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.     

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.     

NMR study on the tautomeric equilibria between the hydrazone imine and diazenyl enamine forms in side chained quinoxalines: Solvent effects and temperature dependence

The reaction of 7-chloro-4-ethoxycarbonylmethylene-4,5-dihydro-1,2,4-triazolo[4,3-a]quinoxaline 6 with 4-ethoxycarbonyl-1-methyl-1H-pyrazole-5-diazonium chloride or 4-cyano-1,3-dimethyl-1H-pyrazole-5-diazonium chloride gave 7-chloro-4-[α-(4-ethoxycarbonyl-1-methyl-1H-pyrazol-5-ylhydrazono)-ethoxycarbonylmethyl]-1,2,4-triazolo[4,3-a]quinoxaline 8a or 7-chloro-4-[α-(4-cyano-1,3-dimethyl-1H-pyrazol-5-ylhydrazono)ethoxycarbonylmethyl]-1,2,4-triazolo[4,3-a]quinoxaline 8b , respectively, while the reaction of 7-chloro-4-ethoxycarbonylmethylene-4,5-dihydrotetrazolo[1,5-a]quinoxaline 7 with 4-ethoxycarbonyl-1-methyl-1H-pyrazole-5-diazonium chloride or 4-cyano-1,3-dimethyl-1H-pyrazole-5-diazomum chloride provided 7-chloro-4-[α-(4-ethoxycarbonyl-1-methyl-1H-pyrazol-5-ylhydrazono)ethoxycarbonylmethyl]tetrazolo[1,5-a]quinoxaline 9a or 7-chloro-4-[α-(4-cyano-1,3-dimethyl-1H-pyrazol-5-ylhydrazono)ethoxycarbonylmethyl]tetrazolo[1,5-a]quinoxaline 9b , respectively. Compounds 8a,b and 9a,b showed the tautomeric equilibria between the hydrazone imine C and diazenyl enamine D forms in dimethyl sulfoxide and/or trifluoroacetic acid, and the effects of solvent and temperature on the tautomer ratios of C to D were studied by the nmr measurements in a series of mixed trifluoroacetic acid/dimethyl sulfoxide media (compounds 8a,b and 9a,b ) and at various temperatures (compounds 8a,b ).     

Surfactants having polyfluoroalkyl chains. II. Syntheses of anionic surfactants having two polyfluoroalkyl chains including a trifluoromethyl group at each tail and their flocculation-redispersion ability for dispersed magnetite particles in water

Anionic surfactants having two polyfluoroalkyl chains per molecule, i.e. the sodium salt of bis(1H, 1H, 2H,2H-heptadeca-fluorodecyl)-2-sulfosuccinate, CF₃(CF₂)₇(CH₂)₂OCOCH₂CH(SO₃Na)COO(CH₂)₂(CF₂)₇CF₃, the sodium salt of bis(1H, 1H, 2H, 2H-tridecafluoro-octyl)-2-sulfosuccinate, CF₃(CF₂)₅(CH₂)₂OCOCH₂CH(SO₃Na)COO(CH₂)₂(CF₂)₅CF₃, and the sodium salt of bis(1H, 1H, 2H, 2H-nonafluorohexyl)-2-sulfosuccinate, CF₃(CF₂)₃(CH₂)₂OCOCH₂CH(SO₃Na)COO(CH₂)₂(CF₂)₃CF₃, have been prepared from maleic anhydride, the corresponding alcohols possessing a polyfluoroalkyl chain and sodium hydrogen sulfite. The flocculation and redispersion abilities of these surfactants for dispersed magnetic particles in water have been examined to investigate the effect of the chain length. It was found that this ability was enhanced by an increase in the chain length. The contact angles for water for pelleted surface-modified magnetite have been measured. In order to compare this ability and the contact angles, data for other fluorinated surfactant have been obtained. The Kraff point, the surface tension and the pNa of the aqueous surfactant solutions have also been measured.     

A highly rigid diamine monomer derived from naturally occurring myo‐inositol and its use for polyamide synthesis

A rigid diamine was synthesized from myo‐inositol, a naturally occurring cyclic hexaol, and used as a monomer to synthesize polyamides. myo‐Inositol was treated with 1,1‐dimethoxycyclohexane to yield a bisketal bearing two hydroxyl groups, and from this bisketal, the target diamine was synthesized in three steps: (1) derivation of the diol into the corresponding bistriflate, (2) nucleophilic substitution of the bistriflate with sodium azide yielding a diazide, and (3) reduction of the diazide to the target diamine. The target diamine readily underwent polycondensation with dicarboxylic acid chloride in solution. The resulting polyamides, whose main chain inherited the rigid 5‐6‐5 system from the diamine monomers, have high glass transition temperatures. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 3436–3443