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Biomedical subjects

K Soda

Publications and source records attributed to K Soda.

At least 73 records · Page 4Linked to original sources
PubMed1998

[Relationship between dietary calcium and bone mineral density before menopause].

To study the relationship between dietary calcium intake and bone mineral density (BMD) among young Japanese females, we recruited 1298 females under 40 years living in Yokohama city for BMD measurement by Computed X-ray densitometer (CXD method) and dietary questionnaire. 1. The average of BMD was 2.75 mm/AI and was highest in the 35 to 39 year old group. 2. Calcium intake (Ca) and protein intake (Protein) were highest in 35 to 39 year old group. 3. BMD, Ca, and Protein were significantly higher in those who had regular dietary habits than those with irregular habits. 4. Among those who had lower Ca, (less than 600 mg per day), the amount of small fish consumed whole was negatively correlated with BMD (p = 0.035), and those with higher consumption of small fish than average had significantly (p = 0.018) lower BMD than those with lower small fish consumption adjusting for age and Ca and protein intake. These findings imply a possibility that small fish accompanied by higher salt intake may influence BMD adversely in this population by an interaction with calcium urinary excretion, which has been suggested by experimental and epidemiologic studies. Dietary composition of Ca may be important for prevention of osteoporosis.

Absorptiometry, Photon↗
PubMed1997

Cysteine sulfinate desulfinase, a NIFS-like protein of Escherichia coli with selenocysteine lyase and cysteine desulfurase activities. Gene cloning, purification, and characterization of a novel pyridoxal enzyme.

Selenocysteine lyase (EC 4.4.1.16) exclusively decomposes selenocysteine to alanine and elemental selenium, whereas cysteine desulfurase (NIFS protein) of Azotobacter vinelandii acts indiscriminately on both cysteine and selenocysteine to produce elemental sulfur and selenium respectively, and alanine. These proteins exhibit some sequence homology. The Escherichia coli genome contains three genes with sequence homology to nifS. We have cloned the gene mapped at 63.4 min in the chromosome and have expressed, purified to homogeneity, and characterized the gene product. The enzyme comprises two identical subunits with 401 amino acid residues (Mr 43,238) and contains pyridoxal 5'-phosphate as a coenzyme. The enzyme catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L-selenocystine to produce L-alanine. Because L-cysteine sulfinic acid was desulfinated to form L-alanine as the preferred substrate, we have named this new enzyme cysteine sulfinate desulfinase. Mutant enzymes having alanine substituted for each of the four cysteinyl residues (Cys-100, Cys-176, Cys-323, and Cys-358) were all active. Cys-358 corresponds to Cys-325 of A. vinelandii NIFS, which is conserved among all NIFS-like proteins and catalytically essential (Zheng, L., White, R. H., Cash, V. L., and Dean, D. R. (1994) Biochemistry 33, 4714-4720), is not required for cysteine sulfinate desulfinase. Thus, the enzyme is distinct from A. vinelandii NIFS in this respect.

Amino Acid Sequence↗
PubMed1997

Spermine inhibits proinflammatory cytokine synthesis in human mononuclear cells: a counterregulatory mechanism that restrains the immune response.

The local production of proinflammatory cytokines mediates the host response to inflammation, infection, and injury, whereas an overexpression of these mediators can injure or kill the host. Recently, we identified a class of multivalent guanylhydrazone compounds that are effective inhibitors of proinflammatory cytokine synthesis in monocytes/macrophages. The structure of one such cationic molecule suggested a molecular mimicry with spermine, a ubiquitous endogenous biogenic amine that increases significantly at sites of inflammation and infection. Here, we addressed the hypothesis that spermine might counterregulate the innate immune response by downregulating the synthesis of potentially injurious cytokines. When spermine was added to cultures of human peripheral blood mononuclear cells stimulated with lipopolysaccharide (LPS), it effectively inhibited the synthesis of the proinflammatory cytokines tumor necrosis factor (TNF), interleukin-1 (IL-1), IL-6, MIP-1alpha, and MIP-1beta. The inhibition of cytokine synthesis was specific and reversible, with significant inhibition of TNF synthesis occurring even when spermine was added after LPS. The mechanism of spermine-mediated cytokine suppression was posttranscriptional and independent of polyamine oxidase activity. Local administration of spermine in vivo protected mice against the development of acute footpad inflammation induced by carrageenan. These results identify a distinct molecular counterregulatory role for spermine in downregulating the monocyte proinflammatory cytokine response.

Animals↗
PubMed1997

New method for incorporating solvent influence into the evaluation of X-ray scattering intensity of proteins in solution.

A new method, the surface integration method, is presented for taking into account the influence of solvent on the intensity of X-ray scattered from proteins in solution. It requires no averaging numerically over the solute orientation. The solvent is modeled by a continuous medium with electrons of uniform density. This method is applied to amino acids, peptides and native proteins to confirm its effectiveness. The solvent influence on the normalized scattering intensity I(K) I(0) is more noticeable for larger solutes and at larger scattering angles, where I(K) is the intensity of scattered X-ray with the magnitude of scattering vector K.

Journal Article↗
PubMed1997

Paracatalytic inactivation of L-2-haloacid dehalogenase from Pseudomonas sp. YL by hydroxylamine. Evidence for the formation of an ester intermediate.

Asp10 of L-2-haloacid dehalogenase from Pseudomonas sp. YL was proposed to act as a nucleophile to attack the alpha-carbon of L-2-haloalkanoic acids to form an ester intermediate, which is hydrolyzed by nucleophilic attack of a water molecule on the carbonyl carbon (Liu, J.-Q, Kurihara, T., Miyagi, M., Esaki, N., and Soda, K. (1995) J. Biol. Chem. 270, 18309-18312). We have found that the enzyme is paracatalytically inactivated by hydroxylamine in the presence of the substrates monochloroacetate and L-2-chloropropionate. Ion spray mass spectrometry demonstrated that the molecular mass of the enzyme inactivated by hydroxylamine during the dechlorination of monochloroacetate is about 74 Da greater than that of the native enzyme. To determine the increase of the molecular mass more precisely, we digested the inactivated enzyme with lysyl endopeptidase and measured the molecular masses of the peptide fragments. The molecular mass of the hexapeptide Gly6-Lys11 was shown to increase by 73 Da. Tandem mass spectrometric analysis of this peptide revealed that the increase is due to a modification of Asp10. When the enzyme was paracatalytically inactivated by hydroxylamine during the dechlorination of L-2-chloropropionate, the molecular mass of the hexapeptide was 87 Da higher. Hydroxylamine is proposed to attack the carbonyl carbon of the ester intermediate and form a stable aspartate beta-hydroxamate carboxyalkyl ester residue in the inactivated enzyme.

Acetates↗
PubMed1997

Endo-beta-Glucanase from Acetobacter xylinum: Purification andCharacterization

A cellulose-producing acetic acid bacterium,Acetobacter xylinum KU-1, abundantly produces an extracellularendo-beta-glucanase (EC 3.2.1.4) in the culture broth. The enzyme was purifiedto homogeneity by DEAE- and CM- Toyopearl 650M ion-exchange chromatography,Butyl-Toyopearl 650M hydrophobic chromatography, and Toyopearl HW-50 gelfiltration. The purified enzyme showed the maximum activity at pH 5 and50°C: it was stable up to 50°C at pH 5, activated by Co2+, andcompetitively inhibited by Hg2+; the apparentKi was 7 &mgr;M. The molecular weight of the enzyme wasdetermined to be about 39,000 by sodium dodesyl sulfate/polyacrylamide gelelectrophoresis, and about 41,000 by Toyopearl HW-50 gel filtration; theenzyme is monomeric. The enzyme hydrolyzed carboxymethylcellulose with anapparent Km of 30 mg/ml and Vmax of 1.2&mgr;M/min. It hydrolyzed cellohexaose to cellobiose, cellotriose andcellotetraose, and also cellopentaose to cellobiose and cellotriose, but didnot act on cellobiose, cellotriose, or cellotetraose.

Journal Article↗
PubMed1997

Non-random ionic-charge distribution responsible for the structural stability and molecular recognition of proteins.

The 'ionic-charge shuffling method' is presented to generate a complete set of electrostatic mutants for a natural protein where ionic charges on the molecular surface of the template protein are exhaustively interchanged with each other. Total Coulomb interaction energies are evaluated for all of the mutants by numerically solving the finite difference Poisson-Boltzmann equation and their distribution in the ensemble is obtained. This method has been applied to five natural proteins to reveal that they have a significantly lower Coulomb energy than the average over the ensemble of their mutants. It is also shown that these natural proteins have a significantly larger and smaller number of pairs of attractive and repulsive ionic groups, respectively, than those expected for their randomly shuffled ensemble: They have been 'designed' through molecular evolution so that a pair of ionic charges with opposite signs may have a higher tendency to be located close to each other, while a pair with the same sign are away from each other.

Ions↗
PubMed1997

Protein stability; optimization of electrostatic contributions by partially neutralizing surface ionic charges.

'Partial Charge-Neutralization Method' is developed to study influence of the relative amount of positive and negative charges in proteins on their structural stability. A given number of either positively or negatively charged groups are neutralized in all of their possible combinations to generate a whole set of distinct species. The Coulomb energy of each species is calculated by numerically solving the Poisson-Boltzmann equation for aqueous solutions. Partial neutralization of lysine residues of tuna cytochrome c in aqueous solution at neutral pH with the Debye-Hückel screening parameter kappa = 1 nm-1 reproduces qualitatively well the destabilization of acetylated cytochrome c observed in physicochemical measurements at pH 7. The stabilization of its molten globule state at pH 2 is also studied with the present method. It is shown that the electrostatic contribution to the structural stability of natural proteins can be optimized by changing the difference in number of their positive and negative charges.

Cytochrome c Group↗
PubMed1997

Cloning and expression of the glutamate racemase gene of Bacillus pumilus.

A glutamate racemase gene (murI) was found in Bacillus pumilus cells and cloned into Escherichia coli WM335, a D-glutamate auxotroph, by means of a genetic complement method. MurI of B. pumilus encodes a 272-amino acid protein with an unusual initiation codon, TTG. The deduced amino acid sequence shows significant similarity with those of glutamate racemases from E. coli (ratio of identical residues, 28%), Pediococcus pentosaceus (44%), and Staphylococcus haemolyticus (49%). B. pumilus MurI was expressed as a fusion protein connected to the N-terminal 12 residues of beta-galactosidase; the fusion protein showed glutamate racemase activity, and resembled the enzyme of P. pentosaceus in physicochemical and enzymological properties.

Amino Acid Isomerases↗
PubMed1997

Mutation of arginine 98, which serves as a substrate-recognition site of D-amino acid aminotransferase, can be partly compensated for by mutation of tyrosine 88 to an arginyl residue.

D-Amino acid aminotransferase is the only aminotransferase that catalyzes the transamination of D-amino acids. We studied the role of the binding site for the alpha-carboxyl group of substrates, which is presumably crucial for the unique stereospecificity of the enzyme. The site-directed mutagenesis of Arg98, which is the putative carboxyl-binding site, as judged on the basis of X-ray crystallographic studies [Sugio, S., Petsko, G.A., Manning, J.M., Soda, K., and Ringe, D. (1995) Biochemistry 34, 9661-9669], by replacement with methionine and lysine, resulted in decreases in the kmax values and increases in the Kd values for both amino donors and amino acceptors. The introduction of another mutation, that of Tyr88, which is located near Arg98 in the spacial structure, by replacement with arginine, in addition to the above Arg98 mutation, resulted in increases in the kmax values but little change in the Kd values. These results suggest that Arg98 constitutes the carboxyl-binding site for the substrate, efficient catalysis by the enzyme being facilitated upon binding. The mutant enzymes are also relieved from inhibition by high concentrations of alpha-ketoglutarate, which is an inherent character of the wild-type enzyme. Therefore, Arg98 is also responsible for the inhibition by alpha-ketoglutarate.

Arginine↗
PubMed1997

Construction of a new leucine dehydrogenase with preferred specificity for NADP+ by site-directed mutagenesis of the strictly NAD+-specific enzyme.

On the basis of sequence comparison between NAD+-dependent leucine dehydrogenase (LeuDH) from Thermoactinomyces intermedius and NADP+-dependent dehydrogenases, a set of amino acid residues that are supposed to determine the coenzyme specificity of LeuDH were assigned. Systematic replacement of these amino acids by others was done with the aim to switch its natural coenzyme specificity to a new one preferring NADP+. Single D203A, double D203A-I204R and triple D203A-I204R-D210R mutation enzymes were constructed. The wild-type LeuDH is inactive with NADP+. However, D203A single mutant exhibited dual specificity for NAD+ and NADP+ with essentially identical k(cat)/Km values for both coenzymes, but the values were three orders of magnitude lower than that of the wild-type enzyme. Introduction of positive charge at 204 together with the removal of the negative charge at 203 in the double mutant D203A-I204R provided the enzyme with significantly high affinity for NADP+. The best k(cat)/Km value for NADP+ was shown for the triple mutant D203A-I204R-D210R: more than 2% of the k(cat)/Km value of the wild-type enzyme. Thus, we succeeded in constructing a mutant LeuDH with a new coenzyme specificity preferring NADP+ which is highly active (specific activity, 19 micromol/mg/min).

Amino Acid Oxidoreductases↗
PubMed1997

Synthesis of optically active amino acids from alpha-keto acids with Escherichia coli cells expressing heterologous genes.

We describe a simple method for enzymatic synthesis of L and D amino acids from alpha-keto acids with Escherichia coli cells which express heterologous genes. L-amino acids were produced with thermostable L-amino acid dehydrogenase and formate dehydrogenase (FDH) from alpha-keto acids and ammonium formate with only an intracellular pool of NAD+ for the regeneration of NADH. We constructed plasmids containing, in addition to the FDH gene, the genes for amino acid dehydrogenases, including i.e., leucine dehydrogenase, alanine dehydrogenase, and phenylalanine dehydrogenase. L-Leucine, L-valine, L-norvaline, L-methionine, L-phenylalanine, and L-tyrosine were synthesized with the recombinant E. coli cells with high chemical yields (> 80%) and high optical yields (up to 100% enantiomeric excess). Stereospecific conversion of various alpha-keto acids to D amino acids was also examined with recombinant E. coli cells containing a plasmid coding for the four heterologous genes of the thermostable enzymes D-amino acid aminotransferase, alanine racemase, L-alanine dehydrogenase, and FDH. Optically pure D enantiomers of glutamate and leucine were obtained.

Alanine Dehydrogenase↗
PubMed1997

Molecular characterization of the mde operon involved in L-methionine catabolism of Pseudomonas putida.

A 15-kb region of Pseudomonas putida chromosomal DNA containing the mde operon and an upstream regulatory gene (mdeR) has been cloned and sequenced. The mde operon contains two structural genes involved in L-methionine degradative metabolism: the already-identified mdeA, which encodes L-methionine gamma-lyase (H. Inoue, K. Inagaki, M. Sugimoto, N. Esaki, K. Soda, and H. Tanaka. J. Biochem. (Tokyo) 117:1120-1125, 1995), and mdeB, which encodes a homologous protein to the homodimeric-type E1 component of pyruvate dehydrogenase complex. A rho-independent terminator was present just downstream of mdeB, and open reading frames corresponding to other components of alpha-keto acid dehydrogenase complex were not found. When MdeB was overproduced in Escherichia coli, the cell extract showed the E1 activity with high specificity for alpha-ketobutyrate rather than pyruvate. These results suggest that MdeB plays an important role in the metabolism of alpha-ketobutyrate produced by MdeA from L-methionine. Accordingly, mdeB encodes a novel E1 component, alpha-ketobutyrate dehydrogenase E1 component, of an unknown alpha-keto acid dehydrogenase complex in P. putida. In addition, we found that the mdeR gene was located on the opposite strand and began at 127 bp from the translational start site of mdeA. The mdeR gene product has been identified as a member of the leucine-responsive regulatory protein (Lrp) family and revealed to act as an essential positive regulator allowing the expression of the mdeAB operon.

Amino Acid Sequence↗
PubMed1997

Bacterial DL-2-haloacid dehalogenase from Pseudomonas sp. strain 113: gene cloning and structural comparison with D- and L-2-haloacid dehalogenases.

DL-2-Haloacid dehalogenase from Pseudomonas sp. strain 113 (DL-DEX) catalyzes the hydrolytic dehalogenation of both D- and L-2-haloalkanoic acids to produce the corresponding L- and D-2-hydroxyalkanoic acids, respectively, with inversion of the C2 configuration. DL-DEX is a unique enzyme: it acts on the chiral carbon of the substrate and uses both enantiomers as equivalent substrates. We have isolated and sequenced the gene encoding DL-DEX. The open reading frame consists of 921 bp corresponding to 307 amino acid residues. No sequence similarity between DL-DEX and L-2-haloacid dehalogenases was found. However, DL-DEX had significant sequence similarity with D-2-haloacid dehalogenase from Pseudomonas putida AJ1, which specifically acts on D-2-haloalkanoic acids: 23% of the total amino acid residues of DL-DEX are conserved. We mutated each of the 26 residues with charged and polar side chains, which are conserved between DL-DEX and D-2-haloacid dehalogenase. Thr65, Glu69, and Asp194 were found to be essential for dehalogenation of not only the D- but also the L-enantiomer of 2-haloalkanoic acids. Each of the mutant enzymes, whose activities were lower than that of the wild-type enzyme, acted on both enantiomers of 2-haloacids as equivalent substrates in the same manner as the wild-type enzyme. We also found that each enantiomer of 2-chloropropionate competitively inhibits the enzymatic dehalogenation of the other. These results suggest that DL-DEX has a single and common catalytic site for both enantiomers.

Amino Acid Sequence↗
PubMed1997

Incidence of ocular complications in rheumatoid arthritis and the relation of keratoconjunctivitis sicca with its systemic activity.

To investigate the incidence of ocular complications in patients with rheumatoid arthritis under modern modalities of treatment and find the relationship between its systemic activity and ocular complications, routine ophthalmological examinations were done as a prospective study in 111 consecutive patients including 89 inpatients and 22 outpatients with rheumatoid arthritis seen from April to May 1995, in a hospital with a special clinic for rheumatology. Keratoconjunctivitis sicca (secondary Sjögren's syndrome) was found in 19 patients (17.1%), scleritis in one patient (0.9%), central retinal vein occlusion in 2 patients (1.8%), and idiopathic retinal hemorrhage in 3 patients (2.7%). Patients with keratoconjunctivitis sicca had significantly higher titers of rheumatoid factor (Mann-Whitney's U-test, p = 0.0048), higher levels of IgM (p = 0.0484), and lower levels of HDL-cholesterol (p = 0.0191), compared to patients without it. The incidence of ocular complications was comparable to the previous studies and keratoconjunctivitis sicca should be considered in patients with high titers of rheumatoid factor.

Adult↗