Protein fluorescence, dynamics and function: exploration of analogy between electronically excited and biocatalytic transition states

Competitive hydrogen bonding influences of fluorophore- urea-adenine system in water: Photophysical and photochemical approaches

Photophysical and photochemical investigation of photoinduced electron transfer (PET)-based acridinedione dye (ADR1) with urea in the presence of a nitrogenous base (adenine) were carried out in water. Urea suppresses the PET resulting in a fluorescence enhancement and the extent of binding is correlated and governed by the number of urea molecules surrounding the close vicinity of dye. On the contrary, adenine forms a true 1:2 complex with dye. Presence of adenine in dye-urea microenvironment results in the displacement of dye from the vicinity of urea molecules. The stability of dye-urea network in the presence of adenine reveals that the microenvironment of dye is governed and influenced by both urea and adenine. Introduction of adenine to dye-urea results in the formation of several hydrogen bonding assemblies that are competitive and influences the excited state characteristics of ADR1 dye. The micro assemblies comprise dye-urea (DU), dye-adenine (DA), urea-adenine (UA), urea-water (UW), urea-urea (UU), and adenine-water (AW) framework and the existence of several competitive hydrogen bonding results in a large variation in fluorescence properties of ADR1 dye. The presence of several assemblies also signifies that no confined phase selectively of DU or DA assemblies exist in any stoichiometric proportion in the aqueous phase. The binding constant, the variation in the fluorescence lifetime and its relative amplitude of DA in the presence of urea authenticate that the binding nature of dye-urea-adenine (DUA) is dependent on the several hydrogen bonding assemblies that coexist at any concentration. The extent of hydrogen bonding of DA is found to be entirely different from that of urea. Further, urea resulted in changes in the transient absorption peak of dye with a large variation in lifetime and shift of the transient absorption peaks. Fluorescence spectral techniques are used as an efficient tool in elucidating the binding nature of DU framework in the presence of non-fluorescent hydrogen-bonding solute like adenine.

Spectroscopic investigation and computational studies on the interaction of Acriflavine with various estrogens

The fluorescence quenching of Acriflavine (AFN) by certain estrogens was examined in aqueous media by employing steady state and time-resolved fluorescence measurements. The absorption spectra of AFN change with significant bathochromic shift in presence of quencher molecules. The quenching behavior was examined by correlating the bimolecular quenching rate constant (k_q) with the free energy change (ΔG). The decrease in quenching rate constant depends on the increase in oxidation potential of quencher molecules. The fluorescence quenching experiments were carried out in different solvents of varying polarities and reveals the possibility of charge transfer quenching mechanism. Lifetime measurements indicate static quenching. The quenching behavior is addressed from bond dissociation enthalpy (BDE) calculations. The antioxidant activity of estrogen compounds were evaluated by deoxyribose oxidation assay.

A new insight into the chemistry of iridium(iii) complexes bearing phenyl phenylphosphonite cyclometalate and chelating pyridyl triazolate: the excited-state proton transfer tautomerism via an inter-ligand PO–H⋯N hydrogen bond

Ir(pdpit)(pppo)(bptz) complex (3) reveals a PO–H–N inter- ligand H-bond from which proton transfer takes place.

Excited-state proton coupled charge transfer modulated by molecular structure and media polarization

Charge and proton transfer reactions in the excited states of organic dyes can be coupled in many different ways. Despite the complementarity of charges, they can occur on different time scales and in different directions of the molecular framework. In certain cases, excited-state equilibrium can be established between the charge-transfer and proton-transfer species. The interplay of these reactions can be modulated and even reversed by variations in dye molecular structures and changes of the surrounding media. With knowledge of the mechanisms of these processes, desired rates and directions can be achieved, and thus the multiple emission spectral features can be harnessed. These features have found versatile applications in a number of cutting-edge technological areas, particularly in fluorescence sensing and imaging.

Site-selective Red-Edge effects

Observation of Red Edge effects is the basis of unique methodology that allows combination of site-photoselection with dynamics of molecular relaxations. The important dynamic information on molecular level can be obtained even by simple recording of steady-state fluorescence using the lifetime as the time marker. The extension to time domain allows distinguishing these relaxations from other dynamic processes that influence the excited-state energies. In this Chapter I briefly discuss the background of this technique and concentrate on quantitative measure of these effects and on importance of their distinction from ground-state heterogeneity. The peculiarity of Trp emission in proteins and the optimal selection of fluorescence probes are discussed. The Red Edge excitations influence dramatically the excited-state reactions that are coupled with dielectric relaxations and this opens a new fascinating prospect for protein and biomembrane studies.

Fast excited-state intramolecular proton transfer and subnanosecond dynamic stokes shift of time-resolved fluorescence spectra of the 5-methoxysalicylic acid/diethyl ether complex

Excited-state intramolecular proton transfer (ESIPT) occurring in the salicylic acid (SA) derivative 5-methoxysalicylic acid (5-MeOSA) in an apolar solvent (cyclohexane) and in the presence of the hydrogen bond accepting agent diethyl ether (DEE) is investigated. Analysis of the directly measured subnanosecond time-resolved emission spectra (TRES) together with conventional steady-state fluorescence and time-correlated single-photon-counting (TCSPC) decays indicates that ESIPT in this system occurs much faster than fluorescence, and that the equilibrium between normal and tautomeric excited states is established before the emission from both states takes place. However, changes in time- and frequency-resolved fluorescence of the 5-MeOSA/DEE complex are observed due to structural relaxation within the complex, which is reflected in the dynamic Stokes shift of the tautomeric fluorescence band. The normal fluorescence band of 5-MeOSA/DEE does not exhibit marked changes within the investigated time range. A single-exponential relaxation time of 460 ps was determined for the dynamic Stokes shift of the tautomeric band, and it is attributed to a geometric change within the 5-MeOSA/DEE complex upon excitation. Since both tautomeric and normal emission bands are well resolved and exhibit different time-dependent behaviors, a double-well potential appears to be adequate to describe the excited state of the system studied.

Heat perturbation of bovine eye lens alpha-crystallin probed by covalently attached ratiometric fluorescent dye 4'-diethylamino-3-hydroxyflavone

Bovine eye lens alpha-crystallin was covalently labeled with 6-bromomethyl-4'-diethylamino-3-hydroxyflavone and studied under native-like conditions and at the elevated temperature (60 degrees C) that is known to facilitate alpha-crystallin chaperone-like activity. This novel SH-reactive two-band ratiometric fluorescent probe is characterized by two highly emissive N*- and T*-bands; the latter appears due to excited state intramolecular proton transfer reaction. The positions of these bands and the ratio of their intensities for the alpha-crystallin-dye conjugate are the sensitive indicators of polarity of the dye environment and its participation in intermolecular hydrogen bonding. Although we found that the dye labels both the SH and the NH2 groups in alpha-crystallin, a recently developed procedure allowed us to distinguish between the heat-induced spectral changes of the dye molecules attached to SH and NH2 groups. We observed that at elevated temperature the environment of the SH-attached dye becomes more polar and flexible. The number of H-bond acceptor groups in the vicinity of the dye decreases. Since alpha-crystallin contains a single Cys residue within the C-terminal domain of its (alpha)A subunit (the (alpha)B subunit contains none), we can attribute the observed effects to temperature-induced changes in the C-terminal domain of this protein.

The binding of novel two-color fluorescence probe FA to serum albumins of different species

The novel two-color ratiometric fluorescence probe FA belonging to a class of 3-hydroxychromone dyes was applied for characterization of binding sites in serum albumins obtained from seven species (bovine, dog, horse, human, pig, rabbit and sheep). On strong and highly specific FA binding to the same location in protein structure, the species-dependent differences were observed in positions of absorption maxima, positions of two fluorescence emission bands and the intensity ratios between them. They were analyzed by multiparametric algorithm that allowed a detailed characterization of probe-binding sites and were characterized by very low polarity, high electronic polarizability and different extent of intermolecular hydrogen bonding. The species-dependent differences were also observed in time-resolved fluorescence emission decays. Fluorescence competition experiments with the drug warfarin, suggested the location of FA binding site within or in proximity to Domain IIA.

Spectral and acid-base features of 3,7-dihydroxy-2,8-diphenyl-4H,6H-pyrano[3,2-g]chromene-4,6-dione (diflavonol)--a potential probe for monitoring the properties of liquid phases

Diflavonol is a molecule that can exist in neutral or anionic form and in several tautomeric forms in ground and excited states. Absorption and emission spectroscopy combined with theoretical calculations have shown that only one tautomer of neutral diflavonol exists in the ground state, but two exist in the excited state. In the latter case, one is the tautomer originating from the ground state tautomer, which exists in strongly protic solvents, the other is the phototautomer occurring in weakly protic or aprotic solvents as a result of the intramolecular transfer of one proton. The OH groups present in diflavonol and involved in weak intramolecular hydrogen bonds exhibit a proton-donating ability reflected by the experimental values of acidity constants or theoretical enthalpies and free energies of proton detachment. The electronically excited molecule is a relatively strong acid when it loses one proton. With increasing basicity of the medium, monoanionic and dianionic forms occur which exhibit spectral characteristics and an emission ability different from those of neutral diflavonol. These interesting features of diflavonol open up possibilities for the analytical use of the compound and its application as a spectral probe sensitive to the properties of liquid phases.

Quantification of allosteric influence of Escherichia coli phosphofructokinase by frequency domain fluorescence

The allosteric properties of the wild-type Escherichia coli phosphofructokinase were compared to the E187A mutant by using frequency-domain techniques. Tryptophan-shifted mutants comprising of double (W311Y/Y55W and W/311F/F188W) and triple (W311Y/Y55W/E187A and W311F/F188W/E187A) amino acid residue changes, which allowed for better fluorescence probing at targeted sites, were also compared to the wild-type and E187A. The additive nature of multiple mutations allowed one to partition the net effect of modifying residue 187. In general, the mutant enzymes displayed greater heterogeneity in sub-state population than did the wild-type enzyme. The semi-cone angle model was used to quantify the extent of depolarization of the fluorophore. Use of the model presupposes that the extent of depolarization directly correlates with the degree of flexibility of the fluorophore. A relationship has been established between the values determined from the semi-cone angle calculations and the thermodynamic components responsible for the allosteric linkage between the regulatory and substrate binding. Coupling interactions giving rise to positive entropy components are manifested by increasing flexibility of the ternary complexes rather than the binary complexes.

Novel two-color fluorescence probe with extreme specificity to bovine serum albumin

We report on strong, highly specific and stochiometric binding to bovine serum albumin of novel fluorescence probe FA, 2-(6-diethylaminobenzo[b]furan-2-yl)-3-hydroxychromone, that exhibits a very characteristic two-band fluorescence spectrum. Both absorption band and two fluorescence bands of FA are very sensitive to non-covalent interactions in the immediate environment of the probe. Multiparametric analysis of this spectroscopic information allows us to conclude that the binding site is characterized by very low polarity, high extent of screening from aqueous environment and unusually high electronic polarizability. The latter suggests the proximal location of probe FA to the aromatic amino acid residues in the binding site. The new probe can be proposed for the study of interaction of ligands and drugs of different nature with serum albumins.

A fluorescence-based method for direct measurement of submicrosecond intramolecular contact formation in biopolymers: an exploratory study with polypeptides

A fluorescent amino acid derivative (Fmoc-DBO) has been synthesized, which contains 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a small, hydrophilic fluorophore with an extremely long fluorescence lifetime (325 ns in H2O and 505 ns in D2O under air). Polypeptides containing both the DBO residue and an efficient fluorescence quencher allow the measurement of rate constants for intramolecular end-to-end contact formation. Bimolecular quenching experiments indicated that Trp, Cys, Met, and Tyr are efficient quenchers of DBO (k(q) = 20, 5.1, 4.5, and 3.6 x 10(8) M(-1) x s(-1) in D2O), while the other amino acids are inefficient. The quenching by Trp, which was selected as an intrinsic quencher, is presumed to involve exciplex-induced deactivation. Flexible, structureless polypeptides, Trp-(Gly-Ser)n-DBO-NH2, were prepared by standard solid-phase synthesis, and the rates of contact formation were measured through the intramolecular fluorescence quenching of DBO by Trp with time-correlated single-photon counting, laser flash photolysis, and steady-state fluorometry. Rate constants of 4.1, 6.8, 4.9, 3.1, 2.0, and 1.1 x 10(7) s(-1) for n = 0, 1, 2, 4, 6, and 10 were obtained. Noteworthy was the relatively slow quenching for the shortest peptide (n = 0). The kinetic data are in agreement with recent transient absorption studies of triplet probes for related peptides, but the rate constants are significantly larger. In contrast to the flexible structureless Gly-Ser polypeptides, the polyproline Trp-Pro4-DBO-NH2 showed insignificant fluorescence quenching, suggesting that a high polypeptide flexibility and the possibility of probe-quencher contact is essential to induce quenching. Advantages of the new fluorescence-based method for measuring contact formation rates in biopolymers include high accuracy, fast time range (100 ps-1 micros), and the possibility to perform measurements in water under air.

The red-edge effects: 30 years of exploration

In 1970, three laboratories independently made a discovery that, for aromatic fluorophores embedded into different rigid and highly viscous media, the spectroscopic properties do not conform to classical rules. The fluorescence spectra can depend on excitation wavelength, and the excited-state energy transfer, if present, fails at the "red" excitation edge. These red-edge effects were related to the existence of excited-state distribution of fluorophores on their interaction energy with the environment and the slow rate of dielectric relaxation of this environment. In these conditions the site-selection can be provided by variation of the energy of illuminating light quanta, and the behaviour of selected species can be followed as a function of time and other variables. These observations found extensive application in different areas of research: colloid and polymer science, molecular biophysics, photochemistry and photobiology. In particular, they led to the development of very productive methods of studying the dynamics of dielectric relaxations in protein and membranes, using the tryptophan emission and the emission of a variety of probes. These studies were extended to the time domain with the observation of new site-selective effects in emission intensity and anisotropy decays. They stimulated the emergence and development of cryogenic energy-selective and single-molecular techniques that became valuable tools in their own right in chemistry and biophysics research. Site-selection effects were discovered for electron-transfer and proton-transfer reactions if they depended on the dynamics of the environment. This review is focused on the progress in the field of red-edge effects, their applications and prospects.

End-to-end diffusion on the microsecond timescale measured with resonance energy transfer from a long-lifetime rhenium metal-ligand complex

We measured the end-to-end diffusion coefficient of an alkyl chain-linked donor-acceptor pair using the time-resolved frequency-domain decay of the donor. The donor was a rhenium metal-ligand complex with a mean decay time ranging from 2.1 to 7.9 microseconds in the absence of the Texas red acceptor. The decay time was used to measure the donor-to-acceptor distance distribution and the mutual diffusion coefficient. Using this long lifetime donor, it was easily possible to determine a diffusion coefficient near 2 x 10(-8) cm2/s and diffusion coefficients as low as 1.3 x 10(-9) cm2/s were measurable. Such long lifetime donors should be valuable for measuring the flexing of peptides on the microsecond timescale, domain motions of proteins and lateral diffusion in membranes. The availability of microsecond decay time luminophores now allows luminescence spectroscopy to be useful generally for studies of microsecond dynamics of biological macromolecules.

Conformational dynamics and molecular interaction reactions of recombinant cytochrome p450scc (CYP11A1) detected by fluorescence energy transfer

Bovine adrenocortical cytochrome P450scc (P450scc) was expressed in Escherichia coli and purified as the substrate bound, high-spin complex (16.7 nmol of heme per mg of protein, expression level in E. coli about 400-700 nmol/l). The recombinant protein was characterized by comparison with native P450scc purified from adrenal cortex mitochondria. To study the interaction of the electron transfer proteins during the functioning of the heme protein, recombinant P450scc was selectively modified with fluorescein isothiocyanate (FITC). The present paper shows that modified P450scc, purified by affinity chromatography using adrenodoxin-Sepharose to remove non-covalently bound FITC, retains the functional activity of the unmodified enzyme, including its ability to bind adrenodoxin. Based on the efficiency of resonance fluorescence energy transfer in the donor-acceptor pair, FITC-heme, we calculated the distance between Lys(338), selectively labeled with the dye, and the heme of P450scc. The intensity of fluorescence from the label dramatically changes during: (a) denaturation of P450scc; (b) changing the spin state or redox potential of the heme protein; (c) formation of the carbon monoxide complex of reduced P450scc; (d) as well as during reactions of intermolecular interactions, such as changes of the state of aggregation, complex formation with the substrate, binding to the electron transfer partner adrenodoxin, or insertion of the protein into an artificial phospholipid membrane. Selective chemical modification of P450scc with FITC proved to be a very useful method to study the dynamics of conformational changes of the recombinant heme protein. The data obtained indicate that functionally important conformational changes of P450scc are large-scale ones, i.e. they are not limited only to changes in the dynamics of the protein active center. The results of the present study also indicate that chemical modification of Lys(338) of bovine adrenocortical P450scc does not dramatically alter the activity of the heme protein, but does result in a decrease of protein stability.

Fluorescence heterogeneity of tryptophans in Na,K-ATPase: evidences for temperature-dependent energy transfer

The intrinsic fluorescence emission kinetics of Na,K-ATPase, a large membrane protein containing 16 tryptophan residues, was studied by time-resolved techniques. The lifetime distributions recovered by the Maximum Entropy Method exhibit a strong dependence on the emission wavelength at temperatures between 37 degrees C and -70 degrees C. From the 'blue' edge of the fluorescence emission spectrum up to the maximum of emission, the lifetime distribution at room temperature is the result of four broad peaks which cover the time range 0.3-7 ns. With increasing emission wavelength, these peaks move to longer lifetimes and the peak at shorter times are suppressed at the red edge, while the longest component (6-7 ns) becomes dominant. With decreasing temperature, the number of lifetime components is reduced for the benefit of the long one. At cryogenic temperatures, the emission decay in the red-edge of the fluorescence spectrum consists of one major slow component (6-7 ns) and a fast one (0.5 ns) associated with a negative pre-exponential term. This is a characteristic feature of an excited-state reaction. The temperature dependence of this fast component and the fluorescence anisotropy decay at low temperature in the red-edge, indicate that this excited state reaction may be accounted for a unidirectional inter-tryptophan fluorescence energy transfer from 'blue' populations of donors to 'red' populations of acceptors. This is also illustrated by the time-resolved emission spectra. In the blue edge of the fluorescence emission spectrum, moreover, the time course of the anisotropy decay suggests the existence of homo-transfer of excitation energy involving 'blue' tryptophan residues. The steady-state anisotropy excitation spectrum in vitrified solvent agrees with this suggestion. These different energy transfer mechanisms may be used as structural probes to detect more accurately conformational changes of the protein elicited by effectors and ion binding or release.

Optical spectroscopy of nicotinoprotein alcohol dehydrogenase from Amycolatopsis methanolica: a comparison with horse liver alcohol dehydrogenase and UDP-galactose epimerase

The NADH absorbance spectrum of nicotinoprotein (NADH-containing) alcohol dehydrogenase from Amycolatopsis methanolica has a maximum at 326 nm. Reduced enzyme-bound pyridine dinucleotide could be reversibly oxidized by acetaldehyde. The fluorescence excitation spectrum for NADH bound to the enzyme has a maximum at 325 nm. Upon excitation at 290 nm, energy transfer from tryptophan to enzyme-bound NADH was negligible. The fluorescence emission spectrum (excitation at 325 nm) for NADH bound to the enzyme has a maximum at 422 nm. The fluorescence intensity is enhanced by a factor of 3 upon binding of isobutyramide (Kd = 59 microM). Isobutyramide acts as competitive inhibitor (Ki = 46 microM) with respect to the electron acceptor NDMA (N,N-dimethyl-p-nitrosoaniline), which binds to the enzyme containing the reduced cofactor. The nonreactive substrate analogue trifluoroethanol acts as a competitive inhibitor with respect to the substrate ethanol (Ki = 1.6 microM), which binds to the enzyme containing the oxidized cofactor. Far-UV circular dichroism spectra of the enzyme containing NADH and the enzyme containing NAD+ were identical, indicating that no major conformational changes occur upon oxidation or reduction of the cofactor. Near-UV circular dichroism spectra of NADH bound to the enzyme have a minimum at 323 nm (Deltaepsilon = -8.6 M-1 cm-1). The fluorescence anisotropy decay of enzyme-bound NADH showed no rotational freedom of the NADH cofactor. This implies a rigid environment as well as lack of motion of the fluorophore. The average fluorescence lifetime of NADH bound to the enzyme is 0.29 ns at 20 degreesC and could be resolved into at least three components (in the range 0.13-0.96 ns). Upon binding of isobutyramide to the enzyme-containing NADH, the average excited-state lifetime increased to 1.02 ns and could be resolved into two components (0.37 and 1.11 ns). The optical spectra of NADH bound to nicotinoprotein alcohol dehydrogenase have blue-shifted maxima compared to other NADH-dehydrogenase complexes, but comparable to that observed for NADH bound to horse liver alcohol dehydrogenase. The fluorescence lifetime of NADH bound to the nicotinoprotein is very short compared to enzyme-bound NADH complexes, also compared to NADH bound to horse liver alcohol dehydrogenase. The cofactor-protein interaction in the nicotinoprotein alcohol dehydrogenase active site is more rigid and apolar than that in horse liver alcohol dehydrogenase. The optical properties of NADH bound to nicotinoprotein alcohol dehydrogenase differ considerably from NADH (tightly) bound to UDP-galactose epimerase from Escherichia coli. This indicates that although both enzymes have NAD(H) as nonexchangeable cofactor, the NADH binding sites are quite different.