A Novel Transition-state Analogue for Lysozyme, 4-O-β-Tri-N-acetylchitotriosyl Moranoline,Provided Evidence Supporting the Covalent Glycosyl-enzyme Intermediate

4-O-β-Di-N-acetylchitobiosyl moranoline (2) and 4-O-β-tri-N-acetylchitotriosyl moranoline (3) were produced by lysozyme-mediated transglycosylation from the substrates tetra-N-acetylchitotetraose, (GlcNAc)₄, and moranoline, and the binding modes of 2 and 3 to hen egg white lysozyme (HEWL) was examined by inhibition kinetics, isothermal titration calorimetry (ITC), and x-ray crystallography. Compounds 2 and 3 specifically bound to HEWL, acting as competitive inhibitors with K_i values of 2.01 × 10⁻⁵ and 1.84 × 10⁻⁶ m, respectively. From ITC analysis, the binding of 3 was found to be driven by favorable enthalpy change (ΔH_r°), which is similar to those obtained for 2 and (GlcNAc)₄. However, the entropy loss (−TΔS_r°) for the binding of 3 was smaller than those of 2 and (GlcNAc)₄. Thus the binding of 3 was found to be more favorable than those of the others. Judging from the K_d value of 3 (760 nm), the compound appears to have the highest affinity among the lysozyme inhibitors identified to date. X-ray crystal structure of HEWL in a complex with 3 showed that compound 3 binds to subsites −4 to −1 and the moranoline moiety adopts an undistorted ⁴C₁ chair conformation almost overlapping with the −1 sugar covalently bound to Asp-52 of HEWL (Vocadlo, Davies, G. J., Laine, R., and Withers, S. G. (2001) Nature 412, 835–838). From these results, we concluded that compound 3 serves as a transition-state analogue for lysozyme providing additional evidence supporting the covalent glycosyl-enzyme intermediate in the catalytic reaction.     

An Efficient Method for the Synthesis of β-d-Ribonucleosides Catalyzed by Metal Iodides

Abstract

Several β-d-ribonucleosides were synthesized in high yields under mild conditions by N-glycosylations of methyl 2,3,5-tri-O-benzoyl-β-d-ribofuranosyl carbonate (1) with trimethylsilylated nucleoside bases in acetonitrile using a catalytic amount of metal iodide such as SnI₂, SbI₃ or TeI₄. A deprotection of N⁶ -benzoyl group of coupling product took place to a considerable extent when N⁶ -benzoyl-N⁶ , N⁹ -bis(trimethylsilyl)adenine was employed as a nucleoside base using SnI₂ or SnCI₂ as a catalyst while it was minimized when SbI₃ or TeI₄ was used. Further, the N-glycosylation of 1 with 7-trimethylsilyltheophylline in the presence of a catalytic amount of metal iodide was more effectively achieved in nitrile solvents other than acetonitrile.

     

Enhanced recovery of lyophilized peptides in shotgun proteomics by using an LC‐ESI‐MS compatible surfactant

LC‐ESI/MS/MS‐based shotgun proteomics is currently the most commonly used approach for the identification and quantification of proteins in large‐scale studies of biomarker discovery. In the past several years, the shotgun proteomics technologies have been refined toward further enhancement of proteome coverage. In the complex series of protocols involved in shotgun proteomics, however, loss of proteolytic peptides during the lyophilization step prior to the LC/MS/MS injection has been relatively neglected despite the fact that the dissolution of the hydrophobic peptides in lyophilized samples is difficult in 0.05–0.1% TFA or formic acid, causing substantial loss of precious peptide samples. In order to prevent the loss of peptide samples during this step, we devised a new protocol using Invitrosol (IVS), a commercially available surfactant compatible with ESI‐MS; by dissolving the lyophilized peptides in IVS, we show improved recovery of hydrophobic peptides, leading to enhanced coverage of proteome. Thus, the use of IVS in the recovery step of lyophilized peptides will help the shotgun proteomics analysis by expanding the proteome coverage, which would significantly promote the discovery and development of new diagnostic markers and therapeutic targets.     

Isolation and Structures of New Peptide Antibiotics,Cirratiomycin A and B

We measured the concentrations of acetyl-CoA and malonyl-CoA in shoots and roots of corn (Zea mays, L., cv. “Peter Corn”). Acetyl-CoA and malonyl-CoA concentrations were found to be relatively constant in shoots and in roots under a light-dark cycle. Acetyl-CoA concentrations were lower in shoots than in roots, whereas malonyl-CoA concentrations were higher in shoots than in roots.     

Heterotrimeric G protein signaling governs the cortical stability during apical constriction in Drosophila gastrulation

During gastrulation in Drosophila melanogaster, coordinated apical constriction of the cellular surface drives invagination of the mesoderm anlage. Forces generated by the cortical cytoskeletal network have a pivotal role in this cellular shape change. Here, we show that the organisation of cortical actin is essential for stabilisation of the cellular surface against contraction. We found that mutation of genes related to heterotrimeric G protein (HGP) signaling, such as Gβ13F, Gγ1, and ric-8, results in formation of blebs on the ventral cellular surface. The formation of blebs is caused by perturbation of cortical actin and induced by local surface contraction. HGP signaling mediated by two Gα subunits, Concertina and G-iα65A, constitutively regulates actin organisation. We propose that the organisation of cortical actin by HGP is required to reinforce the cortex so that the cells can endure hydrostatic stress during tissue folding.     

Minor Differences in Anther Extrusion Affect Resistance to Fusarium Head Blight in Wheat

Fusarium head blight (FHB) remains a serious problem due to yield loss and mycotoxin accumulation in wheat production worldwide. We previously reported that the closed‐flowering (no anther extrusion) characteristic was effective for increasing resistance to FHB infection. In this study, we investigated the relationships between the degree of anther extrusion (AE) and FHB damage using double haploid lines (DHLs), derived from F₁ plants from crosses between closed‐flowering and opened‐flowering varieties. These DHLs exhibited various degrees of AE, and the degree of AE was significantly different among DHLs, regardless of the year and environment (pot‐ or field‐grown). FHB severity was the lowest in closed‐flowering DHLs, and DHLs with partially extruded anthers showed significantly higher FHB symptoms than those with closed‐flowering phenotypes. In general, DHLs with partially extruded anthers also had relatively severe FHB symptoms compared with those exhibiting full anther extrusion. FHB severity was significantly correlated with Fusarium‐damaged kernels and deoxynivalenol concentration. The results of this study showed that partially extruded anthers were considered to be a source of FHB infection. The closed‐flowering phenotype improved resistance to FHB infection. Meanwhile, phenotypes with rapid anther extrusion and ejection also could contribute to the avoidance of FHB infection.     

The establishment and validation of efficient assays for anti-IIa and anti-Xa activities of heparin sodium and heparin calcium

Heparin is used as an anticoagulant drug. The anticoagulation process is mainly caused by the interaction of heparin with antithrombin followed by inhibition of anticoagulant factor IIa and factor Xa. The anti-factor IIa and anti-factor Xa activities of heparin are critical for its anticoagulant effect; however, physicochemical methods that can reflect these activities have not been established. Thus, the measurements of anti-IIa and anti-Xa activities by biological assay are critical for the quality control of heparin products. Currently in the Japanese Pharmacopoeia (JP), the activities of heparin sodium and heparin calcium are measured by an anti-Xa activity assay (anti-Xa assay), but anti-IIa activity is not measured. Here, we established an anti-IIa activity assay (anti-IIa assay) and an anti-Xa assay having good accuracy and precision. When samples having a relative activity of 0.8, 1.0 and 1.2 were measured by the established anti-IIa and anti-Xa assays in nine laboratories, good accuracy (100.0–102.8% and 101.6–102.8%, respectively), good intermediate precision (1.9–2.1% and 2.4–4.2%, respectively) and good reproducibility (4.0–4.8% and 3.6–6.4%, respectively) were obtained. The established anti-IIa and anti-Xa assays have similar protocols, and could be performed by a single person without a special machine. The established assays would be useful for quality control of heparin.