Oligopeptide Synthesis Research Articles

NewL-Amino Acid Ligases Catalyzing Oligopeptide Synthesis from Various Microorganisms

L-Amino acid ligase synthesizes various peptides from unprotected L-amino acids in an ATP-dependent manner. Known L-amino acid ligases catalyze only dipeptide synthesis, but recently we found that RizB of Bacillus subtilis NBRC 3134 catalyzes oligopeptide synthesis. In the present study, we searched for new members of the L-amino acid ligase group that catalyze oligopeptide synthesis. Several hypothetical proteins possessing the ATP-grasp motif were selected by in silico analysis. These recombinant proteins were assayed for L-amino acid ligase activity. We obtained five L-amino acid ligases showing oligopeptide synthesis activities. These proteins showed low similarity in amino acid sequence, but commonly used branched-chain amino acids, such as RizB, as substrates. Furthermore, the spr0969 protein of Streptococcus pneumoniae synthesized longer peptides than those synthesized by RizB, and the BAD_1200 protein of Bifidobacterium adolescentis showed higher activity toward aromatic amino acids than toward branched-chain ones. We also examined some of their characteristics.

Protease-Catalyzed Oligomerization of Hydrophobic Amino Acid Ethyl Esters in Homogeneous Reaction Media Using l-Phenylalanine as a Model System

Enzymatic synthesis of oligopeptides from l-phenylalanine ethyl ester hydrochloride (l-Phe-Et.HCl) and other l-form hydrophobic amino acid ester hydrochlorides in water miscible organic cosolvents was studied. Different proteases, water miscible cosolvents, and effect of different ratios of water miscible cosolvents for protease-catalyzed oligo-phenylalanine [oligo(l-Phe)] were compared. The importance of the use of water miscible cosolvents in transforming reactions from heterogeneous to homogeneous conditions as a potent medium engineering tool for protease-catalyzed oligopeptide synthesis is highlighted. For example, at 0.125 M l-Phe-Et.HCl, 20% (v/v) methanol, 18.6 mg/mL bromelain, in phosphate buffer (0.25M, pH 8), 40 degrees C, for 3 h, oligo(l-Phe) precipitated from the solution to yield 45 +/- 5%, in contrast, in the absence of cosolvent oligo(l-Phe) yield of 29 +/- 5% was obtained. The following reaction conditions were optimized for bromelain catalyzed oligo(l-Phe) synthesis: pH, temperature, substrate, enzyme, and cosolvent concentrations. DP(avg) and chain length distribution in the product peptides were investigated by (1)H NMR and MALDI-TOF.

A NovelL-Amino Acid Ligase fromBacillus subtilisNBRC3134 Catalyzed Oligopeptide Synthesis

L-Amino acid ligase catalyzes dipeptide synthesis from unprotected L-amino acids in an ATP-dependent manner. We have purified a new L-amino acid ligase, RizA, which synthesizes dipeptides whose N-terminus is Arg, from Bacillus subtilis NBRC3134, a microorganism that produces a rhizocticin peptide antibiotic. It was suggested that RizA is probably involved in rhizocticin biosynthesis. In this study, we performed sequence analysis of unknown regions around rizA, and newly identified a gene that encodes a protein that possesses an ATP-grasp motif upstream of rizA. This gene was designated rizB, and its recombinant protein was prepared. Recombinant RizB synthesized homo-oligomers of branched-chain L-amino acids and L-methionine consisting of two to five amino acids in an ATP-dependent manner. RizB also synthesized various heteropeptides. Further examination showed that RizB might elongate a peptide chain at the N-terminus. This is the first report on an L-amino acid ligase catalyzing oligopeptide synthesis.

Novel L-Amino Acid Ligases Catalyzing Oligopeptide Synthesis

L-Amino acid ligase (EC 6.3.2.28) is a microbial enzyme catalyzing formation of an alpha-peptide bond from unprotected L-amino acids in an ATP-dependent manner. The YwfE protein from Bacillus subtilis 168 was the first reported L-amino acid ligase, and it synthesizes various dipeptides. Thereafter, several L-amino acid ligases were newly obtained by in silico analysis using the ATP-grasp motif. But these L-amino acid ligases synthesize only dipeptide and no longer peptide. A novel L-amino acid ligase capable of catalyzing oligopeptide synthesis is required to increase the variety of peptides. We have previously found a new member of L-amino acid ligase, RizA, from B. subtilis NBRC3134, a microorganism that produces the peptide-antibiotic rhizocticin. We newly found that a gene at approximately 9 kbp upstream of rizA encoded a novel L-amino acid ligase RizB. Recombinant RizB synthesized homo-oligomers of branched-chain amino acids consisting of 2 to 5 amino acids, and also synthesized various heteropeptides. RizB is the first reported L-amino acid ligase that catalyzes oligopeptide synthesis. In addition, we obtained L-amino acid ligases showing oligopeptide synthesis activities by in silico analysis using BLAST, which is a set of similarity search programs. These L-amino acid ligases showed low similarity in amino acid sequence, but commonly used branched-chain amino acids, such as RizB, as substrates. Furthermore, the spr0969 protein of Streptococcus pneumoniae synthesized longer peptides than those synthesized by RizB, and the BAD_1200 protein of Bifidobacteria adolescentis showed higher activity toward aromatic amino acids than toward branched-chain ones.

ChemInform Abstract: Enzyme‐Catalyzed Oligopeptide Synthesis — Rapid Regioselective Oligomerization of L‐Glutamic Acid Diethyl Ester Catalyzed by Papain

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Hydrophilic modifications in peptide nucleic acid — Synthesis and properties of PNA possessing 5-hydroxymethyluracil and 5-hydroxymethylcytosine

We have investigated the chemistry for the incorporation of C5-hydroxymethyl-uracil and -cytosine in peptide nucleic acid (PNA) and the subsequent effect of this modification on PNA hybridization behavior. Largely based on literature precedent, we prepared a peptide nucleic acid monomer, possessing 5-hydroxymethyuracil, which was compatible with Fmoc-based oligopeptide synthesis. An improved, large-scale synthesis of 5-hydroxymethylcytosine was developed, as a starting point for the synthesis of a monomer containing this nucleobase. In each case, the hydroxyl group was blocked as a t-butyldiphenylsilyl ether, and the exocyclic amino group of cytosine was additionally blocked with the benzoyl-group. The modified monomers were incorporated into isolated positions in the oligomer sequence using standard protocols. The modified oligomers showed that the 5-hydroxymethyl group is compatible with triplex and duplex formation.Key words: peptide nucleic acid, hydroxymethyluracil, hydroxymethylcytosine, modified nucleobase, hybridization.

A novel strategy for oligopeptide synthesis using a polymer-supported ammonium fluoride

A novel method for the preparation of oligopeptides with a PS-ammonium fluoride in the solution phase is reported. The synthesis of lipid II pentapeptide is efficiently synthesized via a PS-ammonium fluoride without chromatographic purifications. The method reported here is very convenient to synthesize a relatively large amount of oligopeptides with abundantly available Fmoc-protected amino acids in a time efficient manner.

Labeling of proteins and oligopeptides with luminescent lanthanide(III) chelates

Synthesis of a building block that allows introduction of photoluminescent europium(III) and samarium(III) chelates to synthetic oligopeptides on solid phase using standard Fmoc chemistry is described. Upon completion of the oligopeptide synthesis, these conjugates were converted to the corresponding lanthanide(III) chelates by treatment with appropriate lanthanide(III) salt. Also synthesis of a new terpyridine-based europium(III) chelate designed for solution phase protein labeling is demonstrated.

Light directed massively parallel on‐chip synthesis of peptide arrays with t‐Boc chemistry

Peptide and peptidomimetic molecule arrays are emerging powerful tools for parallel screening of binding in proteomics and pharmaceutical discovery research. Up to now the common method of preparing peptide arrays was based on spotting on glass using a library of presynthesized peptides. However, due to the large number of monomers (amino acids) it is not possible to have combinatorial libraries which include all combinations of natural and synthetic amino acids. We describe a very flexible on-chip oligopeptide synthesis method which uses the well developed t-Boc based solid state synthesis chemistry. A very high degree of flexibility is achieved by using light photo generated acids and maskless projection lithography for spatially directed deprotection. Use of microfluidic chips enables moderately high densities, short reaction times and off-the-shelf chemicals. Examples are given from synthesis of metal ion binding peptides and epitope binding assays.

Synthesis and characterization of peptides containing a cyclic Val adduct of diepoxybutane, a possible biomarker of human exposure to butadiene.

1,3-Butadiene, a potential human carcinogen widely used in industry, is oxidized by cytochrome P450 to diepoxybutane (DEB), which is the most mutagenic of the known butadiene metabolites. Assessment of the toxicological significance of DEB formation in humans and animals requires identification of a biomarker uniquely associated with DEB for use in molecular dosimetry studies. We wished to develop a specific and sensitive assay for one such suitable marker, the cyclic adduct 2-(3,4-dihydroxypyrrolidin-1-yl)-3-methylbutyramide (pyr-V), which is formed from addition of DEB to the terminal Val of the alpha- and beta-chains of hemoglobin. We needed to prepare a pure, rigorously characterized DEB-modified N-terminal oligopeptide for raising antibodies both to use in an immunoaffinity purification step and to standardize the assay. In addition, we needed a pure isotopomer to serve as an internal standard for quantitation by LC-MS. Direct modification of the globin sequences by reaction with DEB in vitro proved to be unproductive. We therefore opted to synthesize the cyclic Val adduct and incorporate it by FMOC chemistry into the appropriate oligopeptide sequences. In vitro and in vivo, butadiene is oxidized to enantiomeric and meso forms of DEB. A priori, all three DEB isomers are expected to form pyr-V adducts, resulting in three diastereomeric N-terminal peptides. We therefore synthesized a mixture of the cyclic Val diastereomers as their methyl esters by reaction of DEB with l-Val methyl ester hydrochloride. After protection as the di-O-tert-butyl derivatives, the mixture of 2-(3,4-di-t-butoxypyrrolidin-1-yl)-3-methylbutyric acid diastereomers was incorporated as the N-terminal residue into the 1-11 human globin alpha-chain sequence VLSPADKTNVK. The presence of the three diastereomers was confirmed by two-dimensional correlation NMR spectroscopy and temperature-dependent (1)H NMR. This strategy enabled us to obtain pure, rigorously characterized haptens in quantity for the preparation of polyclonal antibodies. Use of FMOC-protected (2)H(3)-Leu in the automated oligopeptide synthesis provided the required isotopomers for use as internal standard.

Light-directed simultaneous synthesis of oligopeptides on microarray substrate using a photogenerated acid.

Photogenerated acid (PGA) was used as the acid to remove the protection group from amino acids or peptide oligomers. Comparative study of the deprotection using a PGA, trisarylsulfonium antimonyhexafluoride (SSb), and trifluoroacetic acid (TFA) was performed on glass microscope slides. The results showed that PGA can replace TFA in the deprotection step of oligopeptide synthesis with comparable efficiencies. Acids needed for the deprotection step were generated in situ by light activation of the precursor molecule on the microwell substrate. A mask-less laser light illumination system was used to activate the precursor. The accuracy of the amino acid sequence of the synthesized oligopeptide and the location of the synthesis was illustrated by the specific recognition binding of two different models: lead(II) ion-peptide biosensor for lead(II) and human protein p53 (residue 20-25)-mouse MAb DO1. After parallel synthesis of the target peptide models and their analogues based on the predetermined pattern, specific binding treatment, and fluorescence labeling, the fluorescence emission images of the oligopeptide microarray showed fluorescence intensity as a result of specific binding at the correct locations of the array. The stepwise synthesis efficiencies of pentapeptide synthesis on the microwell substrate range are approximately 96-100% and do not decrease with respect to the chain length of the peptide.

A Simplified Reconstitution of mRNA-Directed Peptide Synthesis: Activity of the Epsilon Enhancer and an Unnatural Amino Acid

The study of the early events in translation would be greatly facilitated by reconstitution with easily purified components. Here, Escherichia coli oligopeptide synthesis has been reconstituted using five purified recombinant His-tagged E. coli initiation and elongation factors. Highly purified ribosomes are required to yield products with strong dependencies on the translation factors. Based on HPLC separation of radiolabeled translation products from an mRNA encoding a tetrapeptide, approximately 80% of peptide products are full length, and the remaining 20% are the dipeptide and tripeptide products resulting from pausing or premature termination. Oligopeptide synthesis is enhanced when a commonly used epsilon (enhancer of protein synthesis initiation) sequence is included in the mRNA. The system incorporates a selectable, large, unnatural amino acid and may ultimately form the basis of a pure translation display technology for the directed evolution of peptidomimetic ligands and drug candidates. The recombinant clones can be exploited to prepare initiation factors and initiation complexes for structural studies, to study initiation and elongation in ribosomal peptide synthesis, and to screen for eubacterial-specific drugs.

Polymer‐supported reagents, catalysts, and sorbents: Evolution and exploitation—A personalized view

AbstractThe solid‐phase method for oligopeptide synthesis was introduced by Professor Bruce Merrifield in 1963, but in practice the origins of polymer‐supported reagents, catalysts, and so forth trace back to the early development of ion exchange and catalysis by sulfonic acid resins. This highlight summarizes how the evolution of solid‐phase organic synthesis occurred in parallel with the development of supported reactive species and indicates the interchange between these areas in the last 30 years or so. The treatment is essentially a personalized one as seen from the author's own laboratory in the United Kingdom and is not intended to review the whole field. The emergence of the international series of conferences on polymer‐supported organic chemistry is emphasized as a key development that stimulated and maintained the area before its importance was recognized more widely by both academic and industrial chemists. The requirement of robotic technologies, as the basis for high‐throughput combinatorial and parallel synthesis in the pharmaceutical industry, has brought the relevance of supported chemistry to the attention of all synthetic chemists. At the same time, the recognition that all industrial chemical processes need to meet appropriate environmental standards has focused attention on the use of heterogenized reactive species as a potentially important technology for achieving the greening of chemistry. These two factors have brought polymer‐supported reactive chemistry to center stage, so to speak, and the early principles laid down over 2 decades ago are now being developed and exploited at an amazing rate. From a rather slow start, through a number of ups and downs in its development, the area of polymer‐supported chemistry now seems poised to join the more routine world of synthesis and to become a methodology used by all as and when appropriate. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 2364–2377, 2001

Modeling the performance of immobilized α-chymotrypsin catalyzed peptide synthesis in acetonitrile medium

A model was developed which describes simultaneous reaction and internal diffusion for kinetically controlled, immobilized α-chymotrypsin-catalyzed, oligopeptide synthesis in acetonitrile medium. The model combines the equations that describe the intrinsic kinetics of four different reactions and the physical characteristics of three different support materials, as determined experimentally, to predict the apparent initial activity and nucleophile selectivity of the immobilized biocatalyst. The model is able to predict reasonably well the experimentally observed initial rate and nucleophile selectivity vs. enzyme loading profiles. The reduction in observed initial rate with enzyme loading when fast reactions are carried out with α-chymotrypsin immobilized on celite, and the larger influence of mass transfer limitations on the initial reaction rates than on nucleophile selectivities are correctly predicted by the numerical calculations. The model is general in terms of its application to other systems — enzymes, reactions, support materials and/or kinetic schemes — as long as the intrinsic kinetics and the characteristics of the enzyme and support material are known.

Autocatalytic synthesis of oligoglycine in a simulated submarine hydrothermal system.

A flow reactor simulating a submarine hydrothermal system was constructed for examining the likelihood of oligopeptide synthesis from amino acids alone without recourse to any of condensing agents, templates or metallic ions. We demonstrated that when the initial reactant is glycine, the flow reactor can synthesize both di- and tri-glycine. The initial buildup of the yields of both the oligopeptides was found to be exponential with the elapse of time. The oligopeptide synthesis from glycine in the flow reactor could be autocatalytic.

Antibodies against a peptide sequence located in the linker region of the HMG-1/2 box domains in sera from patients with juvenile rheumatoid arthritis.

To extend our work on the mapping of B cell epitopes on nucleosomal high mobility group (HMG) proteins in the sera of patients with juvenile rheumatoid arthritis (JRA). Seventy-seven pauciarticular-onset JRA serum samples from antinuclear antibody (ANA)-positive patients and 42 polyarticular-onset JRA patient sera found to react with HMG-2 by immunoblotting were used in this study. To identify B cell epitopes on HMG-2, recombinant HMG-2 protein fragments were used in enzyme-linked immunosorbent assay (ELISA) and in competition ELISA experiments with a set of overlapping synthetic peptides. Fine epitope mapping was achieved by oligopeptide synthesis, followed by immunoblotting. Pauciarticular, but not polyarticular, JRA patient sera were found to recognize a lysine-rich major epitope (KKGKKKDP), which is located in the linker region of the HMG box domains of the HMG-2 nonhistone chromosomal protein. No significant immunoreactions were observed in sera from ANA-negative JRA patients and in sera from children with nonrheumatic diseases, indicating that this epitope seems to be specific for pauciarticular-onset JRA. In addition to our previous finding that JRA sera will react with a defined epitope on HMG-17, pauciarticular JRA patient sera were also found to recognize a defined epitope on the HMG-2 protein, thus suggesting the importance of this epitope in the etiology of JRA.

5-Hydroxytryptophan as a building block in oligopeptides using Fmoc/tBu SPPS

One of the initial steps in the development of therapeutic agents is the identification of lead compounds that bind to the target of interest. Use of combinatorial libraries allows the screening of thousands to millions of compounds. To optimize the characteristics of the first generation of compounds, many of their analogues need to be synthesized. In this sense, 5-hydroxytryptophan closely resembles tryptophan. Both, however, are sensitive to oxidation and alkylation during solid-phase peptide synthesis. In an effort to overcome these side reactions during oligopeptide synthesis, we prepared N α-Fmoc-N in-Boc-5-O-benzyl-5-hydroxytryptophan. To evaluate its properties, this building block was incorporated in a pentagastrin analogue using Fmoc/tBu chemistry. After deprotection and cleavage from the support, the products were purified and identified. The fully deprotected peptide was the main compound, contaminated by its 5-O-benzylated analogue. The relative amount of the latter decreased using longer deprotection times.

Polyethylene Glycol–Modified Papain Catalyzed Oligopeptide Synthesis from the Esters ofl-Aspartic andl-Glutamic Acids in Benzene

Comparative studies were made of the polymerization of l-aspartic and l-glutamic acid dialkyl esters using polyethylene glycol–modified papain as a catalyst in phosphate buffer (pH 7.5) and in benzene. Changes in the substrate specificity of papain and in the composition of oligomerized products were observed. In the buffer, the diethyl and di-n-propyl esters of l-glutamic acid were sufficiently converted to high molecular weight oligomers with the accumulation of dimer and trimer, but l-aspartic acid esters were very poor substrates. In benzene, l-aspartic acid esters became more reactive than L-glutamic acid esters. In particular, from l-aspartic acid dimethyl ester the product, which was mainly composed of heptamer to decamer, was obtained in a 90% yield. The reaction in benzene required desalted substrates and a small amount of water to proceed extensively.

The Use of Phosphonitrilic Dichloride Cyclic Trimer in Oligopeptide Synthesis. Synthesis of Isoxazolyl-Prodrugs of Netropsin and Distamycin

Phosphonitrilic dichloride cyclic trimer has been found to be an effective activating agent for the synthesis of oligopeptides containing N-terminal isoxazole-4-carboxamide groups

Polyethylene glycol-modified papain catalyzed oligopeptide synthesis from the esters of L-aspartic and L-glutamic acids in benzene.

Comparative studies were made of the polymerization of L-aspartic and L-glutamic acid dialkyl esters using polyethylene gl¥ col-modified papain as a catalyst in phosphate buffer (pH 7.5) and in benzene. Changes in the substrate specificity of papain and in the composition of oligomerized products were observed. In the buffer, the diethyl and di-n-propyl esters of L-glutamic acid were sufficiently converted to high molecular weight oligomers with the accumulation of dimer and trimer, but L-aspartic acid esters were very poor substrates. In benzene, L-aspartic acid esters became more reactive than L-glutamic acid esters. In particular, from L-aspartic acid dimethyl ester the product, which was mainly composed of heptamer to decamer, was obtained in a 90% yield. The reaction in benzene required desalted substrates and a small amount of water to proceed extensively.