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Kentaro Shimizu

Publications and source records attributed to Kentaro Shimizu.

At least 19 recordsLinked to original sources
PubMed2006

Mechanism of the difference in the binding affinity of E. coli tRNAGln to glutaminyl-tRNA synthetase caused by noninterface nucleotides in variable loop.

Aminoacyl-tRNA synthetases (ARSs) distinguish their cognate tRNAs from many other kinds of tRNAs, despite the very similar tertiary structures of tRNAs. Many researchers have supported the view that this recognition is achieved by intermolecular interactions between tRNA and ARS. However, one of the aptamers of Escherichia coli glutamine specific tRNA, var-AGGU, has a higher affinity to ARS than the wild-type, although the sequence difference only lies in the variable loop located on the opposite side of the binding interface with ARS. To understand the reason for the difference in affinity, we did molecular dynamics simulations on tRNAs and their complexes with ARS. We calculated the enthalpic and entropic contributions to the binding free energy with the molecular mechanics-Poisson-Boltzmann/surface area method and found that the entropic difference plays an important role in the difference in binding free energies. During the molecular dynamics simulations, dynamic rearrangements of hydrogen bonds occurred in the tertiary core region of the wild-type tRNA, whereas they were not observed in the free var-AGGU simulation. Since the internal mobility was suppressed upon complex formation with ARS, the entropy loss in the wild-type was larger than that of the aptamer. We therefore concluded that the sequence difference in the variable loop caused the difference in the internal mobility of the tertiary core region tRNAs and led to the difference in the affinity to ARS through the entropy term.

Amino Acyl-tRNA Synthetases↗
PubMed2006

Potential for assessing quality of protein structure based on contact number prediction.

We developed a novel knowledge-based residue environment potential for assessing the quality of protein structures in protein structure prediction. The potential uses the contact number of residues in a protein structure and the absolute contact number of residues predicted from its amino acid sequence using a new prediction method based on a support vector regression (SVR). The contact number of an amino acid residue in a protein structure is defined by the number of residues around a given residue. First, the contact number of each residue is predicted using SVR from an amino acid sequence of a target protein. Then, the potential of the protein structure is calculated from the probability distribution of the native contact numbers corresponding to the predicted ones. The performance of this potential is compared with other score functions using decoy structures to identify both native structure from other structures and near-native structures from nonnative structures. This potential improves not only the ability to identify native structures from other structures but also the ability to discriminate near-native structures from nonnative structures.

Algorithms↗
PubMed2006

ROKU: a novel method for identification of tissue-specific genes.

BACKGROUND: One of the important goals of microarray research is the identification of genes whose expression is considerably higher or lower in some tissues than in others. We would like to have ways of identifying such tissue-specific genes. RESULTS: We describe a method, ROKU, which selects tissue-specific patterns from gene expression data for many tissues and thousands of genes. ROKU ranks genes according to their overall tissue specificity using Shannon entropy and detects tissues specific to each gene if any exist using an outlier detection method. We evaluated the capacity for the detection of various specific expression patterns using synthetic and real data. We observed that ROKU was superior to a conventional entropy-based method in its ability to rank genes according to overall tissue specificity and to detect genes whose expression pattern are specific only to objective tissues. CONCLUSION: ROKU is useful for the detection of various tissue-specific expression patterns. The framework is also directly applicable to the selection of diagnostic markers for molecular classification of multiple classes.

Algorithms↗
PubMed2006

Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides.

Molecular dynamics (MD) simulation using the reference potential spatial warping algorithm (REPSWA) is a promising method for computing the conformational equilibrium of a system with a rugged energy surface. Its effectiveness has previously been demonstrated using only a simplified model system of a hydrocarbon chain omitting nonbonded interaction terms from the potential energy function. To evaluate the applicability of REPSWA MD simulation to more realistic problems, we applied it to small peptide systems in an aqueous environment. Difficulties were encountered, however, forcing us to devise several modifications. We investigated their effectiveness in comparison to conventional constant-temperature and multicanonical MD simulations. We found that the sampling efficiency of the modified REPSWA MD after a careful optimization of its parameters was better than that of the constant-temperature MD and comparable to that of the multicanonical MD in several cases.

Alanine↗
PubMed2006

Folding free-energy landscape of a 10-residue mini-protein, chignolin.

Chignolin is an artificial mini-protein composed of 10 residues (GYDPETGTWG) that has been shown to cooperatively fold into a beta-hairpin structure in water. We extensively explored the conformational space of chignolin using a 180-ns multicanonical molecular dynamics (MD) simulation and analyzed its folding free-energy landscape. In the MD trajectory, we found structures that satisfy 99% of the experimental restraints and are quite close to the experimentally determined structures with C(alpha) root-mean-square-deviations of less than 0.5 Angstroms. These structures formed a large cluster in the conformational space with the largest probability of existence, agreeing well with the experiment.

Cluster Analysis↗
PubMed2006

Altered gut flora and environment in patients with severe SIRS.

BACKGROUND: The gut is considered an important target organ of injury after severe insult such as sepsis, trauma, and shock. The impact of bacterial translocation or mesenteric lymph on systemic inflammatory response and multiple organ damage has been investigated in animals, but dynamic changes in the gut flora and environment have not been fully clarified in critically ill patients. In the present study, we quantitatively evaluated changes in the gut microflora and environment in patients with severe systemic inflammatory response syndrome (SIRS). METHODS: Twenty-five patients with severe SIRS, who fulfilled the criteria for SIRS, had a serum CRP level >10 mg/dL, and were treated in the intensive care unit for more than 2 days, were included in our study. SIRS was a result of sepsis in 18 patients, trauma in 6, and burn in 1. A fecal sample was used for quantitative evaluation of microflora (bacterial counts of 10 key groups including Bifidobacterium and Lactobacillus) by plate or tube technique and of the gut environment (pH and 9 organic acids by high speed liquid chromatography). Data obtained from patients were compared with corresponding data from healthy volunteers. RESULTS: Analysis of fecal flora confirmed that patients with severe SIRS had significantly lower total anaerobic bacterial counts (especially 2-4 log fewer "beneficial" Bifidobacterium and Lactobacillus) and 2 log higher "pathogenic" Staphylococcus and Pseudomonas group counts than those of healthy volunteers. Concentrations of total organic acids (especially "beneficial" short-chain fatty acids such as acetic acid, propionic acid, and butyric acid) in the feces were significantly decreased in the patients, whereas pH was markedly increased. CONCLUSIONS: The gut flora and environment are significantly altered in patients with severe SIRS. Abnormal gut flora and environment may affect systemic inflammatory response after severe insult.

Adult↗
PubMed2006

[A case of anterior ischemic optic neuropathy associated with Vogt-Koyanagi-Harada disease].

BACKGROUND: Although optic disc swelling is one of the common findings of Vogt-Koyanagi-Harada (VKH) disease, severe visual field loss from optic disc involvement is not common. We report a case of severe visual field contraction from optic disc involvement in VKH disease. CASE REPORT: A 51-year-old woman was diagnosed as having VKH disease and was treated with intravenous pulse methylprednisolone. Exudative retinal detachments disappeared and visual acuity improved, but optic disc swelling was persistent in both eyes. Ten weeks after VKH disease onset, she claimed acute visual field loss in the right eye. Marked optic disc swelling with peripapillary hemorrhages and severe visual field loss were observed in the right eye. Fluorescein angiography showed filling delay and late leakage of the optic disc in the right eye. One month later, right optic disc swelling disappeared, but visual field loss remained. In addition, 5.5 months later, the left optic disc swelled further, and the left visual field was markedly contracted. Hyperbaric oxygen therapy was added. The swelling in the left optic disc gradually decreased and disappeared in one month, but the visual field loss remained. CONCLUSIONS: The optic disc involvement with irreversible visual field loss in this case is thought to be due to anterior ischemic optic neuropathy, which may be a possible complication of VKH disease.

Female↗
PubMed2005

Autosomal dominant leukodystrophy with axonal spheroids and pigmented glia: clinical and neuropathological characteristics.

We report two autopsy cases of siblings with adult-onset autosomal dominant leukodystrophy characterized by destruction of cerebral white matter, large numbers of axonal spheroids and pigmented glia in the fronto-temporal lobes. Both patients presented with motor and cognitive symptoms and aphasia, 2-3 years before death. At autopsy, the brain showed brown coloration and decreased volume of white matter in the frontal and temporal lobes as well as corpus callosum. Microscopically, marked loss of myelin and axons and abundant axonal spheroids without apparent neuronal loss were observed in the frontal and temporal lobes, which was consistent with hereditary diffuse leukodystrophy with spheroids (HDLS). In addition, glial cells, most consistent with macrophages and containing pigments that were stained by Sudan III and PAS, were found in the white matter lesions. The present cases showed overlapping features with HDLS and pigmentary type of orthochromatic leukodystrophy, suggesting that the pathomechanisms of these two diseases are closely related.

Axons↗
PubMed2005

Spinal kyphosis causes demyelination and neuronal loss in the spinal cord: a new model of kyphotic deformity using juvenile Japanese small game fowls.

STUDY DESIGN: Histologic changes in the spinal cord caused by progressive spinal kyphosis were assessed using a new animal model. OBJECTIVES: To evaluate the effects of chronic compression associated with kyphotic deformity of the cervical spine on the spinal cord. SUMMARY OF BACKGROUND DATA: The spinal cord has remarkable ability to resist chronic compression, however, delayed paralysis is sometimes seen following the development of spinal kyphosis. In the past, no animal model to clarify the mechanism of spinal cord damage due to spinal kyphotic deformity has been available. METHODS: Laminectomy and bilateral facetectomy at the C4-C5 level was performed in 52 Japanese small game fowls. Histologic changes in the spinal cord associated with progressive kyphotic deformity were examined at different time points after surgery in each animal. The degree of spinal cord flattening and the severity of demyelination in histologic sections were quantitatively evaluated using an image analyzer, and their association with the kyphotic angle was analyzed. Changes in the microvascular distribution in the spinal cord were also examined by microangiography. RESULTS: In all operated animals, progressive kyphosis developed reproducibly. The kyphotic angle increased gradually until 3 weeks after surgery and stabilized thereafter. There was a significant correlation between the kyphotic angle and the degree of spinal cord flattening. The spinal cord was compressed most intensely at the apex of the kyphosis, where demyelination of the anterior funiculus as well as neuronal loss and atrophy of the anterior horn were observed. Demyelination progressed as the kyphotic deformity became more severe, initially affecting the anterior funiculus and later extending to the lateral and then the posterior funiculus. Angiography revealed a decrease of the vascular distribution at the ventral side of the compressed spinal cord. CONCLUSIONS: Progressive kyphosis of the cervical spine resulted in demyelination of nerve fibers in the funiculi and neuronal loss in the anterior horn due tochronic compression of the spinal cord. These histologic changes seem to be associated with both continuous mechanical compression and vascular changes in the spinal cord.

Animals↗
PubMed2005

Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase.

Carbazole 1,9a-dioxygenase (CARDO) catalyzes the dihydroxylation of carbazole by angular position (C9a) carbon bonding to the imino nitrogen and its adjacent C1 carbon. This reaction is an initial degradation reaction of the carbazole degradation pathway by various bacterial strains. Only a limited number of Rieske non-heme iron oxygenase systems (ROSs) can catalyze this novel reaction, termed angular dioxygenation. Angular dioxygenation is also involved in the degradation pathways of carbazole-related compounds, dioxin, and CARDO can catalyze the angular dioxygenation for dioxin. CARDO consists of a terminal oxygenase component (CARDO-O), and the electron transport components, ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R). CARDO-O has a homotrimeric structure, and governs the substrate specificity of CARDO. Here, we have determined the crystal structure of CARDO-O of Janthinobacterium sp. strain J3 at a resolution of 1.95A. The alpha3 trimeric overall structure of the CARDO-O molecule roughly corresponds to the alpha3 partial structures of other terminal oxygenase components of ROSs that have the alpha3beta3 configuration. The CARDO-O structure is a first example of the terminal oxygenase components of ROSs that have the alpha3 configuration, and revealed the presence of the specific loops that interact with a neighboring subunit, which is proposed to be indispensable for stable alpha3 interactions without structural beta subunits. The shape of the substrate-binding pocket of CARDO-O is markedly different from those of other oxygenase components involved in naphthalene and biphenyl degradation pathways. Docking simulations suggested that carbazole binds to the substrate-binding pocket in a manner suitable for catalysis of angular dioxygenation.

Bacterial Proteins↗
PubMed2005

Late-onset repetitive traumatic flap folds and partial dehiscence of flap edge after laser in situ keratomileusis.

A 25-year-old woman had traumatic flap folds and partial dehiscence of the flap edge in the right eye 5 and 30 months after laser in situ keratomileusis. The period from injury to treatment was 4 hours and 9 days, respectively. With the first injury, the flap was lifted and stretched with moistened sponges to clear the folds. With the second injury, the folds were hard so the flap was lifted and sutured to stretch the folds. The patient recovered visual acuity within 2 weeks.

Accidents, Occupational↗
PubMed2005

Corneal endothelial cell protection with Viscoat and Healon or Healon alone during penetrating keratoplasty.

PURPOSE: To determine the influence of dispersive ophthalmic viscosurgical products (OVPs) on corneal endothelial cell (CEC) density during penetrating keratoplasty (PKP) and on the postoperative intraocular pressure (IOP). METHODS: In 117 eyes of 113 patients, PKP was performed by a single surgeon from April 1, 1998 to April 30, 2002. Loss of CECs and postoperative IOP were evaluated retrospectively after use of Viscoat (sodium hyaluronate 3.0%, chondroitin sulfate 4.0%) plus Healon (sodium hyaluronate 1.0%) (Viscoat/Healon group) or Healon alone (Healon group) during surgery. RESULTS: The average CEC loss was 14.6 +/- 15.5% and 9.0 +/- 10.5% at 1 month, 18.1 +/- 14.6% and 10.1 +/- 7.3% at 3 months, 20.1 +/- 16.3% and 12.2 +/- 10.9% at 6 months, and 31.7 +/- 21.4% and 18.1 +/- 15.5% at 12 months in the Healon (n = 74) and Viscoat/Healon (n = 43) groups, respectively. Patients were stratified into groups with corneal leukoma (n = 61) or bullous keratopathy (n = 56). Loss of CECs was significantly smaller in the Viscoat/Healon group compared with the Healon group irrespective of whether patients had corneal leukoma or bullous keratopathy at 3, 6, and 12 months postoperatively. There was no significant difference of postoperative IOP between the Healon and Viscoat/Healon groups over 12 months of follow-up. CONCLUSION: These results suggest that the addition of Viscoat to Healon decreases CEC loss during PKP and does not affect postoperative IOP.

Adjuvants, Immunologic↗
PubMed2005

Structure, epitope mapping, and docking simulation of a gibberellin mimic peptide as a peptidyl mimotope for a hydrophobic ligand.

Using NMR spectroscopy and simulated annealing calculations, we determined the solution structure of the disulfide-linked cyclized decapeptide ACLPWSDGPC (SD), which is bound to an anti-(gibberellin A(4)) mAb 4-B8(8)/E9 and was found to be the first peptidyl mimotope for a hydrophobic ligand. The resulting structure of the peptide showed a beta-turn-like conformation in residues three to seven and the region converges well (average rmsd 0.54 A). The binding activity and the epitopes of the peptide to the antibody were assessed using saturation transfer difference (STD)-NMR experiments. We also conducted docking simulations between the peptide and the mAb to determine how the peptide is bound to the mAb. Resonances around the beta-turn-like conformation of peptide SD (residues 3-5) showed strong STD enhancement, which agreed well with results from docking simulation between peptide SD and the mAb. Together with the commonality of amino acid residues of the mAb involved in interactions with gibberellin A(4) (GA(4)) and peptide SD, we concluded that peptide SD is bound to the antigen-binding site of mAb 4-B8(8)/E9 as a GA(4) mimic, confirming evidence for the existence of peptide mimics even for hydrophobic ligands.

Amino Acid Sequence↗
PubMed2005

Crystal structure of the terminal oxygenase component of cumene dioxygenase from Pseudomonas fluorescens IP01.

The crystal structure of the terminal component of the cumene dioxygenase multicomponent enzyme system of Pseudomonas fluorescens IP01 (CumDO) was determined at a resolution of 2.2 A by means of molecular replacement by using the crystal structure of the terminal oxygenase component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4 (NphDO). The ligation of the two catalytic centers of CumDO (i.e., the nonheme iron and Rieske [2Fe-2S] centers) and the bridging between them in neighboring catalytic subunits by hydrogen bonds through a single amino acid residue, Asp231, are similar to those of NphDO. An unidentified external ligand, possibly dioxygen, was bound at the active site nonheme iron. The entrance to the active site of CumDO is different from the entrance to the active site of NphDO, as the two loops forming the lid exhibit great deviation. On the basis of the complex structure of NphDO, a biphenyl substrate was modeled in the substrate-binding pocket of CumDO. The residues surrounding the modeled biphenyl molecule include residues that have already been shown to be important for its substrate specificity by a number of engineering studies of biphenyl dioxygenases.

Amino Acid Sequence↗
PubMed2005

A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions.

We describe a fast protein-protein docking algorithm using a series expansion in terms of newly designed bases to efficiently search the entire six-dimensional conformational space of rigid body molecules. This algorithm is an ab initio docking algorithm designed to list candidates of putative conformations from a global conformational space for unbound docking. In our algorithm, a scoring function is constructed from terms that are the inner products of two scalar fields expressing individual molecules. The mapping from a molecule to a scalar field can be arbitrarily defined to express an energy term. Since this scoring scheme has the same expressiveness as that of a method using a fast Fourier transform (FFT), it has the flexibility to introduce various physicochemical energies. Currently, we are using scalar fields that approximate desolvation free energy and steric hindrance energy. Fast calculation of the scoring function for each conformation of the six-dimensional search space is realized by expansion of the fields in terms of basis functions which are combinations of spherical harmonics and modified Legendre polynomials, and the use of only low-order terms, which carry most of the information on the scalar field. We have implemented this algorithm and evaluated the computation time and precision by using actual protein structure data of complexes and their monomers. This paper presents the results for six unbound cases and in all the cases we obtained at least one conformation close to the native structures (interface RMSD < 3.0 A) within the top 1000 candidates with about 40 seconds of computation time using a single Pentium4 2.4 GHz CPU.

Algorithms↗
PubMed2003

DNA microarray cluster analysis reveals tissue similarity and potential neuron-specific genes expressed in cranial sensory ganglia.

Each of four cranial sensory ganglia, trigeminal, geniculate, petrosal, and nodose ganglia, contains multiple kinds of sensory neurons with different cell morphologies and neuronal properties that transmit information about sensory stimuli received peripherally. Here we analyze the complex properties of these neurons from the viewpoint of gene expression using DNA microarrays by cluster analysis. From a total of 8,740 genes, 498 genes were selected as showing tissue-dependent expression on the microarray by hierarchical cluster analysis, and their profiles indicated that, among the four sensory ganglia, the petrosal and trigeminal ganglia are intimately related. Tissue trees of 37 subclusters containing the 498 genes showed that the profiles of gene expression and the subclusters were classified into a smaller number of groups (18 groups) when information on the amounts of expression was added. In situ hybridization analysis of 21 genes selected from 13 different groups was carried out, and the gene expression patterns were classified into eight categories. The putative profiles postulated from the microarray data were essentially consistent with the patterns of expression at the cellular level as shown by in situ hybridization. In conclusion, from the overall analyses of gene expression by DNA microarray, we can identify a number of candidate genes showing neuron type-specific expression in the peripheral ganglia.

Animals↗
PubMed2003

Expression, purification, and characterization of 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase from carbazole-degrader Pseudomonas resinovorans strain CA10.

The two-subunit meta-cleavage enzyme, 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarBaBb), from the carbazole degrader Pseudomonas resinovorans strain CA10 was purified to homogeneity from an Escherichia coli strain carrying the expression vector pUCA503, in which two copies of the carBaBb genes are tandemly linked. SDS-PAGE and gel filtration showed that CarB was a alpha2beta2-heterotetrameric enzyme with subunit molecular masses of approximately 10,000 for CarBa and 29,000 for CarBb. The optimum pH for activity was 8.5 and that of temperature was 35 degrees C. The CarB enzyme had a Km of 14 microM and a kcat/Km of 0.25 microM(-1) s(-1) for 2'-aminobiphenyl-2,3-diol, and the catalytic activities for biphenyl-type catecholic substrates were higher than those for monoaromatic catechol derivatives. The enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, but the enzyme was highly specific for 2,3-dihydroxybiphenyl.

Aminobiphenyl Compounds↗