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Biomedical subjects

K Soda

Publications and source records attributed to K Soda.

At least 91 records · Page 5Linked to original sources
PubMed1997

[Atopic dermatitis and related factors observed at infant physical examination at health centers].

We investigated the incidence of atopic dermatitis and related factors at infant physical examination at health centers. Subjects were 900 infants (290 four-month-old infants, 298 one-year and six month-old infants, 312 three-year-old infants) who participated in infant physical examinations in Kanazawa-ku, Yokohama City. Overall, we analyzed 696 infants whose mothers had cooperated with the survey by completing questionnaires during physical examinations, and who submitted to examination by consulting dermatologists. The incidence of atopic dermatitis was 11.6% in 4-month-old infants, 12.2% in 1.5-year-old infants, and 12.1% in 3-year-old infants. The following were found to be related to the atopic dermatitis of infants. 1. Family history of atopic dermatitis in their mothers and older siblings. 2. Mothers' limited diet during pregnancy (avoiding some food which are suspected allergens). 3. Past history of molluscum contagiosum. 4. The frequency of taking bath. While epidemiological surveys of atopic dermatitis have previously been performed, the criteria at each survey was not identical and results could not be compared precisely. In this survey, 1. Dermatologists specializing in atopic dermatitis performed examinations. 2. All diagnoses were made according to standardized criteria which are applied nationwide. 3. All subjects were from a specific region. Because of this approach, this survey provides important information that can form the basis of comparison for future epidemiological surveys of atopic dermatitis.

Age Factors↗
PubMed1997

[Current status of HIV infection in Yunnan Province of China].

In cooperation with the Chinese Academy of Preventive Medicine and Yunnan Province Provincial Office for AIDS Control and Prevention, we studied the current status of HIV infection intravenous drug users (IVDUs) and other high risk groups in Yunnan province of China. As of the end of 1995, 1,807 HIV cases were officially reported (Positive rate was 0.6%), of which 1,278 (77.9%) were IVDUs, and 24 were their spouses. The majority of cases were found among the Dai minority male farmers near Ruili which borders on Myammar, but HIV also appears to be spreading among the Han people. HIV antibody positive rates among commercial sex workers, pregnant women and blood donors were 0.2%, 0.07% and 0.04%, respectively. A system for surveillance of HIV has been developed, but preventive strategies to cope with HIV epidemic are not sufficient. As HIV/AIDS is now a global issue, (1) the integration and coordination of such preventive strategies in cooperation with community health workers, (2) general health education for condom use promotion and (3) care of psychological vulnerable person such as IVDUs, should be developed.

Acquired Immunodeficiency Syndrome↗
PubMed1997

[The HIV/AIDS Epidemic in Cambodia].

In December 1995 and March 1996, we visited institutes which were conducting epidemiological studied of HIV/AIDS in Cambodia, and obtained data for further collaborative study between Japan and Cambodia. Data included information on AIDS patients and HIV infected persons, and behavioral epidemiology of CSWs (Commercial Sex Workers). The cumulative reported number of AIDS patients and HIV infected persons in Cambodia was 86 and 2,536 cases respectively in 1995. The cause of infection was mostly heterosexual contact with very few cases from injecting drug use (IDU) and other causes. The seroprevalence rate of HIV antibody among donated blood rapidly increased from 0.08% in 1991 to 4.47% in 1995, and those among CSWs and pregnant women were 37.9% and 2.6%, respectively, in 1995. The average rate of condom use among CSWs was 66%, but the rate of usual usage was only 14%. These results indicate that the HIV/AIDS epidemic had spread rapidly through CSWs, that it had been spread among peoples in communities, and that usage of condoms among CSWs was insufficient in Cambodia. Without strong countermeasures against HIV/AIDS in this country, HIV/AIDS epidemic may spread significantly to not only peoples in this country but also those in neighbouring countries in the future.

Acquired Immunodeficiency Syndrome↗
PubMed1996

Site-directed mutagenesis of the amino acid residues in beta-strand III [Val30-Val36] of D-amino acid aminotransferase of Bacillus sp. YM-1.

The beta-strand III formed by amino acid residues Val30-Val36 is located across the active site of the thermostable D-amino acid aminotransferase (D-AAT) from thermophilic Bacillus sp. YM-1, and the odd-numbered amino acids (Tyr31, Val33, Lys35) in the strand are revealed to be directed toward the active site. Interestingly, Glu32 is also directed toward the active site. We first investigated the involvement of these amino acid residues in catalysis by alanine scanning mutagenesis. The Y31A and E32A mutant enzymes showed a marked decrease in k(cat) value, retaining less than 1% of the wild-type enzyme activity. The k(cat) values of V33A and K35A were changed slightly, but the Km of K35A for alpha-ketoglutarate was increased to 35.6 mM, compared to the Km value of 2.5 mM for the wild-type enzyme. These results suggested that the positive charge at Lys35 interacted electrostatically with the negative charge at the side chain of alpha-ketoglutarate. Site-directed mutagenesis of the Glu32 residue was conducted to demonstrate the role of this residue in detail. From the kinetic and spectral characteristics of the Glu32-substituted enzymes, the Glu32 residue seemed to interact with the positive charge at the Schiff base formed between the aldehyde group of pyridoxal 5'-phosphate (PLP) and the epsilon-amino group of the Lys145 residue.

Alanine Transaminase↗
PubMed1996

Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold.

L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation of L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. The crystal structure of the homodimeric enzyme from Pseudomonas sp. YL has been determined by a multiple isomorphous replacement method and refined at 2.5 A resolution to a crystallographic R-factor of 19.5%. The subunit consists of two structurally distinct domains: the core domain and the subdomain. The core domain has an alpha/beta structure formed by a six-stranded parallel beta-sheet flanked by five alpha-helices. The subdomain inserted into the core domain has a four helix bundle structure providing the greater part of the interface for dimer formation. There is an active site cavity between the domains. An experimentally identified nucleophilic residue, Asp-10, is located on a loop following the amino-terminal beta-strand in the core domain, and other functional residues, Thr-14, Arg-41, Ser-118, Lys-151, Tyr-157, Ser-175, Asn-177, and Asp-180, detected by a site-directed mutagenesis experiment, are arranged around the nucleophile in the active site. Although the enzyme is an alpha/beta-type hydrolase, it does not belong to the alpha/beta hydrolase fold family, from the viewpoint of the topological feature and the position of the nucleophile.

Amino Acid Sequence↗
PubMed1996

Stereospecificity of thermostable ornithine 5-aminotransferase for the hydrogen transfer in the L- and D-ornithine transamination.

The thermostable ornithine 5-aminotransferase of a thermophile, Bacillus sp. YM-2, is unique in acting on both enantiomers of ornithine, although less effectively on the D-enantiomer. We studied the stereospecificity of the enzyme for the hydrogen abstraction from C-5 of the substrate moiety and the addition and removal of the hydrogen at C-4' of the cofactor (pyridoxal phosphate and pyridoxamine phosphate) moiety of the external Schiff base intermediate in the transamination of L- and D-ornithine. L- and D-[5-3H]ornithines were prepared by incubation of L- and D-ornithines with the enzyme in 3H2O, respectively. When the L-[5-3H]ornithine was incubated with L-ornithine 5-aminotransferase of a mesophile, Bacillus sphaericus, which catalyzes the stereospecific abstraction of pro-S hydrogen from C-5 of L-ornithine, most of the tritium was released into the solvent. The D-[5-3H]ornithine also reacted with the enzyme of B. sphaericus in the presence or absence of the amino acid racemase of Pseudomonas putida. Tritium was released only in the presence of the racemase, which catalyzes the racemization of ornithine but does not act on C-5 of ornithine. These results show that the Bacillus sp. YM-2 ornithine 5-aminotransferase stereospecifically abstracts the pro-S hydrogen from C-5 of L- and D-ornithine. When the apo form of the enzyme was incubated with pyridoxamine 5'-phosphate that was stereospecifically tritiated at C-4' and 2-oxoglutarate in the presence of L-ornithine or D-ornithine, tritium was released exclusively from (4'S)-[4'-3H]pyridoxamine. Therefore, addition and abstraction of hydrogen at C-4' of the cofactor moiety stereospecifically occur on the si face of the external Schiff base intermediate in the overall transamination catalyzed by Bacillus sp. YM-2 ornithine 5-aminotransferase irrespective of the C-2 configuration of the amino donor.

Amino Acid Isomerases↗
PubMed1996

Interaction of pyridoxal 5'-phosphate with tryptophan-139 at the subunit interface of dimeric D-amino acid transaminase.

The crystal structure of dimeric bacterial D-amino acid transaminase shows that the indole rings of the two Trp-139 side chains face each other in the subunit interface about 10 angstroms from the coenzyme, pyridoxal 5'-phosphate. To determine whether it has a role in the catalytic efficiency of the enzyme or interacts with the coenzyme, Trp-139 has been substituted by several different types of amino acids, and the properties of these recombinant mutant enzymes have been compared to the wild-type enzyme. In the native wild-type holoenzyme, the fluorescence of one of the three Trp residues per monomer is almost completely quenched, probably due to its interaction with PLP since in the native wild-type apoenzyme devoid of PLP, tryptophan fluorescence is not quenched. Upon reconstitution of this apoenzyme with PLP, the tryptophan fluorescence is quenched to about the same extent as it is in the native wild-type enzyme. The site of fluorescence quenching is Trp-139 since the W139F mutant in which Trp-139 is replaced by Phe has about the same amount of fluorescence as the wild-type enzyme. The circular dichroism spectra of the holo and the apo forms of both the wild-type and the W139F enzymes in the far-ultraviolet show about the same degree of ellipticity, consistent with the absence of extensive global changes in protein structure. Furthermore, comparison of the circular dichroism spectrum of the W139F enzyme at 280 nm with the corresponding spectral region of the wild-type enzyme suggests a restricted microenvironment for Trp-139 in the latter enzyme. The functional importance of Trp-139 is also demonstrated by the finding that its replacement by Phe, His, Pro, or Ala gives mutant enzymes that are optimally active at temperatures below that of the wild-type enzyme and undergo the E-PLP --> E-PMP transition as a function of D-Ala concentration with reduced efficiency. The results suggest that a fully functional dimeric interface with the two juxtaposed indole rings of Trp-139 is important for optimal catalytic function and maximum thermostability of the enzyme and, furthermore, that there might be energy transfer between Trp-139 and coenzyme PLP.

Catalysis↗
PubMed1996

Crystallization and preliminary x-ray crystallographic studies of L-2-haloacid dehalogenase from Pseudomonas sp. YL.

The dimeric L-2-haloacid dehalogenase from Pseudomonas sp. YL, (subunit mass, 26179 Da), has been crystallized by vapor diffusion, supplemented by repetitive seeding, against a 50 mM potassium dihydrogenphosphate solution (pH 4.5) containing 15% (w/v) polyethylene glycol 8,000 and 1% (v/v) n-propanol. The crystals belong to the monoclinic space group C2 with unit cell dimensions of a = 92.21 angstrom, b = 62.78 angstrom, c = 50.84 angstrom, and beta = 122.4 degrees, and contain two dehalogenase dimers in the unit cell. They are of good quality and diffract up to 1.5 angstrom resolution.

Crystallography, X-Ray↗
PubMed1996

The ubiquitous cofactor NADH protects against substrate-induced inhibition of a pyridoxal enzyme.

In the usual reaction catalyzed by D-amino acid transaminase, cleavage of the alpha-H bond is followed by the reversible transfer of the alpha-NH2 to a keto acid cosubstrate in a two-step reaction mediated by the two vitamin B6 forms pyridoxal 5'-phosphate (PLP) and pyridoxamine 5'-phosphate (PMP). We report here a reaction not on the main pathway, i.e., beta-decarboxylation of D-aspartate to D-alanine, which occurs at 0.01% the rate of the major transaminase reaction. In this reaction, beta-C-C bond cleavage of the single substrate D-aspartate occurs rather than the usual alpha-bond cleavage in the transaminase reaction. The D-alanine produced from D-aspartate slowly inhibits both transaminase and decarboxylase activities, but NADH or NADPH instantaneously prevent D-aspartate turnover and D-alanine formation, thereby protecting the enzyme against inhibition. NADH has no effect on the enzyme spectrum itself in the absence of substrates, but it acts on the enzyme.D-aspartate complex with an apparent dissociation constant of 16 microM. Equivalent concentrations of NAD or thiols have no such effect. The suppression of beta-decarboxylase activity by NADH occurs concomitant with a reduction in the 415-nm absorbance due to the PLP form of the enzyme and an increase at 330 nm due to the PMP form of the enzyme. alpha-Ketoglutarate reverses the spectral changes caused by NADH and regenerates the active PLP form of the enzyme from the PMP form with an equilibrium constant of 10 microM. In addition to its known role in shuttling electrons in oxidation-reduction reactions, the niacin derivative NADH may also function by preventing aberrant damaging reactions for some enzyme-substrate intermediates. The D-aspartate-induced effect of NADH may indicate a slow transition between protein conformational studies if the reaction catalyzed is also slow.

Amino Acids↗
PubMed1996

Stereospecificity for the hydrogen transfer and molecular evolution of pyridoxal enzymes.

We here describe the stereochemical aspects of the reactions of pyridoxal 5'-phosphate (PLP)-dependent enzymes, and the relationship between the stereochemistry of the enzyme reaction and molecular evolution of the enzyme. The reactions of PLP-dependent enzymes proceed through the formation of an anionic Schiff base intermediate between the substrate and the coenzyme. Three stereochemical possibilities exist for the formation and cleavage of bonds in the intermediate: the reaction occurs stereospecifically on either the si- or the re-face of the planar intermediate, or alternatively, non-stereospecifically on both faces. The stereospecificities for hydrogen transfer between C-4' of the cofactor and substrate in the transamination catalyzed by various PLP-dependent enzymes have been studied. The stereospecificities reflect the active-site structures of the enzymes, especially the topographical situation of a coenzyme-substrate Schiff base and a catalytic base for the hydrogen transfer. The aminotransferases and other PLP-enzymes catalyzing the transamination as a side-reaction so far studied catalyze only the si-face specific hydrogen transfer. This suggests that these PLP enzymes have similar active-site structures and are evolved divergently from a common ancestral protein. We recently established a new method for the identification of stereospecificity for the hydrogen transfer, and found that D-amino acid aminotransferase and branched chain L-amino acid aminotransferase, which have significant sequence similarity to each other, catalyze the re-face hydrogen transfer on the intermediate. The X-ray crystallographic studies of D-amino acid aminotransferase showed that the relative arrangement of the catalytic base of the enzyme active center to the C4' of the bound cofactor is opposite to that of other aminotransferases catalyzing the si-face hydrogen transfer. The folding of D-amino acid aminotransferase is also different from those of the other aminotransferase so far studied. Therefore, the classifications of the aminotransferases based on their primary structures, three dimensional structures, and stereochemistry of their hydrogen transfer coincide with one another. We also found that PLP-dependent amino acid racemases, the primary structures of which are similar to none of the other PLP-enzymes, catalyze the non-stereospecific hydrogen transfer on both faces of the planar intermediate. Stereospecificities for the hydrogen transfer suggest convergent evolution of the PLP-dependent enzymes. The stereochemical aspects of the enzyme reactions give a clue to the molecular evolution of the enzymes as well as the primary structures and three-dimensional structures of the enzymes.

Amino Acids↗
PubMed1996

Fight against infectious diseases.

During early Meiji era in Japan, there were frequent epidemics of fatal acute communicable diseases such as cholera, dysentery and smallpox, and preventive measures and preparations for acute infectious diseases were urgently needed. Together with improvement of scientific preparations, the Communicable Disease Prevention Law was promulgated in 1897. Then gradually until 1940's, the focus of preventive measures have been shifted from acute infectious diseases to chronic ones, particularly tuberculosis. After the World War II, except the short period of social confusion, major legally-defined communicable diseases had been decreasing rapidly mainly due to the use of antibiotics and improvement of environmental sanitation. At the same time, the introduction of preventive vaccination marked a new era for the prevention of infectious diseases and was largely responsible for the remarkable decrease of infant mortality in Japan. Recently the concept of defense by vaccination against infectious diseases has evolved from group-oriented to individual-oriented, so that the Preventive Vaccination Law was drastically revised in 1994. Currently, effective counter-measures against newly emerged infectious diseases, as viral hepatitis, institution-acquired infection, viral hemorrhagic fever etc., have been implemented. For the future, improvement of infections disease surveillance, vaccine development and expansion of vaccination coverage along with monitoring side-effects, preventive health education on AIDS/STDs, addressing the special needs of foreigners living in Japan and international collaboration for disease control abroad are all vital to the success of protection of the public's health from infectious diseases in Japan.

Communicable Disease Control↗
PubMed1996

Epidemiology of AIDS/HIV in Japan.

The data obtained from the national reporting system of acquired immune deficiency syndrome (AIDS) and its causative immune deficiency virus (HIV), the epidemic pattern of AIDS cases and HIV carriers in Japan from 1985 to 1995 could be summarized as follows: 1) the total number of reported AIDS cases and HIV carriers were 1,154 and 3,524 which included 167 and 915 foreigners, respectively; 2) among them the number of HIV carriers in hemophiliacs transmitted through HIV contaminated blood products was 1,806, including 582 AIDS victims; 3) excluding these hemophiliacs, there are 572 AIDS cases (167 foreigners) which shared risk factors for heterosexual contacts (37%) and homosexual contacts (31%), respectively; 4) on the other hand, more than 50% were heterosexuals and only 20% were homosexuals in 1,718 HIV carriers (915 foreigners); 5) the peak incidence is 33% in the 30s in AIDS, while more than 50% are in their 20s; 6) male-to-female ratio was 6.8 in AIDS cases but only 1.1 in HIV carriers; 7) the estimated number of HIV carriers in 2000 was 6,300-8,500 in Japanese and 700-1,700 in foreigners, respectively. From the above mentioned epidemic pattern of AIDS/HIV in Japan, we have to recognize that the recent number of HIV infection is actually increasing and the most of current HIV carriers even in foreigners are infected with HIV in our country and general activities for AIDS prevention in Japan and neighboring Asian countries should be promoted.

Acquired Immunodeficiency Syndrome↗
PubMed1996

[Trace elements as activation factors of enzymes: characteristic enzymes and their activation mechanisms].

We here describe activation mechanisms of three characteristic metalloenzymes by metals. The copper-containing amine oxidase contains a topaquinone residue at the active site. The inactive precursor form of the enzyme, which contains a tyrosine residue at the position corresponding to topaquinone of the matured protein, was isolated and converted to the matured form by incubation with cupric ions through self-processing of the protein. The selenocysteine residue of selenium-containing formate dehydrogenase is synthesized cotranslationally through a process directed by a UGA codon that normally functions as a stop codon. We describe the mechanism of recognition of UGA and specific incorporation of selenium into the protein. Vanadium-containing haloperoxidases afford stable apo forms lacking vanadium. Reconstitution of holo forms by vanadium ions are also described.

Amine Oxidase (Copper-Containing)↗
PubMed1996

Chemical modification of dehalogenase.

Dehalogenase is an enzyme which catalyzes alpha-haloacid into alpha-hydroxyl acid. Chemical modification reactions of dehalogenase YL, 109, and H-2 were carried out by various reagents. The experimental results showed that the activity was not significantly altered by seryl, lysyl, and trpyl reagents but decreased by hisyl, arginyl, and carboxyl reagents. A substitute could protect the active center to chemical modification. It was indicated that hisyl, arginyl, and carboxyl (Glu or Asp) residues would be essential for the activity of dehalogenase.

Hydrolases↗
PubMed1995

Reaction mechanism of L-2-haloacid dehalogenase of Pseudomonas sp. YL. Identification of Asp10 as the active site nucleophile by 18O incorporation experiments.

L-2-Haloacid dehalogenase (EC 3.8.1.2) catalyzes the hydrolytic dehalogenation of L-2-haloacids to produce the corresponding D-2-hydroxy acids. We have analyzed the reaction mechanism of the enzyme from Pseudomonas sp. YL and found that Asp10 is the active site nucleophile. When the multiple turnover enzyme reaction was carried out in H2(18)O with L-2-chloropropionate as a substrate, lactate produced was labeled with 18O. However, when the single turnover enzyme reaction was carried out by use of a large excess of the enzyme, the product was not labeled. This suggests that an oxygen atom of the solvent water is first incorporated into the enzyme and then transferred to the product. After the multiple turnover reaction in H2(18)O, the enzyme was digested with lysyl endopeptidase, and the molecular masses of the peptide fragments formed were measured by an ionspray mass spectrometer. Two 18O atoms were shown to be incorporated into a hexapeptide, Gly6-Lys11. Tandem mass spectrometric analysis of this peptide revealed that Asp10 was labeled with two 18O atoms. Our previous site-directed mutagenesis experiment showed that the replacement of Asp10 led to a significant loss in the enzyme activity. These results indicate that Asp10 acts as a nucleophile on the alpha-carbon of the substrate leading to the formation of an ester intermediate, which is hydrolyzed by nucleophilic attack of a water molecule on the carbonyl carbon atom.

Amino Acid Sequence↗
PubMed1995

Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity.

The three-dimensional structure of D-amino acid aminotransferase (D-AAT) in the pyridoxamine phosphate form has been determined crystallographically. The fold of this pyridoxal phosphate (PLP)-containing enzyme is completely different from those of any of the other enzymes that utilize PLP as part of their mechanism and whose structures are known. However, there are some striking similarities between the active sites of D-AAT and the corresponding enzyme that transaminates L-amino acids, L-aspartate aminotransferase. These similarities represent convergent evolution to a common solution of the problem of enforcing transamination chemistry on the PLP cofactor. Implications of these similarities are discussed in terms of their possible roles in the stabilization of intermediates of a transamination reaction. In addition, sequence similarity between D-AAT and branched chain L-amino acid aminotransferase suggests that this latter enzyme will also have a fold similar to that of D-AAT.

Alanine Transaminase↗