Hydrazide functionalized magnetic nanoparticles for specific extraction of N-terminal serine and threonine peptides.

In this study, we present hydrazide functionalized magnetic nanoparticles as a sorbent prepared by a new and facile method. Scanning electron microscope and Fourier transform infrared were used for characterizing the synthesized nanoparticles. The ability of the sorbent to extract N-terminal serine and threonine peptides was evaluated. The peptides were modified by oxidation of the hydroxyl group in the 1,2-amino alcohol structure before extraction. These aldehyde-forms of peptides were specifically bonded to the hydrazide groups of the sorbent. The formed hydrazone bonds were cleaved in the presence of hydroxylamine reagent. Finally, the oximated peptides were released and quantified with a high-performance liquid chromatography-diode array spectroscopy. The effects of experimental parameters including extraction time, elution time and elution volume on extraction efficiency were also investigated. The required time for the extraction process to reach equilibrium and elution time was only 8 h. The adsorption efficiency of the sorbent was 79 and 77% for peptides with N-terminal serine and threonine, respectively. The sorbent showed good specificity for extracting the peptides. In addition, the extraction efficiency of the sorbent remained constant in the presence of a non-N-terminal serine and threonine peptide as interference.

Depsidomycins B and C: New Cyclic Peptides from a Ginseng Farm Soil-Derived Actinomycete.

LC/MS-based chemical profiling of a ginseng farm soil-derived actinomycete strain, Streptomyces sp. BYK1371, enabled the discovery of two new cyclic heptapeptides, depsidomycins B and C (1 and 2), each containing two piperazic acid units and a formyl group at their N-terminus. The structures of 1 and 2 were elucidated by a combination of spectroscopic and chemical analyses. These new compounds were determined to possess d-leucine, d-threonine, d-valine, and S-piperazic acid based on the advanced Marfey's method and a GITC (2,3,4,6-tetra-O-acetyl-ß-d-glucopyranosyl isothiocyanate) derivatization of their hydrolysates, followed by LC/MS analysis. Depsidomycins B and C displayed significant antimetastatic activities against metastatic breast cancer cells (MDA-MB-231).

Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP.

Genetic and biochemical studies have recently implicated four proteins required in bacteria for the biosynthesis of the universal tRNA modified base N6-threonylcarbamoyl adenosine (t(6)A). In this work, t(6)A biosynthesis in Bacillus subtilis has been reconstituted in vitro and found to indeed require the four proteins YwlC (TsaC), YdiB (TsaE), YdiC (TsaB) and YdiE (TsaD). YwlC was found to catalyze the conversion of L-threonine, bicarbonate/CO(2) and ATP to give the intermediate L-threonylcarbamoyl-AMP (TC-AMP) and pyrophosphate as products. TC-AMP was isolated by HPLC and characterized by mass spectrometry and (1)H NMR. NMR analysis showed that TC-AMP decomposes to give AMP and a nearly equimolar mixture of L-threonine and 5-methyl-2-oxazolidinone-4-carboxylate as final products. Under physiological conditions (pH 7.5, 37 °C, 2 mM MgCl(2)), the half-life of TC-AMP was measured to be 3.5 min. Both YwlC (in the presence of pyrophosphatase) and its Escherichia coli homologue YrdC catalyze the formation of TC-AMP while producing only a small molar fraction of AMP. This suggests that CO(2) and not an activated form of bicarbonate is the true substrate for these enzymes. In the presence of pyrophosphate, both enzymes catalyze clean conversion of TC-AMP back to ATP. Purified TC-AMP is efficiently processed to t(6)A by the YdiBCE proteins in the presence of tRNA substrates. This reaction is ATP independent in vitro, despite the known ATPase activity of YdiB. The estimated rate of conversion of TC-AMP by YdiBCE to t(6)A is somewhat lower than the initial rate from L-threonine, bicarbonate and ATP, which together with the stability data, is consistent with previous studies that suggest channeling of this intermediate.

Preparation of a new crown ether-based chiral stationary phase containing thioester linkage for the liquid chromatographic separation of enantiomers.

A new chiral stationary phase (CSP) containing thioester linkages was prepared by bonding (+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid to mercaptopropylsilica gel. The chiral recognition ability of the new CSP was found to be greater than that of the previously reported CSP containing amide linkages in the resolution of the various alpha-amino acids that were tested, except for that of Met, Ser and Thr. In the resolution of racemic amines and amino alcohols, the new CSP was always better than the one containing amide linkages in terms of the separation factors (alpha) and the resolutions (RS). Given the identical elution orders on the two CSPs, it was concluded that the chiral recognition mechanism is not affected by the change of the linkage type. In addition, the new CSP was found to be quite stable under the acidic mobile phase conditions that were utilized, indicating that the thioester linkage is useful as a tethering group.

Enzymatic formation of glidobactamine: a peptide nucleus of glidobactins A, B and C, new lipopeptide antitumor antibiotics.

Glidobactin deacylating activity was found in a bacterial strain of Pseudomonas sp. Glidobactamine, a key intermediate for acyl analogues of glidobactin, was isolated from the enzymatic degradation products of glidobactins after treatment using a column of fibrous active gel on which the cells of the Pseudomonas strain were immobilized. The chemical structure of glidobactamine was confirmed as the intact peptide moiety of glidobactins by chemical reformation of glidobactin A from glidobactamine and 2,4-dodecadienoic acid which is the constitutive fatty acid of glidobactin A.

Gingival matrix collagen in chronic periodontitis.

The isolation and characterization of cyanogen bromide peptides derived from the human gingival collagen of patients with chronic periodontitis revealed the presence of both Type I and Type III collagens in this tissue. The amount of TYPE III collagen, however, was found to be lower than that in normal gingival tissue. In addition, a non-collagenous protein fraction, accounting for approximately 20% of the insoluble matrix, was relatively rich in acidic, hydrophobic, and hydroxy-containing amino acids. Amino acid analysis, likewise, revealed qualitative and quantitative differences between the normal and diseased tissues.

Ligand-exchange chromatography of amino acids on copper-, cobalt- and zinc-chelex 100.

Procedures for the ligand-exchange chromatography of amino acids on copper-, cobalt-and zinc-Chelex 100 have been examined. Ligand exchange on the copper complex affords a simple and rapid method for the removal of amino acids (except for aspartic and glutamic acids) from dilute solutions. The influence of the pH on the binding of amino acids to the metal complex was also studied. The bound amino acids could be eluted with ammonium hydroxide which also causes a slight metal leakage. Chromatography on cobalt- and zinc-Chelex 100 showed that only the basic amino acids were quantitatively attached to these complexes at pH 8.3-9.5, whereas the others were predominantly EXCLUDED. This procedure can be used for the selective concentration and removal of basic amino acids in the presence of other amino acids.