Intercomparison of small biomolecules by gel filtration and small angle scattering

This paper describes how small angle neutron scattering (SANS) can be used to confirm that gel filtration results are free of dimerization effects. After characterization by analytical gel filtration, concentrated solutions (in heavy water, D2O) of a cobra neurotoxin, a cytotoxin, and a cytotoxin analog are studied by SANS. Small differences in shape are shown to be discernible by means of least-square fits to ellipsoidal models. The parallel axis theorem is then invoked to assess dimerization levels statistically. The results are briefly discussed on the basis of function in relation to structure.

The use of Stokes Raman scattering in time correlated single photon counting: application to the fluorescence lifetime of tyrosinate

The decay kinetics of the tyrosinate form of tyrosine in aqueous solution, pH 11, were investigated by time correlated single photon counting using laser excitation. The lifetime of the single exponential decay was 30.5 +/- 0.2 ps. Stokes Raman scattering was used to determine the instrument response function and the advantages of this approach over the conventional Rayleigh scattering method are discussed.

Resolution of heterogeneous fluorescence into component decay-associated excitation spectra. Application to subtilisins

Direct and indirect methods are described to combine steady-state and picosecond time-resolved fluorescence decay data to generate decay-associated excitation spectra. The heterogeneous fluorescence from a fluorophore mixture that models protein fluorescence was resolved into individual component excitation spectra. The two methods were also used to determine the excitation spectra associated with each of the decay time components for the proteins subtilisin Carlsberg and BPN'. On the basis of associated spectra, the decay components of both proteins were assigned to individual (or groups of) emitting species. The two approaches used to generate the decay-associated excitation spectra are compared and their general application to protein fluorescence studies is discussed.

Correlation of enzyme activities with fluorescence anisotropy of dansyl-labeled cytochrome b5/NADH-cytochrome-b5 reductase systems in phosphatidylcholine vesicles

The changes in steady-state fluorescence lifetimes and anisotropy decay parameters, as well as enzyme activities, of dansyl-labeled cytochrome b5 (DNS-cytochrome b5), on interaction with NADH-cytochrome-b5 reductase in DMPC vesicles, have been measured as a function of temperature. Steady-state fluorescence of DNS-cytochrome b5 in DMPC vesicles with and without cholesterol was increased on interaction with reductase at temperatures both above and below the DMPC phase transition. In all systems three fluorescence decay components of the dansyl label in DNS-cytochrome b5 were observed. In the reductase-containing system, the long (major) decay time component of DNS-cytochrome b5 and the fraction of the total fluorescence associated with this component increased over the temperature range 15-30 degrees C. In time-resolved anisotropy measurements, the order parameters of DNS-cytochrome b5 in DMPC vesicles increased on interaction with reductase at temperatures above the DMPC phase transition, and this increase was even more pronounced in cholesterol-containing vesicles, at temperatures from 15-30 degrees C. The enzyme activity of the DNS-cytochrome-b5 reductase system in DMPC vesicles was also greatly increased in the presence of cholesterol. These results show that interaction of vesicle-bound DNS-cytochrome b5 and NADH-cytochrome-b5 reductase leads to an increased degree of order of the dansyl-labeled cytochrome with little change in its rotational flexibility, and suggests that the increased order can be correlated with increased enzyme activity.

A time-resolved fluorescence study of azurin and metalloazurin derivatives

Nickel and cobalt derivatives of Pseudomonas fluorescens (ATCC 13525) azurin were prepared and their steady-state fluorescence and time-resolved fluorescence monitored. Like the copper-containing native protein, the fluorescence decay of both metallo derivatives was best fit to a sum of three exponentials, whereas the apoazurin from which they were prepared obeyed single-exponential decay kinetics. However, comparison of the lifetimes and fractional of each of the components in these derivatives to those in the oxidized and reduced native proteins revealed significant differences. These results suggest that the presence of a metal center in azurin imparts a conformational heterogeneity which is strongly dependent on the nature of the metal center. Further, the results are used to comment on current ideas concerning the geometry of the active site in this redox protein.

Confirmation that multiexponential fluorescence decay behavior of holoazurin originates from conformational heterogeneity

Homologous azurins from Pseudomonas fluorescens (ATCC 13525) and Pseudomonas aeruginosa (ATCC 10145) were examined by a number of electrophoretic techniques, and their copper to protein stoichiometry was determined by atomic absorption and amino acid analysis. Provided that the spectral ratio (A620/A280 or A625/A280) was 0.53 and there was no evidence of a Soret band in the absorption spectrum, then these criteria can be used to judge the homogeneity of the azurin sample. If the spectral ratio was less than 0.50, evidence suggested a nonreconstitutable, non-trypsin-digestible apoazurin was present. The fluorescence decay of these homogeneous holoazurins included three components, not two as previously reported [Szabo, A. G., et al. (1983) Biophys. J. 41, 233-244]. Whereas the decay times were nearly the same for the azurins from the different sources, the fractional fluorescence of each component varied with the azurin measured. The fluorescence of the corresponding apoazurins, prepared by a refined procedure, obeyed monoexponential decay kinetics. The temperature and pH effects on the fluorescence behavior of these homologous azurins are presented with the pH study suggesting an influence by a group which titrates between pH 5 and pH 7. When taken together these results confirm that the multiexponential decay behavior originates from conformational heterogeneity and not from contamination by an apo form.

Homology of the D-galactose-specific lectins from Artocarpus integrifolia and Maclura pomifera and the role of an unusual small polypeptide subunit

The Maclura pomifera agglutinin (MPA) was purified by affinity chromatography from a seed extract and its properties were compared with those of the Artocarpus integrifolia lectin, jacalin. Reverse-phase high-performance liquid chromatography showed both proteins had multiple forms of a small approximately 20-residue polypeptide chain in addition to the major 12,000 Mr subunit. The amino acid sequences of the small chains and the N-terminal sequences of the large subunits showed considerable similarity between the two proteins, approximately 60% identical residues. The homology of the proteins was confirmed by the similarity of their circular dichroism and fluorescence emission spectra. MPA showed much greater spectral changes upon binding methyl alpha-D-galactoside, suggesting it has complete activity rather than the partial activity found for jacalin. The binding of methyl alpha-D-galactoside by MPA was measured by fluorescence titration; the KA was 1.9 X 10(4) M-1 compared to 3.4 X 10(4) M-1 for jacalin. MPA also precipitated human IgA1 in the same manner as jacalin. The spectra indicate the involvement of tryptophan and tyrosine residues in the binding site of these lectins. Since a tryptophan residue is conserved in all the small subunits, they may form part of the binding site.

Characterization and site-specific mutagenesis of the calcium-binding protein oncomodulin produced by recombinant bacteria

A bacterial expression system for the parvalbumin-like calcium-binding protein oncomodulin has been constructed. This system can yield 50-fold more oncomodulin than the richest known mammalian source, the rat Morris hepatoma 5123. The bacterially produced protein folded correctly as monitored by UV, fluorescence, and 1H nuclear magnetic resonance spectroscopy and is immunologically identical to rat hepatoma oncomodulin. A calcium-specific conformational change is observed in the bacterial oncomodulin similar to that of the hepatoma protein. A modification of the putative calcium-specific CD loop by site-directed mutagenesis, which changed Asp-59 to Glu-59, eliminates calcium-specific effects. In contrast to the native molecule, the mutant Glu-59 now exhibits a magnesium-induced conformational change when monitored by UV difference or fluorescence excitation spectroscopy. The availability of large amounts of bacterially produced oncomodulin combined with the ability to modify at will the metal-binding ligands should now allow dissection of the unusual pairing in oncomodulin of one calcium-specific calmodulin-like site with one calcium/magnesium parvalbumin-like site.

Conformation of bombesin in buffer and in the presence of lysolecithin micelles: NMR, CD, and fluorescence studies

The conformation of the tetradecapeptide hormone bombesin has been studied in buffer and in the presence of lysolecithin micelles, using static and dynamic fluorescence, CD, and one- and two-dimensional nmr. The results obtained show that in buffer bombesin is present in an extended flexible chain, with no evidence for any ordered secondary structure. A marked change in the CD spectrum is observed changing from buffer to the lipid suspension. Concomitantly, the 1H-nmr spectrum of bombesin, in a D2O lipid dispersion, shows the persistence of resonances due to exchangeable protons and in similar conditions the fluorescence intensity increases. We think therefore that these results strongly support the hypothesis that bombesin interacts with the lipid phase, assuming ordered secondary structure. Finally, the marked dependence of tryptophan fluorescence quantum efficiency and order parameter from the hormone concentration in the presence of lysolecithin but not in buffer leads to the conclusion that bombesin can associate into the lipid matrix.

Fluorescence spectral resolution of myelin basic protein conformers in complexes with lysophosphatidylcholine

The structure of (Deibler) myelin basic protein in solution and in a lysolecithin++ lipid complex has been studied by using the emission properties of the single tryptophan residue of the protein (Trp-115). The studies have been carried out using both static and time-resolved fluorescence techniques. Relative to the free protein, the lipid bound myelin basic protein showed a twofold increase in fluorescence intensity and a marked blue-shift in the emission maximum wavelength. The multiexponential fluorescence decays and the decay associated spectra indicated that the protein exists in at least three different conformations both in buffer and in lipids. Fluorescence polarization and acrylamide quenching experiments showed that the tryptophan containing region of the protein is embedded in the lipid matrix. The binding of the protein to the lipid appears to be comparable with that predicted for the interaction of amphipathic helices with nonpolar lipids.

Long-wavelength fluorescence of tyrosine and tryptophan: a classic example of second order diffraction

The recent report of long-wavelength fluorescence of tyrosine and tryptophan solutions [Macias et al. (1987) Biochem. Int. 15, 961-969] prompted an investigation to confirm its authenticity. Similar excitation and emission spectra were recorded in the absence of any filters, but completely disappeared when a 370 nm non-fluorescent cut-off filter was placed between the excitation monochromator and the sample. These results demonstrate that excitation spectra above 400 nm and emission spectra above 550 nm originate from second order diffraction effects.

Lipid-induced changes in the secondary structure of snake venom cardiotoxins

The secondary structures of three snake venom cardiotoxins (from Hemachatus hemachatus, Naja naja atra, and Naja naja naja), in aqueous solution and in a lipid-bound form, were investigated by Fourier-transform infrared spectroscopy. The conformation-sensitive protein infrared bands in the amide I region were analyzed using deconvolution and band-fitting procedures. The spectra of the three cardiotoxins in aqueous buffer are very similar; they indicate a high content of both antiparallel beta-sheet structure and unordered conformation. Moreover, component bands characteristic of turns can also be identified. The binding of cardiotoxins to bilayers of dimyristoylphosphatidyl-glycerol results in an increased content of a beta-structure at the expense of the nonordered conformation. It is suggested that lipid-induced conformational transitions to a beta-structure, similar to that observed with cardiotoxins, may be operative also in membrane interaction of other proteins and peptides, particularly with those which have a small tendency to form alpha-helices.

Conformational properties of azurin in solution as determined from resolution-enhanced Fourier-transform infrared spectra

Infrared spectra of the blue copper protein azurin and of apoazurin from P. fluorescens were obtained in aqueous solution. Using resolution enhancement procedures, a number of component bands were identified in the region of the amide I mode, and these bands were assigned to various components of protein secondary structure. A quantitative analysis of these infrared spectra indicates that the secondary structure of P. fluorescens azurin in solution is very similar to those determined previously by X-ray diffraction for the crystals of azurins from other bacterial species. The major components of this structure are beta strands and turns. Infrared spectra also evince a remarkable thermal stability of the native azurin. A significant unfolding of the protein could only be detected at temperatures above approximately 76 degrees C. While the secondary structure of apoazurin is practically indistinguishable from that of the native protein at room temperature, the thermal stability of the apo form is significantly reduced.

Relation between Ca2+ uptake and fluidity of brush-border membranes isolated from rabbit small intestine and incubated with fatty acids and methyl oleate

The rate of incorporation of oleic acid into isolated brush-border membranes was found to be considerably faster than methyl oleate incorporation under similar experimental conditions. The effects of fatty acids and methyl oleate incorporation on Ca2+ uptake and fluidity were monitored. Whereas treatment with 0.01-0.05 mM oleic acid corresponding to incorporations smaller than 90 nmol/mg protein enhanced Ca2+ transport, exposures to higher concentrations of this fatty acid corresponding to incorporations larger than 150 nmol/mg protein, decreased uptake of this cation. On the other hand, treatment with 0.01-0.2 mM methyl oleate corresponding to incorporations of up to 220 nmol/mg protein had only a stimulatory effect on the Ca2+ uptake. Oleic acid, linoleic acid and methyl oleate decreased the fluorescence anisotropy of membranes labelled with diphenylhexatriene in a dose-dependent manner. In contrast, palmitic acid had little or no effect on the diphenylhexatriene-reportable order of the membrane within the range of concentrations used. Monitored as a function of temperature, the anisotropy values showed a gradual melting for both the control and lipid-treated membranes. The results support the concept that saturated and cis-unsaturated fatty acids dissolve in different lipid domains and this in itself appears to be an important factor defining whether the biological function of the membrane is affected by the uptake. Incorporation of cis-unsaturated fatty acids in domains harboring the Ca2+ uptake process increases Ca2+ uptake in concert with increased diphenylhexatriene-monitored fluidity. However, when concentrations of such fatty acids in these domains become sufficiently great, the presence of a largely increased number of free carboxyl groups at the membrane surface causes inhibition of Ca2+ uptake.

Conformational flexibility of the hormonal peptide bombesin and its interaction with lipids

The conformational flexibility of the tetradecapeptide hormone bombesin has been studied using circular dichroism and fluorescence of its single tryptophan residue. The spectral changes observed indicate that the peptide changed from a random flexible coil in solution to a helical structure in lysolecithin micelles and dimyristoylphosphatidylserine vesicles. The tryptophan residue in the lipid complexes was located in a hydrophobic environment. The interaction with lipids was shown to involve both hydrophobic and electrostatic forces.

Tryptophan interactions of gramicidin A' channels in lipids: a time-resolved fluorescence study

The evolution of the incorporation of cation transport channels into lysolecithin micelles by gramicidin A was followed by measuring the ns time-resolved fluorescence of the tryptophan residues. In all samples, the tryptophan fluorescence could be resolved into three exponentially decaying components. The three decay times ranged from 6 to 8 ns, 1.8 to 3 ns, and 0.3 to 0.8 ns, depending on the emission wavelength. The fractional fluorescence of each component changed with incubation time. The long lifetime component had a reduced contribution to the total fluorescence while the short decay time component increased. The fluorescence spectra could be resolved into three distinct fluorescent components having maxima at 340 nm, 330 nm and 323 nm after 90 min of incubation, and 335 nm, 325 nm and 320 nm after 24 h of incubation. These maxima were, respectively, associated with the long, medium and short decay components. The fluorescence decay behaviour was interpreted as representing three families of tryptophans, the short lifetime component being due to a stacking interaction between tryptophan residues. The variation with incubation time suggests a two-step process in the channel-lipid organization. The first is associated with the conformational change of the polypeptide as it takes up a left-handed helical head-to-head dimer structure in the lipid. The second step is proposed to involve changes originating from membrane assembly and intermolecular interactions between channels as they form hexameric clusters.

Studies on calcium binding to brush-border membranes from rabbit small intestine

A study was made of the uptake of Ca2+ by brush-border membrane vesicles prepared from rabbit small intestine. The process was found to be time, temperature and substrate concentration dependent, displayed saturability, did not depend on added energy sources and occurred optimally in a pH range of 7.5-8.0. Although the transport of D-glucose by these membrane vesicles responded to changes in osmotic pressure as modified by adding cellobiose to the medium, the uptake of Ca2+ was found not to be osmotically-sensitive. Moreover, the equilibrium uptake value obtained when vesicles were exposed to 0.36 mM Ca2+ was some 60-fold higher than the amount that could have been accommodated by the intravesicular space, calculated from the equilibrium uptake of D-glucose. It was concluded from these results that the uptake involved complete binding of the Ca2+ to the membrane. The ionophore A23187 enhanced the rates of uptake and efflux of Ca2+ without affecting equilibrium values, which suggests that the binding of Ca2+ measured under our conditions was to interior sites of the membrane. The binding capacity was decreased in the presence of 10 mM lidocaine as indicated by a diminution of the equilibrium binding values. Generating an electrochemical potential (negative inside) by addition of valinomycin to vesicles pre-equilibrated with K2SO4, enhanced the rate of uptake of Ca2+. Addition of metal ions, on the other hand, inhibited the uptake, La3+ and Tb3+ being most effective followed by Mn2+, Ba2+ and Mg2+. Na+ and K+ were the least inhibitory. The properties of the Ca2+ uptake process found in rabbit brush-border membranes were compared to those of similar processes occurring in other species.

A fluorescence decay time study of tryptophan in isolated hemoglobin subunits

The time-resolved fluorescence behavior of tryptophan residues in isolated human hemoglobin subunits was determined using a sync-pumped dye laser system and time-correlated single photon counting detection. Two decay components having values near 80 ps and 2 ns were found in the fluorescence decay of the alpha-subunit. The data for the beta-chains were best fitted with 3 decay components of 90 ps, 2.5 ns and 6.4 ns. We propose that the decay times correspond to conformations of the proteins in which the disposition of the tryptophan to the heme residue differs.

Conformational changes induced by binding of bivalent cations to oncomodulin, a paravalbumin-like tumour protein

When Mg2+ was added to rat oncomodulin, a paravalbumin-like tumour protein, changes in the c.d. spectrum and tyrosine fluorescence intensity were observed. The addition of Ca2+ resulted in even greater changes in these spectra. The fluorescence excitation spectra of apo- and Mg-oncomodulin were superimposable, whereas that of Ca-oncomodulin was markedly different. The u.v.-absorption spectrum of the Ca2+ form also showed major differences from those of the other two forms. These observations indicate that Ca2+ induced a significant and specific conformational change in the protein that was not observed on binding Mg2+. In contrast, the conformational change induced by either Mg2+ or Ca2+ was identical in the homologous rat parvalbumin. This Ca2+-specific conformational change may be the basis for oncomodulin's Ca2+-dependent protein/protein interaction.

Conformational heterogeneity of the copper binding site in azurin. A time-resolved fluorescence study

Comparison of the fluorescence spectra and the effect of temperature on the quantum yields of fluorescence of Azurin (from Pseudomonas fluorescens ATCC-13525-2) and 3-methylindole (in methylcyclohexane solution) provides substantive evidence that the tryptophan residue in azurin is completely inaccessible to solvent molecules. The quantum yields of azurin (CuII), azurin (CuI), and apoazurin (lambda ex = 291 nm) were 0.052, 0.054, and 0.31, respectively. Other evidence indicates that there is no energy transfer from tyrosine to tryptophan in any of these proteins. The fluorescence decay behavior of each of the azurin samples was found to be invariant with emission wavelength. The fluorescences of azurin (CuII) and azurin (CuI) decay with dual exponential kinetics (tau 1 = 4.80 ns, tau 2 = 0.18 ns) while that of apoazurin obeys single exponential decay kinetics (tau = 4.90). The ratio of pre-exponentials of azurin (CuII), alpha 1/alpha 2, is found to be 0.25, and this ratio increases to 0.36 on reduction to azurin (CuI). The results are interpreted as originating from different interactions of the tryptophan with two conformers of the copper-ligand complex in azurin.

Studies on fluorescence polarization of 1-acyl-2-cis- or trans-parinaroyl sn-3-glycerophosphorylcholines in model systems and microsomal membranes

Fluorescent lecithin probes containing cis- or trans-parinaric acid (PnA) at the 2-position cis-parinaroylphosphatidylcholine (cis-PnPC) and trans-parinaroyl phosphatidylcholine (trans-PnPC)) showed similar behavior to that of the free cis- or trans-parinaric acids (cis-PnA or trans-PnA) in bilayer vesicles of synthetic saturated lecithins. Transition temperatures detected by cis-PnPC were about 1 degree C than those observed with trans-PnPC. In mixed lecithin vesicles, the trans-PnPC probe monitored a higher temperature melting component than did the cis-probe. Both probes were readily incorporated into microsomal membranes and into sonicated vesicles prepared from the microsomal phospholipids. With either cis- or trans-PnPC no change in polarization ratio was observed for microsomal membranes between 40 degrees C and 0 degrees C but this ratio increased with decreasing temperature between 0 degrees C and -5 degrees C. However, vesicles of extracted phospholipids showed a continuous increase in polarization ratio with decreasing temperature between 20 degrees C and -15 degrees C with trans-PnPC and between 5 degrees C and -15 degrees C with cis-PnPC. These results suggest that the two lecithin probes monitor different environments in the membranes and phospholipid vesicles prepared from them.