Biomedical subjects

Kentaro Shimizu

Publications and source records attributed to Kentaro Shimizu.

24 records · Page 2Linked to original sources

PubMed2003

Purification and characterization of meta-cleavage compound hydrolase from a carbazole degrader Pseudomonas resinovorans strain CA10.

2-Hydroxy-6-oxo-6-(2'-aminophenyl)-hexa-2,4dienoic acid [6-(2'-aminophenyl)-HODA] hydrolase, involved in carbazole degradation by Pseudomonas resinovorans strain CA10, was purified to near homogeneity from an overexpressing Escherichia coli strain. The enzyme was dimeric, and its optimum pH was 7.0-7.5. Phylogenetic analysis showed the close relationship of this enzyme to other hydrolases involved in the degradation of monocyclic aromatic compounds, and this enzyme was specific for 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (6-phenyl-HODA), having little activity toward 2-hydroxy-6-oxohepta-2,4-dienoic acid and 2-hydroxymuconic semialdehyde. The enzyme had a Km of 2.51 microM and k(cat) of 2.14 (s(-1)) for 6-phenyl-HODA (50 mM sodium phosphate, pH 7.5, 25 degrees C). The effect of the presence of an amino group or hydroxyl group at the 2'-position of phenyl moiety of 6-phenyl-HODA on the enzyme activity was found to be small; the activity decreased only in the order of 6-(2'-aminophenyl)-HODA (2.44 U/mg) > 6-phenyl-HODA (1.99 U / mg) > 2-hydroxy-6-oxo-6-(2'-hydroxyphenyl)-hexa-2,4-dienoic acid (1.05 U/mg). The effects of 2'-substitution on the activity were in accordance with the predicted reactivity based on the calculated lowest unoccupied molecular orbital energy for these substrates.

Biotransformation↗

PubMed2003

[Recent advances in computed tomography as a diagnostic tool for COPD].

The diagnosis of chronic obstructive pulmonary disease(CODP) has been mainly based on the physiologic impairment(obstructive ventilatory disturbance). However, recent advances in computed tomography including high resolution, helical and multi-detector CTs have made it possible to diagnose patients with CODP morphologically by identifying low attenuation areas on CT. In addition, airway dimensions including luminal area and airway wall thickness have been measurable. CT is now an useful tool for exploring not only parenchymal but also airway abnormality in COPD. These progresses in CT could contribute to elucidate the etiology of COPD, divide COPD patients into two groups, emphysema-dominant and airway disease-dominant patients, and treat them separately.

Humans↗

PubMed2003

Development of an ab initio protein structure prediction system ABLE.

An ab initio protein structure prediction system called ABLE is described. It is based on the fragment assembly method, which consists of two steps: dividing a target sequence into overlapping subsequences (fragments) of short length and assigning a local structure to each fragment; and generating models by assembling the local structures and selecting the models with low potential energy. One of the most important problems in conventional fragment assembly methods is the difficulty of selecting native-like structures by energy minimization only. ABLE thus employs a structural clustering method to select the native-like models from among the generated models. By applying the unit-vector root mean square distance (URMS) as a measure of structure similarity, we achieve more robust, effective structural clustering. When no enough clusters of good quality are obtained, ABLE runs the energy minimization procedure again by incorporating structural restraint conditions obtained from the consensus substructures in the previously generated models. This approach is based on our observation that there is a high probability that the consensus substructures of the generated models have native-like structures. Another feature of ABLE is that in assigning local structures to fragments, it assigns mainchain dihedral angles (phi, psi) to the central residue of each fragment according to a probability distribution map built from candidate sequences similar to each fragment. This enables the system to generate appropriate local structures that may not already exist in a protein structure database. We applied our system to 25 small proteins and obtain near-native folds for more than half of them. We also demonstrate the performance of our structural clustering method, which can be applied to other protein structure prediction systems.

Cluster Analysis↗

PubMed2002

Identification of genes regulating colorectal carcinogenesis by using the algorithm for diagnosing malignant state method.

We studied the expression profiles of various stages of colorectal tumors (adenoma (AD), seven samples; carcinoma (CA), 16 samples) by using cDNA microarrays and developed ADMS (algorithm for diagnosing malignant state) method, selecting 335 clones characteristic of CA state. We, then, applied ADMS to 12 additional samples (five from primary lesions with metastasis and seven metastases); all 16 CAs and 12 metastatic tumors were diagnosed correctly as cancerous states. Although three of the seven ADs were diagnosed as "cancerous," the large size of two of these tumors suggested their potential malignancy. Our strategy for selecting clones characteristic of the malignant state is widely applicable to diagnosis and for predicting the stage of progression during multistep carcinogenesis. Of the 335 clones we selected, 135 were known genes. Included in the 135 genes were tumor suppressor and growth factor-related genes and were consistent with the literature. ADMS is a reliable means for identifying genes useful for the diagnosis of cancer.

Adenoma↗

PubMed2002

New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates.

A new algorithm for parallel calculation of the second derivatives (Hessian) of the conformational energy function of biomolecules in internal coordinates is proposed. The basic scheme of this algorithm is the division of the entire calculation of the Hessian matrix (called "task") into subtasks and the optimization of the assignment of processors to each subtask by considering both the load balancing and reduction of the communication cost. A genetic algorithm is used for this optimization considering the dependencies between subtasks. We applied this method to a glutaminyl transfer RNA (Gln-tRNA) molecule for which the scalability of our previously developed parallel algorithm was significantly decreased when the large number of processors was used. The speedup for the calculation was 32.6 times with 60 processors, which is considerably better than the speedup for our previously reported parallel algorithm. The elapsed time for the calculation of subtasks, data sending, and data receiving was analyzed, and the effect of the optimization using the genetic algorithm is discussed.

Algorithms↗

PubMed2002

Potentiation of slow component of delayed rectifier K(+) current by cGMP via two distinct mechanisms: inhibition of phosphodiesterase 3 and activation of protein kinase G.

1. Regulation of the slowly activating component of delayed rectifier K(+) current (I(Ks)) by intracellular guanosine 3'5' cyclic monophosphate (cGMP) was investigated in guinea-pig sino-atrial (SA) node cells using the whole-cell patch-clamp method. 2. When a cell was dialyzed with pipette solution containing 100 micro M cGMP, I(Ks) started to gradually increase and reached a maximum increase of a factor of 2.37 +/- 0.39 (n = 4) about 10-15 min after rupture of patch membrane. Atrial natriuretic peptide (ANP, 100 nM) also potentiated I(Ks), consistent with intracellular cGMP-induced enhancement of I(Ks). 3. Bath application of a selective blocker of the cGMP-inhibited phosphodiesterase (PDE3) milrinone (100 microM) enhanced I(Ks) by a factor of 1.50 +/- 0.09 (n = 4) but failed to further enhance I(Ks) after a maximum stimulation by intracellular cGMP (100 microM), suggesting that blockade of PDE3 activity is involved in the enhancement of I(Ks). A potent but nonspecific PDE inhibitor 3-isobutyl-1-methylxanthine (IBMX, 100 microM) further increased I(Ks) stimulated by 100 microM milrinone, indicating that PDE subtypes other than PDE3 are also involved in the regulation of basal I(Ks) in guinea-pig SA node cells. 4. Bath application of 100 microM 8-bromoguanosine 3'5' cyclic monophosphate (8-Br-cGMP) increased I(Ks) by a factor of 1.48 +/- 0.11 (n = 5) and this stimulatory effect was totally abolished by cGMP-dependent protein kinase (PKG) inhibitor KT-5823 (500 nM), suggesting that the activation of PKG also mediates cGMP-induced potentiation of I(Ks). 5. These results strongly suggest that intracellular cGMP potentiates I(Ks) not only by blocking PDE3 but also by activating PKG in guinea-pig SA node cells.

1-Methyl-3-isobutylxanthine↗