Effect of ligand binding and conformational changes in proteins on oxygen quenching and fluorescence depolarization of tryptophan residues

K(+) preference at the NaK channel entrance revealed by fluorescence lifetime and anisotropy analysis of site-specifically incorporated (7-hydroxycoumarin-4-yl)ethylglycine

The fluorescent unnatural amino acid, (7-hydroxycoumarin-4-yl)ethylglycine (HC), was site-specifically incorporated at the Phe69 site, close to the entrance of the selectivity filter of the NaK channel. Decreased fluorescence lifetime and elevated time-resolved anisotropy of NaK-F69HC in buffers with high K(+)/Na(+) molar ratios indicated the K(+) preference at the entrance of the NaK channel, consistent with previous crystal structure results of the NaK channel.

Site-dependent excited-state dynamics of a fluorescent probe bound to avidin and streptavidin

The excited-state dynamics of biotin-spacer-Lucifer-Yellow (LY) constructs bound to avidin (Avi) and streptavidin (Sav) was investigated using femtosecond spectroscopy. Two different locations in the proteins, identified by molecular dynamics simulations of Sav, namely the entrance of the binding pocket and the protein surface, were probed by varying the length of the spacer. A reduction of the excited-state lifetime, stronger in Sav than in Avi, was observed with the long spacer construct. Transient absorption measurements show that this effect originates from an electron transfer quenching of LY, most probably by a nearby tryptophan residue. The local environment of the LY chromophore could be probed by measuring the time-dependent polarisation anisotropy and Stokes shift of the fluorescence. Substantial differences in both dynamics were observed. The fluorescence anisotropy decays analysed by using the wobbling-in-a-cone model reveal a much more constrained environment of the chromophore with the short spacer. Moreover, the dynamic Stokes shift is multiphasic in all cases, with a approximately 1 ps component that can be ascribed to diffusive motion of bulk-like water molecules, and with slower components with time constants varying not only with the spacer, but with the protein as well. These slow components, which depend strongly on the local environment of the probe, are ascribed to the motion of the hydration layer coupled to the conformational dynamics of the protein.

Chemical and biological caging effects on the relaxation of a proton-transfer dye

We report studies of the interaction between a proton-transfer dye (1'-hydroxy,2'-acetonaphthone, HAN), with the human serum albumin (HSA) protein and a beta-cyclodextrin derivative (DM-beta-CD) in neutral water solutions. We used steady-state and picosecond time-resolved emission spectroscopy to follow the structural changes of HAN due to the hydrophobicity and confinement effect of these nanocavities. Upon encapsulation, the fluorescence intensity of the 1:1 inclusion complex in both cavities increases, and the emission lifetimes become longer. For the DM-beta-CD complexes, we obtained 430 and 920 ps, whereas for the HSA complexes we obtained 630 ps and 2 ns. Picosecond anisotropy measurements show strong confinement due to protein docking. The rotational time for the CD complex is 660 ps, whereas for the protein complex we find 6 ns. The process of energy transfer from the excited triptophan 214 (Trp214) of HSA to the trapped HAN occurs with high efficiency (71%), and the calculated distance between both chromophores is 17 A. We believe that the results are important for a better understanding of the processes occurring in inclusion complexes such as those in nanopharmacodynamics.

Relaxation Dynamics of Piroxicam Structures within Human Serum Albumin Protein

We report on steady-state and ps-time-resolved emission studies of piroxicam (1) drug within human serum albumin (HSA) protein in cyclodextrin and in neat solvents. The steady-state results indicate that 1 binds to HSA protein and that two binding sites are involved. The fluorescence decays corresponding to site I in subdomain IIA and to site II in subdomain IIIA have time constants of approximately 60 ps and approximately 360 ps, respectively. The results suggest that the anion forms bind to site I, whereas the zwitterionic ones bind to site II. The energy-transfer process from excited tryptophan to 1 can occur with moderate efficiency (50%). The rotational time of 1 encapsulated by HSA indicates diffusion within the protein. These findings can be used for a better understanding of piroxicam and HSA interactions.

Precise boundary element computation of protein transport properties: Diffusion tensors, specific volume, and hydration

A precise boundary element method for the computation of hydrodynamic properties has been applied to the study of a large suite of 41 soluble proteins ranging from 6.5 to 377 kDa in molecular mass. A hydrodynamic model consisting of a rigid protein excluded volume, obtained from crystallographic coordinates, surrounded by a uniform hydration thickness has been found to yield properties in excellent agreement with experiment. The hydration thickness was determined to be delta = 1.1 +/- 0.1 A. Using this value, standard deviations from experimental measurements are: 2% for the specific volume; 2% for the translational diffusion coefficient, and 6% for the rotational diffusion coefficient. These deviations are comparable to experimental errors in these properties. The precision of the boundary element method allows the unified description of all of these properties with a single hydration parameter, thus far not achieved with other methods. An approximate method for computing transport properties with a statistical precision of 1% or better (compared to 0.1-0.2% for the full computation) is also presented. We have also estimated the total amount of hydration water with a typical -9% deviation from experiment in the case of monomeric proteins. Both the water of hydration and the more precise translational diffusion data hint that some multimeric proteins may not have the same solution structure as that in the crystal because the deviations are systematic and larger than in the monomeric case. On the other hand, the data for monomeric proteins conclusively show that there is no difference in the protein structure going from the crystal into solution.

Biotin binding changes the conformation and decreases tryptophan accessibility of streptavidin

Biotin binding reduces the tryptophan fluorescence emissions of streptavidin by 39%, blue shifts the emission peak from 333 to 329 nm, and reduces the bandwidth at half height from 53 to 46 nm. The biotin-induced emission difference spectrum resembles that of a moderately polar tryptophan. Streptavidin fluorescence can be described by two lifetime classes: 2.6 nsec (34%) and 1.3 nsec (66%). With biotin bound, lifetimes are 1.3 nsec (26%) and 0.8 nsec (74%). Biotin binding reduces the average fluorescence lifetime from 1.54 to 0.88 nsec. Biotin does not quench the fluorescence of indoles. The fluorescence changes are consistent with biotin binding causing a conformational change which moves tryptophans into proximity to portions of streptavidin which reduce the quantum yield and lifetimes. Fluorescence quenching by acrylamide revealed two classes of fluorophores. Analysis indicated a shielded component comprising 20-28% of the initial fluorescence with (KSV + V) less than or equal to 0.55 M-1. The more accessible component has a predominance of static quenching. Measurements of fluorescence lifetimes at different acrylamide concentrations confirmed the strong static quenching. Since static quenching could be due to acrylamide binding to streptavidin, a dye displacement assay for acrylamide binding was constructed. Acrylamide does bind to streptavidin (Ka = 5 M-1), and probably binds within the biotin-binding site. In the absence of biotin, none of streptavidin's fluorescence is particularly accessible to iodide. In the presence of biotin, iodide neither quenches fluorescence nor alters emission spectra, and acrylamide access is dramatically reduced. We propose that the three tryptophans which always line the biotin site are sufficiently close to the surface of the binding site to be quenched by bound acrylamide. These tryptophans are shielded from iodide, most probably due to steric or ionic hindrances against diffusion into the binding site. Most of the shielding conferred by biotin binding can be attributed to the direct shielding of these residues and of a fourth tryptophan which moves into the binding site when biotin binds, as shown by X-ray studies (Weber et al., 1989).

Fluorescence lifetime and spectral study of the acid expansion of bovine serum albumin

The fluorescence lifetimes of the tryptophan residues of bovine serum albumin were measured in the native and acid-expanded conformation. A three-exponential process is required to fit the fluorescence decay data. The results are interpreted empirically in terms of two emitting species. The emission at longer wavelength (360 nm) has slower rates of decay than that at shorter wavelength (325 nm). For both emitting species the average lifetime decreases when the N-F transition occurs and shortens further when the protein expands. Rotational correlation times, derived from the decay of the fluorescence anisotropy of the tryptophan residues, suggest that longer emission wavelengths are associated with somewhat shorter correlation times. There is no certain indication of any independent motion of the tryptophans in any conformation, although some very fast process, perhaps Raman scattering, appears to occur. On acid expansion the long correlation times decrease to around 10 ns in the fully expanded form. Static quenching experiments using I- or acrylamide suggest a greater average exposure of the tryptophans when the protein is most greatly expanded. This is despite the fact that the fluorescence emission maximum shifts to shorter wavelength under these conditions. Also, there is no difference in accessibility to quenching between the longer and shorter wavelength emissions.

Investigation of conformational changes in yeast enolase using dynamic fluorescence and steady-state quenching measurements

Conformational changes in yeast enolase were investigated using steady state quenching and dynamic (fluorescence decay and fluorescence anisotropy decay) measurements. The tryptophan fluorescence rotational correlation time increases from 24 to 38 ns on subunit association. The acrylamide quenching constant decreases two-fold when the subunits associate. The conformational metal ion effect suggests a more compact molecule. Under conditions of catalysis, the correlation time decreases 25%, though the sedimentation constant does not change (Holleman, 1973). The enzyme may undergo a hinge-bending motion during catalysis.

Application of a reference convolution method to tryptophan fluorescence in proteins. A refined description of rotational dynamics

A reference method for the deconvolution of polarized fluorescence decay data is described. Fluorescence lifetime determinations for p-terphenyl, p-bis[2-(5-phenyloxazolyl)]benzene and N-acetyltryptophanamide (AcTrpNH2) show that with this method more reliable fits of the decays can be made than with the scatterer method, which is most frequently used. Analysis of the AcTrpNH2 decay with p-terphenyl as the reference compound yields an excellent fit with lifetimes of 2.985 ns for AcTrpNH2 and 1.099 ns for p-terphenyl (20 degrees C), whereas the AcTrpNH2 decay cannot be satisfactorily fitted when the scatterer method is used. The frequency of the detected photons is varied to determine the conditions where pulse pile-up starts to affect the measured decays. At detection frequencies of 5 kHz and 15 kHz, which corresponds to 1.7% and 5% respectively of the rate of the excitation photons no effects are found. Decays measured at 30 kHz (10%) are distorted, indicating that pile-up effects play a role at this frequency. The fluorescence and fluorescence anisotropy decays of the tryptophan residues in the proteins human serum albumin, horse liver alcohol dehydrogenase and lysozyme have been reanalysed with the reference method. The single tryptophan residue of the albumin is shown to be characterized by a triple-exponential fluorescence decay. The anisotropy decay of albumin was found to be mono-exponential with a rotational correlation time of 26 ns (20 degrees C). The alcohol dehydrogenase has two different tryptophan residues to which single lifetimes are assigned. It is found that the rotational correlation time for the dehydrogenase changes with excitation wavelength (33 ns for lambda ex = 295 nm and 36 ns for lambda ex = 300 nm at 20 degrees C), indicating a nonspherical protein molecule. Lysozyme has six tryptophan residues, which give rise to a triple-exponential fluorescence decay. A single-exponential decay with a rotational correlation time of 3.8 ns is found for the anisotropy. This correlation time is significantly shorter than that arising from the overall rotation and probably originates from intramolecular, segmental motion.

Aluminum-induced conformational changes in calmodulin alter the dynamics of interaction with melittin

Studies were undertaken to examine the impact of aluminum-induced structural changes in bovine brain calmodulin on the protein's interface region with melittin, a model for calmodulin's target enzymes. Both steady-state and time-dependent fluorescence characteristics of the single tryptophanyl residue of melittin were employed to derive information on aluminum-related changes in the fluorophore's microenvironment. In the presence of stoichiometric amounts of aluminum ions, calmodulin's target region with melittin appears to be more polar than that with aluminum absent. As a result, upon association of melittin with aluminum-calmodulin, the enhancement of helical arrays is less pronounced. The fluorophore's average microenvironment also is modified such that its apparent lifetime is shortened when aluminum is present. In the presence of aluminum ions, the solvation structure of calmodulin is possibly changed, which may be unfavorable for a proper fit between calmodulin and target proteins.

Structural fluctuations in aspartate transcarbamylase. Succinimide quenching and fluorescence depolarization of tryptophan and tyrosine residues

The effects of binding of various effector ligands on the dynamics of aspartate transcarbamylase (ATCase, c6r6) and on its regulatory (r2) and catalytic (c3) subunits were characterized by examining succinimide quenching of the intrinsic fluorescence, and by measurement of the lifetime-resolved anisotropies. The lifetimes of the tryptophan residues in c3 and c6r6 are about 1.7 ns while those of tyrosine residues in r2 are 2.7 ns. These lifetimes are not significantly altered by the binding of various substrates, substrate analogs and nucleotides. The effects of ligand binding on the accessibility of both tyrosine and tryptophan residues to the quencher are modest in all cases, though the changes are in the same direction as seen using other physicochemical techniques such as hydrogen exchange (M. Lennick and N.M. Allewell, Proc. Natl. Acad. Sci. U.S.A. 78 (1981) 6759). The tryptophan residues in both c3 and c6r6 are immobilized whereas the tyrosine residues of r2 have some motional freedom. Ligands have no effect on the immobilized tryptophan residues in c3 and c6r6, while binding of nucleotides to r2 results in a small decrease in the motional freedom of the tyrosine residues. These results suggest that the protein matrix around the aromatic amino acids in r2, c3 and c6r6 is rather rigid and that local effects of ligands on the dynamics of these residues, and that of the surrounding protein matrix, are minor. They are in general agreement with the results of the crystal structure determination (R.B. Honzatko et al., J. Mol. Biol. 160 (1982) 219).