Characterization of in vivo metabolites of toad venom using liquid chromatography-mass spectrometry

The structures of in vivo metabolites of marinobufotoxin (marinobufagin 3-suberoylarginine ester), marinobufagin, or bufalin which are typical components of toad venom widely used as the traditional Chinese drug, Ch'an Su, are confirmed using authentic samples based on their liquid chromatography-mass spectrometric behavior. A rat is orally administered 2 mg of the previously mentioned components of toad venom, the serum is collected 30 min after the administration, extracted, and then characterized. Marinobufotoxin is hydrolyzed and further epimerized into 3-epimarinobufagin, but marinobufagin 3-hemisuberate is not detected. After the administration of marinobufagin, 3-epimarinobufagin is detected in both the male and female rats, but marinobufagin 3-sulfate is formed only in the female rats. Bufalin is metabolized to 3-epibufalin, which is found to undergo further conjugation resulting in its 3-glucuronide. Furthermore, 3-epibufalin 3-sulfate is formed only in the female rats.     

Rapid determination of fumagillin residues in honey by liquid chromatography-tandem mass spectrometry using the QuEChERS method

A new, rapid, and efficient method for determining the fumagillin residues in honey was developed. The samples extracted were analyzed using LC/MS/MS. Chromatographic separation of fumagillin was performed in gradient mode on a C8 column (100 x 2.0 mm, 5 microm) at 40 degrees C. The mobile phase consisted of a mixture of 2 mM ammonium formate-0.01% formic acid solution and methanol; the flow rate was set to 0.2 mL/min. Under these conditions, it was possible to measure fumagillin and its isomers as a single peak. The sample preparation procedure used is based on the QuEChERS (quick, easy, cheap, effective, rugged, and safe) method, which is fast (approximately 30 min) and uses less organic solvent. The fumagillin was extracted with acetonitrile containing 0.1% formic acid, then purified using a solid-phase extraction method with an Oasis mixed-mode weak anion-exchange cartridge. The overall recovery of fumagillin ranged from 88.1 to 99.4%; the intra- and interassay CVs were <4.5% and <4.9%, respectively. The LOQ was 0.1 microg/kg. LC/MS/MS coupled with the QuEChERS method showed strong potential as a method for determining fumagillin residues in honey.     

Phosphoproteome Profiling Using a Fluorescent Phosphosensor Dye in Two-Dimensional Polyacrylamide Gel Electrophoresis

We validated the novel PhosphoQUANTI SolidBlue Complex (PQSC) dye for the sensitive fluorescent detection of phosphorylated proteins in polyacrylamide- and two-dimensional gel electrophoresis (PAGE and 2DE, respectively). PQSC can detect as little as 15.6 ng of ß-casein, a pentaphosphorylated protein, and 61.3 ng of ovalbumin, a diphosphorylated protein. Fluorescence intensity correlates with the number of phosphorylated residues on the protein. To demonstrate the specificity of PQSC for phosphoproteins, enzymatically dephosphorylated lysates of Swiss 3T3 cells were separated in 2DE gels and stained by PQSC. The fluorescence signals in these gels were markedly reduced following dephosphorylation. When the phosphorylated proteins in Swiss 3T3 cell lysates were concentrated using a phosphoprotein enrichment column, the majority of phosphoproteins showed fluorescence signals in the pI 4–5 range. Finally, we performed phosphoproteome analysis to study differences in the protein phosphorylation profiles of proliferating and quiescent Swiss 3T3 cells. Over 135 discernible protein spots were detected, from which a selection of 15 spots were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF-MS). The PQSC staining procedure for phosphoprotein detection is simple, reversible, and fully compatible with MALDI TOF-MS.     

Monitoring surface-assisted biomolecular assembly by means of evanescent-field-coupled waveguide-mode nanobiosensors

Biological self-assembly is a natural process that involves various biomolecules, and finding the missing partner in these interactions is crucial for a specific biological function. Previously, we showed that evanescent-field-coupled waveguide-mode sensor in conjunction with a SiO₂ waveguide, the surfaces which contain cylindrical nanometric holes produced by atomic bombardment, allowed us to detect efficiently the biomolecular interactions. In the present studies, we showed that the assembly of biomolecules can be monitored using the evanescent-field-coupled waveguide-mode biosensor and thus provide a methodology in monitoring assembly process in macromolecular machines while they are assembling. Evanescent-field-coupled waveguide-mode sensor Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Fluorine in Shark Teeth: Its Direct Atomic‐Resolution Imaging and Strengthening Function

Atomic‐resolution imaging of beam‐sensitive biominerals is extremely challenging, owing to their fairly complex structures and the damage caused by electron irradiation. Herein, we overcome these difficulties by performing aberration‐corrected electron microscopy with low‐dose imaging techniques, and report the successful direct atomic‐resolution imaging of every individual atomic column in the complex fluorapatite structure of shark tooth enameloid, which can be of paramount importance for teeth in general. We demonstrate that every individual atomic column in shark tooth enameloid can be spatially resolved, and has a complex fluorapatite structure. Furthermore, ab initio calculations show that fluorine atoms can be covalently bound to the surrounding calcium atoms, which improves understanding of their caries‐reducing effects in shark teeth.     

Characterization of in vitro metabolites of toad venom using high-performance liquid chromatography and liquid chromatography-mass spectrometry

The characterization of the in vitro metabolites of toad venom, which has been widely used as a traditional Chinese drug, Ch'an Su, has been completed. Toad venom contains bufotoxins (such as marinobufotoxin; marinobufagin 3-suberoylarginine ester) and bufogenins (such as marinobufagin and bufalin) as the main cardiac steroids. An in vitro experiment using the rat or human liver cytosolic fraction disclosed that marinobufotoxin produced marinobufagin, but not its 3-hemisuberate. Marinobufagin was subjected to the enzyme reaction using the rat or human liver microsomal fraction together with NADPH and NAD, which produced 3-dehydromarinobufagin and 3-epimarinobufagin. Marinobufagin produced its 3-sulfate upon treatment with the rat or human liver cytosolic fraction and 3'-phosphoadenosine 5'-phosphosulfate. Bufalin was also subjected to the above enzyme reactions and showed almost the same results except for the result that the hydroxylation occurred at the 5beta-position. On the other hand, small amounts of marinobufagin 3-glucuronide were obtained only by treatment with the human liver microsomal fraction and uridine 5'-diphosphoglucuronic acid. The structures of these metabolites were confirmed using authentic samples regarding their high-performance liquid chromatographic behavior and/or liquid chromatography-mass spectrometry analysis.     

Olefin Polymerization Catalyzed by Double‐Decker Dipalladium Complexes: Low Branched Poly(α‐Olefin)s by Selective Insertion of the Monomer Molecule

Dipalladium complexes of a cyclic bis(diimine) ligand with a double‐decker structure catalyze polymerization of ethylene and α‐olefins and copolymerization of ethylene with 1‐hexene. The polymerization of 1‐hexene yields a polymer that is mainly composed of the hexamethylene unit formed by 2,1‐insertion of the monomer into the palladium–carbon bond, followed by chain‐walking (6,1‐insertion). The polymerization of 4‐methyl‐1‐pentene proceeds by 2,1‐insertion with a selectivity of 92–97 %, and affords the polymer with methyl and 2‐methylhexyl branches. 2,1‐Insertion occurs selectively in all of the polymerization reactions of α‐olefins catalyzed by the dipalladium complexes. Ethylene polymerization with the catalyst at 100 °C lasts over 24 h, whereas the monopalladium–diimine catalyst loses its activity within 8 h at 60 °C. Polyethylene obtained by the dipalladium catalyst is less‐branched and has a higher molecular weight compared to that of the monopalladium catalyst under the same conditions. Copolymerization of ethylene with 1‐hexene affords solid products with melting points and molecular weights that vary depending on the polymerization time, suggesting formation of a block and/or gradient copolymer.     

Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini‐protein,chignolin

The conformational samplings are indispensible for obtaining reliable canonical ensembles, which provide statistical averages of physical quantities such as free energies. However, the samplings of vast conformational space of biomacromolecules by conventional molecular dynamics (MD) simulations might be insufficient, due to their inadequate accessible time‐scales for investigating biological functions. Therefore, the development of methodologies for enhancing the conformational sampling of biomacromolecules still remains as a challenging issue in computational biology. To tackle this problem, we newly propose an efficient conformational search method, which is referred as TaBoo SeArch (TBSA) algorithm. In TBSA, an inverse energy histogram is used to select seeds for the conformational resampling so that states with high frequencies are inhibited, while states with low frequencies are efficiently sampled to explore the unvisited conformational space. As a demonstration, TBSA was applied to the folding of a mini‐protein, chignolin, and automatically sampled the native structure (C_α root mean square deviation < 1.0 Å) with nanosecond order computational costs started from a completely extended structure, although a long‐time 1‐µs normal MD simulation failed to sample the native structure. Furthermore, a multiscale free energy landscape method based on the conformational sampling of TBSA were quantitatively evaluated through free energy calculations with both implicit and explicit solvent models, which enable us to find several metastable states on the folding landscape. © 2015 Wiley Periodicals, Inc.     

Stereoselective synthesis of benzyl-protected β-galactosides by propionitrile-mediated glycosylation

β-Selective galactosylation was studied using a series of 2-O-benzylated phenyl 1-thio-galactosides and glycosyl acceptors in propionitrile with BSP-TTBP-Tf₂O. The glycosylation enabled us to synthesize useful precursors of N-acetyllactosamine and core 1 O-glycoserine derivatives in a highly convergent manner.