer less deep than those in the irregular regions. We have also examined the fractional cholesterol concentration dependencies of diphenylhexatriene (DPH) fluorescence intensity, lifetime, and polarization in DMPC vesicles. DPH fluorescence intensity and polarization also exhibit distinct dips and peaks, respectively, at critical sterol mole fractions for hexagonal superlattices. However, DPH lifetime changes little with sterol mole fraction. As a comparison, the fluorescence properties of DHE and DPH behave differently in response to the formation of sterol regular distribution. Furthermore, finding evidence for sterol regular distribution in both phosphatidylcholine and sphingomyelin membranes raises the possibility that sterol regular distribution may occur within phospholipid/cholesterol enriched domains of real biological membranes.     

Effects of Refractive Index and Viscosity on Fluorescence and Anisotropy Decays of Enhanced Cyan and Yellow Fluorescent Proteins

The fluorescence lifetime strongly depends on the immediate environment of the fluorophore. Time-resolved fluorescence measurements of the enhanced forms of ECFP and EYFP in water–glycerol mixtures were performed to quantify the effects of the refractive index and viscosity on the fluorescence lifetimes of these proteins. The experimental data show for ECFP and EYFP two fluorescence lifetime components: one short lifetime of about 1 ns and a longer lifetime of about 3.7 ns of ECFP and for EYFP 3.4. The fluorescence of ECFP is very heterogeneous, which can be explained by the presence of two populations: a conformation (67% present) where the fluorophore is less quenched than in the other conformation (33% present). The fluorescence decay of EYFP is much more homogeneous and the amplitude of the short fluorescence lifetime is about 5%. The fluorescence anisotropy decays show that the rotational correlation time of both proteins scales with increasing viscosity of the solvent similarly as shown earlier for GFP. The rotational correlation times are identical for ECFP and EYFP, which can be expected since both proteins have the same shape and size. The only difference observed is the slightly lower initial anisotropy for ECFP as compared to the one of EYFP.     

基于激光诱导叶绿素荧光寿命成像技术的植物荧光特性研究

针对植物荧光遥感探测中信号易受干扰的问题, 提出了一种用于评估植物生长状况及环境监测的荧光寿命成像技术. 采用凹透镜对355 nm波长的激光扩束, 再照射植物激发叶绿素荧光, 由增强型电荷耦合器件接收荧光信号. 采用时间分辨测量法, 连续用相同激光脉冲照射植物以激发相同的荧光信号, 同时不断改变激光脉冲触发探测器启动的延时时间, 从而能够得到完整的离散荧光信号分布图像. 对植物特定位置点产生的离散荧光信号进行拟合, 再运用一种改进型的迭代解卷积法可反演高精度的荧光寿命; 进而反演图像各点的荧光寿命以生成植物的荧光寿命分布图. 该方法所绘制的荧光寿命图比荧光强度图能更准确地反映植物内部的叶绿素含量, 并对活体植物叶绿素荧光寿命的物理特性进行了初步研究, 证明叶绿素荧光寿命与植物生理状态存在一定关联; 并且叶绿素荧光寿命与活体植物所处环境存在着复杂的关系. 未来将与生物物理学家们合作, 继续探寻叶绿素荧光寿命与植物生存环境的关系.