Cloning and Sequencing of the xynA Gene Encoding Xylanase A of Aspergillus kawachii

We have cloned the xynA gene coding for xylanase A, a major component of the xylanase family, from Aspergillus kawachii. The cDNA was isolated from an A. kawachii cDNA library by immunoscreening using antibody raised against the purified xylanase A protein. Nucleotide sequence analysis of the cDNA showed a 981-bp open reading frame that encoded a protein of 327 amino acid residues. The signal peptide was composed of 25 amino acid residues and the N-terminus of the mature protein was pyroglutamic acid. The transformed yeast with a cloned cDNA produced xylanase. The genomic DNA was arranged as ten exons and nine introns.     

The γ1 heavy-chain disease FOR protein is present in two molecular forms

Heavy chain disease proteins (FOR) were isolated from human plasma. These proteins were also detected immunochemically in the urine of the patient. The proteins were disulphide-linked Fc-like dimers with molar mass 64.2 kg/mol and sedimentation rate S _20,w ⁰ = = 0.356 ps (3.56 S). Similar amounts of aspartic acid and pyroglutamic acid were found at the N-terminus. After cyanogen bromide cleavage of the FOR proteins, three peptides were isolated and their amino acid composition and partial amino acid sequence was determined. We suggest that two Fc-like proteins of similar sizes are present in the plasma: (1) the first with N-terminal aspartic acid corresponding to position 221 of γ1 EU chain and (2) the second with N-terminal pyroglutamic acid. The first protein and small amounts of related low-molar mass fragments found also in the plasma could be degradation products of the second protein. Evidence is given on structural differences between the FOR proteins and the corresponding portion of the γ1 EU chain.     

Coordination ability of the thyrotropin releasing factor, l-pyroglutamyl-l-histidyl-l-prolinamide(TRF).III. Cu(II) and Ni(II) complexes with TRF and its di- and tripeptide analogues

The results are reported of a spectroscopic and potentiometric study of the copper(II) and nickel(II) complexes of the thyrotropin releasing factor (L-pyroglutamyl-L-histidyl-L-prolinamide, TRF) and some of its di- and tripeptide analogues Spectroscopic techniques used include absorption, circular dichroism and electron paramagnetic resonance spectroscopy TRF and pyroglutamyl-histidine behave similarly. At low pH the metal ions coordinate to the imidazole nitrogen and then cause the ionization of the amide protons of both the peptide linkage and the pyroglutamic acid with equal ease. Hence the concentration of MH_?1 L species is always very low. The C-terminal proline amide residue plays an insignificant role in the complex formation Replacement of pyroglutamic acid with picolinic acid in the hormone molecule causes a major change in the structures of its complexes. The dipeptide analogue, Pic-His. forms dimeric species with Cu(II) that are not found in Cu(II) Pyr-His orCu(II) TRF solutions The introduction of tyrosine residue in the TRF sequence in place of histidine can, in some cases, lead to the direct involvement of proline amide in the binding of metal ions, e.g. , Ni(II) Pyr-Tyr-Pro-NH₂     

Isolation of N-acetylglutamine, pyroglutamic acid and the butyl ester of pyroglutamic acid from human brain

N-acetyl-l -glutamine, pyroglutamic acid, and the butyl ester of pyroglutamic acid were isolated in pure form from an aqueous extract of human brain. These compounds were isolated by combination of paper and ion exchange chromatography. The isolated substance identified as N-acetyl-l -glutamine did not react with the ninhydrin reagent but yielded glutamic acid and ammonia upon acid hydrolysis. An acetyl hydrazide was identified by paper chromatography from hydrazinolysates of the isolated substance. The glutamic acid liberated by hydrolysis had the l -configuration. The results of elementary analysis of the isolated compound were in full accord with the analysis calculated for synthetic N-acetyl-l -glutamine. A large amount of pyroglutamic acid and a substance identical with the butyl ester of pyroglutamic acid were isolated in pure form. The results of our studies suggest that pyroglutamic and the butyl ester derivative were artifacts formed during the isolation and purification procedures.     

CE-UV/VIS and CE-MS for monitoring organic impurities during the downstream processing of fermentative-produced lactic acid from second-generation renewable feedstocks

Background

During the downstream process of bio-based bulk chemicals, organic impurities, mostly residues from the fermentation process, must be separated to obtain a pure and ready-to-market chemical. In this study, capillary electrophoresis was investigated for the non-targeting downstream process monitoring of organic impurities and simultaneous quantitative detection of lactic acid during the purification process of fermentatively produced lactic acid. The downstream process incorporated 11 separation units, ranging from filtration, adsorption and ion exchange to electrodialysis and distillation, and 15 different second-generation renewable feedstocks were processed into lactic acid. The identification of organic impurities was established through spiking and the utilization of an advanced capillary electrophoresis mass spectrometry system.

Results

A total of 53 % of the organic impurities were efficiently removed via bipolar electrodialysis; however, one impurity, pyroglutamic acid, was recalcitrant to separation. It was demonstrated that the presence of pyroglutamic acid disrupts the polymerization of lactic acid into poly lactic acid. Pyroglutamic acid was present in all lactic acid solutions, independent of the type of renewable resource or the bacterium applied. Pyroglutamic acid, also known as 5-oxoproline, is a metabolite in the glutathione cycle, which is present in all living microorganisms. pyroglutamic acid is found in many proteins, and during intracellular protein metabolism, N-terminal glutamic acid and glutamine residues can spontaneously cyclize to become pyroglutamic acid. Hence, the concentration of pyroglutamic acid in the lactic acid solution can only be limited to a certain amount.

Conclusions

The present study proved the capillary electrophoresis system to be an important tool for downstream process monitoring. The high product concentration encountered in biological production processes did not hinder the capillary electrophoresis from separating and detecting organic impurities, even at minor concentrations. The coupling of the capillary electrophoresis with a mass spectrometry system allowed for the straightforward identification of the remaining critical impurity, pyroglutamic acid. Although 11 separation units were applied during the downstream process, the pyroglutamic acid concentration remained at 12,900 ppm, which was comparatively high. All organic impurities found were tracked by the capillary electrophoresis, allowing for further separation optimization.

     

Levansucrase from Acetobacter diazotrophicus SRT4 Is Secreted via Periplasm by a Signal-Peptide-Dependent Pathway

Acetobacter diazotrophicus SRT4 secretes a constitutive levansucrase (LsdA) (EC 2.4.1.10) that is responsible for sucrose utilization. Immunogold electron microscopical studies revealed that LsdA accumulates in the periplasm before secretion. The periplasmic and extracellular forms of the enzyme were purified to homogeneity. Both proteins exhibited similar physical and biochemical characteristics indicating that LsdA adopts its final conformation in the periplasm. The N-terminal sequence of mature LsdA was pGlu-Gly-Asn-Phe-Ser-Arg as determined by PSD-MALDI-TOFMS (post-source decay—matrix-assisted laser desorption/ionization—time-of-flight mass spectrometry). Comparison of this sequence with the predicted precursor protein revealed the cleavage of a 30-residue typical signal peptide followed by the formation of the pyroglutamic acid (pGlu) residue. Thus, in contrast with other Gram-negative bacteria, A. diazotrophicus secretes levansucrase by a signal-peptide-dependent mechanism. Received: 24 March 1999 / Accepted: 30 April 1999     

Neurochemical effects ofl-pyroglutamic acid

The effect ofl-pyroglutamic acid, a metabolite that accumulates in pyroglutamic aciduria, on different neurochemical parameters was investigated in adult male Wistar rats. Glutamate binding, adenylate cyclase activity and G protein coupling to adenylate cyclase were assayed in the presence of the acid.l-pyroglutamic acid decreased Na⁺-dependent and Na⁺-independent glutamate binding Basal and GMP-PNP stimulated adenylate cyclase activity were not affected by the acid. Furthermore, rats received unilateral intrastriatal injections of 10–300 nmol of bufferedl-pyroglutamic acid. Vehicle (0.25 M Tris-Cl, pH 7.35–7.4) was injected into the contralateral striatum. Neurotoxic damage was assessed seven days after the injection by histological examination and by weighing both cerebral hemispheres. No difference in histology or weight could be identified between hemispheres. These results suggest that, although capable of interfering with glutamate binding, pyroglutamate did not cause a major lesion in the present model of neurotoxicity.     

Metabolism and protein transport of a possible pupal cuticle tanning agent in Manduca sexta

Injections of [¹⁴C] glucose and [³H] dopamine have shown the existence of a phenolic conjugate in pharate and tanning pupae. The function and structure of this conjugate is unknown; however, tracer studies have shown it to be ionically associated with a small peptide. Reinjection of this double-labelled peptide results in the transfer of the phenol, but not the label from the glucose to a large protein complex where it is tightly bound. Subsequent tracing of the phenolic-labelled protein complex demonstrated that it crossed the epidermis and became incorporated into the cuticle.     

Antibodies to recombinant fragment 212–276 of protein C specifically recognize the intact human molecule

The peptide fragment Pro²¹²-Ile²⁷⁶ of human protein C was produced as a part of a fusion protein in Escherichia coli. The identity of the peptide was confirmed by immunoblotting experiments using specific antibodies to intact protein C. The peptide Pro²¹²-Ile²⁷⁶ was isolated from the fusion protein after mild hydrolysis with formic acid by gel filtration and reverse-phase HPLC. This peptide fragment was used to produce antibodies specific for the heavy chain of protein C which recognized native protein C present in blood plasma. Antibodies to intact protein C reacted also with the Pro²¹²-Ile²⁷⁶ peptide fragment, indicating that this region is immunogenic in intact protein C and may represent a native epitope.     

Stability and CTL activity of N-terminal glutamic acid containing peptides.

Several cytotoxic T lymphocyte peptide-based vaccines against hepatitis B, human immunodeficiency virus and melanoma were recently studied in clinical trials. One interesting melanoma vaccine candidate alone or in combination with other tumor antigens, is the decapeptide ELA. This peptide is a Melan-A/MART-1 antigen immunodominant peptide analog, with an N-terminal glutamic acid. It has been reported that the amino group and gamma-carboxylic group of glutamic acids, as well as the amino group and gamma-carboxamide group of glutamines, condense easily to form pyroglutamic derivatives. To overcome this stability problem, several peptides of pharmaceutical interest have been developed with a pyroglutamic acid instead of N-terminal glutamine or glutamic acid, without loss of pharmacological properties. Unfortunately compared with ELA, the pyroglutamic acid derivative (PyrELA) and also the N-terminal acetyl-capped derivative (AcELA) failed to elicit cytotoxic T lymphocyte (CTL) activity. Despite the apparent minor modifications introduced in PyrELA and AcELA, these two derivatives probably have lower affinity than ELA for the specific class I major histocompatibility complex. Consequently, in order to conserve full activity of ELA, the formation of PyrELA must be avoided. Furthermore, this stability problem is worse in the case of clinical grade ELA, produced as an acetate salt, like most of the pharmaceutical grade peptides. We report here that the hydrochloride salt, shows higher stability than the acetate salt and may be suitable for use in man. Similar stability data were also obtained for MAGE-3, another N-terminal glutamic acid containing CTL peptide in clinical development, leading us to suggest that all N-terminal glutamic acid and probably glutamine-containing CTL peptide epitopes may be stabilized as hydrochloride salts.     

Protein synthesis in rabbit reticulocytes XXII+: a heat stable dialyzable factor (EIF-I*) modulates Met-tRNAf binding to EIF-1.

The peptide chain initiation factor EIF-1 forms a ternary complex, Met-tRNA_f·EIF-1·GTP in the absence of Mg⁺⁺ and the preformed complex is stable to Mg⁺⁺. However, with homogeneous preparations of EIF-1, addition of Mg⁺⁺ during the initial formation of the ternary complex strongly inhibits the complex formation.A heat stable dialyzable factor (EIF-1¹) which mostly remains associated with the high molecular weight protein complex, EIF-2 (TDF) during purification of the peptide chain initiation factors, has been purified using a phenol extraction procedure. EIF-1¹ restores the Met-tRNA_f binding activity of EIF-1 in the presence of 1 mM Mg⁺⁺; in the presence of EIF-1¹, Met-tRNA_f binding by EIF-1 shows a sharp Mg⁺⁺ optimum around 1 mM. EIF-1¹ is heat stable, alkali stable, dialyzable and pronase sensitive. The same EIF-1¹ preparation also strongly inhibits Met-tRNA_f binding to EIF-1 in the absence of Mg⁺⁺ and stimulates protein synthesis in a mRNA-dependent rabbit reticulocyte lysate system.     

Conformational Studies on Calcium Binding By tBoc-Leu-Pro-Tyr-Ala-NHCH3, a Tyrosine Kinase Substrate,in a Nonpolar Solvent

Abstract

With a view to understanding the structural requirement for tyrosine phosphorylation, we have examined the free and Ca²⁺-bound conformations of the synthetic peptide tBoc-Leu-Pro-Tyr-Ala-NHCH₃, a substrate for a protein tyrosine kinase, using circular dichroism (CD), ¹H and ¹³C nuclear magnetic resonance (NMR) and molecular modeling methods. CD spectrum of the free peptide in water showed a random coil structure, while the spectrum in acetonitrile was indicative of a folded structure containing a type III β-turn. Dihedral angle data derived from J_NH-CH coupling constants, as well as two-dimensional ¹H-COSY and NOESY spectral analyses, showed that the peptide adopts a conformation close to the 3_10- helix. Ca²⁺ binding by the peptide, as monitored by CD spectral changes, was quite weak in water. However, substantial CD spectral changes were observed in the peptide on addition of Ca²⁺ in acetonitrile suggestive of major conformational alterations due to Ca²⁺ binding. Analysis of the binding isotherms at 25°C obtained from CD data in acetonitrile indicated a 2:1 peptide:Ca²⁺ (“sandwich”) complex to be the dominant species with a K_d of about 30μM. A. 1:1 complex was also present and became significant at Ca²⁺:peptide ratios above 1. By comparison, the peptide formed a predominantly 1:1 complex with Mg²⁺ with a K_d of about 40μM. ¹³C-NMR data showed that a mixture of cis and trans conformers (arising from rotation around the Leu-Pro bond) in the free peptide changes over to the all-trans form on coordination of the peptide carbonyl groups to the Ca²⁺ ion. ¹H-NOESY data of the Ca²⁺ complex revealed several interactions involving the sidechains of two peptide molecules in the sandwich. Molecular modeling and energy minimization with and without the input of NOESY-derived distance constraints showed the sandwich complex to be an energetically very favourable conformation. Besides its relevance in terms of the possible involvement of divalent cations in substrate-tyrosine kinase interaction, the conformational characterization of tBoc-Leu-Pro-Tyr-Ala-NHCH₃ and its Ca²⁺ complex should help understand the conformational determinants for Ca²⁺-binding by linear peptides.     

The primary structure of an endocuticular protein from two locust species,Locusta migratoria and Schistocerca gregaria,determined by a combination of mass spectrometry and automatic Edman degradation

The complete primary structures of two variants of a protein, Abd-5, isolated from the endocuticles of the migratory locust Locusta migratoria and the desert locust Schistocerca gregaria, have been determined. The proteins from the two species are N-terminally blocked with pyroglutamic acid. Their sequences differed only in two positions. Comparison of the sequences to those of other cuticular proteins shows that moderate homologies exist to 11 other cuticular proteins from insects representing four different orders. Amino acid residues in certain positions appear to be strictly conserved.     

A positive charge at the N-terminal segment of Discrepin increases the blocking effect of K channels responsible for the IA currents in cerebellum granular cells

Discrepin is a scorpion peptide that blocks preferentially the I_A currents of the voltage-dependent K⁺ channel of rat cerebellum granular cells. It was isolated from the venom of the buthid scorpion Tityus discrepans and contains 38 amino acid residues with a pyroglutamic acid at the N-terminal site. Discrepin has the lowest sequence identity (approx. 50%) among the six members of the α-KTx15 sub-family of scorpion toxins. In order to find out which residues are important for the blocking effects of Discrepin, six mutants were chemically synthesized (V6K, I19R, D20K, T35V, I19R-D20K, I19R-D20K-R21V), correctly folded and their physiological properties were examined. Substitution of residues V6 and D20 for basically charged amino acids increases the blocking activity of Discrepin, specially the mutation V6K at the N-terminal segment of the toxin. Analysis of 3D-structure models of the mutants V6K and D20K supports the idea that basic residues improve their blocking activities, similarly to what happens with BmTx3, a toxic peptide obtained from Buthus martensi scorpion, which has the highest known blocking effects of I_A currents in K⁺ channels of rat cerebellum granular cells.     

Formation of specific amino acid sequences during thermal polymerization of amino acids

The mechanism of the thermal polymerization (at 180°C) of glutamic acid, tyrosine, and glycine has been studied. Glutamic acid is quickly and almost completely converted into pyroglutamic acid. The only dipeptide that is formed by dimerization of the remaining two amino acids is cyclic glycyl-tyrosine (a diketopiperazin). In a secondary reaction pyroglutamic acid interacts with cyclic glycyl-tyrosine and yields pyroglutamyl-glycyltyrosine and pyroglutamyl-tyrosyl-glycine. Other di- or tripeptides are not observed. The preferential appearance of the two pyroglutamyl-peptides has been reported earlier by Nakashima et al. (1977). The present data explain those results. Model experiments show that cyclic glycyl-tyrosine can also be cleaved by other acids or bases. In the presence of acetic acid at 118°C N-acetyl-glycyl-tyrosine is the major product. Partial hydrolysis predominantly yields tyrosyl-glycine. These effects are explained by stereospecific interactions. The results on self-ordering of amino acids during peptide formation are discussed in respect of the origin of prebiotic enzymes and genetic information.     

Characterization and Evaluation of Key Sites in the Peptide Inhibitor of TAB1/p38α Interaction

A combination of computation techniques and peptide mutants have been used to determine the binding site and amino acid residues on the inhibitor peptide that are critical for binding to Mitogen-activated protein kinase 14 (p38α). In our previous research work, the functional peptide, named as PT5, target to p38α, was obtained based on the theoretical complex structure of p38α and [transforming growth factor-β (TGF-β)-activated protein kinase 1 (TAK1)-binding protein 1] (TAB1). Based on the computer-guided ab initio modeling method, the inhibitor peptide PT5 and its mutants were modeled. Furthermore, the 3-D complex structures of PT5 or its mutants and p38α were constructed using molecular docking and dynamics simulation methods. The key residues in the peptide PT5 involved in binding interaction to p38α were predicted. According to the 3-D theoretical complex structure PT5/ p38α, the interaction binding mode between PT5 and p38α was analyzed using distance geometry technology. Mutants of the peptide PT5 was used to evaluate the bio-function when the critical residues were mutated. The mutant experimental results identified the key residues in PT5, i.e. Thr¹¹ and Asp¹² and determined the core sequence of PT5 binding to p38α. Based on the results, optimized peptides compounds could be developed for treating myocardial ischemia/reperfusion (I/R) injury in clinical.     

Stability and CTL-activity of P40/ELA Melanoma Vaccine Candidate

The decapeptide ELA (ELAGIGILTV), a Melan-A/MART-1 antigen immunodominant peptide analogue, is an interesting melanoma vaccine candidate alone or in combination with other tumour antigens. P40, the recombinant outer membrane protein A of Klebsiella pneumoniae (kpOmpA), was recently shown to target dendritic cells and to induce peptide-specific CTLs. Here we investigated the adjuvant role of P40 mixed or chemically conjugated to ELA. This compound is an N-terminal glutamic acid-containing peptide. However, it has been reported that the amino group and the gamma-carboxylic group of glutamic acids easily condense to form pyroglutamic derivatives. Usually, to overcome this stability problem, peptides of pharmaceutical interest were developed with a pyroglutamic acid instead of N-terminal glutamic acid, without loss of pharmacological properties. Unfortunately, the pyroglutamic acid derivative (PyrELA) as well as the N-terminal acetyl capped derivative (AcELA) failed to elicit CTL activity when mixed with P40 adjuvant protein. Despite the apparent minor modifications introduced by PyrELA and AcELA, these two derivatives have probably lower affinity than ELA for the class I Major Histocompatibility Complex. Furthermore, this stability problem is worse in the case of clinical grade ELA, produced as an acetate salt, like most of the pharmaceutical grade peptides. We report here that the hydrochloride shows a higher stability than the acetate and may be suitable for use in man.     

Formation of specific amino acid sequences during carbodiimide-mediated condensation of amino acids in aqueous solution,and computer-simulated sequence generation

Carbodiimide-mediated peptide synthesis in aqueous solution has been studied with respect to self-ordering of amino acids. The copolymerisation of amino acids in the presence of glutamic acid or pyroglutamic acid leads to short pyroglutamyl peptides. Without pyroglutamic acid the formation of higher polymers is favoured.The interactions of the amino acids and the peptides, however, are very complex. Therefore, the experimental results are rather difficult to explain. Some of the experimental results, however, can be explained with the aid of computer simulation programs. Regarding only the tripeptide fraction the copolymerisation of pyroGlu, Ala and Leu, as well as the simulated copolymerisation lead to pyroGlu-Ala-Leu as the main reaction product. The amino acid composition of the insoluble peptides formed during the copolymerisation of Ser, Gly, Ala, Val, Phe, Leu and Ile corresponds in part to the computer-simulated copolymerisation data.     

Formation of specific amino acid sequences during carbodiimide-mediated condensation of amino acids in aqueous solution, and computer-simulated sequence generation

Carbodiimide-mediated peptide synthesis in aqueous solution has been studied with respect to self-ordering of amino acids. The copolymerisation of amino acids in the presence of glutamic acid or pyroglutamic acid leads to short pyroglutamyl peptides. Without pyroglutamic acid the formation of higher polymers is favoured. The interactions of the amino acids and the peptides, however, are very complex. Therefore, the experimental results are rather difficult to explain. Some of the experimental results, however, can be explained with the aid of computer simulation programs. Regarding only the tripeptide fraction the copolymerisation of pyroGlu, Ala and Leu, as well as the simulated copolymerisation lead to pyroGlu-Ala-Leu as the main reaction product. The amino acid composition of the insoluble peptides formed during the copolymerisation of Ser, Gly, Ala, Val, Phe, Leu and Ile corresponds in part to the computer-simulated copolymerisation data.