Biomedical subjects

K Harata

Publications and source records attributed to K Harata.

42 records · Page 3Linked to original sources

PubMed1992

Prominent inclusion effect of dimethyl-beta-cyclodextrin on photoisomerization of the thromboxane synthetase inhibitor (E)-4-(1-imidazoylmethyl)cinnamic acid.

The direct photoisomerization of (E)-4-(1-imidazoylmethyl)-cinnamic acid (IMC), a thromboxane synthetase inhibitor, to its (Z)-isomer at pH 2.0 was decelerated by beta-cyclodextrin (beta-CyD) and heptakis(2,6-di-O-methyl)-beta-cyclodextrin (DM-beta-CyD). The photostationary composition [(Z)-isomer:IMC ratio] was shifted in favor of IMC. These effects were much greater with DM-beta-CyD than with the parent beta-CyD. The quantum yield of the photoisomerization was significantly decreased by complex formation with beta-CyDs, whereas the extinction coefficient of the guest was only slightly decreased. This situation was in sharp contrast to those observed in less polar solvents and suggests that the suppressing mechanism with beta-CyD is different from that with less polar solvent systems. Spectroscopic studies (ultraviolet, circular dichroism, and nuclear magnetic resonance) indicated that IMC is tightly included in an axial mode in the cavity of DM-beta-CyD and that the rotation of the photoreactive site is sterically hindered. The results suggest that the suppressing effect of beta-CyDs on the photoisomerization of IMC results mainly from a steric origin.

Cyclodextrins↗

PubMed1992

X-ray structure of Glu 53 human lysozyme.

The three-dimensional structure of a modified human lysozyme (HL), Glu 53 HL, in which Asp 53 was replaced by Glu, has been determined at 1.77 A resolution by X-ray analysis. The backbone structure of Glu 53 HL is essentially the same as the structure of wild-type HL. The root mean square difference for the superposition of equivalent C alpha atoms is 0.141 A. Except for the Glu 53 residue, the structure of the active site region is largely conserved between Glu 53 HL and wild-type HL. However, the hydrogen bond network differs because of the small shift or rotation of side chain groups. The carboxyl group of Glu 53 points to the carboxyl group of Glu 35 with a distance of 4.7 A between the nearest carboxyl oxygen atoms. A water molecule links these carboxyl groups by a hydrogen bond bridge. The active site structure explains well the fact that the binding ability for substrates does not significantly differ between Glu 53 HL and wild-type HL. On the other hand, the positional and orientational change of the carboxyl group of the residue 53 caused by the mutation is considered to be responsible for the low catalytic activity (ca. 1%) of Glu 53 HL. The requirement of precise positioning for the carboxyl group suggests the possibility that the Glu 53 residue contributes more than a simple electrostatic stabilization of the intermediate in the catalysis reaction.

Amino Acid Sequence↗

PubMed1991

Crystal structure of 2-O-[(S)-2-hydroxypropyl]cyclomaltoheptaose.

2-O-[(S)-2-Hydroxypropyl]cyclomaltoheptaose crystallises in the monoclinic space group P2(1) with unit-cell dimensions a = 15.072(1), b = 10.409(1), c = 20.623(2) A, and beta = 108.52(1) degrees. The structure was solved by X-ray diffraction and refined to an R-value of 0.096. The macrocyclic ring of the cyclomaltoheptaose moiety is less symmetrical than that in cyclomaltoheptaose. The glucose residue that carries the hydroxypropyl group inclines much more with its primary hydroxyl side towards the inside of the macrocycle than the other glucose residues. The molecules are arranged in a herring-bone fashion to form a cage-type packing structure. The hydroxypropyl group is inserted into the cavity of an adjacent molecule related by a two-fold screw axis, and the hydroxyl group is linked to an HO-6 via OH...water...OH hydrogen bonds. The crystal contains 8.5 water molecules which occupy 11 sites. Two water molecules are included at the primary hydroxyl side of the cyclomaltoheptaose cavity.

Carbohydrate Conformation↗

PubMed1991

Synthesis of some 2-O-(2-hydroxyalkyl) and 2-O-(2,3-dihydroxyalkyl) derivatives of cyclomaltoheptaose.

On alkylation of cyclomaltoheptaose with oxiranes, promoted by alkali of low concentration, substitution at secondary positions, particularly at O-2, is favoured. The reaction has been used to prepare the 2-O-[(R)- and (S)-2-hydroxypropyl], 2-O-(2-hydroxy-2-methylpropyl), 2-O-[(R)- and (S)-2,3-dihydroxypropyl], and 2-O-[(R)- and (S)-2,3-dihydroxy-2-methylpropyl] derivatives. Each of these derivatives is less soluble in water than cyclomaltoheptaose, and their complexes with toluene, in contrast to that of cyclomaltoheptaose, are well soluble in water.

Carbohydrate Conformation↗

PubMed1991

The importance of precise positioning of negatively charged carboxylate in the catalytic action of human lysozyme.

The role of aspartic acid 53 of human lysozyme (peptidoglycan N-acetylmuramoylhydrolase, EC 3.2.1.17) has been investigated by a site-directed mutagenesis. In order to clarify the importance of precise positioning of the negatively charged carboxylate group in the active site geometry, both the three-dimensional structure and the enzymatic function of glutamic acid 53 human lysozyme (Glu-53 human lysozyme) have been characterized in comparison with those of wild type enzyme. Glu-53 human lysozyme was crystallized and analysed by X-ray crystallography. No remarkable difference in the conformation of whole molecule except the side chain of 53rd residue was observed. In spite of full retention of the binding activities against either beta-1,4-linked trisaccharide of N-acetylglucosamine ((GlcNAc)3) or the corresponding hexasaccharide ((GlcNAc)6), the conversion of Asp-53 to Glu reduced the enzymatic activities against both bacterial cell substrate and p-nitrophenyl penta-N-acetyl-beta(1----4)-chitopentaoside (p-NO2-(GlcNAc)5) to a few percent of the activities of wild type enzyme. Calculation of electrostatic potential around the reaction center predicted that no significant change in pKa of Glu-35 was caused by the mutation. These results indicate that the precise positioning of the negatively charged carboxylate in the geometry of reaction center is essential for the rate enhancement in the catalytic action of lysozyme, and suggest that Asp-53 of human lysozyme participates in the catalytic action not simply in an electrostatical manner but partly in a nucleophilical manner.

Aspartic Acid↗

PubMedDate not supplied

Crystal structure of asparagine 233-replaced cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011 determined at 1.9 A resolution.

The crystal structure of asparagine 233-replaced cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011 was determined at 1.9 A resolution. While the wild-type CGTase from the same bacterium produces a mixture of mainly alpha-, beta- and gamma-cyclodextrins, catalyzing the conversion of starch into cyclic or linear alpha-1,4-linked glucopyranosyl chains, site-directed mutation of histidine-233 to asparagine changed the nature of the enzyme such that it no longer produced alpha-cyclodextrin. This is a promising step towards an industrial requirement, i.e. unification of the products from the enzyme. Two independent molecules were found in an asymmetric unit, related by pseudo two-fold symmetry. The backbone structure of the mutant enzyme was very similar to that of the wild-type CGTase except that the position of the side chain of residue 233 was such that it is not likely to participate in the catalytic function. The active site cleft was filled with several water molecules, forming a hydrogen bond network with various polar side chains of the enzyme, but not with asparagine-233. The differences in hydrogen bonds in the neighborhood of asparagine-233, maintaining the architecture of the active site cleft, seem to be responsible for the change in molecular recognition of both substrate and product of the mutant CGTase.

Amino Acid Substitution↗