Quantitative estimation of interaction between carbohydrates and concanavalin A by surface plasmon resonance biosensor

We measured the affinity of more than 20 sugars with concanavalin A (ConA) by an optical biosensor (surface plasmon resonance sensor) using asialofetuin (ASF) as an immobilized binding partner of ConA. We determined kinetic parameters of the effects of sugars on the dissociation of ConA from ASF quantitatively, and the structural requirements of the functional groups of sugars for binding with ConA. We found that the affinity of ConA for sugars is dependent on its conformation induced by interaction with the binding partner. In addition, the results showed that optical biosensor system is well mimics the interaction of ConA with sugars in biomembrane.     

Normal mode analysis of oligomeric proteins: Reduction of the memory requirement by consideration of rigid geometry and molecular symmetry

A method is presented to reduce the memory requirement of normal mode analysis applied to systems containing two or more large proteins when these systems exhibit symmetry properties. We use a rigid geometry model (i.e., only the dihedral angles of the polypeptide chain are considered as variables). This model allows a reduction by a factor of 8 on average of the number of variables with a concomitant freezing of the high-frequency modes. The symmetry properties of the system are used to reduce further the number of variables that must be considered in the computation. Application of group theory leads to a factorization of the matrices of interest (the coefficient and the Hessian matrices) into independent blocks along the diagonal. The initial, reducible representation is thus transformed into a number of irreducible representations of smaller dimensions. In the case of the C₂ symmetry group, the method leads to a reduction of the size of the matrices that must be manipulated during the computation (coefficient matrix, Hessian matrix, and eigenvectors matrix) by a factor of 256 compared with the usual normal mode analysis in Cartesian coordinate space. The method is particularly well adapted to the study of the dynamics of oligomeric proteins because these proteins often display symmetry properties (e.g., virus coat proteins, immunoglobulins, hemoglobin, etc.). In favorable cases, in conjunction with X-ray diffuse scattering data, the study of systems showing allosteric properties might be considered. © 1994 by John Wiley & Sons, Inc.     

γ-Radiolysis of 5-fluorouracil and 5-fluorouridine derivatives having sulfur-containing substituents

γ-Radiolysis reactions of eight 5-fluorouracil (5-FU) derivatives having sulfonyl group-containing substituents at the 1-position and five 5-fluorouridine (5-FUR) derivatives having thioureido group-containing substituents were studied under the conditions where hydrated electron (e_aq^?) and hydroxyl radical (HO·) become the principal reactive species. The 5-FU and 5-FUR derivatives were radiolyzed to give 5-FU and 5-FUR, respectively. The efficiency of the reactions depended upon the nature of reactive species and also upon the nature of substituents. The reactivity features of the γ-radiolysis reactions are discussed.     

Reactivity of cobaloxime bound to polystyrene chain by carbon–cobalt σ bond

The (alkyl)-bis(dimethylglyoximato)pyridinecobalt attached to polychloromethylstyrene by a cobalt–carbon bond was prepared by the reaction of Co(II)(DH)₂Py with polychloromethylstyrene in benzene. The fraction of p-vinylbenzyl·Co(DH)₂Py introduced to the polymer was 8.1 and 2.1 mole %. The photodecomposition of the polymer-bonded cobaloxime was investigated by following the change of the visible spectrum. The rate constant k_dec of the polymer-bonded cobaloxime was 1.1 × 10^?2 sec^?1 in benzene; it is one-fourth of that of its monomeric analog, benzyl·Co(DH)₂Py. The k_dec values of the cobaloximes were also measured in benzene–dimethyl sulfoxide mixed solvents, and the polymer effects were discussed. The dependence of the photodecomposition on energy of the irradiation light was investigated, and it was found that the absorption band near 470 nm is important for the photodecomposition of the cobalt–carbon bond. Spectroscopic measurements of the ligand exchange reaction of polymer-bonded cobaloxime with pyridine in dimethyl sulfoxide gave a larger equilibrium constant (1.2 × 10⁴ liter/mole) than that of benzyl·Co(DH)₂Py (9.4 × 10² liter/mole). The kinetic data of the ligand exchange reaction indicated that the larger equilibrium constant for the polymeric system is due to the smaller rate constant of the reverse reaction. The thermodynamic parameters were also obtained.     

Polytheonamides A and B, highly cytotoxic, linear polypeptides with unprecedented structural features, from the marine sponge, Theonella swinhoei

Polytheonamides A and B are highly cytotoxic polypeptides with 48 amino acid residues isolated from the marine sponge, Theonella swinhoei. The structure of polytheonamide B was determined by spectral and chemical methods, especially extensive 2D NMR experiments, which resulted in the unprecedented polypeptide structure; the N-terminal glycine blocked with a 5,5-dimethyl-2-oxo-hexanoyl group, the presence of eight tert-leucine, three beta-hydroxyvaline, six gamma-N-methylasparagine, two gamma-N-methyl-beta-hydroxyasparagine, and beta,beta-dimethymethionine sulfoxide residues. More significantly, it has the sequence of alternating D- and L-amino acids. Polytheonamide A is an epimer of polytheonamide B differing only in the stereochemistry of the sulfoxide of the 44(th) residue.     

The dependence of cyclopolymerizability of acrylic and methacrylic anhydrides on various conditions: New interpretation of temperature dependency of cyclization constant in radical cyclopolymerization of nonconjugated dienes

The cyclization constant K_c in the radical cyclopolymerization of acrylic and methacrylic anhydrides was evaluated in detail under various conditions. No linear relationship between in K_c and 1/T was observed; cyclization was acceleratively enhanced at elevated temperatures. The K_c values also increased with decreased monomer concentration and increased solvent polarity. These increasing dependencies of K_c are ascribed to the increased significance of depropagation, demonstrating a new interpretation of the temperature dependence of the cyclization constant in the radical cyclopolymerization of nonconjugated dienes.     

Structure-specificity relationship of cardiac glycosides as a substrate for glucohydrolase II

Cardenolide glucohydrolase II (CGH II) is a cardenolide-specific glucohydrolase obtained from Digitalis lanata leaves. We investigated the structure-specificity relationship of several cardenolide disaccharides as a substrate for CGH II. Conformation analysis of the substrates was performed using molecular mechanics calculations. The sugar chain conformation of two inert glycosides was significantly different from that of the other glycosides. The other two glycosides, which were weak substrates of CGH II, were suggested to have an intramolecular hydrogen bond between the sugar groups. It was deduced that this hydrogen bond restricts the conformational change of the sugar chain and prevents the glycosides from enzymatic recognition.     

Studies on pyrazines. 29 . High regioselective synthesis of chloropyrazines from 3-substituted pyrazine 1-oxides

Reaction of 3-methoxy- or 3-chloropyrazine 1-oxides with refluxing phosphoryl chloride in the presence of amine led to a high regioselective formation of 3-substituted 2-chloropyrazines. In contrast, the use of chloroacetyl chloride instead of phosphoryl chloride enabled different regioselectivity to yield 6-substituted 2-chloropyrazines, particularly 3-methoxycarbonylpyrazine 1-oxide was almost exclusively converted into methyl 6-chloropyrazinecarboxylate under the conditions without the amine.     

Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen

The carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F has been characterized by X-ray crystallography and absorption and resonance Raman spectroscopy. Nine crystal structures of the [NiFe]hydrogenase in the CO-bound and CO-liberated forms were determined at 1.2-1.4 A resolution. The exogenously added CO was assigned to be bound to the Ni atom at the Ni-Fe active site. The CO was not replaced with H(2) in the dark at 100 K, but was liberated by illumination with a strong white light. The Ni-C distances and Ni-C-O angles were about 1.77 A and 160 degrees, respectively, except for one case (1.72 A and 135 degrees ), in which an additional electron density peak between the CO and Sgamma(Cys546) was recognized. Distinct changes were observed in the electron density distribution of the Ni and Sgamma(Cys546) atoms between the CO-bound and CO-liberated structures for all the crystals tested. The novel structural features found near the Ni and Sgamma(Cys546) atoms suggest that these two atoms at the Ni-Fe active site play a role during the initial H(2)-binding process. Anaerobic addition of CO to dithionite-reduced [NiFe]hydrogenase led to a new absorption band at about 470 nm ( approximately 3000 M(-1)cm(-1)). Resonance Raman spectra (excitation at 476.5 nm) of the CO complex revealed CO-isotope-sensitive bands at 375/393 and 430 cm(-1) (368 and 413 cm(-1) for (13)C(18)O). The frequencies and relative intensities of the CO-related Raman bands indicated that the exogenous CO is bound to the Ni atom with a bent Ni-C-O structure in solution, in agreement with the refined structure determined by X-ray crystallography.