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K Namba

Publications and source records attributed to K Namba.

At least 55 records · Page 3Linked to original sources

Prevention of infection of influenza virus in DQ6 mice, a human model, by a peptide vaccine prepared according to the cassette theory.

We proposed a strategy (cassette theory) in which non-binding peptides for murine major histocompatibility complex (MHC) class II molecules are introduced into a MHC-binding component to render the resultant hybrid peptides bound to the MHC and thus immunogenic in animals carrying the relevant MHC. It was shown that 46F/HA127-133/54A(18mer) peptide which was prepared by introducing hemagglutinin (HA)127-133 of influenza virus into the H-2Ab binding component induced significant T cell responses and antibodies (Ab) specific for HA127-133 in H-2Ab mice. Further we found that the H-2Ab binding component had a supermotif for human class II molecules (i.e. HLA-DQ6). In the present study, a new peptide vaccine, H3-H3, was prepared by combining 46F/HA127-133/54A(18mer) as a carrier and HA127-133 attached to the C terminus of 46F/HA127-133/54A(18mer) as a hapten and the effect of vaccine was examined in DQ6 mice which carry HLA-DQ6 alone as MHC class II molecules and thus may be regarded as a model of the DQ6 positive individuals. Since 46F/HA127-133/ 54A(18mer) induced merely Ab against HA127-133, it was assumed that H3-H3 induced mainly HA127-133 specific Ab in DQ6 mice without undesirable Ab production against the carrier. Indeed, H3-H3 elicited T cell responses and induced HA127-133 specific Ab in DQ6 mice. Furthermore, administration of H3-H3 inhibited growth of influenza virus until 9 weeks after the last immunization in DQ6 mice.

Amino Acid Sequence↗

Domain organization of flagellar hook protein from Salmonella typhimurium.

Hook forms a universal joint, which mediates the torque of the flagellar motor to the outer helical filaments. Domain organization of hook protein from Salmonella typhimurium was investigated by exploring thermal denaturation properties of its proteolytic fragments. The most stable part of hook protein involves residues 148 to 355 and consists of two domains, as revealed by deconvolution analysis of the calorimetric melting profiles. Residues 72-147 and 356-370 form another domain, while the terminal regions of the molecule, residues 1-71 and 371-403, avoid a compact tertiary structure in the monomeric state. These folding domains were assigned to the morphological domains of hook subunits known from EM image reconstructions, revealing the overall folding of hook protein in its filamentous state.

Bacterial Proteins↗

Comparison of gene arrangements of chloroplasts between two centric diatoms, Skeletonema costatum and Odontella sinensis.

We have cloned and sequenced 3.4 kbp, 2.5 kbp, 1.9 kbp, 1.6 kbp and 0.5 kbp segments of a marine centric diatom, Skeletonema costatum, chloroplast DNA. These segments contain 28 genes. The genes which are not encoded on chloroplast genomes of chlorophyll a+b plants are found such as the psaD, ycf33, ycf35 and ycf47 genes. The gene sequences were compared with that of Odontella sinensis. At nucleic acid level, the ycf genes have lower homologies (69-87%) with O. sinensis than the other genes (78-100%), and some differences in the gene arrangement are found between two centric diatoms, O. sinensis and S. costatum.

Chloroplasts↗

[View of development of fluoroquinolones].

The global resurgence of tuberculosis and the emergence of multidrug-resistant tuberculosis have emphasized an urgent need for new, effective antimycobacterial drugs. A new antimycobacterial drugs should have a different mechanism of action to the standard drugs and should not show cross-resistance with them. Favorable pharmacokinetic properties, low incidence of side effects and low cost are the characteristics that would make antimycobacterial drugs suitable for extensive use. The fluoroquinolones would appear to fulfill most of the criteria for an ideal class of antimycobacterial drugs. The fluoroquinolones have been proposed for the treatment of Mycobacterium tuberculosis (M. tuberculosis) infections, with the results of in vitro, animal model and clinical studies suggesting that ofloxacin, ciprofloxacin, sparfloxacin and levofloxacin are the most promising of these drugs. However, these fluoroquinolones should not be used as first-line drugs, but rather, they should be reserved for treatment of tuberculosis that is resistant to rifampicin and isoniazid. Recently, a new investigational fluoroquinolone derivative, AM-1155, DU-6859a and CS-940, have excellent in vitro activity against M. tuberculosis, further studies are required to assess its clinical activity. We discussed the future of view of development of fluoroquinolones for mycobacterial diseases on the basis of structure-activity and structure-side-effect relationship studies. The comparative analysis enabled us to elucidate the structural requirements for the antimycobacterial activity and side-effects of fluoroquinolones. In addition, we summarized the newer methods for high-throughput screening of compounds against M. tuberculosis and discussed the problem of development of fluoroquinolones for mycobacterial diseases.

Anti-Infective Agents↗

[Imipenem/cilastatin sodium and other beta-lactams for respiratory tract infections: clinical benefit and treatment days for cure].

Therapeutic efficacy and the treatment days for cure of imipenem/cilastatin sodium (IPM/CS) in treatment of pulmonary infections were prospectively determined in comparison with those of beta-lactams other than carbapenems mainly ceftazidime (CAZ) or sulbactam/cefoperazone (SBT/CPZ). The overall response rate was 84.9% (62/73) in the IPM/CS group and 74.7% (56/75) in the beta-lactam group, the difference not being significant. In the subjects having underlying respiratory diseases, the response rate was 91.1% (41/45) and 73.9% (34/46) in the IPM/CS and beta-lactam groups, respectively. In patients with infections secondary to chronic respiratory disease, the rate was 91.2% (31/34) in the former group and 66.7% (24/36) in the latter group, respectively. The differences were significant for both stratified analyses. The treatment days for cure judged by the attending physician were 12.9 +/- 0.6 days in the IPM/CS group, and 14.5 +/- 0.7 days in the beta-lactam group. The difference was not, however, significant. In patients with mild to moderate infections, the treatment days for cure was 12.0 +/- 0.6 days (n = 64) in the IPM/CS group and 14.3 +/- 0.7 days (n = 70) in the beta-lactam group. In patients with underlying respiratory disease, the treatment days for cure were 11.8 +/- 0.7 days (n = 45) and 14.7 +/- 0.9 days (n = 46) in the IPM/CS and beta-lactam groups, respectively. In patients with infections secondary to chronic respiratory disease, the days were 11.1 +/- 0.7 days (n = 34) and 14.7 +/- 1.1 days (n = 36), respectively. Thus, IPM/CS therapy significantly reduced the number of treatment days until cure. There was, however, no significant difference between the two therapy groups in treatment of the patients with severe infections, those without underlying respiratory disease, or those with pneumonia and/or lung abscess. The treatment days for cure were also assessed by the members of review committee taking into consideration of body temperature, leukocyte count, and C-reactive protein. As the result, it was 6.9 +/- 0.5 days in the IPM/ CS and 10.3 +/- 0.7 days in the beta-lactam groups; respectively, and the difference was significant. Time (days) until cure was also compared between the two groups using survival time analysis, confirming a more rapid response in the IPM/CS group. Although IPM/CS therapy was associated with a shorter response time as assessed by both the attending physicians and the review committee, there were considerable differences between the results of these judgements. Thus, the duration of treatment with injectable antibiotics requires reevaluation in the future. No significant differences were observed between the groups with respect to parameters indicating side effects and laboratory abnormalities. There were no severe symptoms or laboratory findings, and symptoms and changes in laboratory values, if any resolved during the course of therapy or after the withdrawal of treatment. In conclusion, IPM/CS seems to be very useful as first-line therapy for respiratory tract infections and for shortening the duration of treatment.

Adult↗

Prominent increase of macrophage migration inhibitory factor in the sera of patients with uveitis.

PURPOSE: To investigate pathogenesis underlying endogenous uveitis, macrophage migration inhibitory factor (MIF) was quantified in sera of patients. METHODS: Sera were obtained from the 55 patients with uveitis (24 with Behçet's disease; 9 with Vogt-Koyanagi-Harada's [VKH] disease; 22 with sarcoidosis) and 58 healthy control subjects. MIF levels were determined by a human MIF enzyme-linked immunosorbent assay. RESULTS: The mean MIF levels in the sera of the patients with Behçet's disease, VKH disease, and sarcoidosis and of healthy control subjects were 60.4+/-9.0 (mean+/-SE) ng/ml, 16.5+/-2.9 ng/ml, 27.1+/-5.6 ng/ml, and 5.4+/-0.04 ng/ml, respectively. The average levels of MIF in the sera of uveitis patients were significantly higher (P < 0.0001) than those of healthy control subjects. The high levels of MIF were especially noted in patients with Behçet's disease at the ocular exacerbation stage and patients with sarcoidosis at the severe uveitis stage. CONCLUSIONS: Significant increase of MIF in sera was characteristic of uveitis, and MIF may be a usefull laboratory parameter to use to comprehend the clinical course of uveitis.

Behcet Syndrome↗

Mechanism of self-association and filament capping by flagellar HAP2.

HAP2 forms a capping structure, which binds very tightly to the distal end of flagellar filaments and still allows insertion of flagellin subunits below the cap by an unknown mechanism. Terminal regions of HAP2 from Salmonella typhimurium were found to be quickly degraded by various proteases, indicating that HAP2 also possesses disordered terminal regions like other axial proteins of bacterial flagellum. Removal of these portions by trypsin results in a fragment of 40 kDa (HP40), which lacks 42 NH2-terminal and 51 COOH-terminal residues. HAP2 in solution readily associates into a decameric structure without any significant population of intermediate oligomeric forms. The HP40 fragments, however, do not form decamers, while they can assemble into pentamers, as revealed by chemical cross-linking and analytical ultracentrifugation. Decameric HAP2 also dissociates into pentamers and smaller oligomers upon a heat induced conformational transition around 36 degreesC. While the highly mobile terminal regions are immobilized in decameric HAP2 complexes, they are still largely disordered in the pentameric state. These results demonstrate that the intersubunit interactions within the pentamers are mainly through the HP40 portions, whereas the terminal regions are responsible for association of pentamers into decameric complexes. Several observations indicate that HAP2 performs its capping function as a pentamer. We suggest that binding of the pentameric HAP2 cap to the filament is mediated by the highly flexible terminal regions. Indeed, HP40 fragments are unable to cap the end of filaments, while removal of about 30 residues from both terminal regions of HAP2 results in a highly reduced capping ability. A model is presented to explain the molecular mechanism of capping, in which conformational entropy in the disordered terminal regions moderates the otherwise too tight HAP2-filament interactions to allow insertion of flagellin subunits below the cap.

Amino Acid Sequence↗

A structural feature in the central channel of the bacterial flagellar FliF ring complex is implicated in type III protein export.

The FliF ring complex, which consists of the M-S ring and a proximal portion of the rod of the flagellar basal body, is the base structure for the bacterial flagellar assembly. The FliF ring is also thought to be part of the export apparatus for flagellar proteins from its amino acid sequence homology to proteins involved in type III protein export systems. We established a new purification procedure for the FliF ring particles and carried out electron microscopic image analyses in their two distinct forms: well-dispersed single particles in the presence of salt and ordered monolayer arrays of hexagonal packing formed in the absence of salt. In both cases, the axial projection maps showed a common feature, a pair of concentric rings: the inner ring corresponds to the proximal rod; the outer ring represents the thick, edge portion of the M-S ring. However, the central channel of the FliF ring, the putative pathway for the flagellar protein export, appeared to show distinct structural features in the two forms. This suggests that a domain of FliF partially occupies the central channel to be involved in the export and gate mechanism, and the domain changes its conformation depending on the ionic strength.

Amino Acid Sequence↗

Role of the outermost subdomain of Salmonella flagellin in the filament structure revealed by electron cryomicroscopy.

A mutant strain of Salmonella typhimurium, SJW46, has flagellar filaments supercoiled in the same form as the wild-type strain, SJW1103, and swims normally. However, its flagellar filaments are mechanically unstable and show anomalous behaviors of polymorphism. Flagellin from SJW46 has a large central deletion from Ala204 to Lys292 of SJW1103 flagellin, which has been thought to be located in the outer surface of the filament. Since the filament structure is determined by intersubunit interactions of the terminal regions in the densely packed core of the filament, no serious involvement of the deleted portion was expected in the filament stability and polymorphism. In order to locate the deleted portion and to understand the underlying mechanism of these anomalous characteristics, we carried out structure analysis of the L-type straight filament reconstituted from a mutant flagellin of SJW46 (SJW46S) and compared the structure with that of the SJW1660 filament, which is also the L-type but composed of flagellin with no deletion. The deleted portion was identified as the outermost subdomain, and the structure in the core region showed no appreciable differences. The structure revealed the previously identified folding of flagellin in further detail, and the significance of intersubunit interactions between outer domains, which are present in the SJW1660 filament but absent in the SJW46 filament. This suggests that these contacts have a significant contribution to the filament stability and polymorphic behavior, despite the fact that the contacting surface area occupies only a minor portion of the whole intersubunit interactions.

Caulobacter crescentus↗

Computer-Aided Diagnosis (CAD) for Mammography: Preliminary Results.

PURPOSE: To evaluate the CAD system for screening mammograms. MATERIALS AND METHODS: Mammograms of patients with asymptomatic breast cancerwere examined retrospectively. A total of 260 screening mammograms from 65 patients (bilateral cranio-caudal and medio-lateral-oblique views from each) were tested by using the CAD system (ImageChecker M1000 system, R2 Technology, Los Altos, CA, USA). Results: With 0.58 microcalcifications marks/film and 0.20 mass marks/film set as the false positive rate, 100% of microcalcifications cases and 79% of mass cases were detected correctly. Conclusion: The CAD system has the potential to become a second reader. Further developments are expected to improve the accuracy of detection of mass lesions

Journal Article↗

Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism.

BACKGROUND: 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding. RESULTS: We have determined the crystal structure of IPMDH from Thiobacillus ferrooxidans (Tf) complexed with 3-isopropylmalate (IPM) at 2.0 A resolution by the molecular replacement method. The structure shows a fully closed conformation and the substrate-binding site is quite similar to that of ICDH except for a region around the gamma-isopropyl group. The gamma group is recognized by a unique hydrophobic pocket, which includes Glu88, Leu91 and Leu92 from subunit 1 and Val193' from subunit 2. CONCLUSIONS: A large movement of domain 1 is induced by substrate binding, which results in the formation of the hydrophobic pocket for the gamma-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The C beta and C gamma atoms of Glu88 interact with the gamma-isopropyl moiety of IPM and are central to the recognition of substrate. The acidic tip of Glu88 is likely to interact with the nicotinamide mononucleotide (NMN) ribose of NAD+ in the ternary complex. This structure clearly explains the substrate specificity of IPMDH.

3-Isopropylmalate Dehydrogenase↗

Multiple-step method for making exceptionally well-oriented liquid-crystalline sols of macromolecular assemblies.

X-ray fiber diffraction is potentially powerful in solving the atomic structure of filamentous assemblies of macromolecules, as demonstrated for tobacco mosaic virus. However, it requires extremely well-oriented sols to allow for extraction of intensities on closely located layer-lines. A high degree of orientation requires a high filament concentration to restrain the orientational freedom, but orienting concentrated sols is hampered by their high viscosity. Here, we report a systematic method that reproducibly produces extremely good orientation, which involves three steps; liquid crystallization, centrifugation and magnetic orientation. We found that a slow centrifugation can trigger a dynamic self-orientation process to form perfectly homogeneous liquid-crystalline sols, and further centrifugation to concentrate sols followed by magnetic orientation produces exceptionally well-oriented sols. The best-oriented flagellar sol showed a disorientation angle of 0.6 degrees as 1sigma of its Gaussian distribution. The new method has been successfully applied to many other systems, such as tobacco mosaic virus and F-actin.

Actins↗

Assembly characteristics of flagellar cap protein HAP2 of Salmonella: decamer and pentamer in the pH-sensitive equilibrium.

The cap of the bacterial flagellum is an oligomeric assembly of HAP2 protein (also called FliD), tightly attached to the tip of the flagellar filament. Flagellar growth does not occur in fliD-deficient mutants because flagellin monomers transported through the central channel of the flagellum leak out without polymerizing at the distal end. The structure of the cap complex is not known yet. An in vitro assembly of HAP2 proteins was found to have a pentagonal shape, while its molecular mass corresponded roughly to that of a dodecamer. To characterize the structure and assembly behavior of the complex formed in vitro in more detail, the stoichiometry of the complex and the association equilibrium have been studied. Crosslinking experiments now clearly show that the HAP2 complex is decameric. The assembly equilibrium is mainly between the monomer and decamer with a minor population of intermediate oligomers involved, and is highly dependent on the solution pH as well as the salt concentration: the fraction of the decamer sharply rises as the pH decreases from 8.5 to 8.0; the physiological concentration of salt partially suppresses the decamer formation. A preferential crosslinking within a pentameric unit together with a bipolar feature of the complex particle observed by electron microscopy suggests that the decamer is a bipolar pair of pentamers. Because of the polar nature of the filament cap structure, the pentamer is suggested to be the cap complex with its decamer forming surface involved in interactions with the filament.

Bacterial Proteins↗

Plugging interactions of HAP2 pentamer into the distal end of flagellar filament revealed by electron microscopy.

Bacterial flagellum has a cap structure tightly attached to its distal end. The cap is an oligomeric assembly of HAP2 protein (also called FliD) and plays an essential role in the filament growth in vivo by preventing flagellin monomers from leaking out without polymerization. Electron micrographs of the HAP2 complex formed in solution showed exclusively a pentagonal shape, called "star-cap", which was thought to be the end-on view of the cap. The molecular mass roughly corresponded to a dodecamer of HAP2, and therefore a double-layered star-cap was modeled to be the cap. Here, we have observed the side view of the complex in electron micrographs. The images clearly show a rectangular shape, about 80 A wide and 180 A long, with a bipolar feature in its long axis, indicating that the complex is a bipolar pair of pentamers. A thin plate feature is identified at each end of the particle, which looks exactly like the one observed as the structure of the native filament cap. Together with the structure of the filament previously analyzed by electron cryomicroscopy, the results suggest that the cap is a pentamer with its thin plate exposed to the solvent and the other half plugged into the hole at the distal end of the filament, which is almost twice wider than its central channel. This also allows us to model the axial domain arrangement of flagellin subunit in the filament.

Bacterial Proteins↗

Effect of the length and effective diameter of F-actin on the filament orientation in liquid crystalline sols measured by x-ray fiber diffraction.

We examined factors that affect the filament orientation in F-actin sols to prepare highly well-oriented liquid crystalline sols suitable for x-ray fiber diffraction structure analysis. Filamentous particles such as F-actin spontaneously align with one another when concentrated above a certain threshold concentration. This alignment is attributed to the excluded volume effect of the particles. In trying to improve the orientation of F-actin sols, we focused on the excluded volume to see how it affects the alignment. The achievable orientation was sensitive to the ionic strength of the solvent; the filaments were better oriented at lower ionic strengths, where the effective diameter of the filament is relatively large. Sols of longer filaments were better oriented than those of shorter filaments at the same concentration, but the best achievable orientation was limited, probably because of the filament flexibility. The best strategy for making well-oriented F-actin sols is therefore to concentrate F-actin filaments of relatively short length (<1 micrometer) by slow centrifugation in a low-ionic-strength solvent (<30 mM).

Actins↗

Quasi- and nonequivalence in the structure of bacterial flagellar filament.

In supercoiled forms of flagellar filaments, which are thought to be produced by combinations of two distinct subunit lattices, the lattices are elastically deformed in 11 different ways, depending on their azimuthal positions on the circumference of a tube with 11 protofilaments. Those two interactions are nonequivalent as opposed to quasiequivalent ones in elastically deformed lattices of otherwise identical interactions. The term nonequivalence is defined to represent different bonding interactions, and quasiequivalent is used to describe deformed but conserved bonding interactions. By using two distinct lattices that were accurately determined by x-ray fiber diffraction, 10 possible supercoiled forms of flagellar filaments were simulated, based on a bistable-subunit packing model. Comparison to the observed forms showed good agreement, indicating that the model and determined lattice parameters effectively represent realistic features of the structure. The simulated quasiequivalent lattices have been compared to the two nonequivalent lattices, revealing an interesting feature: the maximum deviation in the intersubunit distance by elastic deformation is almost three-quarters of the difference between the two distinct lattices, demonstrating a balanced coexistence of a well-defined conformational distinction and extensive adaptability in the molecular structure of flagellin and its packing interactions.

Bacteria↗

Structure and switching of bacterial flagellar filaments studied by X-ray fiber diffraction.

Bacterial motility involves switching between the left and right supercoiled states of the flagellar filament. The polymorphism of this assembly of identical flagellin molecules has presented a structural puzzle. Supercoiling has been attributed to coexistence of two conformational states of the 11 nearly axially aligned protofilament strands of subunits. The helical parameters of straight filaments in the left (L) and right (R) lattice states have now been accurately determined by X-ray fiber diffraction. The 9 A resolution electron density map of the R-type filament, refined from the X-ray data, reveals the interlocked alpha-helical segments of the core portion, which constitute the inner and outer tubes. While the inner-tube domain interactions remain invariant, the strand joints in the outer tube can switch between the L- and R-state by 2-3 A axial shifts, which change the strand periodicity of approximately 50 A by 0.8 A. This bi-stable quaternary switching results in supercoiling. Based on the measured helical parameters of the L and R lattices and the switching model, the twist and curvature calculated for the ten possible supercoils are in quantitative accord with observed supercoiled forms of flagellar filaments.

Crystallography, X-Ray↗