A time-resolved fluorescence study of 4',6'-diamidine-2-phenylindole dihydrochloride binding to polynucleotides

At phosphate/dye (P/D) ratios greater than 30 the quantum yield of 4',6'-diamidine-2-phenylindole dihydrochloride (DAPI)-DNA and DAPI-poly(d(A-T)) complexes was found to be 0.62 and 0.66, respectively. Contrary to earlier reports a fluorescence enhancement of DAPI-poly(d(G-C)) complexes was observed with a quantum yield of 0.22. Time-resolved fluorescence measurements of complexes with a P/D ratio of 150:1 indicate that there were three fluorescent components in DAPI-DNA complexes with lifetimes of 3.86, 1.79 and 0.13 ns. In DAPI-poly(d(A-T)) complexes the lifetimes were 3.91, 1.20 and 0.11 ns. Also, three components with lifetimes of 3.98, 0.87 and 0.12 ns were found in DAPI-poly(d(G-C)) complexes. At low P/D ratios (< 5) another binding form of DAPI was observed which was assigned to the interaction of one or more molecules of DAPI with one previously bound to DNA. It is concluded that DAPI does not exhibit A-T binding specificity and that at high P/D ratios there are two types of binding having similar binding constants.

Internal motion of lysozyme studied by time-resolved fluorescence depolarization of tryptophan residues

The internal motion of lysozyme was described by the steady-state and time-resolved fluorescence anisotropy of its tryptophan residues. The fluorescence of mutant lysozymes W62Y- and W108Y-lysozyme, in which Trp62 or Trp108 of hen egg white lysozyme was replaced with a tyrosine residue, could be respectively assigned to Trp108 or Trp62 at the longer wavelength region of the total fluorescence spectrum. The segmental motion of Trp62 as shown by its fluorescence anisotropy decay was described with two components originating from the fluctuational rotation of an indole moiety about the Calpha-Cbeta bond and rotational wobble of the peptide segment adjacent to Trp62. Although Trp62 showed a high degree of motional freedom, its motion was significantly suppressed by the interaction of the mutant protein with a trimer of N-acetyl-D-glucosamine. By contrast, the segmental motion of Trp108 is hindered by the local cage structure at temperatures below 30 degreesC, but Relief from restricted motion occurred on the formation of ligand complex or by thermal agitation. Because of overlaps of the fluorescence spectrum, it is difficult to assign the segmental motion of Trp28 or Trp111, the other two tryptophan residues in lysozyme. However, a careful analysis of the fluorescence anisotropy decay of W62Y- and W108Y-lysozyme showed that the fluctuation of the hydrophobic matrix box was greater than that expected from lysozyme's crystal structure, although it was suppressed by the binding of the ligand to the active site of lysozyme.

Preparation of enantiomerically pure L-7-azatryptophan by an enzymatic method and its application to the development of a fluorimetric activity assay for tryptophanyl-tRNA synthetase

The reaction of D,L-7-azatryptophan (D,L-7AW) with tryptophanyl-tRNA synthetase (TrpRS), adenosine triphosphate (ATP), and Mg2+ in the presence of inorganic pyrophosphatase results in the formation of a highly fluorescent l-7AW-adenylate complex. Detection of this complex is based on its enhanced fluorescence at 315 nm excitation and 360 nm emission after the addition of ATP. This stereoselective reaction was used to develop an activity assay for TrpRS using commercially available racemic D,L-7AW. The assay can be used to determine the activity of TrpRS from samples which contain less than 1 nmol of enzyme in 250 microL of sample. Thus the enzyme activity can be assessed without resorting to a radioactive assay of tRNATrp acylation. A secondary use of the stereoselective assay was for confirming the presence of pure L-7AW, D-7AW, or mixtures of the two enantiomers. D-7AW and L-7AW were prepared by reacting D,L-7AW with chloroacetic anhydride to form N-chloroacetyl-D,L-7AW (ClAc-7AW) followed by stereospecific proteolytic digestion of ClAc-7AW using carboxypeptidase A to produce the free L-7AW. The L-7AW could be separated from unreacted N-chloroacetyl-7AW by reverse-phase HPLC. The TrpRS-based assay was able to unambiguously discriminate between the two enantiomers of 7AW. The assay was then used to identify which enantiomer of 7AW was present in resolved fractions of the tripeptide L-lysyl-D,L-7-azatryptophyl-L-lysine. Digestion of the resolved tripeptides with protease enzymes produced the free L or D enantiomer of 7AW, which was easily identified using the TrpRS assay procedure.

Primary Sequence and Refined Tertiary Structure ofPseudomonas fluorescensHolo Azurin at 2.05 Å

This paper reports the primary sequence and refined crystal structure of Pseudomonas fluorescens holoazurin. The crystal structure has been determined by molecular replacement on the basis of the molecular model of azurin from Alcaligenes denitrificans, and refined by the method of molecular dynamics simulation and energy-restrained least-squares methods. P. fluorescens was crystallized in the orthorhombic space group P2(1)2(1)2(1) with unit-cell dimensions a = 31.95, b = 43.78, c = 78.81 A. The asymmetric unit is composed of only one molecule. The final R value is 16.7% for 6691 reflections to a resolution of 2.05 A. This azurin structure shows some interesting features at His35 and His83. Part of the main chain of strand 3 including His35 O are involved in the contact between two symmetrically related molecules. P. fluorescens is also compared with the other azurin structures in terms of primary sequence, crystal packing, solvent structure and Cu-site geometry. The difference in fluorescence decay behavior of two holoazurins from P. fluorescens and P. aeruginosa and the correlation between the fluorescence quenching and electron transfer are discussed.

Identification of a chameleon-like pH-sensitive segment within the colicin E1 channel domain that may serve as the pH-activated trigger for membrane bilayer association

In vitro, the channel-forming domain of colicin E1 requires activation by acidic pH (<4.5) or detergents. The activation of this domain to its insertion-competent state results in an increased ability of the protein to dock onto and to form channels in artificial membranes. Fluorescence methods were used to characterize the conformational changes occurring in a channel-forming peptide of colicin E1 in solution with pH. The 178-residue thermolytic fragment of colicin E1 contains three Trp residues, W-424, W-460, and W-495. In order to study the structural and dynamic requirements for activation of the C-terminal domain of colicin E1, single-Trp-containing peptides were prepared by site-directed mutagenesis. All of the mutant peptides displayed in vitro channel activity and cellular cytotoxicity similar to the those of wild-type peptide. Two Trp residues, W-413 and W-424, exhibited pH-sensitive fluorescence parameters. Upon acidification (pH 6.0 --> 3.5), the fluorescence quantum yield of W-413 and W-424 increased 50% and 80%, respectively, indicating a significant change in the local environment of the peptide segment containing these two Trp residues. The fluorescence decay of W-413 and W-424 was best fit by three fluorescence decay components, two of which were sensitive to pH. However, only small changes in spectral shape and position were observed for W-424 fluorescence, whereas there were larger changes in these fluorescence parameters for W-413. The quantum yields for the Trp residues in the seven other single-Trp mutant peptides and the wild-type peptide were distinct but only slightly affected by changes in pH. Time-resolved fluorescence measurements showed that W-460, -484, and -495 each had two fluorescence decay components with similar decay times, with one component dominating the fluorescence decay behavior. Furthermore, the individual fluorescence decay times for all the single-Trp peptides, except for W-413 and W-424, were insensitive to pH changes. At pH 3.5, the fluorescence of the wild-type peptide was fit by three decay time components, with the two longer decay times being quite different from the fluorescence decay times of the single-Trp mutant proteins (W-424, -460, and -495, the naturally occurring Trp residues). In contrast, at pH 6.0, the wild-type peptide showed double-exponential decay kinetics. Time-resolved fluorescence anisotropy decay measurements of the three single-Trp mutant proteins, containing a naturally occurring Trp residue, suggest that local segmental motion of the peptide as reported by each of the three tryptophans is highly restricted and largely insensitive to changes in pH. On the other hand, the anisotropy decay profiles of the wild-type protein were consistent with energy transfer occurring between Trp residues, likely between W-460 and W-495. These steady-state and time-resolved fluorescence results show that W-413 and W-424 report conformational changes which may be associated with the insertion-competent state and reside on the protein segment(s) which form the pH-activated trigger of the channel peptide.

Site-specific replacement of amino acid residues in the CD site of rat parvalbumin changes the metal specificity of this Ca2+/Mg(2+)-mixed site toward a Ca(2+)-specific site

Rat parvalbumin (PV) and oncomodulin (OM) display considerable sequence similarity and structural similarity, but differ in the affinity and selectivity of metal binding to their CD site, a Ca2+/Mg(2+)-mixed site in PV and a Ca(2+)-specific site in OM. In an attempt to identify the structural basis for these differences, mutations were introduced in the previously generated [W102]PV mutant, which contains a unique tryptophan as a conformational-sensitive fluorescent probe inside the hydrophobic core. In the present report, we substituted selected amino acid residues in the CD site of PV by those present at identical positions in OM. One mutant protein, named [F66, W102]PV, has one new substitution in which isoleucine at position 66 was exchanged by phenylalanine. The second mutant protein, [I46, I50, L58, F66, W102]PV, has four new substitutions, namely V46-->I, L50-->I, I58-->L and I66-->F. Tryptophan fluorescence and difference spectrophotometry indicated that the mutations do not alter significantly the hydrophobic core. Both mutant proteins display two metal-binding sites of identical affinities with intrinsic affinity constants K'Ca2+ of 2.9 x 10(7) M-1 for [F66, W102]PV and 1.7 x 10(7) M-1 for [I46, I50, L58, F66, W102]PV and K'Mg2+ of 3.1 x 10(4) M-1 for [F66, W102]PV and 1.9 x 10(4) M-1 for [I46, I50, L58, F66, W102]PV. Thus, the five-residue substitution, but not the two-residue one, leads to a small decrease of affinity compared to [W102]PV (K'Ca2+ = 2.7 x 10(7) M-1, K'Mg2+ = 4.4 x 10(4) M-1). Despite these similarities, the Mg2+ effect on Ca2+ binding is different for the two mutant parvalbumins: the Ca(2+)-binding isotherms of [F66, W102]PV undergo a parallel shift upon increasing Mg2+ concentrations, which indicates that the Mg2+ effect on the two Ca(2+)-binding sites is the same and quantitatively very similar to that described for [W102]PV. In [I46, I50, L58, F66, W102]PV, Mg2+ antagonizes the binding of the second Ca2+ (likely at the EF site) much more than that of the first Ca2+ (likely the CD site). According to the competition equation, the two sites display KMg2+.compet values of 390 M-1 and 3.9 x 10(3) M-1, respectively. These data indicate that (a) the single I66-->F mutation does not modify the cation binding parameters. (b) Multiple modifications in the hydrophobic core still do not change the affinity for Ca2+ and Mg2+, but strongly affect the Mg2+ antagonism and probably the selectivity of the CD site.

A concerted tryptophanyl-adenylate-dependent conformational change in Bacillus subtilis tryptophanyl-tRNA synthetase revealed by the fluorescence of Trp92

A semi-conserved tryptophan residue of Bacillus subtilis tryptophanyl-tRNA synthetase (TrpRS) was previously asserted to be an essential residue and directly involved in tRNATrp binding and recognition. The crystal structure of the Bacillus stearothermophilus TrpRS tryptophanyl-5'-adenylate complex (Trp-AMP) shows that the corresponding Trp91 is buried and in the dimer interface, contrary to the expectations of the earlier assertation. Here we examine the role of this semi-conserved tryptophan residue using fluorescence spectroscopy. B. subtilis TrpRS has a single tryptophan residue, Trp92. 4-Fluorotryptophan (4FW) is used as a non-fluorescent substrate analog, allowing characterization of Trp92 fluorescence in the 4-fluorotryptophanyl-5'-adenylate (4FW-AMP) TrpRS complex. Complexation causes the Trp92 fluorescence to become quenched by 70%. Titrations, forming this complex under irreversible conditions, show that this quenching is essentially complete after half of the sites are filled. This indicates that a substrate-dependent mechanism exists for the inter-subunit communication of conformational changes. Trp92 fluorescence is not efficiently quenched by small solutes in either the apo- or complexed form. From this we conclude that this tryptophan residue is not solvent exposed and that binding of the Trp92 to tRNATrp is unlikely. Time-resolved fluorescence indicates conformational heterogeneity of B. subtilis Trp92 with the fluorescence decay being best described by three discrete exponential decay times. The decay-associated spectra (DAS) of the apo- and complexed-TrpRS show large variations of the concentration of individual fluorescence decay components. Based on recent correlations of these data with changes in the local secondary structure of the backbone containing the fluorescent tryptophan residue, we conclude that changes observed in Trp92 time-resolved fluorescence originate primarily from large perturbations of its local secondary structure. The quenching of Trp92 in the 4FW-AMP complex is best explained by the crystal structure conformation, in which the tryptophan residue is found in an alpha-helix. The amino acid residue cysteine is observed clearly within the quenching radius (3.6 angstroms) of the conserved tryptophan residue. These tryptophan and cysteine residues are neighbors, one helical turn apart. If this local alpha-helix was disrupted in the apo-TrpRS, this disruption would concomitantly relieve the putative cysteine quenching by separating the two residues. Hence we propose a substrate-dependent local helix-coil transition to explain both the observed time-resolved and steady-state fluorescence of Trp92. A mechanism can be further inferred for the inter-subunit communication involving the substrate ligand Asp132 and a small alpha-helix bridging the substrate tryptophan residue and the conserved tryptophan residue of the opposite subunit. This putative mechanism is also consistent with the observed pH dependence of TrpRS crystal growth and substrate binding. We observe that the mechanism of TrpRS has a dynamic component, and contend that conformational dynamics of aminoacyl-tRNA synthetases must be considered as part of the molecular basis for the recognition of cognate tRNA.

Steady-state and time-resolved fluorescence studies on the ligand-induced conformational change in an active lysozyme derivative, Kyn62-lysozyme

The ligand-induced conformational change of an active lysozyme derivative, Kyn62-lysozyme, in which Trp62 of hen egg-white lysozyme (EC 3.2.1.17) was selectively modified to kynurenine, was investigated by steady-state and time-resolved fluorescence spectroscopy. Kyn62 formed an intramolecular energy transfer donor-acceptor pair with a tryptophan residue as a donor. The energy transfer was related to the conformation of the active site. The spectral overlap integral (J) of the kynurenine-tryptophan pair is large as it was determined to be 4.92 x 10(-15) M-1 cm3. Time-resolved fluorescence properties of Kyn62-lysozyme and its complex with a trimer of N-acetyl-D-glucosamine [(GlcNAc)3] show that the energy donor is Trp28 or Trp111 in the hydrophobic matrix box of the free Kyn62-lysozyme. In the complex, it appears that the kynurenine residue drastically changed its orientation or approached closer to Trp108 to accept more efficiently the excitation energy from Trp108 on the binding of Kyn62-lysozyme with (GlcNAc)3.

Probing local secondary structure by fluorescence: time-resolved and circular dichroism studies of highly purified neurotoxins

The relationship between beta-sheet secondary structure and intrinsic tryptophan fluorescence parameters of erabutoxin b, alpha-cobratoxin, and alpha-bungarotoxin were examined. Nuclear magnetic resonance and x-ray crystallography have shown that these neurotoxins have comparable beta-sheet, beta-turn, and random coil secondary structures. Each toxin contains a single tryptophan (Trp) residue within its beta-sheet. The time-resolved fluorescence properties of native erabutoxin b and alpha-cobratoxin are best described by triple exponential decay kinetics, whereas native alpha-bungarotoxin exhibits more than four lifetimes. The disulphide bonds of each toxin were reduced to facilitate carboxymethylation and amidocarboxymethylation. The two different toxin derivatives of all three neurotoxins displayed triple exponential decay kinetics and were completely denatured as evidenced by circular dichroism (random coil). The concentration (c) values of the three fluorescence decay times (time-resolved fluorescence spectroscopy (TRFS)) were dramatically different from those of the native toxins. Each neurotoxin, treated with different concentrations of guanidinium hydrochloride (GuHCl), was studied both by circular dichroism and TRFS. Disappearance of the beta-sheet secondary structural features with increasing concentrations of GuHCl was accompanied by a shift in the relative contribution (c value) of each fluorescence decay time (TRFS). It was found that certain disulphide residues confer added stability to the beta-sheet secondary structure of these neurotoxins and that the center of the beta-sheet is last to unfold. These titrations show that Trp can be used as a very localized probe of secondary structure.

Bifunctional fusion proteins consisting of a single-chain antibody and an engineered lanthanide-binding protein

The combination of an antibody fragment with a lanthanide chelating protein has desirable characteristics for fluorescence-based immunoassays and tumor radioimmunotherapy. As a model for this design, a fusion protein consisting of a single-chain antibody linked to an engineered version of oncomodulin, a protein with two Ca(2+)-binding motifs (the CD and EF loops), was produced by secretion from Escherichia coli in good yield. The single-chain antibody was specific for a Salmonella O-polysaccharide. The CD loop of oncomodulin had been redesigned to bind lanthanide ions with high affinity. The fusion protein was shown to have antigen-binding activity that was comparable to that of the unfused single-chain antibody, to bind Tb3+ with very high affinity and to give strong, sensitized Tb3+ luminescence via excitation of the tryptophan residue in the CD loop. A second fusion protein containing a 30-residue helix-loop-helix motif as the lanthanide-binding component was also prepared, but showed considerably lower solubility. Competition for Tb3+ binding by a series of metal chelators indicated that the affinities of the oncomodulin and 30 residue fusions for Tb3+ were approximately 10(11) M-1 and 10(7) M-1, respectively. Time-resolved lanthanide luminescence photography of electrophoresis gels demonstrated that the helix-loop-helix Ca(2+)-binding could be used to specifically visualize the scFv fragment.

A protease assay using time-resolved lanthanide luminescence from an engineered calcium binding protein substrate

OBJECTIVES

The objective of this work was to demonstrate the utility of luminescence from lanthanides bound to a mutant of the Ca2+ binding protein, oncomodulin, to monitor protease activity.

DESIGN AND METHODS

A mutant of oncomodulin with a cysteine residue at position 57 located in the CD binding loop was conjugated to a salicylic acid group. The luminescence of Tb3+ resulting from electronic energy transfer from the salicylic acid group was monitored using time resolved lanthanide luminescence in the presence of proteolytic enzymes.

RESULTS

Low detection limits for subtilisin (150 pg), chymotrypsin (2.5 ng), cathepsin B (3.5 ng), and HIV-1 protease (25 ng) were found.

CONCLUSION

The simplicity of the assay coupled with its high level of sensitivity make it useful for the detection of protease at very low concentrations.

Location of diphenyl-hexatriene and trimethylammonium-diphenyl-hexatriene in dipalmitoylphosphatidylcholine bilayers by neutron diffraction

Neutron scattering experiments have been performed on oriented dipalmitoylphosphatidylcholine (DPPC) bilayers containing diphenylhexatriene (DPH) or its trimethylammonium analog (TMA-DPH). DPH and TMA-DPH were either protonated or deuterated in one of the phenyl rings which afforded by using proton-deuterium contrast methods the location of these fluorescent probes in the model membrane. Both probes exhibit bimodal distributions in DPPC. The position, population and orientation in the two sites vary depending upon the physical state of the bilayer (gel or fluid) and the presence or absence of the TMA group. In gel (L beta') phase lipids DPH is located close and parallel to the bilayer surface (site I) and near the bilayer center, oriented at approximately 30 degrees with respect to the normal to the surface (site II). On going to the fluid (L alpha) phase, a distribution of orientations around the parallel to the surface is only observed for site II. Orientation of DPH in site I is unchanged. In the gel phase TMA-DPH is found in a position close and parallel to the bilayer surface (site I) and in a position (site II) oriented at an angle of approximately 25 degrees with respect to the bilayer normal, with the trimethylammonium group anchored in the head group domain. On going to the fluid phase there is a change in molecular orientation of each of the sites. In site I the molecule penetrates deeper in the bilayer and adopts a approximately 20 degrees tilt with respect to the surface, with an orientational distribution of +/- 10 degrees. In site II the molecule becomes perpendicular to the membrane surface. Changes in population of sites, both with DPH and TMA-DPH, are observed on going from low to high temperatures. They are however difficult to quantitate due to experimental conditions. The H2O-2H2O exchange experiments afforded an estimate of the water layer thickness as well as the maximum penetration of water into the interior of the bilayer.

Probing alpha-helical secondary structure at a specific site in model peptides via restriction of tryptophan side-chain rotamer conformation

The relationship between alpha-helical secondary structure and the fluorescence properties of an intrinsic tryptophan residue were investigated. A monomeric alpha-helix forming peptide and a dimeric coiled-coil forming peptide containing a central tryptophan residue were synthesized. The fluorescence parameters of the tryptophan residue were determined for these model systems at a range of fractional alpha-helical contents. The steady-state emission maximum was independent of the fractional alpha-helical content. A minimum of three exponential decay times was required to fully describe the time-resolved fluorescence data. Changes were observed in the decay times and more significantly, in their relative contributions that could be correlated with alpha-helix content. The results were also shown to be consistent with a model in which the decay times were independent of both alpha-helix content and emission wavelength. In this model the relative contributions of the decay time components were directly proportional to the alpha-helix content. Data were also analyzed according to a continuous distribution of exponential decay time model, employing global analysis techniques. The recovered distributions had "widths" that were both poorly defined and independent of peptide conformation. We propose that the three decay times are associated with the three ground-state chi 1 rotamers of the tryptophan residue and that the changes in the relative contributions of the decay times are the result of conformational constraints, imposed by the alpha-helical main-chain, on the chi 1 rotamer populations.

Myelin basic protein interaction with zinc and phosphate: fluorescence studies on the water-soluble form of the protein

The interaction of myelin basic protein (MBP) with zinc and phosphate ions has been studied by using the emission properties of the single tryptophan residue of the protein (Trp-115). The studies have been carried out by means of both static and time-resolved fluorescence techniques. The addition of either zinc to MBP in the presence of phosphate or phosphate to MBP in the presence of zinc resulted in an increase of fluorescence intensity and a blue shift of the emission maximum wavelength. Furthermore, a concomitant increase in the scattering was also detected. Anisotropy decay experiments demonstrated that these effects are due to the formation of MBP molecules into large aggregates. A possible physiological role for such interaction is discussed.

Detection of calcium binding proteins on polyacrylamide gels using time-resolved lanthanide luminescence photography

Methods were developed for using the luminescent lanthanides Tb3+ and Eu3+ for the specific staining of calcium-binding proteins, as well as the nonspecific staining of proteins, on polyacrylamide gels. These methods involve equilibration of the gel after electrophoresis in solutions containing the appropriate lanthanide and a weak competitive chelating agent, such as N-(2-hydroxyethyl)iminodiacetic acid or nitrilotriacetic acid. This staining has the potential for complete reversibility using stronger chelating agents such as EDTA or diethylenetriaminepentaacetic acid, to allow for recovery of the protein. Specific staining produces an intense luminescent signal from those metal-binding proteins which have been modified either chemically or via site-directed mutagenesis. Gels were photographed using a time-resolved fluorescence camera system.

Crystallization and preliminary crystallographic studies of the crystals of the azurin Pseudomonas fluorescens

The Azurin Pseudomones fluorescens has been crystallized in the presence of ammonium sulfate and Tris buffer at pH 7.5. The crystals diffract to 2.05 A using a FAST system. The space group is P2(1)2(1)2(1) with a = 31.95, b = 43.78, and c = 78.81 A.

Characterization of aminoacyl-adenylates in B. subtilis tryptophanyl-tRNA synthetase, by the fluorescence of tryptophan analogs 5-hydroxytryptophan and 7-azatryptophan

The tryptophan analogs 5-hydroxytryptophan (5HW) and 7-azatryptophan (7AW) are capable of being biosynthetically incorporated into bacterial proteins and can be used as intrinsic fluorescence probes of protein structure, function and dynamics. A prerequisite for analog incorporation is their recognition by tryptophanyl-tRNA synthetase (TrpRS) and the formation of the analog aminoacyladenylate in the enzyme's active site. The binding of 5HW and 7AW to B. subtilis TrpRS and the stability of the corresponding aminoacyladenylates of 5HW and 7AW were examined using their unique spectroscopic properties. The adenylate of 7AW in the active site of TrpRS exhibited intense fluorescence with a 10.5 ns fluorescence decay time. Enzyme-bound 7AW-adenylate was a long-lived intermediate with a half-life of over 9 hours. Enzyme-bound 5HW-adenylate fluorescence was quenched compared to that of 5HW in solution. The 5HW-adenylate/TrpRS complex was much less stable than that of 7AW, with a half-life of 33 minutes. Rapid hydrolysis of the 5HW-adenylate may explain the apparent proofreading observed which prohibits 5HW incorporation into proteins in the presence of tryptophan. Hydrolysis of the adenylates of both analogs restored the fluorescence parameters towards those of the analogs in solution. Neither 1-methyltryptophan nor 5-methoxytryptophan were capable of forming long-lived aminoacyladenylate intermediates in TrpRS. This study provides perspectives on the usefulness of 5HW and 7AW as intrinsic fluorescence probes of protein structure. The enhanced fluorescence of 7AW suggests its location in a buried hydrophobic environment in the protein. Exposure to water results in significant fluorescence quenching. These studies clearly demonstrate the utility of Trp analogs for the elucidation of molecular details of protein structure and dynamics.

Structure-activity correlations of melanotropin peptides in model lipids by tryptophan fluorescence studies

Steady-state and time-resolved fluorescence spectroscopy were employed in the study of the structure and interactions of alpha-MSH (alpha-melanocyte-stimulating hormone) and its analogs, [Nle4,D-Phe7]-alpha-MSH (MSH-I) and Ac-[Nle4,Asp5,D-Phe7,Lys10]-alpha-MSH(4-10)-NH2 (MSH-II). In aqueous buffer, the fluorescence parameters of the single tryptophan of alpha-MSH and MSH-I were similar and did not allow any distinction between these molecules. On the other hand, the tryptophan fluorescence of MSH-II was notably different, reflecting its cyclic lactam turn structure. In the presence of acidic lipid vesicles, the fluorescence properties of the peptides were different, indicating structural changes on incorporation of the peptide into the liquid-crystalline phase of the lipid. No evidence of interaction was observed in the presence of the neutral lipid dimyristoylphosphatidylcholine (DMPC). The association constants for lipid-peptide interactions were compared for binding isotherms which either neglected or accounted for electrostatic effects through Gouy-Chapman potential functions. The relative order of association constants in either treatment was MSH-II > MSH-I > alpha-MSH. These results parallel the reported biological activities that show increased potencies and prolongation of response for the analogs, MSH-II and MSH-I, as compared to the native hormone, alpha-MSH. Time-resolved fluorescence results showed that the fluorescence decay of melanotropins is best described by triple-exponential kinetics. In the lipid-peptide complex, there was a change in the relative concentrations of the components, with the intermediate-lifetime component predominating compared to those in solution.(ABSTRACT TRUNCATED AT 250 WORDS)

A novel peptide designed for sensitization of terbium (III) luminescence

Several synthetic peptides, modelled from a Ca(2+)-binding loop of the EF-hand family of proteins, were prepared containing cysteine residues. The peptide, GDKNADGFICFEEL, was labelled covalently at the cysteine residue (loop position 9) with iodoacetamidosalicylic acid. This novel conjugate is a metal-binding loop containing a salicylic acid side chain that could not only chelate Tb3+ in conjunction with the other chelating groups in the sequence, but could also sensitize Tb3+ luminescence. The loop had a high Tb3+ affinity, with stoichiometric binding observed under experimental conditions. The luminescence from the Tb(3+)-peptide complex was more than 10-fold greater than the luminescence reported from a related peptide which contained Trp as the Tb3+ donor at loop position 7. This peptide has significant potential for use in lanthanide-based time-resolved luminescence immunoassays.

Metal binding properties of recombinant rat parvalbumin wild-type and F102W mutant

Rat parvalbumin (PV), an EF-hand type Ca(2+)-binding protein, was expressed in Escherichia coli and mutated by replacing a Phe at position 102 with a unique Trp in order to introduce a distinct fluorescent label into the protein. Mass spectroscopy and NMR data indicate that the recombinant wild-type (PVWT) and F102W mutant (PVF102W) proteins have the expected molecular weight and retain the native structure. Both proteins contain two non-cooperative Ca2+/Mg(2+)-binding sites with intrinsic affinity constants, KCa and KMg, of 2.4 +/- 0.9 x 10(7) M-1 and of 2.9 +/- 0.2 x 10(4) M-1, respectively, for PVWT, and KCa and KMg, of 2.7 +/- 1.1 x 10(7) M-1 and of 4.4 +/- 0.3 x 10(4) M-1, respectively, for PVF102W. Based on the highly similar metal binding properties of PVWT and PVF102W the latter protein was used to study cation-dependent conformational changes. Trp fluorescence emission and UV difference spectra of PVF102W indicated that the Trp residue at position 102 is confined to a hydrophobic core and conformationally strongly restricted. Upon Ca2+ or Mg2+ binding the structural organization of the region around the Trp is hardly affected, but there are significant changes in its electrostatic environment. The conformational change upon binding of Ca2+ and Mg2+, as monitored by UV difference spectrophotometry, increases linearly from 0 to 2 cations bound, indicating that the binding of both ions contributes equally to the structural organization in this protein.

Self-association of Ca(2+)-binding peptides induced by lanthanide ions: a fluorescence study

In this study a Ca(2+)-binding 14mer peptide was synthesized with the sequence GDKNADGCIEFEEL, allowing covalent attachment of sulfhydryl-reactive fluorescent molecules at position 7 of the 12-residue, metal-binding loop (underlined). This provided the opportunity to select donor molecules with suitable spectral characteristics for sensitized excitation of chelated terbium (Tb3+) or europium (Eu3+) ions. N-(1-Pyrene)-iodoacetamide and 7-diethylamino-3-((4'-iodoacetylamino)phenyl)-4-methylcoumarin were attached to the peptide and titrations carried out with terbium or europium stock solutions. It was possible to observe lanthanide ion binding to the loop in stoichiometric quantities, but maximal lanthanide luminescence was achieved with a large excess of lanthanide present, due to metal-induced peptide association. Obtaining maximal lanthanide luminescence is important in the development of systems for use in sensitive clinical diagnostic and time-resolved luminescence-based immunoassay applications.

Acrylamide quenching of the intrinsic fluorescence of tryptophan residues genetically engineered into the soluble colicin E1 channel peptide. Structural characterization of the insertion-competent state

Colicin E1 or any of its COOH-terminal channel peptides can be activated in vitro by acidic (< 4.5) pH or detergents. In its activated or insertion-competent state, the colicin E1 thermolytic (178 residue) channel peptide demonstrated an increased ability to bind and form channels in artificial membranes. An earlier report [Merrill et al. (1990) Biochemistry 29, 5829-5836] indicated that the structural change occurring in the channel peptide upon activation was not a large unfolding but seemingly involves a more subtle conformational change. To probe the solution structure of the colicin channel peptide and the structural changes occurring upon activation, 12 single-tryptophan-containing mutant peptides have been prepared. All of the peptides displayed cellular cytotoxicity comparable to the wild-type peptide. Fluorescence quenching by acrylamide of each Trp residue genetically engineered into the channel peptide indicated that tryptophyls located at positions 355, 367, 393, 413, and 443 report significant conformational changes which are associated with the insertion-competent state. Calculation of the bimolecular quenching constants for each single-Trp peptide showed that there are three classes of Trp residues found in the native colicin E1 channel peptide. None of the Trp residues were found to be completely inaccessible to acrylamide (buried). The NH2-terminal region near Trp-355 and -367 along with the COOH-terminal hydrophobic domain, including Trp-484, -495, and -507, was largely buried in the channel peptide soluble structure. Two peptide segments, one containing Trp-393, -404, and -413 and a second encompassing Trp-431 and -443, were moderately to very exposed regions in the soluble channel peptide.(ABSTRACT TRUNCATED AT 250 WORDS)

A study of sensitized lanthanide luminescence in an engineered calcium-binding protein

In this study, the CD loop of the Ca(2+)-binding protein oncomodulin was replaced by a high-affinity, metal-binding sequence that was found to reverse the order of fill of the two sites in the protein. A cysteine was included at position 7 of this sequence, i.e., DKNADGCIEFEE. The cysteine allowed covalent attachment of chromophores to the loop that could subsequently be tested for their ability to sensitize the luminescence of Tb3+ or Eu3+ bound in the loop. 7-Diethylamino-3-((4'-iodoacetylamino)phenyl)-4-methylcoumarin was the most efficient Eu3+ sensitizer studied, consistent with a mechanism of energy transfer that involves the triplet state of the donor. 4-Iodoacetamidosalicylic acid was the most efficient Tb3+ donor tested. Levels of lanthanide ion and labeled C3 as low as 5 x 10(-10) mol/liter could be detected. This protein chelator system has potential to be a useful, flexible complement to the organic chelators currently used in lanthanide-based, time-resolved luminescence immunoassays.

Optical absorption and fluorescence spectroscopy studies of ground state melanin-cationic porphyrins complexes

Optical absorption and fluorescence spectroscopies were employed in the study of the interaction between synthetic L-dopa (dihydroxyphenylalanine) melanin and the cationic porphyrins tetrakis(4-N-methylpyridyl) porphyrin (TMPyP), tetrakis(4-N-benzylpyridyl)porphyrin (TBzPyP), zinc tetrakis(4-N-methylpyridyl)porphyrin (ZnTMPyP) and zinc tetrakis (4-N-benzylpyridyl)porphyrin (ZnTBzPyP). Optical absorption and fluorescence properties of the porphyrins were dependent on the symmetry of the central ring. No evidence was found for dimerization of the porphyrins in phosphate buffer, pH 7, in the concentration range between 4 x 10(-8) to 5 x 10(-5) M. Addition of L-dopa melanin red shifted the optical absorption spectra of porphyrins, concomitant to broadening and reduction in intensity of the bands. L-Dopa melanin also strongly quenched the fluorescence of the porphyrins. Time resolution of the fluorescence decay of porphyrins showed at least two lifetimes that were only slightly modified in the presence of melanin. The interaction between melanin and porphyrin resulted in the formation of non-fluorescent ground state complexes. It was found that there are two different classes of binding sites in melanin for complexation with cationic porphyrins and the values of dissociation constants are of the order of 10(-8) M. These values and the number of binding sites are dependent on the nature of the porphyrins. It was shown that the binding has electrostatic origin, but it is also affected by metal coordination and hydrophobic interaction.

A new intrinsic fluorescent probe for proteins. Biosynthetic incorporation of 5-hydroxytryptophan into oncomodulin

The tryptophan analog, 5-hydroxytryptophan (5HW), has a significant absorbance between 310-320 nm, which allows it to act as an exclusive fluorescence probe in protein mixtures containing a large number of tryptophan residues. Here for the first time a method is reported for the biosynthetic incorporation of 5HW into an expressed protein, the Y57W mutant of the Ca2+ binding protein, oncomodulin. Fluorescence anisotropy and time-resolved fluorescence decay measurements of the interaction between anti-oncomodulin antibodies and the 5HW-incorporated oncomodulin conveniently provide evidence of complex formation and epitope identification that could not be obtained with the natural amino acid. This report demonstrates the significant potential for the use of 5HW as an intrinsic probe in the study of structure and dynamics of protein-protein interactions.

Conformation of parathyroid hormone: time-resolved fluorescence studies

Conformational and environmental changes in the functionally significant amino-terminal region of human parathyroid hormone (hPTH), induced by solvent or by complexation with acidic lipid, have been investigated. Structural perturbations were monitored by their effect on the fluorescence decay kinetics of the single tryptophyl residue at position 23. Data for the intact hormone were compared with those for its 1-34 and 13-34 analogues. Deletion of the 35-84 sequence had no significant effect on the structure of hPTH in the region of Trp-23, nor was there any evidence for interaction of this region with the 1-12 sequence. On the basis of a comparison of the results of this study with structural information available from other spectroscopic techniques, we propose that the local structure in the region of Trp-23 of aqueous solutions of hPTH and hPTH 1-34 has helical character. This local structure was not stable in aqueous hPTH 13-34, but was present in hPTH and its analogues, both on complexation with acidic lipid and in helix-promoting solvents. The tryptophyl fluorescence of the lipid-bound peptides was characteristic of an aqueous environment. Triple-exponential fluorescence decay kinetics were observed for the tryptophyl residue of hPTH and its deletion analogues. This can be explained in terms of ground-state heterogeneity due to the presence of three C alpha-C beta rotamers of the tryptophanyl indole side chain. Assuming this model, we show that the calculated fractional concentrations of the decay time components correlate with the likely rotamer populations and with their expected dependence on the main-chain conformation.(ABSTRACT TRUNCATED AT 250 WORDS)

Comparison of terbium (III) luminescence enhancement in mutants of EF hand calcium binding proteins

The luminescent isomorphous Ca2+ analogue, Tb3+, can be bound in the 12-amino acid metal binding sites of proteins of the EF hand family, and its luminescence can be enhanced by energy transfer from a nearby aromatic amino acid. Tb3+ can be used as a sensitive luminescent probe of the structure and function of these proteins. The effect of changing the molecular environment around Tb3+ on its luminescence was studied using native Cod III parvalbumin and site-directed mutants of both oncomodulin and calmodulin. Titrations of these proteins showed stoichiometries of fill corresponding to the number of Ca2+ binding loops present. Tryptophan in binding loop position 7 best enhanced Tb3+ luminescence in the oncomodulin mutant Y57W, as well as VU-9 (F99W) and VU-32 (T26W) calmodulin. Excitation spectra of Y57F, F102W, Y65W oncomodulin, and Cod III parvalbumin revealed that the principal Tb3+ luminescence donor residues were phenylalanine or tyrosine located in position 7 of a loop, despite the presence of other nearby donors, including tryptophan. Spectra also revealed conformational differences between the Ca2+- and Tb(3+)-bound forms. An alternate binding loop, based on Tb3+ binding to model peptides, was inserted into the CD loop of oncomodulin by cassette mutagenesis. The order of fill of Tb3+ in this protein reversed, with the mutated loop binding Tb3+ first. This indicates a much higher affinity for the consensus-based mutant loop. The mutant loop inserted into oncomodulin had 32 times more Tb3+ luminescence than the identical synthetic peptide, despite having the same donor tryptophan and metal binding ligands. In this paper, a ranking of sensitivity of luminescence of bound Tb3+ is made among this subset of calcium binding proteins. This ranking is interpreted in light of the structural differences affecting Tb3+ luminescence enhancement intensity. The mechanism of energy transfer from an aromatic amino acid to Tb3+ is consistent with a short-range process involving the donor triplet state as described by Dexter (Dexter, D. L. (1953) J. Chem. Phys. 21, 836). This cautions against the use of the Förster equation in approximating distances in these systems.

The tyrosyl fluorescence of angiotensin II in alcoholic solvents

Angiotensin II is an octapeptide hormone and contains a single tyrosyl residue and no tryptophyl residues. Intramolecular interactions of the tyrosyl residue with, for example, ionizable side chains or hydrogen bond acceptors can potentially perturb its fluorescence properties. The intrinsic fluorescence of angiotensin II was used to determine if the interactions of the tyrosyl residue were altered, as a consequence of conformational changes induced by certain alcoholic solvents. Steady state and time-resolved fluorescence data for angiotensin II in neutral aqueous buffer, isopropanol and 1,2=propanediol, provided no evidence for specific conformations, which facilitated intramolecular association of the tyrosyl residue with other moieties. Multiexponential decay kinetics in which the decay times were <5 ns were observed in all cases. No fluorescence which could be attributed to tyrosinate anion was detected in the solvent systems studied.

Metal-induced changes in the fluorescence properties of tyrosine and tryptophan site-specific mutants of oncomodulin

Oncomodulin is a 108-residue, oncodevelopmental protein containing two calcium-binding sites identified as the CD- and EF-loops. The protein contains no tryptophan and only two tyrosine residues, one which is a calcium ligand in the CD-loop (Tyr-57) and one which lies in the flanking D-helix of this loop (Tyr-65). Site-specific mutagenesis was performed to yield five mutants, two with phenylalanine substituted for tyrosine in positions 57 and 65 and three with tryptophan substituted into position 57 in the CD-loop, position 65 in the D-helix, and position 96 in the EF-loop. The single Tyr-containing mutants demonstrated that position 57 was perturbed to a significantly greater extent than position 65 upon calcium binding. Although both tyrosine residues responded to decalcification, the fluorescence intensity changes were in opposite directions, with the more dominant Tyr-57 accounting for the majority of the intrinsic fluorescence observed in native oncomodulin. The substitution of tryptophan for each tyrosyl residue revealed that in both positions the tryptophan resided in polar, conformationally heterogeneous environments. The environment of Trp-57 was affected by Ca2+ binding to a much greater extent compared to that of Trp-65. Only 1 equiv of Ca2+ was required to produce greater than 70% of the Trp fluorescence changes in positions 57 and 65, indicating that Ca2+ binding to the higher affinity EF-loop had a pronounced effect on the protein structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Fluorescence and CD studies on the conformation of the gastrin releasing peptide in solution and in the presence of model membranes

The conformation of the heptacosapeptide hormone, gastrin releasing peptide, has been studied in buffer and in the presence of lipids, using static and dynamic fluorescence and CD. The results obtained show that, in buffer, the hormone exists in a collection of flexible, random coil type conformers, characterized by a beta-turn between residues 14-19. On the other hand, organic solvents can induce some degree of ordered secondary structure in the peptide chain. The marked changes, observed in CD and fluorescence spectra upon addition of lysolecitin micelles and dimyristoylphosphatidylserine vesicles, clearly show that the peptide interacts with lipids, assuming a lipid specific configuration. Interestingly, no significative spectroscopic changes are produced by exposure to dimyristoylphosphatidylcholine vesicles both in the gel and liquid-chrystalline phases, suggesting a requirement for negatively charged lipids during the process of hormone-membrane interaction.

A calcium-specific conformational response of parvalbumin

The single tryptophan containing isotype III parvalbumin from codfish (Gadus callarius) was purified by a modified procedure and was shown to be homogeneous by a number of biochemical techniques. Sequence analysis established the location of the single tryptophan in position 102 of the 108 amino acid primary sequence. Atomic absorption spectroscopy showed that trichloroacetic acid (TCA) precipitation was more effective in parvalbumin decalcification compared to the more commonly used method of EGTA treatment. Magnesium induced steady-state fluorescence spectral changes of the EGTA-treated, but not the TCA-treated, parvalbumin. Steady-state fluorescence and circular dichroism spectra showed that calcium, but not magnesium, induced a conformational response in the TCA-treated protein. The fluorescence decay of the calcium-loaded native (holo) cod III parvalbumin was best described by two decay time components. By contrast, three lifetime components were necessary to describe the fluorescence decay of the metal-free (apo) protein. The decay-associated spectra of each temporal component were obtained. Collectively, these results demonstrate that it is possible for a parvalbumin to display a calcium-specific response.

Comparison of metal ion-induced conformational changes in parvalbumin and oncomodulin as probed by the intrinsic fluorescence of tryptophan 102

The calcium-induced conformational changes of the 108-amino acid residue proteins, cod III parvalbumin and oncomodulin, were compared using tryptophan as a sensitive spectroscopic probe. As native oncomodulin is devoid of tryptophan, site-specific mutagenesis was performed to create a mutant protein in which tryptophan was placed in the identical position (residue 102) as the single tryptophan residue in cod III parvalbumin. The results showed that in the region probed by tryptophan-102, cod III parvalbumin experienced significantly greater changes in conformation upon decalcification compared to the oncomodulin mutant, F102W. Addition of 1 eq of Ca2+ produced greater than 90% of the total fluorescence response in F102W, while in cod III parvalbumin, only 74% of the total was observed. Cod III parvalbumin displayed a negligible response upon Mg2+ addition. In contrast, F102W did respond to Mg2+, but the response was considerably less when compared to Ca2+ addition. Time-resolved fluorescence showed that the tryptophan in both proteins existed in at least two conformational states in the presence of Ca2+ and at least three conformational states in its absence. Comparison with quantum yield measurements indicated that the local electronic environment of the tryptophan was significantly different in the two proteins. Collectively, these results demonstrate that both cod III parvalbumin and oncomodulin undergo Ca2(+)-specific conformational changes. However, oncomodulin is distinct from cod III parvalbumin in terms of the electronic environment of the hydrophobic core, the magnitude of the Ca2(+)-induced conformational changes, and the number of calcium ions required to modulate the major conformational changes.

Terbium luminescence in synthetic peptide loops from calcium-binding proteins with different energy donors

Fourteen 14-mer peptides corresponding to a consensus sequence of metal-binding loops from proteins of the calmodulin family were synthesized. The effect of varying both the position in the binding loop, and the type of aromatic side chains as energy donors for enhancement of terbium luminescence, was studied. It was concluded that tryptophan in loop position 7 gave optimal luminescence enhancement, and that the additional inclusion of a tyrosine in the loop at positions 2 or 4 could further boost emission from the bound terbium. In all further cases energy transfer from aromatic residues at positions other than 7 was markedly less efficient. These results suggest that the peptides assume a configuration which allows a hexadentate ligand structure around the bound terbium ion. This is consistent with a Dexter-type electron exchange model of energy transfer.

Fluorescence decay kinetics of the tryptophyl residues of myoglobin: effect of heme ligation and evidence for discrete lifetime components

The fluorescence decay kinetics of the tryptophyl residues of sperm whale and yellowfin tuna myoglobin have been determined by using time-correlated single photon counting, with picosecond resolution. Purification by HPLC techniques resulted in the isolation of samples that exclusively displayed picosecond decay kinetics. Lifetimes of 24.4 ps for Trp14 and 122.0 ps for Trp7 were found for oxy sperm whale myoglobin (pH 7), which agree with theoretical predictions [Hochstrasser, R. M., & Negus, D. K. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 4399-4403]. The effects of ligand binding and pH on the decay kinetics were investigated, and the results were shown to be consistent with the known crystal structures. Data for the met form of sperm whale myoglobin were analyzed both in terms of a sum of discrete exponential components and as a continuous gamma distribution of exponential decays. The results were not found to support the existence of multiple, structurally distinct conformation states in myoglobin.