Phenylthiohydantoin Amino Acids Research Articles

Determination of sequence and absolute configuration of peptide amino acids by HPLC–MS/CD-based detection of liberated N-terminus phenylthiohydantoin amino acids

We report a method for the simultaneous determination of the sequence and absolute configuration of peptide amino acids using a combination of Edman degradation and HPLC–MS/CD. Phenylthiohydantoin (PTH) derivatives of 20 pairs of standard d- and l-amino acids were synthesized by the Edman reaction. The CD spectra of the derivatives revealed that each pair of the PTH derivatives exhibited the absorption with opposite signs at around 270 nm. These standard PTH derivatives showed well-resolved resolution without interference from byproducts in the ion chromatogram and clear positive/negative CD absorptions when subjected on a reversed phase HPLC–MS system coupled with a CD-2095 HPLC detector. This method was applied for the detection of a synthetic pentapeptide and a natural depsipeptide (halicylindramide C). The sequence and configuration of the pentapeptide and up to eight residues of halicylindramide C were successfully analyzed by this method. The amino acid configuration of the pentapeptide was also determined successfully by subjecting its acid hydrolysates to the Edman reaction followed by HPLC–MS/CD.

Assessment of the Wound Healing Property of the Ethanolic Seed Extract of Eleusine coracana Linn using the Chorioallantoic Membrane Model

Access to readily available material for wound healing is very important. The wound healing property of Eleusine coracana a food source in Nigeria was therefore investigated. The ethanolic crude extract of the seed flour was prepared using maceration and qualitative phytochemical screening was carried out on the crude extract using standard methods. The antimicrobial activity of the E. coracana extract was determined using the disc diffusion method against E. coli, S. aureus, P. aeruginosa, and C. tetani. The wound healing property assay was carried out using the Chorioallantoic Membrane Model (CAM) at 50mg, 100mg, 150mg, and 200mg/ml concentration with the basic Fibroblast Growth Factor (bFGF) as the positive control. The crude extract was further fractionated into Hexane, Methanolic, and Aqueous fractions and then subjected to amino acid content analysis using the Applied Biosystems Phenylthiohydantoin (PTH) Amino Acid Analyzer. The phytochemical screening reveals the presence of alkaloids, steroids, terpenes, flavonoids, carbohydrates, glycoside, and protein. E. coli and S. aureus were susceptible to the E. coracana extract at a Minimum Inhibitory Concentration (MIC) of 50µg/ml while the P. aeruginosa was only susceptible at 200µg/ml and C. tetani was not susceptible at all the concentrations used. An increase in percentage angiogenesis was observed at all doses of the extract used indicating good wound healing properties. The amino acid profile reveals the presence of glycine, a proline that is important in wound healing. The E. coracana seeds, therefore, have wound healing properties based on the CAM model.

Sensor Array Based Determination of Edman Degradated Amino Acids Using Poly(p‐phenyleneethynylene)s

A cross‐reactive optical sensor array based on poly(p‐phenyleneethynylene)s (PPEs) determines Edman degraded amino acids. We report a sensor array composed of three anionic PPEs P1–P3, and their electrostatic complexes with metal ions (Fe2+, Cu2+, Co2+). We recorded distinct fluorescence intensity response patterns as “fingerprints” of this chemical tongue toward standard phenylthiohydantoin (PTH) amino acids—degradation products of the Edman process. These “fingerprints” were converted into canonical scores by linear discrimination analysis (LDA), which differentiates all of the PTH‐amino acids. This array discriminates PTH‐amino acid residues degraded from an oligopeptide through Edman sequencing. This approach is complementary to chromatography approaches which rely on mass spectrometry; our array offers the advantage of simplicity.

Thermodynamic enantioseparation behavior of phenylthiohydantoin-amino acid derivatives in supercritical fluid chromatography on polysaccharide chiral stationary phases.

Thirteen pairs of enantiomers belonging to the same structural family (phenylthiohydantoin-amino acids) were analyzed on two polysaccharide chiral stationary phases, namely, tris-(3,5-dimethylphenylcarbamate) of amylose (Chiralpak AD-H) or cellulose (Chiralcel OD-H) in supercritical fluid chromatography with a carbon dioxide/methanol mobile phase (90:10 v/v). Five different temperatures (5, 10, 20, 30, 40°C) were applied to evaluate the thermodynamic behavior of these enantioseparations. On the cellulose stationary phase, the retention, and separation trends were most similar among the set of probe analytes, suggesting that the chiral cavities in this stationary phase have little diversity, or that all analytes accessed the same cavities. Conversely, the retention and separation trends on the amylose phase were much more diverse, and could be related to structural differences among the set of probe analytes (carbon chain length in the amino acid residue, secondary amine in proline, existence of covalent rings, or formation of pseudo-rings via intramolecular hydrogen bonds). The large variability of behaviors on the amylose phase suggests that the chiral-binding sites in this chiral stationary phase have more variety than on the cellulose phase, and that the analytes did access different cavities.

Preparation, purification and common characteristics of anticoagulant peptide from peloid

Aim. To obtain the peloid extract containing peptide anticoagulant, to separate it from co-extracted compounds, to confirm the chemical structure of the purified anticoagulant, to characterize the amino acid profile and to evaluate its effect on blood clotting activity in vitro and the effect on hemostasis in laboratory animals. Methods. The anticoagulant was derived from lake Taraskul (Tyumen region) peloid. The effector was prepared and purified by original method including extraction, sedimentation of humic acids by salting-out, and removal of fulvic acids and low molecular weight fractions of humic acids by ion exchange chromatography. Purity and homogeneity of gained anticoagulant was evaluated by high performance liquid chromatography and polyacrylamide gel electrophoresis. The chemical composition of the active substance was determined by acid hydrolysis and identification of phenylthiohydantoin amino acid derivatives by reversed-phase high performance liquid chromatography. Specific anticoagulant activity was evaluated by substance’s influence on effect of thrombin-dependent conversion of fibrinogen to fibrin and serum thrombin clotting time after being administered to laboratory animals. Results. Peptide anticoagulant was isolated of the peloid and purified. Its activity is realized at the stage of thrombin and fibrinogen interaction. The substance prolongs the fibrin clotting time both in a model test system and when administered intravenously to rats. The anticoagulant effect of the peptide when administered to animals lasts at least 60 min, and no significant toxic effects appear. Conclusion. An isolated active substance might be a basis for the drug development of anticoagulants.

Molecular Cloning and Characterization of First Organic Matrix Protein from Sclerites of Red Coral, Corallium rubrum

We report here for the first time the isolation and characterization of a protein from the organic matrix (OM) of the sclerites of the alcyonarian, Corallium rubrum. This protein named scleritin is one of the predominant proteins extracted from the EDTA-soluble fraction of the OM. The entire open reading frame (ORF) was obtained by comparing amino acid sequences from de novo mass spectrometry and Edman degradation with an expressed sequence tag library dataset of C. rubrum. Scleritin is a secreted basic phosphorylated protein which exhibits a short amino acid sequence of 135 amino acids and a signal peptide of 20 amino acids. From specific antibodies raised against peptide sequences of scleritin, we obtained immunolabeling of scleroblasts and OM of the sclerites which provides information on the biomineralization pathway in C. rubrum.

Multi-linear gradient elution optimization for separation of phenylthiohydantoin amino acids using pareto optimality method

Multi-linear gradient elution was applied for simultaneous optimization of resolution and analysis times for ten phenylthiohydantoin amino acids (PTH-AAs) in liquid chromatography. Relation of lnK upon φ for each analyte was determined using isocratic retention time data, and gradient retention time of analytes was predicted using fundamental equation of gradient elution. Then a grid search program was used to predict retention time of solutes in variable space. Two different chromatographic goals-analysis time and minimum difference between adjacent peaks- were simultaneously evaluated using Pareto optimality method. Gradient program in optimum condition was: initially 24% CH3OH/Water for 10 min, linear ramp to 34% over 5 min, to 29% over 5 min, and to 70% over 20 min. The average of calculated relative error in the prediction of the retention time in optimal conditions was -1.67% that shows a good agreement between predicted and experimental values of the chromatographic retention time in optimal condition.

Analysis of PTH‐Cysteine by Adsorptive Stripping Square‐Wave Voltammetry

AbstractThe aim of this work is the study of cysteine by its derivative form. Cysteine derivation is done by Edman degradation and we obtain the phenylthiohydantoin of cysteine. Edman degradation is one of the most usual procedures for sequentate proteins. From this reaction, the phenylthiohydantoin amino acid derivative (PTH‐amino acid) from the N‐terminal one is obtained, leaving the new amino terminus for the next degradation cycle. To identify the produced PTH‐derivative, a square‐wave cathodic stripping voltammetry method is developed. In this work we show the results obtained for the optimization the instrumental and chemical conditions, and we can conclude that it is an electrochemically irreversible system with adsorptive reduction phemomenon. Under the best conditions we found a new method to analyze proteins with LOD of 2 μg L−1 and LOQ of 5 μg L−1, a RSD less than 10% and a Er minor than 9%. Results of the application of this methodology to a real protein are included.

Response surface methodology and support vector machine for the optimization of separation in linear gradient elution

Experimental design methodology was used to optimize the linear gradient elution chromatography. The effect of initial mobile phase composition (phi(in)), initial isocratic time (t(in)), and gradient time (t(G)) on the retention times of phenyl thiohydantoin aminoacids (PTH-amino acids) was investigated. The experiments were performed according to Box-Behnken experimental design to map the chromatographic response surface. Then multiple linear regression and support vector machine (SVM) methods were used to fit the retention times of solutes. Results shows the SVM models have better ability to predict retention time and used for grid search in factor space. The SVM models were verified, as good agreement was observed between the predicted and experimental values of retention time in the optimal condition.

A Barley Xyloglucan Xyloglucosyl Transferase Covalently Links Xyloglucan, Cellulosic Substrates, and (1,3;1,4)-β-D-Glucans

Molecular interactions between wall polysaccharides, which include cellulose and a range of noncellulosic polysaccharides such as xyloglucans and (1,3;1,4)-beta-D-glucans, are fundamental to cell wall properties. These interactions have been assumed to be noncovalent in nature in most cases. Here we show that a highly purified barley xyloglucan xyloglucosyl transferase HvXET5 (EC 2.4.1.207), a member of the GH16 group of glycoside hydrolases, catalyzes the in vitro formation of covalent linkages between xyloglucans and cellulosic substrates and between xyloglucans and (1,3;1,4)-beta-D-glucans. The rate of covalent bond formation catalyzed by HvXET5 with hydroxyethylcellulose (HEC) is comparable with that on tamarind xyloglucan, whereas that with (1,3; 1,4)-beta-D-glucan is significant but slower. Matrix-assisted laser desorption ionization time-of-flight mass spectrometric analyses showed that oligosaccharides released from the fluorescent HEC:xyloglucan conjugate by a specific (1,4)-beta-D-glucan endohydrolase consisted of xyloglucan substrate with one, two, or three glucosyl residues attached. Ancillary peaks contained hydroxyethyl substituents (m/z 45) and confirmed that the parent material consisted of HEC covalently linked with xyloglucan. Similarly, partial hydrolysis of the (1,3;1,4)-beta-D-glucan:xyloglucan conjugate by a specific (1,3;1,4)-beta-D-glucan endohydrolase revealed the presence of a series of fluorescent oligosaccharides that consisted of the fluorescent xyloglucan acceptor substrate linked covalently with 2-6 glucosyl residues. These findings raise the possibility that xyloglucan endo-transglucosylases could link different polysaccharides in vivo and hence influence cell wall strength, flexibility, and porosity.

An N-Linked Glycan Modulates the Interaction between the CD1d Heavy Chain and β2-Microglobulin

Human CD1d molecules consist of a transmembrane CD1 (cluster of differentiation 1) heavy chain in association with beta(2)-microglobulin (beta(2)m). Assembly occurs in the endoplasmic reticulum (ER) and involves the initial glycan-dependent association of the free heavy chain with calreticulin and calnexin and the thiol oxidoreductase ERp57. Folding and disulfide bond formation within the heavy chain occurs prior to beta(2)m binding. There are four N-linked glycans on the CD1d heavy chain, and we mutated them individually to ascertain their importance for the assembly and function of CD1d-beta(2)m heterodimers. None of the four were indispensable for assembly or the ability to bind alpha-galactosyl ceramide and to present it to human NKT cells. Nor were any required for the CD1d molecule to bind and present alpha-galactosyl ceramide after lysosomal processing of a precursor lipid, galactosyl-(alpha1-2)-galactosyl ceramide. However, one glycan, glycan 2 at Asn-42, proved to be of particular importance for the stability of the CD1d-beta(2)m heterodimer. A mutant CD1d heavy chain lacking glycan 2 assembled with beta(2)m and transported from the ER more rapidly than wild-type CD1d and dissociated more readily from beta(2)m upon exposure to detergents. A mutant expressing only glycan 1 dissociated completely from beta(2)m upon exposure to the detergent Triton X-100, whereas a mutant expressing only glycan 2 at Asn-42 was more stable. In addition, glycan 2 was not processed efficiently to the complex form in mature wild-type CD1d molecules. Modeling the glycans on the published structure indicated that glycan 2 interacts significantly with both the CD1d heavy chain and beta(2)m, which may explain these unusual properties.

Evolutional Design of a Hyperactive Cysteine- and Methionine-free Mutant of Escherichia coli Dihydrofolate Reductase

We developed a strategy for finding out the adapted variants of enzymes, and we applied it to an enzyme, dihydrofolate reductase (DHFR), in terms of its catalytic activity so that we successfully obtained several hyperactive cysteine- and methionine-free variants of DHFR in which all five methionyl and two cysteinyl residues were replaced by other amino acid residues. Among them, a variant (M1A/M16N/M20L/M42Y/C85A/M92F/C152S), named as ANLYF, has an approximately seven times higher k(cat) value than wild type DHFR. Enzyme kinetics and crystal structures of the variant were investigated for elucidating the mechanism of the hyperactivity. Steady-state and transient binding kinetics of the variant indicated that the kinetic scheme of the catalytic cycle of ANLYF was essentially the same as that of wild type, showing that the hyperactivity was brought about by an increase of the dissociation rate constants of tetrahydrofolate from the enzyme-NADPH-tetrahydrofolate ternary complex. The crystal structure of the variant, solved and refined to an R factor of 0.205 at 1.9-angstroms resolution, indicated that an increased structural flexibility of the variant and an increased size of the N-(p-aminobenzoyl)-L-glutamate binding cleft induced the increase of the dissociation constant. This was consistent with a large compressibility (volume fluctuation) of the variant. A comparison of folding kinetics between wild type and the variant showed that the folding of these two enzymes was similar to each other, suggesting that the activity enhancement of the enzyme can be attained without drastic changes of the folding mechanism.

Identification of the electrophoretic peaks of the phenylthiohydantoin derivatives of amino acids

Two techniques for identifying the peaks of phenylthiohydantoin (PTH) amino acids separated under the conditions of micellar electrokinetic chromatography were compared. The first technique is linear regression analysis, in which the retention time of an amino acid is a function of the retention times of two retention-time standards. The second technique takes into account hydrophobicity constants logD′, which were calculated using the ACD/LC Simulator 8.0 program package from ACDLabs (Canada). These constants provide an opportunity to calculate the relative migration times of PTH amino acids taking into account the velocity of the electroosmotic flow. The first technique allows us to identify the electrophoretic peaks of all 16 amino acids separated; the second procedure allows us to predict the elution order of the electrophoretic peaks; the use of a correlation equation gives better results.

The Crystal Structure of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines for the Design of Inhibitors Specific for the Bacterial Forms

Peptide deformylase (PDF) inhibitors have a strong potential to be used as a new class of antibiotics. However, recent studies have shown that the mitochondria of most eukaryotes, including humans, contain an essential PDF, PDF1A. The crystal structure of the Arabidopsis thaliana PDF1A (AtPDF1A), considered representative of PDF1As in general, has been determined. This structure displays several similarities to that of known bacterial PDFs. AtPDF1A behaves as a dimer, with the C-terminal residues responsible for linking the two subunits. This arrangement is similar to that of Leptospira interrogans PDF, the only other dimeric PDF identified to date. AtPDF1A is the first PDF for which zinc has been identified as the catalytic ion. However, the zinc binding pocket does not differ from the binding pockets of PDFs with iron rather than zinc. The crystal structure of AtPDF1A in complex with a substrate analog revealed that the substrate binding pocket of PDF1A displays strong modifications. The S1' binding pocket is significantly narrower, due to the creation of a floor from residues present in all PDF1As but not in bacterial PDFs. A true S3' pocket is created by the residues of a helical CD-loop, which is very long in PDF1As. Finally, these modified substrate binding pockets modify the position of the substrate in the active site. These differences provide guidelines for the design of bacterial PDF inhibitors that will not target mitochondrial PDFs.

Simultaneous optimization of the resolution and analysis time in micellar liquid chromatography of phenyl thiohydantoin amino acids using Derringer's desirability function

The chemometrics approach was applied for simultaneous optimization of resolution and analysis time of nine phenyl thiohydantoin amino acids in micellar liquid chromatography. Derringer's desirability function, a multi-criteria decision making method, was tested for the evaluation of the two different chromatographic performance goals. The effect of five experimental parameters on a chromatographic response function formed using two sigmoidal desirability functions was investigated. The sigmoidal functions were used to transform the optimization criteria, resolution and analysis time, into the desirability values. The factors studied were the concentration of sodium dodecyl sulfate, alkyl chain length of the alcohol used as the organic modifier, organic modifier content, mobile phase pH and temperature. The experiments were performed according to a face-centred cube response surface experimental design to map the chromatographic response surface. Then, calculated chromatographic response functions were fitted to a polynomial model. The obtained regression model was characterized by both descriptive and predictive ability ( R 2 = 0.988 and R cv 2 = 0.973 ). The model was verified, as good agreement was observed between the predicted and experimental values of the chromatographic response function in the optimal condition. Based on the results of the study, combination of response surface mapping with Derringer's desirability function allows to predict the best operating condition in micellar liquid chromatography of phenyl thiohydantoin amino acids with respect to resolution and analysis time.

Inactivation of Brain myo-Inositol Monophosphate Phosphatase by Pyridoxal-5'-Phosphate

Myo-inositol monophosphate phosphatase (IMPP) is a key enzyme in the phosphoinositide cell-signaling system. This study found that incubating the IMPP from a porcine brain with pyridoxal-5'-phosphate (PLP) resulted in a time-dependent enzymatic inactivation. Spectral evidence showed that the inactivation proceeds via the formation of a Schiff's base with the amino groups of the enzyme. After the sodium borohydride reduction of the inactivated enzyme, it was observed that 1.8 mol phosphopyridoxyl residues per mole of the enzyme dimer were incorporated. The substrate, myo-inositol-1-phosphate, protected the enzyme against inactivation by PLP. After tryptic digestion of the enzyme modified with PLP, a radioactive peptide absorbing at 210 nm was isolated by reverse-phase HPLC. Amino acid sequencing of the peptide identified a portion of the PLP-binding site as being the region containing the sequence L-Q-V-S-Q-Q-E-D-I-T-X, where X indicates that phenylthiohydantoin amino acid could not be assigned. However, the result of amino acid composition of the peptide indicated that the missing residue could be designated as a phosphopyridoxyl lysine. This suggests that the catalytic function of IMPP is modulated by the binding of PLP to a specific lysyl residue at or near its substrate-binding site of the protein.

Determination of amino acids in Sargassum fusiforme by high performance capillary electrophoresis

High performance capillary electrophoresis (HPCE) was developed for quantitative determination of 18 phenylthiohydantoin (PTH)–amino acids. The influence of electrolyte concentration, pH, organic modifier and applied voltage on HPCE performance was investigated. The HPCE separation of a PTH–amino acids mixture was much improved by adding organic modifier and Tris–boric acid buffer to the run buffer. After optimization of the method, 17 PTH–amino acids in a solution containing 18 PTH–amino acids could be separated using 400 mmol l −1 Tris–boric acid, 1.0 mmol l −1 diethylamine at pH 9.5 adjusted with 0.1 mol l −1 NaOH as a run buffer, voltage of 25 kV was applied, temperature was maintained at 25 °C, detection wavelength was 254 nm. The precision ( n = 7) of this method is less than 3.2% (peak area) and 1.1% (migration time) of relative standard deviation (R.S.D.). Linearity was established over the concentration range 50–1000 μM of each derivative, with correlation coefficients ( r) ranging between 0.9904 and 0.9993. The detection limits (S/N = 3) range from 2 to 48 μmol l −1. The method was applied to determine amino acids in Sargassum fusiforme, a marine algae collected from Tongtou County of Zhejiang Province in China with satisfactory results.

Evidence for Domain-specific Recognition of SK and Kv Channels by MTX and HsTx1 Scorpion Toxins

Maurotoxin (MTX) and HsTx1 are two scorpion toxins belonging to the alpha-KTx6 structural family. These 34-residue toxins, cross-linked by four disulfide bridges, share 59% sequence identity and fold along the classical alpha/beta scaffold. Despite these structural similarities, they fully differ in their pharmacological profiles. MTX is highly active on small (SK) and intermediate (IK) conductance Ca(2+)-activated (K(+)) channels and on voltage-gated Kv1.2 channel, whereas HsTx1 potently blocks voltage-gated Kv1.1 and Kv1.3 channels only. Here, we designed and chemically produced MTX-HsTx1, a chimera of both toxins that contains the N-terminal helical region of MTX (sequence 1-16) and the C-terminal beta-sheet region of HsTx1 (sequence 17-34). The three-dimensional structure of the peptide in solution was solved by (1)H NMR. MTX-HsTx1 displays the activity of MTX on SK channel, whereas it exhibits the pharmacological profile of HsTx1 on Kv1.1, Kv1.2, Kv1.3, and IK channels. These data demonstrate that the helical region of MTX exerts a key role in SK channel recognition, whereas the beta-sheet region of HsTx1 is crucial for activity on all other channel types tested.

The Hippocampal Cholinergic Neurostimulating Peptide, the N-terminal Fragment of the Secreted Phosphatidylethanolamine-binding Protein, Possesses a New Biological Activity on Cardiac Physiology

Phosphatidylethanolamine-binding protein (PEBP), alternatively named Raf-1 kinase inhibitor protein, is the precursor of the hippocampal cholinergic neurostimulating peptide (HCNP) corresponding to its natural N-terminal fragment, previously described to be released by hippocampal neurons. PEBP is a soluble cytoplasmic protein, also associated with plasma and reticulum membranes of numerous cell types. In the present report, using biochemistry and cell biology techniques, we report for the first time the presence of PEBP in bovine chromaffin cell, a well described secretion model. We have examined its presence at the subcellular level and characterized this protein on both secretory granule membranes and intragranular matrix. In addition, its presence in bovine chromaffin cell and platelet exocytotic medium, as well as in serum, was reported showing that it is secreted. Like many other proteins that lack signal sequence, PEBP may be secreted through non-classic signal secretory mechanisms, which could be due to interactions with granule membrane lipids and lipid rafts. By two-dimensional liquid chromatography-tandem mass spectrometry, HCNP was detected among the intragranular matrix components. The observation that PEBP and HCNP were secreted with catecholamines into the circulation prompted us to investigate endocrine effects of this peptide on cardiovascular system. By using as bioassay an isolated and perfused frog (Rana esculenta) heart preparation, we show here that HCNP acts on the cardiac mechanical performance exerting a negative inotropism and counteracting the adrenergic stimulation of isoproterenol. All together, these data suggest that PEBP and HCNP might be considered as new endocrine factors involved in cardiac physiology.

Temperature- and pH-responsive aminopropyl-silica ion-exchange columns grafted with copolymers of N-isopropylacrylamide

We have designed copolymers of N-isopropylacrylamide, environmentally-responsive polymers, which respond to temperature and other external stimuli. In this study, we designed and synthesized copolymers that introduced ion-exchange groups. These copolymers responded to the temperature and the pH, and the copolymer-grafted aminopropyl silica beads were used as HPLC packing materials. This stationary phase altered the properties from hydrophilic to hydrophobic and from charge to non-charge by temperature and pH changes. We studied the separations of organic acids and phenylthiohydantoin-amino acids using environmentally-responsive chromatography, and confirmed the effects of the ion-exchange groups. The elution behaviors of these samples were controlled by the temperature changes without organic solvents in the mobile phase. It was confirmed that the interactions between the solute and stationary phase could be freely controlled by the temperature and the pH. Environmentally-responsive chromatography is expected to be applicable to the separation of pharmaceuticals and biomolecules, such as peptides, proteins and nucleic acids.