A biuret-derived, MS-cleavable cross-linking reagent for protein structural analysis: A proof-of-principle study.

Chemical cross-linking combined with mass spectrometry (XL-MS) and computational modeling has evolved as an alternative method to derive protein 3D structures and to map protein interaction networks. Special focus has been laid recently on the development and application of cross-linkers that are cleavable by collisional activation as they yield distinct signatures in tandem mass spectra. Building on our experiences with cross-linkers containing an MS-labile urea group, we now present the biuret-based, CID-MS/MS-cleavable cross-linker imidodicarbonyl diimidazole (IDDI) and demonstrate its applicability for protein cross-linking studies based on the four model peptides angiotensin II, MRFA, substance P, and thymopentin.

Quantitative measurement of urinary proteins in 2018: advantages, disadvantages, limits.

Today, there is no reference method for the measurement of urinary proteins. The difficulties are that urine is a very complex biological fluid, and that there are a high intra-and inter-individual variability in the protein excretion rate. Progress has been made during the last thirty years, but high analytical variability persists among the colorimetric or turbidimetric methods used for urinary proteins measurement.

Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841.

Biuret deamination is an essential step in cyanuric acid mineralization. In the well-studied atrazine degrading bacterium Pseudomonas sp. strain ADP, the amidase AtzE catalyzes this step. However, Rhizobium leguminosarum bv. viciae 3841 uses an unrelated cysteine hydrolase, BiuH, instead. Herein, structures of BiuH, BiuH with bound inhibitor and variants of BiuH are reported. The substrate is bound in the active site by a hydrogen bonding network that imparts high substrate specificity. The structure of the inactive Cys175Ser BiuH variant with substrate bound in the active site revealed that an active site cysteine (Cys175), aspartic acid (Asp36) and lysine (Lys142) form a catalytic triad, which is consistent with biochemical studies of BiuH variants. Finally, molecular dynamics simulations highlighted the presence of three channels from the active site to the enzyme surface: a persistent tunnel gated by residues Val218 and Gln215 forming a potential substrate channel and two smaller channels formed by Val28 and a mobile loop (including residues Phe41, Tyr47 and Met51) that may serve as channels for co-product (ammonia) or co-substrate (water).

[Application research of protein test by using biuret reagent].

OBJECTIVE: To investigate the biuret reagent to detect proteins in the application, the impact of different test conditions for test results. METHODS: The biuret method to select three different instruments, reagents, calibrators are arranged in combination to form 27 sets of detection systems, each detection system is a combination of 5 serum samples for testing, 5 measured values obtained, the selection process normality good a serum for the study to determine the mean value of all AST after culling outliers obtained in order to calculate the various detection systems use a combination of biuret reagent to detect proteins bias. RESULTS: The use of different detection equipment to detect proteins biuret reagent bias, homogeneity of variance (P = 0.467), the difference was not statistically significant (F = 1.688, P = 0.421). different detection reagents using biuret reagent to detect proteins bias, homogeneity of variance (P = 0.574), a statistically significant difference (F = 5.784, P = 0.011). different calibrators use biuret reagent to detect proteins bias, homogeneity of variance (P = 0.467), the difference was statistically significant (F = 5.289, P = 0.000). CONCLUSION: Biuret reagent in the detection of protein applications, impact detection reagents and calibrators will test result, during the test than when it is necessary to detect deviation detection reagents and calibrators due to be considered.

In silico and in vitro comparative activity of novel experimental derivatives against Leishmania major and Leishmania infantum promastigotes.

This in silico and in vitro comparative study was designed to evaluate the effectiveness of some biurets (K1 to K8) and glucantime against Leishmania major and Leishmania infantum promastigotes. Overall, eight experimental ligands and glucantime were docked using AutoDock 4.3 program into the active sites of Leishmania major and Leishmania infantum pteridine reductase 1, which were modeled using homology modeling programs. The colorimetric MTT assay was used to find L. major and L. infantum promastigotes viability at different concentrations of biuret derivatives in a concentration and time-dependent manner and the obtained results were expressed as 50% and 90% of inhibitory concentration (IC50 and IC90). In silico method showed that out of eight experimental ligands, four compounds were more active on pteridine reductase 1. K3 was the most active against L. major promastigotes with an IC50 of 6.8 µM and an IC90 of 40.2 µM, whereas for L. infantum promastigotes was K8 with IC50 of 7.8 µM. The phenylethyl derivative (K7) showed less toxicity (IC50s>60 µM) in both Leishmania strains. Glucantime displayed less growth inhibition in concentration of about 20 µM. In silico and especially docking results in a recent study were in accordance with the in vitro activity of these compounds in presented study and compound K3, K2 and K8 showed reasonable levels of selectivity for the Leishmania pteridine reductase 1.

Catalytic signal amplification using [Fe(III)(biuret-amide)]-mesoporous silica nanoparticles: visual cyanide detection.

Catalytic signal amplification was used for the colorimetric detection of CN(-) in aqueous media by using the enzyme catalase in tandem with mesoporous silica nanoparticle based synthetic HRP enzyme mimic Fe-MSNs. Signal amplification up to a maximum of eight fold was observed for the reporter "oxidized TMB" with respect to the added CN(-) ion.

One pot glucose detection by [Fe(III)(biuret-amide)] immobilized on mesoporous silica nanoparticles: an efficient HRP mimic.

An [Fe(III)(biuret-amide)] complex has been immobilized onto mesoporous silica nanoparticles via Cu(I) catalyzed azide-alkyne click chemistry. This hybrid material functions as an efficient peroxidase mimic and was successfully used for the quantitative determination of hydrogen peroxide and glucose via a one-pot colorimetric assay.

Preparation and properties of a coated slow-release and water-retention biuret phosphoramide fertilizer with superabsorbent.

In this investigation, a novel water-insoluble slow-release fertilizer, biuret polyphosphoramide (BPAM), was formulated and synthesized from urea, phosphoric acid (H(3)PO(4)), and ferric oxide (Fe(2)O(3)). The structure of BPAM was characterized by Fourier transform infrared (FTIR) spectroscopy. Subsequently, a coated slow-release BPAM fertilizer with superabsorbent was prepared by ionic cross-linked carboxymethylchitosan (the core), acrylic acid, acrylamide, and active carbon (the coating). The variable influences on the water absorbency were investigated and optimized. Component analysis results showed that the coated slow-release BPAM contained 5.66% nitrogen and 11.7% phosphorus. The property of water retention, the behavior of slow release of phosphorus, and the capacity of adsorption of cations were evaluated, and the results revealed that the product not only had good slow-release property and excellent water retention capacity but also higher adsorption capacities of cations in saline soil.

Synthesis and cytotoxicity of some biurets against human breast cancer T47D cell line.

Design, synthesis and cytotoxicity of several known and novel biurets against human breast cancer T47D cell line in comparison to doxorubicin are described. Biurets incorporating 2-methyl quinoline-4-yl and benzo[d]thiazol-2-ylthio moieties showed higher cytotoxicity and decreased cell viability in a concentration- and time-dependent manner.

Electroosmotic sampling. Application to determination of ectopeptidase activity in organotypic hippocampal slice cultures.

We hypothesize that peptide-containing solutions pulled through tissue should reveal the presence and activity of peptidases in the tissue. Using the natural zeta-potential in the organotypic hippocampal slice culture (OHSC), physiological fluids can be pulled through the tissue with an electric field. The hydrolysis of the peptides present in the fluid drawn through the tissue can be determined using capillary HPLC with electrochemical detection of the biuret complexes of the peptides following a postcolumn reaction. We have characterized this new sampling method by measuring the flow rate, examining the use of internal standards, and examining cell death caused by sampling. The sampling flow rate ranges from 60 to 150 nL/min with a 150 microm (ID) sampling capillary with an electric field (at the tip of the capillary) from 30 to 60 V/cm. Cell death can be negligible with controlled sampling conditions. Using this sampling approach, we have electroosmotically pulled Leu-enkephalin through OHSCs to identify ectopeptidase activity in the CA3 region. These studies show that a bestatin-sensitive aminopeptidase may be critical for the hydrolysis of exogenous Leu-enkephalin, a neuropeptide present in the CA3 region of OHSCs.

5'-Uridyl derivatives of N-glycosyl allophanic acid and biuret.

(2',3'-O-Isopropylidene-5'-uridyl) 4-(2,3,4,6-tetra-O-acetyl-beta-d-glycopyranosyl)allophanates were obtained in the reactions of 2',3'-O-isopropylidene-uridine and O-peracetylated beta-d-gluco-, galacto- and xylopyranosylamines, and OCNCOCl. 2,3,4,6-Tetra-O-acetyl-beta-d-glucopyranosyl isocyanate and N-(2',3'-O-isopropylidene-5'-uridyl)urea gave 1-(2,3,4,6-tetra-O-acetyl-beta-d-glucopyranosyl)-5-(2',3'-O-isopropylidene-5'-uridyl)biuret. Deprotection of the beta-d-gluco configured allophanate and biuret was carried out by standard methods.

Synthesis of new glycosyl biuret and urea derivatives as potential glycoenzyme inhibitors.

O-peracetylated 1-(beta-D-glucopyranosyl)-5-phenylbiuret was prepared in the reaction of O-peracetylated beta-D-glucopyranosylisocyanate and phenylurea. The reaction of O-peracetylated N-beta-D-glucopyranosylurea with phenylisocyanate furnished the corresponding 1-(beta-D-glucopyranosyl)-3,5-diphenyl- as well as 3-(beta-D-glucopyranosyl)-1,5-diphenyl biurets besides 1-(beta-D-glucopyranosyl)-3-phenylurea. O-Peracetylated 1-(beta-D-glucopyranosyl)-5-(beta-D-glycopyranosyl)biurets were obtained in one-pot reactions of O-peracetylated beta-D-glucopyranosylamine with OCNCOCl followed by a second glycopyranosylamine of beta-D-gluco, beta-D-galacto and beta-D-xylo configurations. O-Acyl protected 1-(beta-D-glucopyranosyl)-3-(beta-D-glycopyranosylcarbonyl)ureas were obtained from the reaction of beta-D-glucopyranosylisocyanate with C-(glycopyranosyl)formamides of beta-D-gluco and beta-D-galacto configurations. The O-acyl protecting groups were removed under acid- or base-catalyzed transesterification conditions, except for the N-acylurea derivatives where the cleavage of the N-acyl groups was faster than deprotection. Some of the new compounds exhibited moderate inhibition against rabbit muscle glycogen phosphorylase b and human salivary alpha-amylase.

Comparative assessment of early acute lung injury in mice and rats exposed to 1,6-hexamethylene diisocyanate-polyisocyanate aerosols.

The aliphatic diisocyanate monomer 1,6-hexamethylene diisocyanate (HDI) is used as a building block for non-volatile polycondensation products, such as HDI-isocyanurate (HDI-IC) and HDI-biuret (HDI-BT). This paper describes the results from acute inhalation studies with these types of polyisocyanate aerosols in OF1 and C57BL/6J mice and in Wistar rats. The modifying role of different concentrations of residual HDI in HDI-BT on pulmonary irritation was also addressed. These data close data gaps for acute mouse inhalation studies in direct comparison with rats. The sensory irritant potency was examined in OF1 mice during a 3h nose-only exposure to the polyisocyanate aerosols. Concurrent with exposure, breathing patterns suitable to distinguish upper/lower respiratory tract irritation where examined. Functional measurements in barometric plethysmographs (Penh) addressed changes in respiratory function in C57BL/6J mice exposed for 6h up to 16h postexposure. These measurements revealed that these polyisocyanates elicit changes slow in onset suggestive of pulmonary irritation rather than upper airway irritation. This conclusion was supported by similarly exposed OF1 mice exposed to non-irritant, surface active respirable particles of amorphous silica. In C57BL/6J mice and Wistar rats, nose-only exposed for 6h to 10mg/m(3) of aerosolized HDI-BT HDI (0.1% or 2% residual HDI), the pulmonary irritation potency was comparatively assessed by bronchoalveolar lavage (BAL) on postexposure day 1. Similarly air-exposed animals served as concurrent controls. Most changes in BAL suggestive of acute pulmonary irritation were more pronounced in Wistar rats than in C57BL/6J mice. A conclusive dependence of BAL endpoints on the residual content of residual HDI monomer in the polyisocyanate was not found. The results of this study show that mice may be particularly suitable to functionally analyze at which location of the respiratory tract predominant irritation may occur. However, with regard to analysis of lower respiratory tract irritation, rats were demonstrated to be more susceptible than mice. In summary, this study supports the conclusion that data from rat inhalation studies with these types of isocyanates appear to be more conservative and less variable than the respective data from mice.

Preparation of guanine and diaminopurine from biuret. Part III.

Because of their potential prebiotic origin and relative chemical stability, urea, biuret, formic acid, and glycine amide might have played a role in the assembly process of purine bases. In this paper, we describe a short reaction path to purine nucleobases from these acyclic precursors. The formation of different purines was verified by UV and NMR spectroscopy, as well as by mass spectrometry.

Vibrational circular dichroism spectroscopy of a spin-triplet bis-(biuretato) cobaltate(III) coordination compound with low-lying electronic transitions.

Vibrational absorption (VA) and vibrational circular dichroism (VCD) spectroscopy was applied in the analysis of vibrational and low lying electronic transitions of a triplet ground state cobalt(III) coordination compound. The spectroscopic measurements were performed on the tetrabutylammonium salt of (6S,7S)-1,3,5,8,10,12-hexaaza-2,4,9,11-tetraoxo-6,7-diphenyl-dodecanato(4-)cobaltate(III) in DMSO solution and in potassium bromide pellets. The chiral anion exhibits an unusual geometry for cobalt(III), being four-coordinate, planar, and paramagnetic with an intermediate spin state. The spectroscopic results were compared to measurements performed on the free ligand and to theoretical calculations using density functional theory (B3LYP/TZVP). The results of the VCD analysis of the coordination compound identified an electronic, dipole-forbidden, magnetic dipole-allowed low-lying d-d transition located in the mid infrared, as well as several amide stretch transitions located in the fingerprint region (1800-1100 cm(-1)), in both the liquid and solid phase. VCD signals were found to be 5-10 times higher than expected, indicating enhancement of the vibrational CD signals, caused by coupling of the vibrational transitions with the close-lying electronic transition.

Synthesis of N- and S-bis-protected lactosyl isothiobiurets.

Several N,S-bis(hepta-O-acetyllactosyl)-1-aryl-2-isothiobiuret compounds have been synthesised for the first time by the reaction of S-(hepta-O-acetyl-beta-lactosyl)-1-arylisothiocarbamides and hepta-O-acetyl-beta-lactosyl isocyanate. The identities of these newly synthesised compounds were established on the basis of elemental analysis and IR, (1)H NMR, (13)C NMR and mass spectral studies.

Felinine stability in the presence of selected urine compounds.

The stability of felinine, an amino acid present in feline urine, was investigated. Synthetic felinine was unstable in the urine of a selection of mammals. Felinine was found to stable in feline urine in which urea had been degraded. Synthetic felinine was found to react specifically with urea and did not react with urea analogues such as biuret or thiourea or other nucleophilic compounds such as ammonia which is more nucleophilic or acetamide and water which are less nucleophilic than urea. The reaction of urea and felinine was independent of pH over the range of 3-10. Urea did not react with N-acetyl-felinine suggesting a felinine N-terminal interaction with urea. Mass spectral analysis of the reaction products showed the presence of carbamylated felinine and fragmentation ions derived from carbamyl-felinine. The physiological relevance of felinine carbamylation is yet to be determined.

The electronic structure and spectra of spin-triplet ground state bis(biuretato)cobalt(III) coordination compounds.

The planar coordination compounds of cobalt(III) with bis(biuretato) ligands are highly unusual due to their intermediate spin triplet ground state. Density functional theory (DFT) and time-dependent DFT have been applied in a study of the structure and electronic spectroscopy of this type of coordination compounds. The investigations included prediction and spectroscopic measurements of the absorption and circular dichroism (CD), as well as an experimental study of the magnetic CD. The results obtained by TD-DFT were in excellent agreement with the observed spectral features, both regarding the d-d and the charge transfer regions. There was noted a systematic blue-shift of the TD-DFT results compared to experiment, corresponding to an offset of ca. 0.5 microm(-1) and a scaling factor of 1.25 for the transition energies. The DFT results are rationalized in terms of a qualitative MO analysis.