Enhanced conformational diversity search of CDR-H3 in antibodies: role of the first CDR-H3 residue

Through a conformation search by a simulation calculation, the relationships between the amino acid sequences and the conformations of the third complementarity-determining region of the antibody heavy chain (CDR-H3) were investigated to characterize the large conformational varieties of antibodies. Here, we focused on the structural role of the first CDR-H3 residue, and we selected two antibodies, 28B4 and PLG, whose CDR-H3 conformations are significantly different, having Trp and Gly at the first position, respectively. Multicanonical molecular dynamics simulations, with the advantage of enhanced sampling efficiency, were performed for the CDR-H3 fragments of 28B4 and PLG, and a modified CDR-H3 model of 28B4, where the first Trp residue was substituted with Gly. When the first CDR-H3 residue is Trp, almost all of the observed CDR-H3 loops were bent at the first residue. In contrast, when the first residue is Gly, large varieties of loop conformations were observed. The structural role of this Gly residue is discussed from the perspective of the other antibody structures in the database. When the surrounding residues were included in the calculations, CDR-H3 loop structures similar to those in the crystal structures were reproduced as the major conformations for both the 28B4 and PLG antibodies.     

Metabolic regulation of leptin production in adipocytes: a role of fatty acid synthesis intermediates

In addition to a signal arising from the physical "stretching" of the adipocytes, metabolic and endocrine regulation of leptin production seems to operate in adipocytes. There is however a paucity of literature examining direct role of fatty acid synthesis in regulating adipocytes leptin production. To clarify the relation between fatty acid synthesis and leptin release in adipocytes, we examined leptin release from primary cultured rat epididymal adipocytes with several substances relevance to de novo fatty acid syntyhesis. Bezafibrate (0.5 or 1.0 mM), known to inhibit acetyl-CoA carboxylase, decreased leptin release to 60.3 +/- 7.2 or 47.3 +/- 11.9%, while cerulenin (15, 30, or 75 mM), an inhibitor of fatty acid synthase, increased it by 20.5 +/- 7.7, 58.5 +/- 12.1 or 105.0 +/- 35.0% of the control. Exogenous pyruvate (2.5, 5.0, or 10.0 mM) and malonyl-CoA (10, 20, or 40 mM), substrates and intermediate of fatty acid synthesis, increased leptin release by 11.0 +/- 3.3, 21.5 +/- 5.4, or 61.0 +/- 10.7%, and 11.1 +/- 3.0, 41.1 +/- 9.7 or 56.7 +/- 7.9% of the control, respectively. Considering difference in the site of action of bezafibrate and cerulenin along fatty acid synthesis pathway, one plausible explanation is that malonyl-CoA levels act as a signal of fuel availability to trigger leptin synthesis and/or secretion in adipocytes. Keywords: Leptin secretion; Fatty acid synthesis; Malonyl-CoA; Rat adipocytes.     

Design and synthesis of dysidiolide analogs from vitamin D3: novel class of Cdc25A inhibitors

Potent dysidiolide analogs were synthesized by structural hybridization of dysidiolide and vitamin D(3). These analogs exhibited strong inhibitory activity toward dual-specificity phosphatase Cdc25A (IC(50)=0.44-0.89 microM).     

Differential requirement of EGFR signaling for the expression of defective proventriculus gene in the Drosophila endoderm and ectoderm

A homeobox gene, defective proventriculus (dve), is expressed in various tissues including the ventral ectoderm and midgut. Here, we show the expression pattern of dve in the ventral ectoderm, in which dve expression is induced by Spitz, a ligand for Drosophila epidermal growth factor receptor (EGFR). In spitz mutants, dve expression is only lost in the ventral ectoderm and overexpression of Spitz induces ectopic dve activation in the ventral ectoderm. Dve expression in the middle midgut depends on Decapentaplegic (Dpp) signaling, while expression of a dominant-negative form of Drosophila EGFR (DER(DN)) also causes a marked decrease in dve expression in the middle midgut. Furthermore, heterozygous mutation of thick veins (tkv), a Dpp receptor, strongly enhances the effect of DER(DN). These results indicate that EGFR signaling is crucial for dve expression in the ventral ectoderm and is required in the middle midgut where it cooperates with Dpp signaling.     

Ceriporic acid C, a hexadecenylitaconate produced by a lignin-degrading fungus, Ceriporiopsis subvermispora

A lignin-degrading basidiomycete, Ceriporiopsis subvermispora produces a series of alkyl- and alkenylitaconates (ceriporic acids). Previously, two alkylitaconic acids with tetradecyl and hexadecyl side chains were isolated and identified as 1-heptadecene-2,3-dicarboxylic acid (ceriporic acid A) and 1-nonadecene-2,3-dicarboxylic acid (ceriporic acid B). In the present study, one hexadecenylitaconate (ceriporic acid C) was isolated and its chemical structure was analyzed by glycolation and subsequent (1) trimethylsilation, or (2) acetalation with acetone and acetone-d6. Analyses of the isolated metabolite demonstrated that the hexadecenylitaconic acid was (Z)-1,10-nonadecadiene-2,3-dicarboxylic acid. The structure of the side chain in ceriporic acid C was the same as that of hexadecenylcitraconate, chaetomellic acid B. Thus, it was found that ceriporic acids share close structural similarity with alk(en)yl citraconate derivatives, chaetomellic acids and other lichen lactones, protolichesterinic, lichesterinic, and murolic acids.     

Effect of initial glucose concentration and inoculation level of lactic acid bacteria in shrimp waste ensilation

Fermentation conditions and microorganisms were determined, based on acid production, glucose concentration as carbohydrate source. Inoculation levels to obtain a stable shrimp waste silage were also determined. Shrimp waste ensilation was an efficient method of preservation, allowing the recovery of chitin and another added-value products such as pigments, proteins and enzymes. From the various lactic acid bacteria tested, Lactobacillus pentosus and Lactobacillus sp. (B2) were the best lactic acid producers, although small quantities of acetic acid were detected in samples inoculated with Lactobacillus pentosus. Therefore B2 was chosen for the analysis of glucose consumption as well as for the determination of optimum inoculation levels. The best results were obtained at 10% (w/w wet basis) and 5% (v/w wet basis) respectively. Presence of starters and initial glucose concentration were critical factors in the fermentation of shrimp waste. High initial glucose and starter concentrations reduced the time and increased the amount of lactic acid produced. The fermentation pattern changed during ensilation from hetero to homofermentative. Shrimp waste ensilation prevented the growth of spoilage microorganisms keeping their microbial counts steady and pH values within the acid region.     

Improvement of shark type I collagen with microbial transglutaminase in urea

In the presence of urea, type I collagen could form a gel with crosslinks with microbial transglutaminase (MTGase). Collagen self-assembly was accelerated with the addition of MTGase. The proportion of reconstructed collagen fibrils was raised with the addition of MTGase. MTGase-treated collagen gel remained gelled at high temperatures at which collagen denatured. By treatment with MTGase, collagen could form the gel under impossible condition to collagen self-assembly, and that denaturation temperature was raised.     

Suppression of antibody production by TNF-related apoptosis-inducing ligand (TRAIL)

TNF-related apoptosis-inducing ligand (TRAIL), a type II membrane protein belonging to the TNF family, induces apoptotic cell death in various types of tumor cells. However, little is known about its pathological and physiological functions in the immune system. In this study, we showed that administration of neutralizing anti-TRAIL mAb markedly increased serum auto-Ab levels, particularly of IgG1 subclass, in autoimmune-prone C3H/HeJ gld/gld mice without affecting lymphocytosis and lymphocytes populations. In an experimental system where TNP-specific Ab production was induced by immunization with TNP-modified syngeneic B lymphoma cells, expression of TRAIL on these cells significantly reduced TNP-specific Ab production, especially of IgG1 subclass, without affecting T cell priming. These results suggest a new role for TRAIL in the suppression of Ab production.