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Biomedical subjects

N Yasuoka

Publications and source records attributed to N Yasuoka.

At least 37 records · Page 2Linked to original sources
PubMed1996

Significance of angiotensin I-converting enzyme and angiotensin II type 1 receptor gene polymorphisms as risk factors for coronary heart disease.

The D allele of an insertion/deletion (I/D) polymorphism in the angiotensin I-converting enzyme (ACE) gene is associated with a risk of myocardial infarction, and the relative risk associated with the ACE D allele is increased by the C allele of an angiotensin II type 1 receptor (AT1R) gene polymorphism (an A-->C transversion at nucleotide position 1166) [28]. The relation of the ACE and AT1R gene polymorphisms to coronary heart disease and the severity of coronary artery stenosis has now been investigated in 133 patients with myocardial infarction (MI) or angina pectoris who underwent coronary angiography and in 258 control subjects. The frequency of the ACE DD genotype as compared with non-DD was significantly higher in the patients who experienced an MI and in the low-risk patients than that in the controls (P < 0.05). The DD genotype showed a significantly increased risk of MI (odds ratio 1.85). The frequency of the AT1R A/C genotypes did not differ between the patients and the controls. The severity of coronary stenosis in the patients was estimated by the number of affected vessels (> 75% stenosis) and the coronary score of Gensini. Neither the number of affected vessels nor the coronary score differed among the ACE I/D genotypes. However, the number of affected vessels was significantly greater in patients with the AT1R AC genotype than in those with the 4A genotype (1.93 +/- 0.27 vs. 1.27 +/- 0.99; P < 0.05) (CC genotype was not found in the patients). After excluding patients with diabetes mellitus, the coronary score of those with the AC genotype was also significantly higher than in those with the AA genotype (51.7 +/- 34.4 vs. 18.2 +/- 23.3; P < 0.01). These results suggest that the ACE D allele is associated with the occurrence of myocardial infarction, while the AT1R C allele is involved in the development of the coronary artery stenosis.

Adult↗
PubMed1996

High-resolution crystal structures of two polymorphs of cytochrome c' from the purple phototrophic bacterium rhodobacter capsulatus.

The structures of two polymorphs of cytochrome c' from Rhodobacter capsulatus (RCCP) strain M110 have been determined by the molecular replacement method. Iron anomalous scattering data were used to confirm the molecular replacement solution. The structures were refined at 1.72 angstrom and 2.0 angstrom resolution to R-values of 15.0% and 16.3%, respectively. The RCCP molecule is a dimer and each of the identical 129 residue subunits folds as a four-helical bundle with a covalently bound heme group in the center. This structural motif resembles that of cytochromes c' reported from Rhodospirillum molischianum (RMCP), Rhodospirillum rubrum (RRCP), Chromatium vinosum (CVCP), Achromobacter xyloseoxidans (AXCP) and Alcaligenes denitrificans (ADCP). However, the architecture of the RCCP dimer, that is, the mode of association of subunits, differs substantially from that of the other cytochromes c'. In the RCCP dimer, the subunits are roughly parallel with each other and only helix B of each subunit participates in formation of the dimer interface. Measurement of the solvent-accessible surface area indicates that the dimer interface is smaller in RCCP than in the other cytochromes c'. In RMCP, CVCP, RRCP, AXCP and ADCP the subunits cross each other to form an X shape, and two helices, A and B, of each subunit interact across the dimer interface. These results are consistent with hydrodynamic measurements, which show that there is an equilibrium between monomers and dimer in RCCP, whereas the dimer is the predominant form in the other cytochromes c' for which structures have been determined. Structural comparison of the six cytochromes c' reveal that they can be divided into two groups. In group 1 cytochromes c', CVCP and RCCP, the amino acid sequences and the folding of subunits are arranged in such a way as to allow the formation of a deep channel between helices B and C with direct solvent accessibility to the heme sixth ligand position. There is no such channel in group 2 cytochromes c', RMCP, RRCP, AXCP and ADCP. This may account, in part, for the differences in carbon monoxide binding.

Amino Acid Sequence↗
PubMed1996

Crystallization and preliminary X-ray study of a new crystal form of cytochrome c' from Rhodobacter capsulatus.

A new crystal form of diheme cytochrome c' from Rhodobacter capsulatus has been obtained and preliminary crystallographic experiments have been performed. The crystals belong to the space group P2(1)2(1)2 with unit-cell dimensions of a = 47.82, b = 72.59, c = 34.32 A. The assumption that an asymmetric unit of the crystal contains one half of the homodimer molecule indicates that the monomers in the dimeric molecule may be related by a crystallographic twofold axis. Crystals diffract up to 1.7 A resolution using the X-ray beam from synchrotron radiation, and 11 127 unique structure factors were obtained with an R(merge) of 7.1% from 52 922 indexed reflections. Structure analysis by means of molecular-replacement methods is now underway.

Journal Article↗
PubMed1996

Concerted movement of side chains in the haem vicinity observed on ligand binding in cytochrome c' from rhodobacter capsulatus.

We have determined the structure of n-butylisocyanide-bound Rhodobacter capsulatus cytochrome c'. This is the first example of a ligand-bound structure of a class IIa cytochrome c. Compared with the structure of native cytochrome c', there are significant conformational changes of amino acid residues in the haem vicinity, accompanied by a rearrangement of the hydrogen bonding pattern. The results suggest that rearrangements resulting from ligand binding could drive dimer dissociation in some species and also that the haem propionate may participate in proton transfer.

Amino Acid Sequence↗
PubMed1996

A novel nonsense mutation in exon 1 and a transition in intron 3 of the lipoprotein lipase gene.

We examined the lipoprotein lipase (LPL) gene by single strand conformation polymorphism (SSCP) and by restriction fragment length polymorphism (RFLP) analysis in 106 patients with hypertriglyceridemia to screen for novel mutations and to study the contribution of LPL genetic defects in hypertriglyceridemia. We found a single incidence of a homozygous novel nonsense mutation (216G-->A; -14Tryptophan-->stop codon) in exon 1 and 6 cases heterozygous for a single transition (C-->T) at six bp upstream from splicing acceptor site of intron 3. These mutations were not found in 105 normolipidemic controls. The proband homozygous for the nonsense mutation in exon 1, a 74 year old woman, had mild hyperchylomicronemia and her post-heparin plasma showed no LPL protein. However, four heterozygous among family members did not demonstrate hypertriglyceridemia. The frequency of heterozygosity for the C-->T transition in intron 3 was significantly different from that in normolipidemic controls. Therefore, it was suggested that the mutation is involved in hypertriglyceridemia. All of the heterozygotes were men with 4 patients having impaired glucose tolerance or diabetes mellitus. These observations suggest that this polymorphism in intron 3 combined with other as yet undefined factors may be related to hypertriglyceridemia.

Adult↗
PubMed1995

Relationship of low-density lipoprotein particle size to plasma lipoproteins, obesity, and insulin resistance in Japanese men.

OBJECTIVE: To determine the clinical characteristics of patients with small low-density lipoprotein (LDL) particles among Japanese men with mild glucose intolerance and to investigate the relationship of LDL particle size to the levels of other plasma lipoproteins, obesity, insulin resistance, and blood pressure (BP). RESEARCH DESIGN AND METHODS: The subjects were 40 men with impaired glucose tolerance or diabetes treated by diet alone, and 40 healthy men matched for age and body mass index (BMI) were used as control subjects. LDL particle size was measured using gradient gel electrophoresis. RESULTS: Of the 40 patients with glucose intolerance, 19 had small LDL (particle size < 25.5 nm) compared with only 4 of the 40 control subjects. In the patients with small LDL, the plasma levels of cholesterol, triglycerides, and apolipoprotein B, the fasting serum immunoreactive insulin, and the waist-to-hip ratio were all higher than in the patients with normal LDL (particle size > or = 25.5 nm), while the high-density lipoprotein cholesterol level was lower. However, there were no significant differences in BMI, BP, or insulin sensitivity in a euglycemic clamp study between the small-LDL and normal-LDL subgroups. CONCLUSIONS: Japanese men with glucose intolerance frequently have small LDL, and this abnormality is associated with other dyslipoproteinemias and increased waist-to-hip ratio.

Aged↗
PubMed1995

Polymorphism of the angiotensin converting enzyme gene and clinical aspects of IgA nephropathy.

To investigate the relationship between the insertion/deletion (I/D) polymorphism of the angiotensin converting enzyme (ACE) gene and the onset and progression of IgA nephropathy, we studied this polymorphism in 48 patients (21 males and 27 females) with IgA nephropathy and 104 normal controls (51 males and 53 females) using the polymerase chain reaction method. There was no difference in either the genotype or allele frequency of the I/D polymorphism between the patients and normal controls (D allele frequency; 0.303 and 0.325, respectively). But, the mean slope of the reciprocal of the serum creatinine concentration was significantly steeper (p < 0.05) in the patients with the D allele (-0.0104 +/- 0.007 dl.mg-1.month-1) than those without the D allele (-0.0055 +/- 0.008 dl.mg-1.month-1). The mean percentage of the glomeruli with sclerosis or segmental lesions obtained from each renal biopsy specimen was significantly larger (p < 0.02) in the patients with the D allele (49.5 +/- 17.8%) than in those without (33.3 +/- 22.9%). These results suggest that 1. the ACE gene polymorphism is not related to the onset of IgA nephropathy, but 2. the progression of IgA nephropathy may be influenced by the polymorphism which may be involved in glomerular hypertension.

Adult↗
PubMed1994

A detailed comparison of the refined structures of cytochrome c3 molecules from two strains in Desulfovibrio vulgaris: the relationship between the heme structures and their redox properties.

The refined structures of the cytochrome c3 molecules from Desulfovibrio vulgaris Miyazaki and Hildenborough have been compared in detail. Though there are no significant differences of the overall structure and spatial arrangement of four heme groups between two molecules, there are some unique features with regard to the local structures near the heme pockets. Two of the heme groups show significant differences including a hydrogen bonding scheme between the imidazole rings and water molecules in heme pocket. The water molecule near the heme 1 pocket in Miyazaki cytochrome c3 is replaced by the C delta 1 atom of Leu9 in the Hildenborough structure. The rotation around the C alpha-C beta bond of Leu9 results in the increase of the solvent accessibility of the portion of the heme 1 edge. On the other hand, in heme3 one water molecule is additionally included in the hydrogen bonding network with a N delta 1 atom of the imidazole ring and carbonyl oxygen atom of the main chain in Hildenborough cytochrome c3. This additional hydrogen bonding network will contribute to the possible passage between the imidazole ring and the molecular surface. These features have been related to the upfield shift of the C2 proton signals of NMR spectra and the low redox potentials of the cytochrome c3 molecules of Desulfovibrio vulgaris Hildenborough in comparison with those from Miyazaki.

Amino Acid Sequence↗
PubMed1994

[A case of IgA nephropathy associated with psoriasis vulgaris].

Nephrotic syndrome due to IgA nephropathy was found in a 45-year-old man with psoriasis vulgaris. He was first diagnosed as psoriasis vulgaris at 20 years age and had exhibited proteinuria since 37 years of age. Recently, he developed nephrotic syndrome with unfavorable progression of psoriasis. The conditions of psoriasis and nephrotic syndrome were consistently parallel, and both diseases responded to corticosteroid therapy. The specimens from renal biopsy showed mesangial proliferative glomerulonephritis and sclerosis with mesangial deposition of IgA. Therefore, we diagnosed this case as IgA nephropathy. Twelve cases with chronic glomerulonephritis associated with psoriasis vulgaris have been published. All biopsied specimens from these cases showed mesangial deposition of IgA. Immune abnormalities have been reported in both diseases. The pathogenesis of psoriasis vulgaris and IgA nephropathy may be related through an immune mechanism.

Adult↗
PubMed1992

XELE--a polypeptide model-building program for a graphics workstation.

A model-building program, XELE, for use in protein crystallography has been written in C under UNIX on a graphics workstation. This program makes full use of the X Window system to display the electron density distribution and to manipulate the polypeptide model, and therefore is named XELE. It utilizes a fast three-dimensional rendering package, Dorè, and is portable to other types of graphics workstations. A part of the program for the man-machine interface uses the library of X Window and X Toolkit, and therefore is highly interactive. The structure analysis program package, PROTEIN, is also implemented in an interactive mode using X Window, and has been interfaced with XELE.

Computer Graphics↗
PubMed1991

Evaluation of x-ray diffraction data from protein crystals by use of an imaging plate.

A system has been developed which uses an imaging-plate diffraction apparatus to obtain structure factors for protein crystals. The latter is connected to a graphics workstation through an Ethernet. Pixel data from an imaging plate are transferred via the Ethernet to a workstation and processed to give the structure factors. The quality and precision of the diffraction data were examined from the point of view of spatial uniformity, linearity with exposure, decay with time, and reproducibility. X-rays from an 55Fe source and Debye-Scherrer rings from Si powder were used for calibration purposes. Finally, diffraction data were obtained and evaluated for lysozyme and cytochrome c-553 using this system. The results were satisfactory in terms of sensitivity and precision.

Protein Conformation↗
PubMed1991

1H NMR studies on ferricytochrome c3 from Desulfovibrio vulgaris Miyazaki F and its interaction with ferredoxin I.

The 1H NMR signals of the heme methyl, propionate and related chemical groups of cytochrome c3 from Desulfovibrio vulgaris Miyazaki F (D.v. MF) were site-specifically assigned by means of 1D NOE, 2D DQFCOSY and 2D TOCSY spectra. They were consistent with the site-specific assignments of the hemes with the highest and second-lowest redox potentials reported by Fan et al. (Biochemistry, 29 (1990) 2257-2263). The site-specific heme assignments were also supported by NOE between the methyl groups of these hemes and the side chain of Val18. All the results contradicted the heme assignments for D.v. MF cytochrome c3 made on the basis of electron spin resonance (Gayda et al. (1987) FEBS Lett., 217 57-61). Based on these assignments, the interaction of cytochrome c3 with D.v. MF ferredoxin I was investigated by NMR. The major interaction site of cytochrome c3 was identified as the heme with the highest redox potential, which is surrounded by the highest density of positive charges. The stoichiometry and association constant were two cytochrome c3 molecules per monomer of ferredoxin I and 10(8) M-2 (at 53 mM ionic strength and 25 degrees C), respectively.

Binding Sites↗
PubMed1991

Effects of amino acid substitution on three-dimensional structure: an X-ray analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 2 A resolution.

The three-dimensional structure of cytochrome c3 from Desulfovibrio vulgaris Hildenborough has been determined by use of the molecular replacement method and refined at 2.0 A resolution. A suitable crystal of the cytochrome c3 was obtained from buffer solution (25 mM Tris-HCl, pH 7.4), with 75% ethanol as the precipitating reagent. Crystallographic data are as follows: a = 43.17 A, b = 62.91 A, c = 41.17 A, orthorhombic, P2(1)2(1)2(1) and Z = 4. Constrained least-squares refinement and a molecular dynamics procedure with a simulated structure annealing method yielded a crystallographic R-factor of 0.212. The similarity in the folding pattern of both cytochromes c3 is established, the mean deviation of the polypeptide backbone between the two structures being 0.367 A. Most of the amino acids substitutions from DvMF were located on the surface of the molecule, and in particular, S27 and V86 were placed near the propionic acid of the heme group so as to hang over the heme and the cleft of the molecule.

Amino Acid Sequence↗
PubMed1990

Elastic anisotropy of bivalve hinge-ligament.

Compressive stress-strain properties of an elastic ligament of a bivalve, Pseudocardium sachalinensis were investigated in the swollen state in water. The ligament is a calcified tissue, composed of calcium carbonate and insoluble protein which is rich in methionine S-oxide residue [Kikuchi, Y. and Tamiya, N., J. Biochem. (Tokyo) 89, 1975-1976 (1981)]. X-ray diffraction study showed that calcium carbonate existed only in orthorhombic aragonite form, and that all the crystal c-axes of the unit cell orientate nearly in the growing direction of the ligament. The uniaxial compression modulus for the growing direction was appreciably larger than those for the other two directions, while the anisotropy of the modulus was absent for a decalcified ligament. Thus the mechanical anisotropy of the ligament could be explained by means of the uniaxially oriented structure of aragonite crystals being dispersed in a nearly isotropic protein matrix.

Animals↗
PubMed1990

S-class cytochromes c have a variety of folding patterns: structure of cytochrome c-553 from Desulfovibrio vulgaris determined by the multi-wavelength anomalous dispersion method.

The three-dimensional structure of cytochrome c-553 isolated from sulfate-reducing bacterium, Desulfovibrio vulgaris Miyazaki F strain, has been determined by the multi-wavelength anomalous dispersion technique with use of synchrotron radiation. The result shows that bacterial S-class cytochromes c have a variety of folding patterns. The relative location of two a-helices at amino- and carboxyl-terminals and the style of bonding to the heme group show "cytochrome c folding," but other regions of the structure are different from those of other cytochromes c previously reported. The results also give useful information about the location of sulfate-reducing bacterium on the phylogenetic tree of the bacterial cytochromes c superfamily.

Amino Acid Sequence↗
PubMed1988

Crystallization and preliminary X-ray studies on human epidermal growth factor.

Single crystals of human epidermal growth factor have been prepared from a polyethylene glycol solution and characterized by X-ray diffraction. The crystals grow in a space group of P2(1) with unit cell dimensions of a = 32.7, b = 32.5, c = 22.3 A, and beta = 96.9 degrees. They contain a single molecule per asymmetric unit and show better diffraction than 2.5 A.

Crystallization↗