Fluorescence spectroscopic investigations of the dynamic properties of proteins, membranes and nucleic acids

Solvation dynamics on the diffusion timescale elucidated using energy-represented dynamics theory

Photoexcitation of a solute alters the solute-solvent interaction, resulting in the nonequilibrium relaxation of the solvation structure, often called a dynamic Stokes shift or solvation dynamics. Thanks to the local nature of the solute-solvent interaction, the characteristics of the local solvent environment dissolving the solute can be captured by the observation of this process. Recently, we derived the energy-represented Smoluchowski-Vlasov (ERSV) equation, a diffusion equation for molecular liquids, which can be used to analyze the solvation dynamics on the diffusion timescale. This equation expresses the time development for the solvent distribution on the solute-solvent pair interaction energy (energy coordinate). Since the energy coordinate can effectively treat the solvent flexibility in addition to the position and orientation, the ERSV equation can be utilized in various solvent systems. Here, we apply the ERSV equation to the solvation dynamics of 6-propionyl-2-dimethylamino naphthalene (Prodan) in water and different alcohol solvents (methanol, ethanol, and 1-propanol) for clarifying the differences of the relaxation processes among these solvents. Prodan is a solvent-sensitive fluorescent probe and is thus widely utilized for investigating heterogeneous environments. On the long timescale, the ERSV equation satisfactorily reproduces the relaxation time correlation functions obtained from the molecular dynamics (MD) simulations for these solvents. We reveal that the relaxation time coefficient on the diffusion timescale linearly correlates with the inverse of the translational diffusion coefficients for the alcohol solvents because of the Prodan-solvent energy distributions among the alcohols. In the case of water, the time coefficient deviates from the linear relationship for the alcohols due to the difference in the extent of importance of the collective motion between the water and alcohol solvents.

Triplet state spectroscopy reveals involvement of the buried tryptophan residue 310 in Glyceraldehyde-3-phosphate dehydrogenase (GAPD) in the interaction with acrylamide

Using conventional steady state and time resolved fluorescence study of the interaction between a multi-tryptophan protein and a quencher, it is difficult, if not impossible to identify the particular tryptophan residue/residues involved in the interaction. In this work we have exemplified the above contention using a multi-tryptophan protein, Glyceraldehyde-3-phosphate dehydrogenase (GAPD) from rabbit muscle having three tryptophan (Trp) residues at positions 84, 193 and 310 and a neutral quencher acrylamide in Tris buffer of pH 7.5. From the steady state and time resolved fluorescence quenching (at 298 K) with acrylamide Ksv, K and kq for the system have been calculated. Low temperature phosphorescence (LTP) spectra at 77 K of GAPD in suitable cryosolvent is known to exhibit two (0,0) bands corresponding to two tryptophan residues 193 and 310. Using the LTP study of free GAPD and GAPD - acrylamide it is possible to identify that the buried Trp 310 residue is specifically involved in the interaction with acrylamide. This is possible without doing any site-directed mutagenesis of GAPD which contains Trp residues at 84, 193 and 310. Tyrosine 320 is also specifically quenched. The results have been corroborated using the molecular docking studies. Molecular Dynamics simulation supports our contention of the involvement of Trp 310 and also shows that the other nearest residues of acrylamide are Val175 and Val232.

The life of the cell membrane: A paradigmatic reading from Deleuze and Guattari

While the Fluid Mosaic model (FMM) is widely accepted as an account of the cell membrane's structure-function, its inability to explain certain phenomena has led to the lipid rafts hypothesis (nanodomains) that spontaneous spatiotemporal enriched zones of sphingolipids-cholesterol-protein exist within the membrane. In this text, we propose a novel approach that conceives the cell membrane as a living entity. The questions regarding the FMM revolve around the fact that, although these molecular components are present in many cell types, the membrane does not react in the same way to every external agent; for example, a virus evokes a particular response: why is there some marked specificity of virus (or toxin) attack on one (or some) of these cell types and not to other cell types that nevertheless have a similar membrane protein constitution? The crucial question, to explain this selectivity, would be what determines the specificity of attack on some cells and not others? While FMN assumes a dynamism between macrostates at the intramolecular, intermolecular, and/or collective levels in the membrane, the approach of the lipid raft model presupposes a much greater and more complex dynamics of microstates (even nano-states) of these molecular components. In other words, it implies higher and instantaneous mobility as assemblages ("intentional") and thus, of the membrane itself (as a collective), in response to changes in the internal and external physicochemical environment over a broad spatiotemporal scale. This suggests a mechanism of membrane adaptation in the face of evolutionary constraints. In this text, we propose a paradigmatic approach, from Deleuze-Guattari's philosophy: to conceive the cell membrane as living and not as a mere molecular conglomerate with particular functions and mechanical processes between molecules. For this, we employ the functional concepts of territory and machinic assemblage, whence the vitality of the membrane would allow us to postulate instantaneous updates, within wider spatiotemporal scales in its composition in contrast with the model that dominates as a more plausible explanation nowadays, that does not include smaller spatiotemporal events. If we resort to the concept of territory and its different media components, we could offer a more plausible explanation of the vigorous dynamism in the composition of the cell membrane since it would allow more subtle and complex differentiations between media and thus make visible the constant and instant changes. We propose that the model of nanodomains, understood as a process of dynamic territorialization, offers a more complex and subtle explanation of the instantaneous changes in the cell membrane's composition. This approach expands the explanatory framework for cellular phenomena and reveals their spatiotemporal complexity in accordance with other research.

Energy Transfer Characteristics of Lipid Bilayer Membranes of Liposomes Examined with Picosecond Time-Resolved Raman Spectroscopy

A number of biochemical reactions proceed inside biomembranes. Since the rate of a chemical reaction is influenced by chemical properties of the surrounding environment, it is important to examine the chemical environment inside the biomembranes. Although the energy transfer characteristics are a basic and important property of a reaction medium, experimental investigation of the thermal conducting capabilities of the biomembranes is a challenging task. We have examined the energy transfer characteristics of lipid bilayer membranes of liposomes, a good model system for the biomembrane, with picosecond time-resolved Raman spectroscopy. The cooling kinetics of the first excited singlet (S1) state of trans-stilbene solubilized within the lipid bilayer membranes is observed as a peak shift of the 1570 cm-1 Raman band of S1 trans-stilbene. The cooling rate constant of S1 trans-stilbene is obtained in six lipid bilayer membranes formed by phospholipids with different hydrocarbon chains, DSPC, DPPC, DMPC, DLPC, DOPC, and egg-PC. We estimate the thermal diffusivity of the lipid bilayer membranes with a known correlation between the cooling rate constant and the thermal diffusivity of the solvent. The thermal diffusivity estimated for the liquid-crystal-phase lipid bilayer membranes is 8.9 × 10-8 to 9.4 × 10-8 m2 s-1, while that for the gel-phase lipid bilayer membranes is 8.4 × 10-8 to 8.5 × 10-8 m2 s-1. The difference in thermal diffusivity between the two phases is explained by a one-dimensional diffusion equation of heat.

Bio-membranes: Picosecond to second dynamics and plasticity as deciphered by solid state NMR

Since the first membrane models in the 1970s, the concept of biological membranes has evolved considerably. The membrane is now seen as a very complex mixture whose dynamic behavior is even more complex. Solid-state NMR is well suited for such studies as it can probe the movements of the membrane from picoseconds to seconds. Two NMR observables can be used: motionally averaged spectra and relaxation times. They bring information on order parameters, phase transitions, correlation times, activation energies and membrane elasticity. Spectra are used to determine the nature of the membrane phase. The order parameters can be measured directly from spectra that are dominated by quadrupolar, dipolar and chemical shielding magnetic interactions and allow describing the lipid membrane as being very rigid at the glycerol and chain level and very fluid at its center and surface. Correlation times and activation energies can be measured for intramolecular motions (pico to nanoseconds), molecular motions (nano to 100 ns) and collective modes of membrane deformation (microseconds). Sterols modulate membrane phases, order parameters, correlation times and membrane elasticity. In general terms, sterols tend to act to reduce the impact of environmental changes on molecular order and dynamics. They can be described as regulators of membrane dynamics by keeping them in a state of dynamics that changes very little when the temperature or other factors change. The presence of such large-scale membrane dynamics is proposed as a means of adapting to evolutionary constraints.

Characterization of dissolved black carbon and its binding behaviors to ceftazidime and diclofenac pharmaceuticals: Employing the molecular weight fractionation

As the ubiquitous component of the aquatic environment, dissolved organic matter (DOM) readily bind with residual pharmaceutical contaminants (PCs) and influence their environmental behaviors. However, the binding mechanisms between dissolved black carbon (DBC), a vital part of the natural DOM pool, and PCs were poorly researched. In this study, the bulk DBC was divided into four fractions in molecular weight (MW) via an ultrafiltration system, and the properties of DBC and their binding interaction with two kinds of typical PCs (ceftazidime (CAZ) and diclofenac (DCF)) were explored concretely. The results showed that low MW component was the main contributor to bulk DBC, and the aromaticity increased with the increase of MW. The categories of chemical structures and fluorescent substances in different MW DBC were similar. Multispectral techniques showed that the oxygen-enriched compounds in DBC had the higher affinity to CAZ/DCF. The -NH-, -COOH, -NH₂ groups in CAZ molecules appeared to form the hydrogen bond with DBC. Fluorescence quenching experiments were analyzed, and the binding mechanisms were specifically expounded from the thermodynamic perspective. The fluorophore of fulvic acid-like compounds (FA) were quenched by both static and dynamic quenching mechanisms, while only static quenching occurred for humic acid-like compounds (HA). For bulk DBC, the hydrogen bond and van der Waals force were the major forces in the HA-CAZ system, while the hydrophobic force made the primary contribution to the HA-DCF system, which might be ascribed to the higher hydrophobic nature of DCF. Notably, with the increase of HA MW, the main binding mode of HA-CAZ/DCF changed from hydrophobic force to hydrogen bond and van der Waals force gradually, which also directly proved that various noncovalent interactions co-driven the binding processes. Our findings are beneficial to better assess the fate of DBC and PCs and the corresponding complexes in the aquatic environment.

Classification of fluorescent anisotropy decay based on the distance approach in the frequency domain

Frequency-domain (FD) fluorometry is a widely utilized tool to probe unique features of complex biological structures, which may serve medical diagnostic purposes. The conventional data analysis approaches used today to extract the fluorescence intensity or fluorescence anisotropy (FA) decay data suffer from several drawbacks and are inherently limited by the characteristics and complexity of the decay models. This paper presents the squared distance (D²) technique, which categorized samples based on the direct frequency response data (FRD) of the FA decay. As such, it improves the classification ability of the FD measurements of the FA decay as it avoids any distortion that results from the challenged translation into time domain data. This paper discusses the potential use of the D² approach to classify biological systems. Mathematical formulation of D² technique adjusted to the FRD of the FA decay is described. In addition, it validates the D² approach using 2 simulated data sets of 6 groups with similar widely and closely spaced FA decay data as well as in experimental data of 4 samples of a fluorophore-solvent (fluorescein-glycerol) system. In the simulations, the classification accuracy was above 95% for all 6 groups. In the experimental data, the classification accuracy was 100%. The D² approach can help classify samples whose FA decay data are difficult to extract making FA in the FD a realistic diagnostic tool. The D² approach offers an advanced method for sorting biological samples with differences beyond the practical temporal resolution limit in a reliable and efficient manner based on the FRD of their time-resolved fluorescence measurements thereby achieving better diagnostic quality in a shorter time.

Generative adversarial network enables rapid and robust fluorescence lifetime image analysis in live cells

Fluorescence lifetime imaging microscopy (FLIM) is a powerful tool to quantify molecular compositions and study molecular states in complex cellular environment as the lifetime readings are not biased by fluorophore concentration or excitation power. However, the current methods to generate FLIM images are either computationally intensive or unreliable when the number of photons acquired at each pixel is low. Here we introduce a new deep learning-based method termed flimGANE (fluorescence lifetime imaging based on Generative Adversarial Network Estimation) that can rapidly generate accurate and high-quality FLIM images even in the photon-starved conditions. We demonstrated our model is up to 2,800 times faster than the gold standard time-domain maximum likelihood estimation (TD_MLE) and that flimGANE provides a more accurate analysis of low-photon-count histograms in barcode identification, cellular structure visualization, Förster resonance energy transfer characterization, and metabolic state analysis in live cells. With its advantages in speed and reliability, flimGANE is particularly useful in fundamental biological research and clinical applications, where high-speed analysis is critical.

Optical properties of the human lens constituents

The absorption and fluorescence properties of the metabolomic (MET), water-soluble and urea-soluble protein fractions from the middle-age, aged, and cataractous human lenses have been measured. At 280nm and 300nm the major lens absorbers are crystallins, which absorb more than 90% of light in the UV-B region (280-315nm). In middle-aged lenses, the absorption at 360nm is mostly provided by UV filters contained in the MET fraction. With aging, and especially with the cataract development, the absorption of MET fraction in UV-A region (315-400nm) decreases due to the drop of the UV filter concentration, while the absorption of protein fractions increases due to the accumulation of post-translational modifications. Consequently, the contribution of the MET fraction into the total lens absorption at 360nm decays from 63% in middle-aged lenses to 25% in aged lenses to 3% in cataractous lenses. The fluorescence yield of the MET fraction from cataractous lenses also significantly increases. Therefore, the protection of the lens tissue against UV radiation in aged and cataractous lenses weakens: the absorption of UV-A light is mostly provided by modified crystallins and non-UV-filter metabolites, which are photochemically more active than the UV filters. The obtained data indicate that the aged and cataractous human lenses are more vulnerable to UV-A light than the middle-aged lenses.

Light and life in Baltimore--and beyond

Baltimore has been the home of numerous biophysical studies using light to probe cells. One such study, quantitative measurement of lateral diffusion of rhodopsin, set the standard for experiments in which recovery after photobleaching is used to measure lateral diffusion. Development of this method from specialized microscopes to commercial scanning confocal microscopes has led to widespread use of the technique to measure lateral diffusion of membrane proteins and lipids, and as well diffusion and binding interactions in cell organelles and cytoplasm. Perturbation of equilibrium distributions by photobleaching has also been developed into a robust method to image molecular proximity in terms of fluorescence resonance energy transfer between donor and acceptor fluorophores.

Wavelength-selective fluorescence as a novel tool to study organization and dynamics in complex biological systems

The dynamics exhibited by a given component of a large macromolecule such as a folded globular protein or an organized supramolecular assembly like the biological membrane is a function of its precise localization within the larger system. A set of approaches based on the red edge effect in fluorescence spectroscopy, which can be used to monitordirectly the environment and dynamics around a fluorophore in a complex biological system, is reviewed in this article. A shift in the wavelength of maximum fluorescence emission toward higher wavelengths, caused by a shift in the excitation wavelength toward the red edge of the absorption band, is termed the red edge excitation shift (REES). This effect is mostly observed with polar fluorophores in motionally restricted media such as very viscous solutions or condensed phases. This phenomenon arises from the slow rates of solvent relaxation around an excited-state fluorophore, which is a function of the motional restriction imposed on the solvent molecules in the immediate vicinity of the fluorophore. Utilizing this approach, it becomes possible to probe the mobility parameters of the environment itself (which is represented by the relaxing solvent molecules) using the fluorophore merely as a reporter group. Further, since the ubiquitous solvent for biological systems is water, the information obtained in such cases will come from the otherwise 'optically silent' water molecules. This makes REES and related techniques extremely useful in biology since hydration plays a crucial modulatory role in a large number of important cellular events.

Differential phospholipid substrates and directional transport by ATP-binding cassette proteins ABCA1, ABCA7, and ABCA4 and disease-causing mutants

ABCA1, ABCA7, and ABCA4 are members of the ABCA subfamily of ATP-binding cassette transporters that share extensive sequence and structural similarity. Mutations in ABCA1 cause Tangier disease characterized by defective cholesterol homeostasis and high density lipoprotein (HDL) deficiency. Mutations in ABCA4 are responsible for Stargardt disease, a degenerative disorder associated with severe loss in central vision. Although cell-based studies have implicated ABCA proteins in lipid transport, the substrates and direction of transport have not been firmly established. We have purified and reconstituted ABCA1, ABCA7, and ABCA4 into liposomes for fluorescent-lipid transport studies. ABCA1 actively exported or flipped phosphatidylcholine, phosphatidylserine, and sphingomyelin from the cytoplasmic to the exocytoplasmic leaflet of membranes, whereas ABCA7 preferentially exported phosphatidylserine. In contrast, ABCA4 transported phosphatidylethanolamine in the reverse direction. The same phospholipids stimulated the ATPase activity of these ABCA transporters. The transport and ATPase activities of ABCA1 and ABCA4 were reduced by 25% in the presence of 20% cholesterol. Nine ABCA1 Tangier mutants and the corresponding ABCA4 Stargardt mutants showed significantly reduced phospholipid transport activity and subcellular mislocalization. These studies provide the first direct evidence for ABCA1 and ABCA7 functioning as phospholipid transporters and suggest that this activity is an essential step in the loading of apoA-1 with phospholipids for HDL formation.

Emerging approaches to probing ion channel structure and function

Ion channels, as membrane proteins, are the sensors of the cell. They act as the first line of communication with the world beyond the plasma membrane and transduce changes in the external and internal environments into unique electrical signals to shape the responses of excitable cells. Because of their importance in cellular communication, ion channels have been intensively studied at the structural and functional levels. Here, we summarize the diverse approaches, including molecular and cellular, chemical, optical, biophysical, and computational, used to probe the structural and functional rearrangements that occur during channel activation (or sensitization), inactivation (or desensitization), and various forms of modulation. The emerging insights into the structure and function of ion channels by multidisciplinary approaches allow the development of new pharmacotherapies as well as new tools useful in controlling cellular activity.

Live-cell imaging reveals multiple interactions between Epstein-Barr virus nuclear antigen 1 and cellular chromatin during interphase and mitosis

Epstein-Barr virus (EBV) establishes a life-long latent infection in humans. In proliferating latently infected cells, EBV genomes persist as multiple episomes that undergo one DNA replication event per cell cycle and remain attached to the mitotic chromosomes. EBV nuclear antigen 1 (EBNA-1) binding to the episome and cellular genome is essential to ensure proper episome replication and segregation. However, the nature and regulation of EBNA-1 interaction with chromatin has not been clearly elucidated. This activity has been suggested to involve EBNA-1 binding to DNA, duplex RNA, and/or proteins. EBNA-1 binding protein 2 (EBP2), a nucleolar protein, has been proposed to act as a docking protein for EBNA-1 on mitotic chromosomes. However, there is no direct evidence thus far for EBP2 being associated with EBNA-1 during mitosis. By combining video microscopy and Förster resonance energy transfer (FRET) microscopy, we demonstrate here for the first time that EBNA-1 and EBP2 interact in the nucleoplasm, as well as in the nucleoli during interphase. However, in strong contrast to the current proposed model, we were unable to observe any interaction between EBNA-1 and EBP2 on mitotic chromosomes. We also performed a yeast double-hybrid screening, followed by a FRET analysis, that led us to identify HMGB2 (high-mobility group box 2), a well-known chromatin component, as a new partner for EBNA-1 on chromatin during interphase and mitosis. Although the depletion of HMGB2 partly altered EBNA-1 association with chromatin in HeLa cells during interphase and mitosis, it did not significantly impact the maintenance of EBV episomes in Raji cells.

Effect of a high surface-to-volume ratio on fluorescence-based assays

In the work discussed in this paper, the effect of a high surface-to-volume ratio of a microfluidic detection cell on fluorescence quenching was studied. It was found that modification of the geometry of a microchannel can provide a wider linear range. This is a phenomenon which should be taken into consideration when microfluidic systems with fluorescence detection are developed. The dependence of the linear range for fluorescein on the surface-to-volume ratio was determined. Both fluorescence inner-filter effects and concentration self-quenching were taken into consideration. It was found that inner-filter effects have little effect on the extent of the linear range on the microscale.

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Modern biomolecular mass spectrometry and its role in studying virus structure, dynamics, and assembly

Over a century since its development, the analytical technique of mass spectrometry is blooming more than ever, and applied in nearly all aspects of the natural and life sciences. In the last two decades mass spectrometry has also become amenable to the analysis of proteins and even intact protein complexes, and thus begun to make a significant impact in the field of structural biology. In this Review, we describe the emerging role of mass spectrometry, with its different technical facets, in structural biology, focusing especially on structural virology. We describe how mass spectrometry has evolved into a tool that can provide unique structural and functional information about viral-protein and protein-complex structure, conformation, assembly, and topology, extending to the direct analysis of intact virus capsids of several million Dalton in mass. Mass spectrometry is now used to address important questions in virology ranging from how viruses assemble to how they interact with their host.

Effects of mutations in Aedes aegypti sterol carrier protein-2 on the biological function of the protein

Sterol carrier protein-2 (SCP-2) is a nonspecific intracellular lipid carrier protein. However, the molecular mechanism of ligand selectivity and the in vivo function of SCP-2 remain unclear. In this study, we used site-directed mutagenesis to investigate the ligand selectivity and in vivo function of the yellow fever mosquito sterol carrier protein-2 protein (AeSCP-2). Mutations to amino acids in AeSCP-2 known to interact with bound ligand also weakened NBD-cholesterol binding. Substitution of amino acids in the ligand cavity changed the ligand specificity of mutant AeSCP-2. Overexpressing wild-type AeSCP-2 in the Aedes aegypti cultured Aag-2 cells resulted in an increase in the level of incorporation of [(3)H]cholesterol. However, overexpressing mutants that were deleterious to the binding of NBD-cholesterol in AeSCP-2 showed a loss of ability to enhance uptake of [(3)H]cholesterol in cultured cells. Interestingly, when [(3)H]palmitic acid was used as the substrate for incorporation in vivo, there was no change in the levels of incorporation with overexpression of wild-type protein or mutated AeSCP-2s. The in vivo data suggest that AeSCP-2 is involved in sterol uptake, but not fatty acid uptake. This is the first report that the cholesterol binding ability may directly correlate with AeSCP-2's in vivo function in aiding the uptake of cholesterol.

HIV-1 Vpr oligomerization but not that of Gag directs the interaction between Vpr and Gag

During HIV-1 assembly, the viral protein R (Vpr) is incorporated into newly made viral particles via an interaction with the C-terminal domain of the Gag polyprotein precursor Pr55(Gag). Vpr has been implicated in the nuclear import of newly made viral DNA and subsequently in its transcription. In addition, Vpr can affect the cell physiology by causing G(2)/M cell cycle arrest and apoptosis. Vpr can form oligomers, but their roles have not yet been investigated. We have developed fluorescence lifetime imaging microscopy-fluorescence resonance energy transfer-based assays to monitor the interaction between Pr55(Gag) and Vpr in HeLa cells. To that end, we used enhanced green fluorescent protein-Vpr that can be incorporated into the virus and tetracysteine (TC)-tagged Pr55(Gag)-TC. This TC motif is tethered to the C terminus of Pr55(Gag) and does not interfere with Pr55(Gag) trafficking and the assembly of virus-like particles (VLPs). Results show that the Pr55(Gag)-Vpr complexes accumulated mainly at the plasma membrane. In addition, results with Pr55(Gag)-TC mutants confirm that the (41)LXXLF domain of Gag-p6 is essential for Pr55(Gag)-Vpr interaction. We also report that Vpr oligomerization is crucial for Pr55(Gag) recognition and its accumulation at the plasma membrane. On the other hand, Pr55(Gag)-Vpr complexes are still formed when Pr55(Gag) carries mutations impairing its multimerization. These findings suggest that Pr55(Gag)-Vpr recognition and complex formation occur early during Pr55(Gag) assembly.

Fluorescence lifetime imaging: association of cortical actin with a PIP3-rich membrane compartment

We have used fluorescence lifetime imaging (FLIM) to study actin and plasma membrane dynamics in B16-F1 melanoma cells. In the absence of a FRET acceptor, significant changes in the fluorescence lifetime of GFP were induced simply by linking the fluorophore to different functional probes, including beta-actin, the PH domains of PLCdelta and Akt, the Ras farnesylation signal, and the neuromodulin palmitoylation signal (MEM). In contrast, the lifetime of GFP-actin was constant despite the many different local environments of G- and F-actin within the cell. Treatment with cytochalasin D but not latrunculin A significantly shortened the lifetime of GFP-beta-actin in the absence of a FRET acceptor. Robust lifetime shifts were observed using either a GFP-RFP chimera or co-transfection of GFP-MEM with RFP-MEM. In contrast to previous reports we observed a photobleaching-dependent change in the lifetime of GFP which could complicate the interpretation of FRET experiments. Of the membrane probes tested only the fluorescence lifetime of GFP-Akt was influenced by the presence of mRFP-actin, suggesting that the cortical actin meshwork is associated with a PIP3-enriched compartment of the plasma membrane. These results will aid in the design of new FRET-based approaches to study cytoskeletal interactions at the molecular level.

Modulation of inhibition of ferrochelatase by N-methylprotoporphyrin

Protoporhyrin IX ferrochelatase catalyses the terminal step of the haem-biosynthetic pathway by inserting ferrous iron into protoporphyrin IX. NMPP (N-methylprotoporphyrin), a transition-state analogue and potent inhibitor of ferrochelatase, is commonly used to induce haem deficiency in mammalian cell cultures. To create ferrochelatase variants with different extents of tolerance towards NMPP and to understand further the mechanism of ferrochelatase inhibition by NMPP, we isolated variants with increased NMPP resistance, bearing mutations in an active-site loop (murine ferrochelatase residues 248-257), which was previously shown to mediate a protein conformational change triggered by porphyrin binding. The kinetic mechanisms of inhibition of two variants, in which Pro255 was replaced with either arginine (P255R) or glycine (P255G), were investigated and compared with that of wild-type ferrochelatase. While the binding affinity of the P255X variants for NMPP decreased by one order of magnitude in relation to that of wild-type enzyme, the inhibition constant increased by approximately two orders of magnitude (K(i)(app) values of 1 microM and 2.3 microM for P255R and P255G respectively, as against 3 nM for wild-type ferrochelatase). Nonetheless, the drastically reduced inhibition of the variants by NMPP was not paralleled with a decrease in specificity constant (kcat/K(m, protoporhyrin IX)) and/or catalytic activity (kcat). Further, although NMPP binding to either wild-type ferrochelatase or P255R occurred via a similar two-step kinetic mechanism, the forward and reverse rate constants associated with the second and rate-limiting step were comparable for the two enzymes. Collectively, these results suggest that Pro255 has a crucial role in maintaining an appropriate protein conformation and modulating the selectivity and/or regiospecificity of ferrochelatase.

Pseudo real-time method for monitoring of the limiting anisotropy in membranes

Data acquisition and analysis of the time-resolved fluorescence anisotropy is typically a time consuming process preventing usage of this experimental method for monitoring of time-dependent phenomena. We describe a method for pseudo real-time monitoring of the limiting fluorescence anisotropy r(infinity) allowing to track changes of the membrane order occurring on the time scale of minutes. Principle and performance of the method is demonstrated in the time domain with the time-correlated single photon counting detection. DMPC liposomes stained with 1,6-diphenyl-1,3,5-hexatriene (DPH) have been used to test influence of the diffusion membrane potential on the membrane order during the temperature-induced phase transition in DMPC membranes. It has been found that the transmembrane field of the order of -70 mV increases the phase transition temperature by about 1.5 degrees C-2 degrees C. It is proposed that the full advantage of the method can be utilized with a gated detection, which besides a faster data acquisition brings additional advantage of excitation light suppression. The method can be also used for imaging.

Fluorescence resonance energy transfer analysis of the antagonist- and partial agonist-occupied states of the cholecystokinin receptor

Changes in receptor conformation are believed to be key for ligand-induced regulation of cellular signaling cascades. However, little information exists about specific conformations of a receptor. We recently applied fluorescence resonance energy transfer to determine distances from distinct points distributed over the surface and within the helical bundle of the cholecystokinin receptor to the amino terminus of a full agonist CCK analogue (Harikumar, K. G., Pinon, D. I., Wessels, W. S., Dawson, E. S., Lybrand, T. P., Prendergast, F. G., and Miller, L. J. (2004) Mol. Pharmacol. 65, 28-35). Here, we apply the same experimental strategy to determine distances from the same receptor positions to an analogous point at the amino terminus of structurally related partial agonist (Alexa488-Gly-[(Nle(28,31))CCK-26-32]phenethyl ester) and antagonist (Alexa488-Gly-[(D-Trp31, Nle(28,31))CCK-26-32]phenethyl ester) ligands. A high degree of spectral overlap and fluorescence transfer was observed for ligand-occupied fluorescent-tagged receptors with no transfer observed for the ligand-occupied pseudo-wild type null cysteine-reactive mutant receptor (C94S). For the partial agonist, calculated distances to receptor positions 94, 102, 204, and 341, representing sites within the helical confluence, and the first, second, and third loops, were 21 +/- 0.4, 18 +/- 0.4, 25 +/- 1, and 17 +/- 1 angstroms, not different from those measured previously for the analogous full agonist. For the antagonist, the analogous distances were 21 +/- 2, 28 +/- 2, 15 +/- 1 and 21 +/- 1 angstroms. Distances to the first and third loops were longer and the distance to the second loop was shorter for the antagonist relative to both the full and partial agonist probes, whereas all three probes demonstrated similar distances to the intrahelical reference point. This supports the possibilities of changes in the conformation of the probe and/or the receptor induced by structurally similar ligands having distinct intrinsic biological activities.

Measurement of Intermolecular Distances for the Natural Agonist Peptide Docked at the Cholecystokinin Receptor Expressed in Situ Using Fluorescence Resonance Energy Transfer

Fluorescence resonance energy transfer is a powerful biophysical technique used to analyze the structure of membrane proteins. Here, we used this tool to determine the distances between a distinct position within a docked agonist and a series of distinct sites within the intramembranous confluence of helices and extracellular loops of the cholecystokinin (CCK) receptor. Pseudo-wild-type CCK receptor constructs having single reactive cysteine residues inserted into each of these sites were developed. The experimental strategy included the use of the full agonist, Alexa488-CCK, bound to these receptors as donor, with Alexa568 covalently bound to the specific sites within the CCK receptor as acceptor. Site-labeling was achieved by derivatization of intact cells with a novel fluorescent methanethiosulfonate reagent. A high degree of spectral overlap was observed between receptor-bound donor and receptor-derivatized acceptors, with no transfer observed for a series of controls representing saturation of the receptor binding site with nonfluorescent ligand and use of a null-reactive CCK receptor construct. The measured distances between the fluorophore within the docked agonist and the sites within the first (residue 102) and third (residue 341) extracellular loops of the receptor were shorter than those directed to the second loop (residue 204) or to intramembranous helix two (residue 94). These distances were accommodated well within a refined molecular model of the CCK-occupied receptor that is fully consistent with all existing structure-activity and photoaffinity-labeling studies. This approach provides the initial insights into the conformation of extracellular loop regions of this receptor and establishes clear differences from analogous loops in the rhodopsin crystal structure.

Environment and mobility of a series of fluorescent reporters at the amino terminus of structurally related peptide agonists and antagonists bound to the cholecystokinin receptor

Fluorescence is a powerful biophysical tool for the analysis of the structure and dynamics of proteins. Here, we have developed two series of new fluorescent probes of the cholecystokinin (CCK) receptor, representing structurally related peptide agonists and antagonists. Each ligand had one of three distinct fluorophores (Alexa(488), nitrobenzoxadiazolyl, or acrylodan) incorporated in analogous positions at the amino terminus just outside the hormone's pharmacophore. All of the probes bound to the CCK receptor specifically and with high affinity, and intracellular calcium signaling studies showed the chemically modified peptides to be fully biologically active. Quenching by iodide and measurement of fluorescence spectra, anisotropy, and lifetimes were used to characterize the response of the fluorescence of the probe in the peptide-receptor complex for agonists and antagonists. All three fluorescence indicators provided the same insights into differences in the environment of the same indicator in the analogous position for agonist and antagonist peptides bound to the CCK receptor. Each agonist had its fluorescence quenched more easily and showed lower anisotropy (higher mobility of the probe) and shorter lifetime than the analogous antagonist. Treatment of agonist-occupied receptors with a non-hydrolyzable GTP analogue shifted the receptor into its inactive low affinity state and increased probe fluorescence lifetimes toward values observed with antagonist probes. These data are consistent with a molecular conformational change associated with receptor activation that causes the amino terminus of the ligand (situated above transmembrane segment six) to move away from its somewhat protected environment and toward the aqueous milieu.

Plasma membrane polarity of polymorphonuclear leucocytes from children with primary ciliary dyskinesia

BACKGROUND

Polymorphonuclear leucocytes (PMN) from subjects with primary ciliary dyskinesia (PCD) can have abnormal locomotory systems. The locomotory activity of PMN is the result of biochemical events mediated by the plasma membrane. In this study we investigated plasma membrane polarity of PMN from children with PCD.

DESIGN

Membrane polarity was studied in 11 children with PCD and in healthy controls by measuring the steady-state fluorescence excitation and emission spectra of 2-dimethylamino[6-lauroyl]naphthalene (Laurdan), which is known to be incorporated at the hydrophobic-hydrophilic interface of the bilayer, displaying spectral sensitivity to the polarity of its surroundings. Laurdan shows a marked steady-state emission red shift in polar solvents, with respect to nonpolar solvents. Moreover, the effect of the microtubule disassembling agent colchicine on PMN membrane polarity was evaluated.

RESULT

Our results show a red shift of the fluorescence excitation and emission spectra of Laurdan in PMN from the PCD group with respect to the control group. These data indicate an increase in membrane polarity of PMN from the PCD group. Treatment of PMN with colchicine induced a red shift in the Laurdan excitation and emission spectra with the same trend observed in PMN from the PCD group.

CONCLUSION

PMN from children with PCD are characterized by an increased plasma membrane polarity. These changes could be the basis of the modifications in the locomotory activities of PMN. The observed alterations may be attributed to abnormalities in the cytoskeleton.

Time-resolved and steady-state fluorescence quenching of N-acetyl-L-tryptophanamide by acrylamide and iodide

We examined the time-resolved and steady-state fluorescence quenching of N-acetyl-L-tryptophanamide (NATA) by acrylamide and iodide, over a range of viscosities in propylene glycol. The quenching of NATA by acrylamide and iodide results in heterogeneity of the intensity decay which increases with the quencher concentration. We attribute the complex decays of NATA to transient effects in diffusion and the nature of the fluorophore-quencher interaction. These data were compared using the phenomenological radiation boundary condition (RBC) and distance-dependent quenching (DDQ) models for collisional quenching. We used global analysis of the time-resolved frequency-domain and steady-state data to select between the models. Consideration of both the frequency-domain and steady state data demonstrate that the quenching rate depends exponentially on the fluorophore-quencher distance, indicating the validity of the DDQ model. The rate constants for acrylamide and iodide quenching, at the constant distance of 5 A, were found to be near 10(13) s-1 and 10(9) s-1, respectively. These rates reflect electron transfer and exchange interactions as the probable quenching mechanisms, respectively.

Light quenching of fluorescence: a new method to control the excited state lifetime and orientation of fluorophores

Experimental studies have recently demonstrated that fluorescence emission can be quenched by laser light pulses from modern high-repetition rate lasers, a phenomenon we call "light quenching." In this overview article, we describe the possible effects of light quenching on the steady-state and time-resolved intensity and anisotropy of fluorophores. One can imagine two classes of experiments. Light quenching can occur within the single excitation pulse, or light quenching can be accomplished with a second time-delayed quenching pulse. The extent of light quenching depends on the amplitude of the emission spectrum at the quenching wavelength. Different effects are expected for light quenching by a single laser beam (within a single laser pulse) or for a time-delayed quenching pulse. Depending upon the polarization of the light quenching beam, light quenching can decrease or increase the anisotropy. Remarkably, the light quenching can break the usual z-axis symmetry of the excited state population, and the measured anisotropy (or polarization) depends upon whether the observation axis is parallel or perpendicular to the propagation direction of the light quenching beam. The polarization can increase to unity under selected conditions. Quenching with time-delayed light pulses can result in step changes in the intensity or anisotropy, which is predicted to result in oscillations in the frequency-domain intensity and anisotropy decays. These predicted effects of light quenching, including oscillations in the frequency-domain data, were demonstrated to occur using selected fluorophores. The increasing availability and use of pulsed laser sources requires consideration of the possible effects of light quenching and offers the opportunity for a new class of two-pulse or multiple-pulse time-resolved experiments where the sample is prepared by the excitation pulse and subsequent quenching pulses to modify the excited state population, followed by time- or frequency-domain measurement of the optically prepared excited fluorophores.

Influence of vesicle curvature on fluorescence relaxation kinetics of fluorophores

The effect of membrane curvature on the fluorescence decay of 2-p-toluidinyl-naphthalene-6-sulfonic acid (TNS), 2-(9-anthroyloxy) stearic acid (2-AS) and 12-(9-anthroyloxy)-stearic acid (12-AS) was investigated for egg lecithin vesicles of average diameter dm = 22 nm and 250 nm. The biexponential fluorescence decay of TNS at the red edge of the emission spectrum was analysed according to the model of Gonzalo and Montoro [1]. Over the entire temperature range (1-40 degrees C) the small TNS labelled vesicles showed significantly shorter solvent relaxation times tau(r) than their larger counterparts (e.g. 1.3 ns compared with 2.1 ns at 5 degrees C), indicating a higher mobility of the hydrated headgroups in the highly curved, small vesicles. The fluorescence decay of both AS derivatives is also biexponential. While the shorter decay times (1-3 ns) are practically identical for small and large vesicles, the longer decay times (5-14 ns) are identical only for 12-AS but not for 2-AS. This indicates that the microenvironment is similar in small and large vesicles deep in the membrane in spite of the differences in curvature.

Steady-state fluorescence studies on lipase-vesicle interactions

The interaction of lipase from Candida cylindracea (CCL) with positively charged polymerizable surfactant vesicles was studied by the use of steady-state fluorescence techniques. The phase transition of vesicles composed of nonpolymerized and polymerized N-allylbis[2-(hexadecanoyloxy)ethyl]methylammonium bromide (ABHEMA Br) was determined in the absence of lipase, by measuring the change in fluorescence anisotropy of the membrane probe 1,6-diphenyl-1,3,5-hexatriene (DPH). The phase transition temperature for nonpolymerized vesicles is 49 degrees C and for the polymerized analogues 45 degrees C. Fluorescence anisotropy and resonance energy transfer measurements were used to illustrate the incorporation of the lipase in the vesicle membrane. These studies demonstrated that CCL is incorporated into the hydrophobic bilayer of the vesicle. By using an interfacial membrane probe 1-[4-(trimethylammonium)phenyl]-6-phenyl-1,3,5-hexatriene p-toluene sulphonate, TMA-DPH) and an internal membrane probe (DPH), it could be determined that the enzyme is incorporated more efficiently into nonpolymerized vesicles, and that the penetration of the enzyme into the bilayer is less deep in the case of the polymerized vesicles.

Oxygen diffusion-concentration in erythrocyte plasma membranes studied by the fluorescence quenching of anionic and cationic pyrene derivatives

Fluorescence quenching by oxygen of cationic [pyrene-(CH2)nN(CH3)3+; n = 1, 4, and 11] and anionic [pyrene-(CH2)nCO2-, n = 3, 8, 11, and 15] probes was investigated in erythrocyte plasma membranes (leaky) in order to assess the ability of oxygen molecules to interact with solutes located at different positions in the membrane. The pseudounimolecular quenching rate constants measured increase, both for cationic and anionic probes, when n increases. These results are interpreted in terms of an increased oxygen solubility toward the center of the membrane interior, and imply that lateral diffusion contributes more than transverse diffusion to total oxygen mobility. For all of the probes considered, quenching rates increase when n-alkanols are added. The effect observed increases when n decreases and when the size of the n-alkanol alkyl chain increases. Arrhenius-type plots for the quenching rate constants show noticeable downward curvatures. Average (0-40 degrees C) activation energies are approximately 6 kcal/mol.

Selective modification of the catalytic subunit of cAMP-dependent protein kinase with sulfhydryl-specific fluorescent probes

The catalytic subunit of cAMP-dependent protein kinase contains only two cysteine residues, and the side chains of both Cys 199 and Cys 343 are accessible. Modification of the catalytic subunit by a variety of sulfhydryl-specific reagents leads to the loss of enzymatic activity. The differential reactivity of the two sulfhydryl groups at pH 6.5 has been utilized to selectively modify each cysteine with the following fluorescent probes: 3,6,7-trimethyl-4-(bromomethyl)-1,5-diazabicyclo[3.3.0]octa-3,6-diene- 2,8-dione, N-(iodoacetyl)-N'-(5-sulfo-1-naphthyl)ethylenediamine, and 4-[N-[(iodoacetoxy)ethyl]-N-methyl-amino]-7-nitrobenz-2-oxa-1,3-diazole. The most reactive cysteine is Cys 199, and exclusive modification of this residue was achieved with each reagent at pH 6.5. Modification of Cys 343 required reversible blocking of Cys 199 with 5,5'-dithiobis(2-nitrobenzoic acid) followed by reaction of Cys 343 with the fluorescent probe at pH 8.3. Treatment of this modified catalytic subunit with reducing reagent restored catalytic activity by unblocking Cys 199. In contrast, catalytic subunit that was selectively labeled at Cys 199 by the fluorescent probes was catalytically inactive. Even though Cys 199 is presumably close to the interaction site between the regulatory subunit and the catalytic subunit, all of the modified C-subunits retained the capacity to aggregate with the type II regulatory subunit in the absence of cAMP, and the resulting holoenzymes were dissociated in the presence of cAMP.(ABSTRACT TRUNCATED AT 250 WORDS)

Interaction of clathrin coat proteins with unilamellar and multilamellar vesicles of phosphatidylcholine

The binding of clathrin and accessory coat proteins to small unilamellar vesicles and to liposomes of uncharged phospholipids has been followed by chromatography, 31P-NMR, ESR and fluorescence anisotropy. At pH 6.5 and at an ionic strength value (0.1 M Mes) close to that used during the purification of clathrin-coated vesicles, the proteins do not restore the characteristic network found around the natural vesicles. Instead, a limited fusion leads to enlarged structures in which the perturbation of the dynamics of the phospholipids decreases gradually with the depth in the membrane. While the rate of motion of the outer polar heads is lowered, the order parameter of doxyl groups located either under or in the vicinity of the glycerol backbone is not affected by the proteins. In the inner core of the membrane, the main thermotropic transition of the hydrocarbon chains is unchanged. All the effects are the results of interactions limited to the membrane surface. The electrostatic nature of these interactions is evidenced when the embedded spin labels have a charge protruding at the membrane surface. An 'anchoring' effect appears which is due to the charged groups of the proteins. The lateral diffusion of the probes is reduced and, at low ionic strength, a cationic derivative no longer detects the thermotropic transition of the hydrocarbon chains. These results indicate that, although it is known that clathrin and accessory proteins bind to membranes by a series of protein-protein interactions, this system is not devoid of lipid-protein interactions, at least when it is not organized as in the natural system.

Time-resolved emission spectra of hemoglobin on the picosecond time scale

We used front-face illumination to examine the steady-state and time-resolved emission from the intrinsic tryptophan emission of human hemoglobin (Hb). Experimental conditions were identified which eliminated all contributions of scattered light. The sensitivity obtained using front-face optics was adequate to allow measurement of the wavelength-dependent frequency response of the emission to 2 GHz. The intensity decays displayed pico- and nanosecond components in the emission at all wavelengths from 315 to 380 nm. The contribution of the picosecond component decreased from 72 to 37% over this range of wavelengths. Frequency-domain measurements were used to calculate the time-resolved emission spectra and decay-associated emission spectra. These spectra indicate that the picosecond components of the emission display maxima near 320 nm, whereas the nanosecond components are centered at longer wavelengths near 335 nm. The nanosecond components appear to be due to residual impurities which remain even in highly purified samples of Hb. However, we cannot eliminate the possibility that some of these components are due to Hb itself.