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Biomedical subjects

Mikio Kataoka

Publications and source records attributed to Mikio Kataoka.

At least 37 records · Page 2Linked to original sources
PubMed2004

Solution structure of the tandem Src homology 3 domains of p47phox in an autoinhibited form.

The phagocyte NADPH oxidase is a multisubunit enzyme responsible for the generation of superoxide anions (O(2).) that kill invading microorganisms. p47(phox) is a cytosolic subunit of the phagocyte NADPH oxidase, which plays a crucial role in the assembly of the activated NADPH oxidase complex. The molecular shapes of the p47(phox) tandem SH3 domains either with or without a polybasic/autoinhibitory region (PBR/AIR) at the C terminus were studied using small angle x-ray scattering. The tandem SH3 domains with PBR/AIR formed a compact globular structure, whereas the tandem SH3 domains lacking the PBR/AIR formed an elongated structure. Alignment anisotropy analysis by NMR based on the residual dipolar couplings revealed that the tandem SH3 domains with PBR/AIR were in good agreement with a globular module corresponding to the split half of the intertwisted dimer in crystalline state. The structure of the globular module was elucidated to represent a solution structure of the tandem SH3 domain in the autoinhibited form, where the PBR/AIR bundled the tandem SH3 domains and the linker forming a closed structure. Once PBR/AIR is released by phosphorylation, rearrangements of the SH3 domains may occur, forming an open structure that binds to the cytoplasmic proline-rich region of membrane-bound p22(phox).

Dimerization↗
PubMed2004

Resonance Raman spectroscopy reveals the origin of an intermediate wavelength form in photoactive yellow protein.

Photoactive yellow protein (PYP) is a bacterial blue light receptor containing a 4-hydroxycinnamyl chromophore, and its absorption maximum is 446 nm. In a dark state, the hydroxyl group of the chromophore is deprotonated and forms hydrogen bonds with Tyr42 and Glu46. Either removal of a hydrogen bond with Tyr42 or addition of chaotropes such as thiocyanate produces a blue-shifted species called an intermediate wavelength form, in which absorption maximum ranges from 355 to 400 nm. To examine the structural origin of the intermediate wavelength form, we have performed resonance Raman investigations of wild-type PYP and some mutants (Tyr42 --> Ala, Tyr42 --> Phe, Glu46 --> Gln, and Thr50 --> Val) in the presence or absence of potassium thiocyanate. These studies show that the chromophore of the intermediate wavelength form is protonated, implying an increase in a pK(a) of the chromophore. Hence, the removal of the hydrogen bond between Tyr42 and chromophore or partial protein denaturation in the presence of thiocyanate results in a spectral blue-shift. Quantum chemical calculations based on density functional theory further support the idea that the pK(a) of the chromophore is increased by removing a hydrogen bond or by increasing the dielectric constant in the vicinity of the chromophore.

Alanine↗
PubMed2004

[A case of idiopathic bronchiolitis obliterans accompanied with pneumothorax and pulmonary atypical mycobacteriosis].

A 22-year-old man was urgently admitted for pneumothorax. He continued complaining of exertional dyspnea and dry cough after the pneumothorax healed. About three months later, an atypical pulmonary mycobacteriosis by mycobacterium kansasii was identified. Exertional dyspnea increased after chemotherapy was administered, and the patient was readmitted because of difficulty in daily life activities. Chest radiographs and CT scans showed bilateral pulmonary hyperinflation and a narrowed heart shadow. There was also marked combined ventilatory impairment, as identified by a respiratory function test. Furthermore, the histological findings of surgically removed lung tissue revealed accumulation of lymphocytes in the wall of a small bronchus. Idiopathic bronchiolitis obliterans was diagnosed from the clinical course and clinical findings. The patient is now being monitored and is awaiting lung transplantation.

Adult↗
PubMed2003

Role of an N-terminal loop in the secondary structural change of photoactive yellow protein.

Photoactive yellow protein (PYP) is photoconverted to its putative active form (PYP(M)) with global conformational change(s). The changes in the secondary structure were studied by far-UV circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy using PYP, which lacks N-terminal 6, 15, or 23 amino acid residues (T6, T15, and T23, respectively). Irradiation of truncated PYPs induced the loss of the CD signal, where the maximal difference was located at 222 nm. The reduction of the CD signal was significantly larger than the calculated CD of the N-terminal helices, indicating that it is mainly accounted for by the unfolding and/or structural change of the helices located outside the N-terminal region. The difference FTIR spectra between dark and photosteady states recorded using the solution samples demonstrated that large absorbance changes in the amide mode of the beta-sheet were reduced and downshifted by truncation. The structural change of the beta-sheet is therefore closely correlated with the N-terminal loop. NaCl decelerates the decay of intact PYP(M) and T6(M) at low concentrations (<500 mM) but accelerates decay at high concentrations (>1000 mM). For T15(M) and T23(M), NaCl accelerates their decay at >100 mM but never decelerates their decay, suggesting that the electrostatic interaction, which plays an important role for the recovery of PYP from PYP(M), is lost by removing positions 7-15. The electrostatic interaction between this region and the beta-scaffold is likely to promote the conformational change of PYP(M) for recovery of PYP.

Bacterial Proteins↗
PubMed2003

Effects of the difference in the unfolded-state ensemble on the folding of Escherichia coli dihydrofolate reductase.

The unfolded state of a protein is an ensemble of a large number of conformations ranging from fully extended to compact structures. To investigate the effects of the difference in the unfolded-state ensemble on protein folding, we have studied the structure, stability, and folding of "circular" dihydrofolate reductase (DHFR) from Escherichia coli in which the N and C-terminal regions are cross-linked by a disulfide bond, and compared the results with those of disulfide-reduced "linear" DHFR. Equilibrium studies by circular dichroism, difference absorption spectra, solution X-ray scattering, and size-exclusion chromatography show that whereas the native structures of both proteins are essentially the same, the unfolded state of circular DHFR adopts more compact conformations than the unfolded state of the linear form, even with the absence of secondary structure. Circular DHFR is more stable than linear DHFR, which may be due to the decrease in the conformational entropy of the unfolded state as a result of circularization. Kinetic refolding measurements by stopped-flow circular dichroism and fluorescence show that under the native conditions both proteins accumulate a burst-phase intermediate having the same structures and both fold by the same complex folding mechanism with the same folding rates. Thus, the effects of the difference in the unfolded state of circular and linear DHFRs on the refolding reaction are not observed after the formation of the intermediate. This suggests that for the proteins with close termini in the native structure, early compaction of a protein molecule to form a specific folding intermediate with the N and C-terminal regions in close proximity is a crucial event in folding. If there is an enhancement in the folding reflecting the reduction in the breadth of the unfolded-state ensemble for circular DHFR, this acceleration must occur in the sub-millisecond time-range.

Circular Dichroism↗
PubMed2003

Concentration-dependent tetramerization of bovine visual arrestin.

The oligomeric states of bovine visual arrestin in solution were studied by small-angle x-ray scattering. The Guinier plot of arrestin at the concentration ranging from 0.4 mg/ml to 11.1 mg/ml was approximated with a straight line, and the apparent molecular weight was evaluated by the concentration-normalized intensity at zero angle (I(0)/conc). Using ovalbumin as a molecular weight standard, it was found that arrestin varied from monomer to tetramer depending on the concentration. The I(0)/conc decreased at high-salt concentration, but was independent of temperature. The simulation analysis of the concentration-dependent increase of I(0)/conc demonstrated that the tetramerization is highly cooperative, and arrestin at the physiological concentration is virtually in the equilibrium between monomer and tetramer. The concentration of arrestin monomer, which is considered to be an active form, remains at an almost constant level even if the total concentration of arrestin fluctuates within the physiological range. The scattering profile of arrestin tetramer in solution was in good agreement with that in the crystal, indicating that the quaternary structure in solution is essentially identical to that in crystal. Small-angle x-ray scattering was applied to a binding assay of phosphorylated rhodopsin and arrestin in the detergent system, and we directly observed their association as the increase of I(0)/conc.

Animals↗
PubMed2003

The role of interleukin-8 in interstitial pneumonia.

OBJECTIVE: A variety of inflammatory cells accumulate in the lungs of patients with interstitial lung disease. The potential for IL-8 to be released from these cells into the lungs of patients with idiopathic interstitial pneumonia (IIP), interstitial pneumonia with collagen vascular disease (IP-CVD), sarcoidosis (SAR) and hypersensitivity pneumonitis (HP) was investigated. METHODOLOGY: IL-8 levels were assessed by enzyme-linked immunosorbent assay in BAL fluid and serum, and the expression of IL-8 in the lungs of these patients was evaluated by immunohistochemistry. RESULTS: Serum IL-8 levels were significantly elevated in patients with IIP (P < 0.05) and SAR (P < 0.01). In BAL fluid, the IL-8 level was significantly higher in patients with IIP (P < 0.05), IP-CVD (P < 0.01), SAR (P < 0.01) and HP (P < 0.01). In several cases, IL-8 level correlated with neutrophil density. The IL-8 immunopositive cells were type II pulmonary epithelial cells and alveolar and interstitial macrophages in patients with IIP and IP-CVD. CONCLUSIONS: IL-8 is likely to be a key factor in the pathogenesis of fibrosis of the lung and in lung injury.

Airway Resistance↗
PubMed2003

Propionibacterium acnes DNA detected in bronchoalveolar lavage cells from patients with sarcoidosis.

BACKGROUND AND AIM OF THE WORK: The causes of sarcoidosis are unknown. Propionibacterium acnes is so far the only bacterium to be found in sarcoid lymph nodes. We attempted to detect P. acnes DNA in cells recovered by bronchoalveolar lavage (BAL) from patients with sarcoidosis. METHODS: BAL cells from 30 patients with histologically proven sarcoidosis and 30 controls with other lung diseases were examined by a nested polymerase chain reaction (PCR) for 16S rRNA of P. acnes. BAL cells from three recent sarcoid patients and two control patients were also examined by in situ PCR to locate P. acnes DNA. Clinical findings in sarcoid patients with and without positive results by PCR were compared. RESULTS: P. acnes DNA was detected in BAL cells from 21 (70%) sarcoid patients and 7 (23%) control patients. In situ signals of P. acnes DNA were detected in the cytoplasm of 0.2% to 2.8% of alveolar macrophages from sarcoid patients, but from no cells of the control patients. Gallium-67 uptake by lung parenchyma was found in about half of the sarcoid patients with P. acnes DNA, but in none of the other sarcoid patients. More of these patients with such DNA had lung parenchymal shadows in chest X-ray films and were in more advanced stages of the disease than the other sarcoid patients. CONCLUSIONS: Detection of P. acnes DNA in BAL cells was significantly more common in the patients with confirmed sarcoidosis. Detection was associated with some indices of disease activity in the lung.

Adult↗
PubMed2002

Light-induced global conformational change of photoactive yellow protein in solution.

The light-induced global conformational change of photoactive yellow protein was directly observed by small-angle X-ray scattering (SAXS). The N-terminal 6, 15, or 23 amino acid residues were enzymatically truncated (T6, T15, or T23, respectively), and their near-UV intermediates were accumulated under continuous illumination for SAXS measurements. The Kratky plot demonstrated that illumination induced partial loss of globularity. The change in globularity was marked in T6 but very small in T15 and T23, suggesting that structural change in positions 7-15 mainly reduces the globularity. The radius of gyration (R(g)) estimated by Guinier plot was increased by 1.1 A for T6 and 0.7 A for T15 and T23 upon illumination. As T23 lacks most of the N-terminal loop, structural change in the main part composed of the PAS core, helical connector, and beta-scaffold caused an increase of R(g) by 0.7 A. The structural change of positions 7-15 caused an additional increase by 0.4 A. The decrease of R(g) upon truncation of positions 7-15 for dark state was 0.3 A, while that for the intermediate was 0.7 A, suggesting that this region moves outward on formation of the intermediate. These results indicate that a light-induced structural change of PYP takes place in the main part and N-terminal 15 amino acid residues. The former induces only dimensional increase, but the latter results in additional change in shape.

Bacterial Proteins↗
PubMed2002

Role of C-terminal region of Staphylococcal nuclease for foldability, stability, and activity.

The role of the C-terminal region of Staphylococcal nuclease (SNase) was examined by deletion mutation. Deletions up to eight residues do not affect the structure and function. The structure and enzymatic activity were partially lost by deleting Ser141-Asn149 (Delta141-149), and deletion of Trp140-Asn149 (Delta140-149) resulted in further loss of structure and activity. A 13-residue deletion showed the same effect as the 10-residue deletion. Both Ser141Gln and Ser141Ala mutations for an eight-residue deletion mutant did not alter properties as well as Ser141A1a for full-length SNase. In contrast, Trp140Ala mutation for Delta141-149 shows the same effect as the deletion of Trp140. Trp140Ala mutation for full-length SNase causes the loss of native structure. These observations indicate the significance of the 140th and the 141st residues. The side-chain of the 140th residue is required to be tryptophan; however, the backbone of the 141st residue is solely critical for foldability, but the side-chain information is not crucial. All of the mutants that take a non-native conformation show enzymatic activity and inhibitor-induced folding, suggesting that foldability is required for the activity.

Amino Acid Sequence↗
PubMed2002

Themodynamic and transport properties of intermediate states of the photocyclic reaction of photoactive yellow protein.

Themodynamic and transport properties of intermediate states of the photocyclic reaction of photoactive yellow protein (PYP) were studied by a combination of the pulsed laser-induced transient grating (TG), transient lens (TrL), and photoacoustic (PA) spectroscopies from tens of nanoseconds to hundreds of milliseconds. The diffusion coefficients (D) of PYP in the ground state (pG) and of the second intermediate state (pB) were determined by the TG analysis, and it was found that D of pG is about 1.2 times larger than D of pB. At the same time, D at various denatured conditions were measured using guanidine hydrochloride as the denaturant. D of completely unfolded protein is about 0.4 times that of the native form. The enthalpy of pB is estimated to be 60 kJ/mol by the TrL method with an assumption that the volume change of pB is not sensitive to the temperature. Since the enthalpy of the first intermediate state (pR) is as high as 160 kJ/mol, it implies that most of the photon energy is stored as the strain of the protein in pR, and this may be the driving force for the successive reaction to pB. From the temperature dependence of the volume change, the difference in the thermal expansion coefficients between pG and pR was calculated. All of the characteristic features of PYP, the negative volume change, the larger thermal expansion coefficient, and the slower diffusion process, indicate that the intermediate pR and pB are reasonably interpreted in terms of the unfolded (loosened) protein structure.

Bacterial Proteins↗
PubMed2002

Structural change of site-directed mutants of PYP: new dynamics during pR state.

The energetics, protein dynamics, and diffusion coefficients of three mutants of photoactive yellow protein, R52Q, P68A, and W119G, were studied by the transient grating and pulsed laser-induced photoacoustic method. We observed a new dynamics with a lifetime of approximately 1 micro s in the transient grating signal, which is silent by the light absorption technique. This fact indicates that, after the structure change around the chromophore is completed (pR(1)), the protein part located far from the chromophore is still moving to finally create another pR (pR(2)) species, which can transform to the next intermediate, pB. Although the kinetics of pR(2)-->pB-->pG are very different depending on the mutants, the enthalpies of the first long-lived (in micro seconds, 100-micro s range) intermediate species (pR(2)) are similar and very high for all mutants. The diffusion coefficients of the parent (pG) and pB species of the mutants are also similar to that of the wild-type photoactive yellow protein. From the temperature dependence of the volume change, the difference in the thermal expansion coefficients taken as indicator of the flexibility of the structure between pG and pR(2) is measured. They are also similar to that of the wild-type photoactive yellow protein. These results suggest that the protein structures of pR(2) and pB in these mutants are globally different from that of pG, and this structural change is not altered so much by the single amino acid residue mutation. This is consistent with the partially unfolded nature of these intermediate species. On the other hand, the volume changes during pR(1)-->pR(2) are sensitive to the mutations, which may suggest that the volume change reflects a rather local character of the structure, such as the chromophore-protein interaction.

Acoustics↗
PubMed2002

Time-resolved X-ray diffraction reveals movement of F helix of D96N bacteriorhodopsin during M-MN transition at neutral pH.

D96N bacteriorhodopsin has two photointermediates with the deprotonated Schiff base: the M and MN intermediates. We measure the time-resolved x-ray diffraction of the D96N purple membrane after flash photoexcitation (pH 7.0, 25 degrees C). The data clearly show the M-MN transition during the D96N photocycle. Low-resolution projection maps of these states show that the F helix of the MN intermediate shifts from its original position and this shift is much larger than that of the M intermediate. This indicates that the F helix moves in the M-MN transition of the D96N bacteriorhodopsin photocycle. Moreover, the existence of the MN intermediate in the D96N photocycle under neutral pH indicates that the MN intermediate is not peculiar to the alkaline condition. It is notable that the structural transition of M-MN is independent of the protonation state of the Schiff base. Therefore, the F helix movement precedes reprotonation of the Schiff base in the bacteriorhodopsin photocycle. Our previous study showed that the M-MN transition is hydration-dependent and that the MN intermediate is more hydrated than the M intermediate. Considering this together with the present results, we conclude that the movement of the F helix causes hydration of the cytoplasmic side, which promotes the reprotonation of the Schiff base.

Amino Acid Substitution↗
PubMed2002

Effect of organic anions on the photoreaction of photoactive yellow protein.

In order to clarify changes in the structure and surface properties of photoactive yellow protein (PYP) upon light absorption, the spectroscopic properties and solution structure of its photo-intermediate (PYP(M)) were examined in the presence of various anions. At identical ionic strengths, citrate slowed the decay rate of PYP(M) more than acetate. Although the absorption spectrum in the dark was not affected by organic anions, citrate induced a 5-nm blue shift of the absorption maximum for PYP(M). Solution X-ray scattering experiments indicated that the radius of gyration (Rg) and apparent molecular weight in the dark were constant in all buffer systems. However, the Rg of PYP(M) in citrate buffer at high concentration was 16.2 (+/-0.2) A, while the Rg of PYP(M) in acetate buffer was 15.6 (+/-0.2) A. The apparent molecular weight increased 7% upon PYP(M) formation in citrate buffer at high concentration compared to other conditions. These results suggest that citrate molecules specifically bind to PYP(M). A cluster of basic amino acid residues with a hydrogen bond donor would be exposed upon PYP(M) formation and responsible for the specific binding of citrate.

Acetates↗
PubMed2002

Mechanistic pathways for the photoisomerization reaction of the anchored, tethered chromophore of the photoactive yellow protein and its mutants.

We show by way of physical organic reasoning that the currently known photochemical results of the chromophore of photoactive yellow protein (PYP) are consistent with that expected of a least volume-demanding process for an anchored, tethered chromophore. The primary photoreaction, interestingly, does not appear to involve a hula-twist process. However, the latter might be involved during subsequent transition of dark intermediates. Absorption data of intermediates obtained from a microsecond time-resolved spectroscopic study of three PYP mutants (E46Q, T50V and R52Q) are consistent with the above analyses.

Bacterial Proteins↗