Radical production simulated by photoirradiation of the diol dehydratase-adeninylpentylcobalamin complex

In the course of structural studies of diol dehydratase-cobalamin complexes, it was found that the electron density corresponding to the cyano group of the enzyme-bound cyanocobalamin is almost not observable at room temperature and very low even at cryogenic temperatures, suggesting its dissociation from the Co atom upon X-ray irradiation. On the contrary, the adenine moiety of the enzyme-bound adeninylpentylcobalamin was clearly located in the electron density map. When the enzyme-adeninylpentylcobalamin complex was illuminated with visible light, the electron density between the C5' and Co atoms disappeared, and the temperature factors of the atoms comprising the pentamethylene group became much larger than those in the dark. This indicates a Co-C bond cleavage and that the adenine moiety remains held by hydrogen bonds with some residues in the enzyme. Thus, the formation of an adenine-anchored radical upon illumination was demonstrated crystallographically with this complex. These observations clearly indicate that homolysis of the Co-C bond of alkylcobalamin takes place upon illumination with visible light but is not readily cleaved during X-ray irradiation.

Collagenofibrotic glomerulonephropathy associated with immune complex deposits

A 66-year-old Japanese male, who suffered from persistent proteinuria and leg edema, underwent renal biopsy. Light microscopy revealed marked narrowing of the glomerular capillary lumen with a diffuse accumulation of weakly PAS-positive material. By electron microscopy, abundant abnormal collagen fibers were observed predominantly in the subendothelial space and occasionally in the mesangial matrix. The fibers had a periodicity of about 60 nm and were immunoreactive for anti-type III collagen. Subendothelial electron-dense deposits were also found in some of the capillary walls. The serum level of procollagen III peptides was elevated and changed in parallel with the amount of proteinuria during the patient's clinical course. On the basis of these findings, a diagnosis of the collagenofibrotic glomerulonephropathy was made. A review of the literature, including 29 similar or identical cases, failed to reveal the etiology and pathogenesis of this disease. We suggest that this disease may be divided into two different clinical subtypes, an adult-onset type and a pediatric type.

How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex

BACKGROUND

Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for enzymatic radical reactions. The adenosyl radical, a catalytic radical in these reactions, is formed by homolysis of the cobalt-carbon bond of the coenzyme, although the mechanism of cleavage of its organometallic bond remains unsolved.

RESULTS

We determined the three-dimensional structures of diol dehydratase complexed with adeninylpentylcobalamin and with cyanocobalamin at 1.7 A and 1.9 A resolution, respectively, at cryogenic temperatures. In the adeninylpentylcobalamin complex, the adenine ring is bound parallel to the corrin ring as in the free form and methylmalonyl-CoA-mutase-bound coenzyme, but with the other side facing pyrrole ring C. All of its nitrogen atoms except for N(9) are hydrogen-bonded to mainchain amide oxygen and amide nitrogen atoms, a sidechain hydroxyl group, and a water molecule. As compared with the cyanocobalamin complex, the sidechain of Seralpha224 rotates by 120 degrees to hydrogen bond with N(3) of the adenine ring.

CONCLUSIONS

The structure of the adenine-ring-binding site provides a molecular basis for the strict specificity of diol dehydratase for the coenzyme adenosyl group. The superimposition of the structure of the free coenzyme on that of enzyme-bound adeninylpentylcobalamin demonstrated that the tight enzyme-coenzyme interactions at both the cobalamin moiety and adenine ring of the adenosyl group would inevitably lead to cleavage of the cobalt-carbon bond. Rotation of the ribose moiety around the glycosidic linkage makes the 5'-carbon radical accessible to the hydrogen atom of the substrate to be abstracted.

New crystal forms and low resolution structure analysis of 20S proteasomes from bovine liver

20S proteasomes from higher eukaryotes have immunological functions rather than those from archibacteria or yeast. To clarify the mechanism of the sorting and production of antigen-presenting peptides, it is important and worthwhile to determine the structure of mammalian proteasomes using a third generation synchrotron radiation source. Here we report new crystal forms of 20S proteasomes from bovine liver and preliminary structure analysis of them. The crystals belong to the same space group but have different cell dimensions. One crystal (form I) belongs to space group P2(1)2(1)2(1) with unit cell dimensions of a = 124.8, b =197.4, c =323.8 A, and diffracts to 3.0 A resolution. The other crystal (form II) belongs to the same space group with a =115.1, b =205.6, c =316. 0 A, and diffracts to 4.0 A resolution. The diffraction data for the form I crystal provided an interpretable electron density map for presenting the structural differences from yeast proteasomes.

How do the x-ray structure and the NMR structure of FMN-binding protein differ?

The crystal structure of FMN-binding protein (FMN-bp) from Desulfovibrio vulgaris Miyazaki F was solved by the multiple isomorphous replacement method and refined to an R factor of 15.1% at 1.3 A resolution. FMN-bp exists in a dimeric form in the crystal, in contrast to the monomeric structure determined by NMR. R.m.s. deviations between the crystal structure and the solution structure are more than 2 A, which implies significant differences. There are some hydrophobic residues in the interface between the two monomers. In particular, Leu122 in the C-terminus has a close contact with the o-xylene moiety of FMN, while solvent molecules may cover the o-xylene moiety in the solution structure.

Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-Ray structure analysis

The single-stranded DNA (ssDNA) binding protein from Escherichia coli (EcoSSB) plays a central role in DNA replication, recombination and repair. The tertiary structure of EcoSSB was determined at 2.2 A resolution. This is rather higher resolution than previously reported. Crystals were grown from the homogeneous intact protein but the EcoSSB tetramer in the crystals contains truncated subunits lacking a part of the C-terminal. The structure determined includes biologically important flexible loops and C-terminal regions, and revealed the existence of concavities. These concavities include the residues important for ssDNA binding. An ssDNA can be fitted on the concavities and further stabilized through interactions with the loops forming flexible lids. It seems likely to play a central role in the binding of ssDNA.

A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase

BACKGROUND

Diol dehydratase is an enzyme that catalyzes the adenosylcobalamin (coenzyme B12) dependent conversion of 1,2-diols to the corresponding aldehydes. The reaction initiated by homolytic cleavage of the cobalt-carbon bond of the coenzyme proceeds by a radical mechanism. The enzyme is an alpha2beta2gamma2 heterooligomer and has an absolute requirement for a potassium ion for catalytic activity. The crystal structure analysis of a diol dehydratase-cyanocobalamin complex was carried out in order to help understand the mechanism of action of this enzyme.

RESULTS

The three-dimensional structure of diol dehydratase in complex with cyanocobalamin was determined at 2.2 A resolution. The enzyme exists as a dimer of heterotrimers (alphabetagamma)2. The cobalamin molecule is bound between the alpha and beta subunits in the 'base-on' mode, that is, 5,6-dimethylbenzimidazole of the nucleotide moiety coordinates to the cobalt atom in the lower axial position. The alpha subunit includes a (beta/alpha)8 barrel. The substrate, 1,2-propanediol, and an essential potassium ion are deeply buried inside the barrel. The two hydroxyl groups of the substrate coordinate directly to the potassium ion.

CONCLUSIONS

This is the first crystallographic indication of the 'base-on' mode of cobalamin binding. An unusually long cobalt-base bond seems to favor homolytic cleavage of the cobalt-carbon bond and therefore to favor radical enzyme catalysis. Reactive radical intermediates can be protected from side reactions by spatial isolation inside the barrel. On the basis of unique direct interactions between the potassium ion and the two hydroxyl groups of the substrate, direct participation of a potassium ion in enzyme catalysis is strongly suggested.

Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution

BACKGROUND

The active site of [NiFe] hydrogenase, a heterodimeric protein, is suggested to be a binuclear Ni-Fe complex having three diatomic ligands to the Fe atom and three bridging ligands between the Fe and Ni atoms in the oxidized form of the enzyme. Two of the bridging ligands are thiolate sidechains of cysteinyl residues of the large subunit, but the third bridging ligand was assigned as a non-protein monatomic sulfur species in Desulfovibrio vulgaris Miyazaki F hydrogenase.

RESULTS

The X-ray crystal structure of the reduced form of D. vulgaris Miyazaki F [NiFe] hydrogenase has been solved at 1.4 A resolution and refined to a crystallographic R factor of 21.8%. The overall structure is very similar to that of the oxidized form, with the exception that the third monatomic bridge observed at the Ni-Fe site in the oxidized enzyme is absent, leaving this site unoccupied in the reduced form.

CONCLUSIONS

The unusual ligand structure found in the oxidized form of D. vulgaris Miyazaki F [NiFe] hydrogenase was confirmed in the reduced form of the enzyme, with the exception that the electron density assigned to the monatomic sulfur bridge had almost disappeared. On the basis of this finding, as well as the observation that H2S is liberated from the oxidized enzyme under an atmosphere of H2 in the presence of its electron carrier, it was postulated that the monatomic sulfur bridge must be removed for the enzyme to be activated. A possible mechanism for the catalytic action of the hydrogenase is proposed.

Crystallization and preliminary crystallographic studies of FMN-binding protein from Desulfovibrio vulgaris miyazaki F

The flavin mononucleotide binding protein from Desulfovibrio vulgaris (Miyazaki F) was crystallized using the vapour-diffusion method. The crystal belongs to the monoclinic space group P21 with unit-cell parameters a = 37.2, b = 84.6, c = 41.1 A, beta = 94.1 degrees, contains two molecules per asymmetric unit and diffracts beyond 1.2 A resolution with a synchrotron radiation X-ray source.

Crystallization and preliminary x-ray study of two crystal forms of Klebsiella oxytoca diol dehydratase-cyanocobalamin complex

Two crystal forms of Klebsiella oxytoca diol dehydratase complexed with cyanocobalamin have been obtained and preliminary crystallographic experiments have been performed. The crystals belong to two different space groups, depending on the crystallization conditions. One crystal (form I) belongs to space group P212121 with unit-cell parameters a = 76.2, b = 122.3, c = 209. 6 A, and diffracts to 2.2 A resolution using an X-ray beam from a synchrotron radiation source. The other crystal (form II) belongs to space group P21 with unit-cell parameters a = 75.4, b = 132.7, c = 298.8 A, beta = 91.9 degrees, and diffracts to 3.0 A resolution. For the purpose of structure determination, a heavy-atom derivative search was carried out and some mercuric derivatives were found to be promising. Structure analysis by the multiple isomorphous replacement method is now under way.

Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms

The structures of two crystal forms (form I, P3221, a = b = 43.7, c = 50.7 A; form II, P21, a = 27.3, b = 44.9, c = 51.2 A and beta = 90. 6 degrees ) of the rubredoxin from Desulfovibrio vulgaris Miyazaki F have been solved by the molecular-replacement method. Form I has been refined at a resolution of 2.0 A to an R value of 20.8% and includes 32 water molecules. Form II includes 86 water molecules and has been refined at 1.9 A resolution to an R value of 17.5%. In form II, there are three molecules in the asymmetric unit with the molecules related by a non-crystallographic 32 symmetry axis. In both crystal forms, it was found that only a few residues effectively participate in the formation of intermolecular contacts along both the crystallographic (form I) and the non-crystallographic (form II) 32 axes. The crystal structure of the form II crystal is compared with those of other rubredoxin molecules from anaerobic bacteria. From this comparison, a similarity in the core region, which is composed of aromatic residues and includes the active centre, has been revealed.

Basis for monomer stabilization in Rhodopseudomonas palustris cytochrome c' derived from the crystal structure

The crystal structure of an unusual monomeric cytochrome c' from Rhodopseudomonas palustris (RPCP) has been determined at 2.3 A resolution. RPCP has the four-helix (helices A, B, C and D) bundle structure similar to dimeric cytochromes c'. However the amino acid composition of the surface of helices A and B in RPCP is remarkably different from that of the dimeric cytochromes c'. This surface forms the dimer interface in the latter proteins. RPCP has seven charged residues on this surface contrary to the dimeric cytochromes c', which have only two or three charged groups on the corresponding surface. Moreover, hydrophobic residues on this surface of RPCP are two to three times fewer than in dimeric cytochromes c'. As a result of the difference in amino acid composition, the A-B surface of RPCP is rather hydrophilic compared with dimeric cytochromes c'. We thus suggest that RPCP is monomeric in solution because of the hydrophilic nature of the A-B surface. The amino acid composition of the A-B surface is similar to that of Rhodobacter capsulatus cytochrome c' (RCCP), which is an equilibrium admixture of monomer and dimer. The charge distribution of the A-B surface in RCCP, however, is considerably different from that of RPCP. Due to the difference, RCCP can form dimers by both ionic and hydrophobic interactions. These dimers are quite different from those in proteins which form strong dimers such as in Chromatium vinosum, Rhodospirillum rubrum, Rhodospirillum molischianum and Alcaligenes. Cytochrome c' can be classified into two types. Type 1 cytochromes c' have hydrophobic A-B surfaces and they are globular. The A-B surface of type 2 cytochromes c' is hydrophilic and they take a monomeric or flattened dimeric form.

A case of Gitelman's syndrome with chondrocalcinosis

A 45-year-old Japanese woman, treated for Bartter's syndrome for 14 years, presented with complaints of numbness in her extremities and polyarthralgia. She was diagnosed to have Gitelman's syndrome with chondrocalcinosis, which were effectively treated with spironolactone and magnesium supplementation. Gitelman's syndrome is a primary renal tubular disorder characterized by hypomagnesemia and hypocalciuria with normal calcemia. The persistent hypomagnesemia is one of the causes of chondrocalcinosis, and many cases of Bartter's syndrome with hypomagnesemia are associated with chondrocalcinosis attributed to a tubular magnesium defect. We summarize the reported cases with Bartter's syndrome and chondrocalcinosis, referring to the possibility of Gitelman's syndrome.

Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis

BACKGROUND

The hydrogenase of Desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. The Ni-Fe active center of Desulfovibrio hydrogenase has an unusual ligand structure with non-protein ligands. An atomic model at high resolution is required to make concrete assignment of the ligands which coordinate the Ni-Fe center. These in turn will provide insight into the mechanism of electron transfer, during the reaction catalysed by hydrogenase.

RESULTS

The X-ray structure of the hydrogenase from Desulfovibrio vulgaris Miyazaki has been solved at 1.8 A resolution and refined to a crystallographic R factor of 0.229. The overall folding pattern and the spatial arrangement of the metal centers are very similar to those found in Desulfovibrio gigas hydrogenase. This high resolution crystal structure enabled us to assign the non-protein ligands to the Fe atom in the Ni-Fe site and revealed the presence of a Mg center, located approximately 13 A from the Ni-Fe active center.

CONCLUSIONS

From the nature of the electron-density map, stereochemical geometry and atomic parameters of the refined structure, the most probable candidates for the four ligands, coordinating the Ni-Fe center, have been proposed to be diatomic S=O, C triple bond O and C triple bond N molecules and one sulfur atom. The assignment was supported by pyrolysis mass spectrometry measurements. These ligands may have a role as an electron sink during the electron transfer reaction between the hydrogenase and its biological counterparts, and they could stabilize the redox state of Fe(II), which may not change during the catalytic cycle and is independent of the redox transition of the Ni. The hydrogen-bonding system between the Ni-Fe and the Mg centers suggests the possible.

Lobular form idiopathic glomerulonephritis with massive subendothelial and paramesangial immune deposits, a three-year follow-up case

We report a patient with unusual glomerulonephritis. A 24-year-old Japanese female was hospitalized in October 1995 because of nephrotic syndrome. Lobular form glomerulonephritis with mesangial proliferation associated with massive wide-spread accumulation of slightly eosinophilic, periodic acid Schiff-positive amorphous materials in the luminal side of the capillary walls and paramesangial area was observed in the renal biopsy specimen. Immunofluorescent study revealed massive strong staining for IgM and C4 along the capillary walls and in the mesangium. Deposits of IgA, IgG, C3 and fibrinogen were also observed. Electron microscopy showed normal thickness of the capillary basement membrane and a large amount of subendothelial and paramesangial electron dense, finely granular deposits without fibrils or tubular structures. There were no clinical or laboratory findings of systemic diseases, such as systemic lupus erythematosus and cryoglobulinemia. Therefore, we believed that this case involved an unusual idiopathic glomerular disease with massive subendothelial and paramesangial immune deposits. Glomerulonephritis in this patient appeared to be resistant to treatment with corticosteroids and that this glomerulopathy may be a progressive disease as shown during the 3-year observation. Furthermore, our patient had idiopathic hyperprolactinemia and subclinical hypothyroidism. However, the relationship between glomerulonephritis and endocrinopathy in our patient is unknown.

Structure of Cytochromec' fromRhodobacter capsulatusStrain St Louis: An Unusual Molecular Association Induced by Bridging Zn Ions

Rhodobacter capsulatus strain St Louis cytochrome c' (RCCP-SL) has been crystallized and the structure solved by molecular replacement. It was refined at 2.1 A resolution to an R value of 18.4%, and compared with Rhodobacter capsulatus strain M110 cytochrome c' (RCCP-M110). Although these two proteins are very similar in sequence and structure, the intermolecular interaction is largely different. In RCCP-M110, the molecules dimerize through interaction of helix B to form an antiparallel arrangement. When crystallized in the presence of Zn ions, molecules of RCCP-SL were found to be arranged as linear polymers connected by the bridging Zn ions. The changes in conformation of the side chains induced by binding of the Zn ions, by the substitution of Glu90 for Asp90, and by the different arrangement of the molecules, are discussed in detail.

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.

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.

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.

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.

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.

Systemic lupus erythematosus relapse with lupus cystitis

A 45-year-old woman who had been diagnosed as having systemic lupus erythematosus (SLE) at the age of 28 years and who had been in remission developed severe urinary frequency, watery diarrhea, vomiting and weight loss. She also developed acute renal failure and her serological examination was consistent with active SLE. She had a markedly decreased urinary bladder capacity of 20 ml with hydroureteronephrosis. Histopathological study of her urinary bladder biopsy specimen showed mucosal edema, infiltration by lymphocytes and granulocytes, and deposition of IgA in the epithelium and submucosal region. We diagnosed this as a case of lupus cystitis. The patient's symptoms were alleviated by bilateral nephrostomy and corticosteroid therapy. In the present episode the patient showed none of the usual symptoms of SLE. This case and others reported in the literature show that lupus cystitis presents with specific signs and symptoms and therefore, this syndrome may represent a specific clinical manifestation of SLE.

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.

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.

[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.

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.

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.

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.

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.

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.