Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase

Two molecular dynamics (MD) simulations totaling 25 ns of simulation time of monomeric scytalone dehydratase (SD) were performed. The enzyme has a ligand-binding pocket containing a cone-shaped alpha+beta barrel, and the C-terminal region covers the binding pocket. Our simulations clarified the difference in protein dynamics and conformation between the liganded protein and the unliganded protein. The liganded protein held the ligand molecule tightly and the initial structure was maintained during the simulation. The unliganded protein, on the other hand, fluctuated dynamically and its structure changed largely from the initial structure. In the equilibrium state, the binding pocket was fully solvated by opening of the C-terminal region, and the protein dynamics was connected with hydration water molecules entry into and release from the binding pocket. In addition, the cooperative motions of the unliganded protein and the hydration water molecules produced the path through the protein interior for ligand binding.     

Characterization of human residual catalase of an acatalasemic patient by isoelectric focusing and sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by electrophoretic blotting and immunodetection

Isoelectric points and subunit sizes of catalases in human blood and human cultured skin fibroblasts from acatalasemic and normal subjects were analyzed by isoelectric focusing in agarose gel and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, respectively, followed by electroblotting to polyvinylidene difluoride membranes for immunodetection. The results indicated that the isoelectric point of residual catalase in the C fraction prepared from acatalasemic erythrocytes was identical with that of catalase prepared from normal erythrocytes. The residual catalase in homogenates of acatalasemic cultured skin fibroblasts also reacted with anticatalase rabbit serum and had an isoelectric point identical with that of normal catalase. Subunit sizes of normal and acatalasemic catalases in the C fractions of erythrocytes were also found to be identical on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, followed by electroblotting and immunoenzymatic amplification. The results indicated no substantial difference in molecular size and charge of catalase proteins between normal and acatalasemic erythrocytes and fibroblasts.     

Trapping effect of eugenol on hydroxyl radicals induced by L-DOPA in vitro

Many researchers have stated that eugenol might inhibit lipid peroxidation at the stage of initiation, propagation, or both, and many attempts have been made to elucidate the mechanism of its antioxidant activity. Nevertheless, details of its mechanism are still obscure. This study was carried out to investigate the trapping effect of eugenol on hydroxyl radical generated from L-3,4-dihydroxyphenylalanine (DOPA) in MiliQ water and the generation mechanism of the hydroxyl radical by this system which uses no metallic factor. This was studied by adding L-DOPA and 5,5-dimethyl-1-pyrroline N-oxide (DMPO) to phosphate buffered saline (PBS) or MiliQ water, and the generation of hydroxyl radical was detected on an ESR spectrum. By this method, the effect of antioxidants was detected as a modification of ESR spectra. We found that the eugenol trapped hydroxyl radicals directly, because it had no iron chelating action, did not trap L-DOPA semiquinone radical and inhibited hydroxyl radicals with or without iron ion.     

Chain-growth polycondensation for well-defined aramide. Synthesis of unprecedented block copolymer containing aramide with low polydispersity

Poly(p-benzamide) with a defined molecular weight and a low polydispersity and a block copolymer containing this well-defined aramide was synthesized. Phenyl 4-aminobenzoate, which would yield poly(p-benzamide), did not polymerize under the conditions of chain-growth polycondensation. However, phenyl 4-(4-octyloxybenzylamino)benzoate (1b) polymerized at room temperature in the presence of base and phenyl 4-nitrobenzoate (2) as an initiator in a chain-growth polycondensation manner to give well-defined aromatic polyamides having the 4-octyloxybenzyl groups as a protecting group on nitrogen in an amide. It was confirmed by a model reaction that deprotection of this protecting group proceeded completely with trifluoroacetic acid (TFA) without breaking the amide linkage. The utility of this approach to poly(p-benzamide) with a low polydispersity was demonstrated by the synthesis of block copolymers. Thus, phenyl 4-(octylamino)benzoate (1a) polymerized in the presence of 2 and base, followed by addition of 1b and base to the reaction mixture of the prepolymer to yield the block copolymer of 1a and 1b with a controlled molecular weight and a low polydispersity. The block copolymer was treated with TFA, resulting in a soluble block copolymer of poly(N-octyl-p-benzamide) and poly(p-benzamide). The SEM images of the supramolecular assemblies of the block copolymer showed mum-sized bundles and aggregates of flake structures.     

A theory of adsorption kinetics with time delay and its application to overshoot and oscillation in the surface tension of gelatin solution

A theory of adsorption kinetics with time delay [Ohshima et al. (1992) Colloid Polym. Sci. 270:707] is developed and applied to the surface tension of a polymer solution. It is found that the general appearance of the overshoot and oscillation in the time course of the surface tension of aqueous gelatin solution observed by Sato and Ueberreiter [(1979) Makromol. Chem. 180:829, 1107; (1979) Polym. Prepr. Am. Chem. Soc. Div. Polym. Chem. 20:907) can be explained by the present theory.     

Cloning, sequencing, and functional analysis of the biosynthetic gene cluster of macrolactam antibiotic vicenistatin in Streptomyces halstedii

Vicenistatin, an antitumor antibiotic isolated from Streptomyces halstedii, is a unique 20-membered macrocyclic lactam with a novel aminosugar vicenisamine. The vicenistatin biosynthetic gene cluster (vin) spanning approximately 64 kbp was cloned and sequenced. The cluster contains putative genes for the aglycon biosynthesis including four modular polyketide synthases (PKSs), glutamate mutase, acyl CoA-ligase, and AMP-ligase. Also found in the cluster are genes of NDP-hexose 4,6-dehydratase and aminotransferase for vicenisamine biosynthesis. For the functional confirmation of the cluster, a putative glycosyltransferase gene product, VinC, was heterologously expressed, and the vicenisamine transfer reaction to the aglycon was chemically proved. A unique feature of the vicenistatin PKS is that the loading module contains only an acyl carrier protein domain, in contrast to other known PKS-loading modules containing certain activation domains. Activation of the starter acyl group by separate polypeptides is postulated as well.