Internal Tryptophan Research Articles

Novel signal-on immunosensors for rapid and sensitive detection of Microcystin-LR

Microcystins are a group of hepatotoxins produced by cyanobacteria present in surface water. We developed two Quenbodies (Q-bodies) as effective and reliable fluorescent sensors to detect microcystin with leucine and arginine (MC-LR) within 3 min. The designed single-chain variable region of antibody 3A8 was used to prepare Q-bodies by conjugating the fluorescent dye ATTO520 or tetramethylrhodamine (TAMRA) to its N-terminus. The fluorescence of Q-bodies was quenched by the internal tryptophan residues of antibody via photo-induced electron transfer, whereas it significantly increased upon the binding of MC-LR. The limit of detection and EC50 were 0.45 ng/mL and 20.43 ng/mL, respectively, for TMARA-labeled Q-body, and 8.6 ng/mL and 251.6 ng/mL for ATTO520-labeled Q-body. Combining the Q-bodies enabled sensitive and wide-range detection of MC-LR. The recovery rates for river water samples spiked with MC-LR ranged from 94.8% to 120.0%, suggesting their potential applications in MC-LR monitoring in nature.

Rapid detection of the neonicotinoid insecticide imidacloprid using a quenchbody assay.

Contamination of the land and water by neonicotinoid insecticide residues is currently a severe environmental problem. However, the traditional methods for pesticide residue analysis are time consuming and laborious. To tackle this problem, here we describe a novel quenchbody (Q-body) immunoassay reagent that allows the rapid and sensitive detection of imidacloprid, one of the most frequently used neonicotinoid pesticides, in aqueous solution. A Q-body comprises an antibody Fab fragment that is site-specifically labeled with a fluorescent dye. The Fab fragment quenches the dye with its internal tryptophan residues via photoinduced electron transfer. The subsequent addition of imidacloprid stabilizes the antibody structure and displaces the quenched dye to the outside of the protein, resulting in increased fluorescence. The constructed Q-body assay exhibited a high dynamic range and a low limit of detection (10ngmL-1), and the entire assay procedure could be completed in a few minutes. The assay showed a low cross-reactivity with possible interfering analogous compounds, indicating that it has a good selectivity. Hence, the developed Q-body assay has excellent potential as a universal technology for monitoring neonicotinoid residues in environmental and food samples. Graphical abstract A novel quenchbody (Q-body) immunoassay reagent that allows the rapid and sensitive detection of imidacloprid, one of the most frequently used neonicotinoid pesticides, in aqueous solution was developed. The addition of imidacloprid stabilizes the Q-body structure and displaces the quenched dye to the outside of the protein, resulting in increased fluorescence. The constructed Q-body assay exhibited a high dynamic range and a low limit of detection (10ngmL-1), and completed in a few minutes.

Tryptophan-Dependent Control of Colony Formation After DNA Damage via Sea3-Regulated TORC1 Signaling inSaccharomyces cerevisiae

The Saccharomyces cerevisiae Iml1 complex inhibits TORC1 signaling and SEACAT antagonizes the Iml1 complex. Conditions in which SEACAT functions to inhibit Iml1 and, hence, TORC1 signaling, remain largely unknown. The SEACAT member Sea3 was linked previously to telomere maintenance and DNA repair via genome-wide genetic and physical interaction studies. Therefore, we questioned whether Sea3 functioned through TORC1 to influence these pathways. Deletion of SEA3 delayed the emergence of telomerase-independent survivors that use break-induced replication (BIR) to maintain their telomeres. Similarly, sea3∆ mutants exhibited a delay in colony formation in a BIR assay strain after double-strand break (DSB) induction as well as on the DNA-damaging agent bleomycin. Deletion of IML1 rescued the impaired growth of sea3∆ mutants after DNA damage, consistent with Sea3 functioning as a regulator of TORC1 signaling. The delay was not attributable to slowed DSB repair or termination of the DNA damage checkpoint but to tryptophan auxotrophy. High levels of tryptophan in yeast peptone dextrose media did not rescue the delay in colony formation, suggesting a defect in tryptophan import, although levels of the high-affinity tryptophan permease Tat2 were not perturbed in the sea3Δ mutant. Addition of quinolinic acid, an intermediate of the de novo NAD+ biosynthetic pathway, however, rescued the delay in colony formation in the sea3Δ mutant. Together, these findings highlight the importance of enforcement of TORC1 signaling and suggest that internal tryptophan levels influence growth recovery post DNA damage through the role of tryptophan in NAD+ synthesis.

π-Cation interactions as the origin of the weak absorption at 532 nm observed in tryptophan-containing polypeptides

We have previously reported that bovine serum albumin (BSA) and other proteins that do not contain prosthetic groups exhibited a weak light absorption in the visible, only detectable by pulsed laser-induced optoacoustic spectroscopy (LIOAS). Human serum albumin (HSA) exhibited signals 25% higher than those observed with BSA. Signals comparable to those obtained with BSA were observed with poly(L-Trp, L-Lys), poly(L-Trp, L-Arg) or poly(L-Trp, L-Orn) at pH 7.0. No signals were obtained when tryptophan was replaced by other amino acids or when free tryptophan or the tripeptide Lys-Trp-Lys was assayed (pH 7.0). Tryptophan in HCl 5 N produced LIOAS signals similar to those produced by tryptophan-containing copolymers. Moreover, the absorption peak could be observed in a UV-VIS spectrophotometer. Therefore, the LIOAS signals obtained with BSA, HSA, and tryptophan-containing random copolymers may be attributed to a new transition of the indole moiety of their tryptophan residues when "protonated". Tryptophan residues of proteins are known to participate in π-cation interactions, which are important in protein stability and function. As a matter of fact, HSA and BSA contain an internal tryptophan in close proximity to lysine and arginine residues and therefore suitable for π-cation interactions. The strength of this type of interaction strongly depends on distances and relative orientations of both amino acid residues. Accordingly, these interactions should be highly sensitive to conformational changes. Based on preliminary results that have shown that LIOAS signal at 532 nm depended on the aggregation state of BSA and/or on the oxidation state of its Cys-34, we postulate that the LIOAS signal observed with proteins and tryptophan-containing polypeptides are related to Trp-Lys or Trp-Arg interactions and that the intensity of the signal depends on the strength of such interactions.

Conformational Dynamics in a Truncated Epidermal Growth Factor Receptor Ectodomain

Structural studies have revealed two forms of the monomeric epidermal growth factor receptor (EGFR) ectodomain: a compact (tethered) form stabilized by interdomain interactions and an extended (untethered) form in the presence of ligand. An important question is whether the ligand induces a conformational transition from a tethered to untethered form or whether there is a preexisting conformational equilibrium between tethered and untethered states. To distinguish between these two possibilities, we investigated a truncated receptor, EGFR501 (spanning residues 1-501), that contains the minimal elements required for high-affinity ligand binding in solution. Conformational transitions and dynamics were inferred by means of fluorescence from five internal tryptophan residues that are located within or close to the ligand-binding domains of EGFR501. A preexisting conformational equilibrium between tethered and untethered states in EGFR501 was deduced from (1) the nonlinear Arrhenius temperature dependence of fluorescence and (2) fluorescence polarization showing independently mobile domains. In contrast, the ligand-EGFR501 complex revealed a linear Arrhenius temperature dependence of fluorescence and increased fluorescence polarization due to a lack of significant interdomain motions. The data suggest that the role of the ligand is to trap the EGFR501 in the untethered state that is transiently formed in solution through a preexisting conformational equilibrium.

A Homogeneous Fluorescence Resonance Energy Transfer System for Monitoring the Activation of a Protein Switch in Real Time

A homogeneous fluorescence resonance energy transfer (FRET) system for the real-time monitoring of exchange factor-catalyzed activation of a ras-like small GTPase is described. The underlying design is based on supramolecular template effects exerted by protein-protein interactions between the GTPase adenosine diphosphate ribosylation factor (ARF) and its effector protein GGA3. The GTPase is activated when bound to guanosine triphosphate (GTP) and switched off in its guanosine diphosphate (GDP)-bound state. Both states are accompanied by severe conformational changes that are recognized by GGA3, which only binds the GTPase "on" state. GDP-to-GTP exchange, i.e., GTPase activation, is catalyzed by the guanine nucleotide exchange factor cytohesin-2. When GGA3 and the GTPase ARF1 are labeled with thoroughly selected FRET probes, with simultaneous recording of the fluorescence of an internal tryptophan residue in ARF1, the conformational changes during the activation of the GTPase can be monitored in real time. We applied the FRET system to a multiplex format that allows the simultaneous identification and distinction of small-molecule inhibitors that interfere with the cytohesin-catalyzed ARF1 activation and/or with the interaction between activated ARF1-GTP and GGA3. By screening a library of potential cytohesin inhibitors, predicted by in silico modeling, we identified new inhibitors for the cytohesin-catalyzed GDP/GTP exchange on ARF1 and verified their increased potency in a cell proliferation assay.

The Tryptophan Phosphorescence of Porcine and Mutant Bovine Odorant-Binding Proteins: A Probe for the Local Protein Structure and Dynamics

Vertebrate odorant-binding proteins (OBPs) are small extracellular proteins belonging to the lipocalin superfamily. They have been supposed to play a role in events of odorant molecules detection by carrying, deactivating, and/or selecting odorant molecules. The OBPs share a conserved folding pattern, an eight-stranded beta-barrel flanked by an alpha-helix at the C-terminal end of the polypeptide chain. The beta-barrel creates a central nonpolar cavity whose role is to bind and transport hydrophobic odorant molecules. These proteins reversibly bind odorant molecules with dissociation constants ranging from nanomolar to micromolar range. In this work, we have studied the structural features of the OBP from pig and from cow by phosphorescence spectroscopy. The obtained results demonstrate that the indolic phosphorescence of the two studied proteins can be readily detected at ambient temperature solutions and that it is owed exclusively to the internal tryptophan residue located next to the ligand binding cavity, which is generally conserved in the mammalian OBPs. In addition, while both the phosphorescence spectrum and the lifetime yield a picture of the fold of the studied protein in good agreement with the protein crystallographic structures, the triplet probe points out that in solution the polypeptide structure of the both investigated OBPs exists as a multiplicity of slowly interconverting protein conformations. Finally, this work also demonstrates that it is possible to directly detect the binding of the ligands to OBPs as variations of the protein luminescence features, thus, representing the very first observation reported in the literature so far that a fast and direct assay can be used for monitoring the binding of ligands to OBPs.

Disruption of the disulfide bridge in azurin from Pseudomonas aeruginosa

In the family of small blue-copper proteins azurins are unique in that they contain a disulfide bridge close to the amino-terminal end. It is situated in the ‘south’ side of the molecule, about 25 Å away from the copper. Site-specific mutagenesis was used to exchange one or both of the cysteines in the bridge for serines in Pseudomonas aeruginosa azurin. In the double mutant Cys3Ser-Cys26ser the Type 1 Cu is converted into Type 2, and the fluorescence of the single internal tryptophan shows that it becomes exposed to a polar environment. The circular dichroism spectrum indicates a loss of β-structure. Thus, this mutation prevents the correct folding of the protein and the formation of the metal-binding site. Single mutants, Cys3Ser or Cys26Ser, can at least in part form native-like structures as shown by optical, EPR, fluorescence and CD spectroscopy. The Cys3Ser mutant can form a stable intermolecular disulfide bond which promotes the native conformation of the protein.

Oxygen fluorescence quenching studies with single tryptophan-containing proteins

The work of Lakowicz and Weber [Biochemistry 12, 4161 (1973)] demonstrated that molecular oxygen is a powerful quencher of tryptophan fluorescence in proteins. Here we report studies of the oxygen quenching of several proteins that have a single, internal tryptophan residue. Among these are apoazurin (Pseudomonas aeruginosa), asparaginase (Escherichia coli), ribonuclease T1 (Aspergillus oryzae), and cod parvalbumin. Both fluorescence intensity and phase lifetime quenching data are reported. By comparison of these data we find that there is a significant degree of apparent static quenching in these proteins. The dynamic quenching rate constants,k q, that we find are low compared to those for tryptophan residues in other proteins. For example, for apoazurin we find an apparentk q of 0.59×10(9) M (-1) s(-1) at 25°C. This value is the lowest that has been reported for the oxygen quenching of tryptophan fluorescence.

Use of engineered proteins with internal tryptophan reporter groups and pertubation techniques to probe the mechanism of ligand-protein interactions: investigation of the mechanism of calcium binding to calmodulin.

Stopped-flow kinetic and fluorescence spectroscopic analyses, including solvent and temperature perturbations, of five isofunctional structural mutants of calmodulin indicate that calcium binding to calmodulin follows the order site III, site IV, site I, site II, with dissociation occurring in the reverse order. Each of the isofunctional structural mutants contains a single tryptophan residue, introduced by site-specific mutagenesis, as an internal spectroscopic reporter group that was used as a probe of local conformational change. Calcium binding was studied by using flow dialysis or by using fluorescence spectroscopy and monitoring the change in the single tryptophan residue in each calcium-binding site. Calcium removal was examined by using EDTA and monitoring tryptophan fluorescence or by using Quin 2 and monitoring the change in the chromophoric chelator. Computational analysis of the data suggests a rate-limiting step for dissociation between calcium removal from sites I/II and sites III/IV. Unexpected results with the site IV isofunctional mutant (Q135W-CaM) indicated cross-talk between the amino and carboxyl terminal halves of CaM during the calcium-binding mechanism. Studies with ethylene glycol provided empirical data that suggest the functional importance of the electrostatic potential of CaM, or the molarity of water, in the calcium-binding process. Altogether, the data allowed a kinetic extension of the sequential, cooperative model for calcium binding to calmodulin and provided values for additional parameters in the model of calcium binding to CaM, a prototypical member of the family of proteins required for calcium signal transduction in eukaryotic cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Kinetics of haloperidol binding to monoclonal antibodies as measured by direct fluorescence quenching

Monoclonal antibodies which bind small neurogenic ligands may mimic certain aspects of the stereospecific binding present in the natural biological receptor, and may prove useful in designing engineered protein receptors, provided their interactions are correctly understood. We report here the kinetic and equilibrium characteristics of ligand-antibody complexes of haloperidol, a dopaminergic antagonist, with three of its monoclonal antibodies as studied by fluorescence quenching techniques. These antibodies possessed moderate to high affinity constants, ranging from 10 5 to 10 9 M −1, and caused fluorescence quenching of a fluorescein-labeled haloperidol as well as quenching (40–60%) of the internal tryptophan fluorescence. The dissociation rates of the ligand from the complexes were measured at different conditions of temperature, pH and ionic strength. The results provide important information regarding the kinetic and thermodynamic parameters of the binding pockets of these antibodies.

A high resolution fluorescence decay and depolarization study of human plasma apolipoproteins.

Abstract— Human plasma apolipoprotein A‐I (apoA‐I) and apolipoprotein C‐I (apoC‐I) were investigated by time‐resolved fluorescence decay and depolarization. The tryptophyl fluorescence of apoA‐I undergoes a double‐exponential decay with lifetimes of 1.07 and 3.43 ns which remain unchanged over the range of apoA‐I concentration studied.The time‐resolved fluorescence of both native and denatured forms of apoC‐I exhibits an unusual tryptophyl fluorescence decay that was best fit to a triexponential function with lifetimes at 3.7 ± 0.2, 1.1 ± 0.1 and 0.1 ns at 2°C. The native and denatured forms of apoC‐I had rotational correlation times of 1.42 and 1.19 ns at 20°C respectively. A shorter rotational correlation time associated with the internal tryptophan motions was not observed or resolved.The decay of tryptophyl fluorescence in apoC‐I/DPPC/cholesterol complex at 20°C is also triexponential with lifetimes at 4.94, 1.28 and 0.21 ns, which are longer than those of the uncomplexed forms. Two rotational correlation times of 28.32 and 0.59 ns at 20°C were resolved by fluorescence depolarization measurements. The long rotational time remained constant with temperatures above 30°C. Also, the temperature dependence of the order parameter, S2, resembled a lipid phase transition curve with a transition midpoint at 38°C. The tryptophan and thus apoC‐I are found to be affected by the bulk changes in the lipid.

Phosphorescence anisotropy of liver alcohol dehydrogenase in the crystalline state. Apparent glasslike rigidity of the coenzyme-binding domain.

Phosphorescence anisotropy from internal tryptophan (Trp) residues in proteins which are in the crystalline state may provide an experimental approach suitable to study the flexibility of rather rigid segments of protein structure. The phosphorescence anisotropy of Trp-314 in liver alcohol dehydrogenase, which is enclosed within the beta-sheet forming the coenzyme-binding domain, was measured with the protein free in solution and in the crystalline state. In contrast to the free protein, where the rotational correlation time reflects the tumbling rate of the whole macromolecule, there is effectively no loss in anisotropy in the crystalline state. At room temperature, the triplet lifetime of 0.5 s implies that the rotational correlation time of the indole side chain must be larger than 1 s. Anisotropy data show that fluctuations of the indole ring about the average position can only be of limited amplitude (cone of semiangle less than 15 degrees) and that the resistance opposed by the beta-sheet to out-of-plane rotational motions is equivalent to a viscosity larger than 2.5 X 10(8) P, a value which confirms the particular rigidity anticipated for such an assembly of secondary structure.

Viscosity dependence of the solute quenching of the tryptophanyl fluorescence of proteins.

We have studied the viscosity dependence of the acrylamide quenching of the fluorescence on the internal tryptophan residues in cod parvalbumin and ribonuclease T1, as well as the model systems. N-acetyl-L-tryptophanamide and glucagon. For the latter systems, the apparent rate constant, kq(app), for acrylamide quenching shows a typical diffusion-limited behavior. For parvalbumin and ribonuclease T1, however, the viscosity dependence of kq(app) is quite different. There is little change in the kq(app) values on increasing the bulk viscosity from 1 to 10 cP (by addition of glycerol), but a further increase from 10 to 100 cP results in a significant reduction in the kq(app). Both an unfolding mechanism and a quencher penetration mechanism are considered to explain the results. Only the penetration mechanism is found to be consistent, and our data are interpreted as indicating that the rate-limiting step for quenching goes from being that of diffusion through the protein matrix, at low viscosity, to diffusion through the bulk solvent, at high viscosity. By also considering the Kramers' relationship in fitting our data, we are able to obtain insight regarding the coupling between internal fluctuations in the structure of the protein and motion of the bulk solvent. For parvalbumin and ribonuclease T1, the internal dynamics are found to be very weakly coupled to the bulk.

Tryptophan uptake and hydroxylation in rat forebrain synaptosomes.

Tryptophan uptake, hydroxylation, and decarboxylation in isolated synaptosomes were studied to assess how their properties may determine the rate of serotonin synthesis in the presynaptic nerve terminals of the brain. Simultaneous measurements of the rates of uptake, hydroxylation, and decarboxylation in the presence and absence of various inhibitors showed that tryptophan hydroxylase is rate-limiting for serotonin synthesis in this model system. There was significant direct decarboxylation of tryptophan to tryptamine. Measurement of tryptophan hydroxylase flux with varying internal concentrations of tryptophan allowed the determination of the Km of tryptophan hydroxylase in synaptosomes for tryptophan of 120 +/- 15 microM. Depolarisation of synaptosomes with veratridine caused both a reduction in the internal tryptophan concentration and an apparent activation of tryptophan hydroxylase. This activation did not occur in the absence of Ca2+ or in the presence of trifluoperazine. Synaptosomal serotonin synthesis and brain stem-soluble tryptophan hydroxylase were inhibited by low concentrations of noradrenaline or dopamine. Dibutyryl cyclic AMP, glucagon, insulin, and vasopressin were observed to have no effect on tryptophan uptake or hydroxylation in synaptosomes.

Characteristics of tryptophan accumulation by isolated rat forebrain synaptosomes.

Uptake of 10 microM L-tryptophan into isolated rat brain synaptosomes was studied to assess its effect on the rate of serotonin synthesis from tryptophan. The initial rate of uptake was rapid, being two orders of magnitude above the rate of tryptophan hydroxylation. Uptake was highly concentrative, the concentration ratio across the plasma membrane at equilibrium being approximately 9. This concentration ratio was decreased to about 1 in the presence of high concentrations of amino acids transported by the L-type neutral amino acid uptake system. A mixture of the large neutral amino acids at physiological concentrations decreased the internal tryptophan concentration to 58% of that in their absence. Large tryptophan concentration ratios were observed in experiments in which Na+ in the medium was replaced with choline+. The concentrative uptake of tryptophan was energy-dependent, being decreased by inclusion of cyanide and omission of glucose. The concentration gradient was abolished by veratridine or rotenone. Time courses of the changes in ATP content and tryptophan concentration ratio on addition of these and other agents established that tryptophan uptake is probably not driven by ATP hydrolysis or efflux of other amino acids, but by the plasma membrane potential.

Fluorimetric studies of tryptophyl exposure in concanavalin A

Studies of the iodide ion quenching of the intrinsic fluorescence of Concanavalin A indicate that 50% of the tryptophyl fluorescence originates from exposed residues. This agrees with the X-ray crystallographic determination that two of the four tryptophan residues in a Concanavalin A monomer are on the surface. Previous studies have indicated that conformational changes induced by sugar binding alter the environment of aromatic residues. The present investigation finds that neither the specific binding of α-methyl- d-mannoside nor alteration of the Concanavalin A quaternary structure changes the number or accessibility of the solvent-exposed tryptophan residues. It therefore appears that the major conformational transitions in Concanavalin A do not affect steric access to the surface tryptophans and the effects previously observed may be ascribed to structurally internal tryptophan residues.

Room temperature phosphorescence and the dynamic aspects of protein structure.

While the phosphorescence of aromatic chromophores in solution is normally quenched through diffusion of dissolved oxygen and other solvent-mediated processes, the phosphorescence of some proteins in solution is observed at room temperature. The tryptophan phosphorescence arises from residues which are hindered from interaction with oxygen by the folding of the polypeptide chains. Measurements of the phosphorescence lifetime of horse liver alcohol dehydrogenase (alcohol: NAD(+) oxidoreductase, EC 1.1.1.1) as a function of oxygen concentration indicate that internal tryptophan residues are periodically exposed to oxygen. This permits the calculation of rate constants for conformational oscillations in the enzyme. The present article illustrates the feasibility of employing phosphorescence in the study of proteins in solution in general and the utility of such experiments in probing the dynamic aspects of protein structure.

Physiological studies of biosynthetic indole excretion in Bacillus alvei.

Bacillus alvei excretes indole during early exponential growth in acid-hydrolyzed casein medium. l-Threonine is the amino acid responsible for "early" indole excretion, and the amount of indole excreted is directly related to the amount of l-threonine in the medium. "Early-indole" excretion can be prevented by the continuous addition of serine (3.1 mumoles per ml per hr) or by substituting a mutant with an impaired ability to degrade serine. The addition of serine to a culture during the period of indole excretion halts the excretion and stimulates indole utilization. Threonine is a competitive inhibitor of serine (K(i) = 0.6 m) in the tryptophan synthetase B reaction. The internal tryptophan concentration increases during the period of indole excretion, suggesting that threonine acts by increasing the activity of the tryptophan pathway. This view is supported by experiments demonstrating that anthranilic acid and indoleacrylic acid also stimulate indole excretion. A metabolic explanation is offered and discussed.

Factors affecting increased production of tryptophan synthetase by a TD mutant of Neurospora crassa.

Matchett, William H. (University of California, San Diego, La Jolla, Calif.) and John A. DeMoss. Factors affecting increased production of tryptophan synthetase by a td mutant of Neurospora crassa. J. Bacteriol. 83:1294-1300. 1962.-Mutant td 201 of Neurospora crassa produces a tryptophan synthetase in significantly larger amount than the parental wild-type strain. Evidence obtained in the present investigation indicates that tryptophan synthetase formation in this mutant is subject to end product regulation by a pool of internal tryptophan. An accelerated rate of formation of enzyme was observed when the level of internal tryptophan fell below the value of 1 mumole per g dry weight of mycelium. It is concluded, therefore, that the high level of enzyme found in this strain results from release of repression. In experiments with the parental wild-type strain, no such release of repression was observed. The significance of these results for the problem concerning the nature of the mutation giving rise to mutant td 201 is discussed. Evidence indicating a marked effect of growth temperature upon metabolism of externally supplied tryptophan is presented.