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Toshio Shimizu

Publications and source records attributed to Toshio Shimizu.

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

ConPred_elite: a highly reliable approach to transmembrane topology predication.

The function of transmembrane (TM) proteins is closely correlated to their TM topology; large quantities of highly reliable TM topology data are becoming increasingly required. We present a new consensus approach for TM topology prediction (ConPred_elite) that can predict the whole topology with accuracies of 0.98 for prokaryotic and 0.95 for eukaryotic proteins on a dataset of experimentally-characterized TM topologies. The predicted yield on the dataset is 30.4% for prokaryotic and 21.5% for eukaryotic proteins. Applying ConPred_elite to predicted TM proteins extracted from 29 prokaryotic and 10 eukaryotic proteomes, we obtained 3871 and 7271 highly reliable TM topologies (yields, 19.8 and 13.3%), respectively. The predicted TM topology data may contribute to further research into a comprehensive functional classification and identification of TM proteins based on information of the topology.

Archaeal Proteins↗
PubMed2004

Proteome-wide classification and identification of mammalian-type GPCRs by binary topology pattern.

G protein-coupled receptors (GPCRs), a large eukaryotic protein family, have proved difficult to comprehensively detect and functionally identify by homology searches and domain detection, because they are highly divergent and their sequences share strikingly little similarity. Transmembrane (TM) topology pattern analysis has been used to classify TM proteins, and such patterns are conserved within GPCRs of similar function. Here, we developed a stepwise binary topology pattern (BTP) method for GPCR classification and identification and used it to identify and classify mammalian-type GPCRs in the genomes of 10 different eukaryotic species. A binary topology pattern was obtained for each functional class or group by assigning binary loop threshold lengths of "0" (short loop) or "1" (long loop). The GPCR-classification ability of the BTP method had quite high accuracies for classifying GPCR functions at the class level (Classes A, B, C, Frizzled/Smoothened, Non-GPCR, based on the GPCRDB classification scheme), with many classes being classified with 100% accuracy. Sufficiently high accuracies were also maintained at the functional group level, 0.945 over 15 functional groups. Proteome-wide mammalian-type GPCR searches in 10 eukaryotic genomes (H. sapiens, M. musculus, F. rubripes, C. intestinalis, A. thaliana, D. melanogaster, A. gambiae, C. elegans, P. falciparum, S. cerevisiae) using the BTP method showed much higher classification/identification in non-mammalian genomes than typical BLAST searches, in which a higher number of sequences were classified as Non-GPCR. This stepwise BTP method should prove useful for the identification and functional classification of GPCRs from the genomes of a wide range of species.

Animals↗
PubMed2004

Proteome-wide functional classification and identification of prokaryotic transmembrane proteins by transmembrane topology similarity comparison.

We propose a new method for classifying and identifying transmembrane (TM) protein functions in proteome-scale by applying a single-linkage clustering method based on TM topology similarity, which is calculated simply from comparing the lengths of loop regions. In this study, we focused on 87 prokaryotic TM proteomes consisting of 31 proteobacteria, 22 gram-positive bacteria, 19 other bacteria, and 15 archaea. Prior to performing the clustering, we first categorized individual TM protein sequences as "known," "putative" (similar to "known" sequences), or "unknown" by using the homology search and the sequence similarity comparison against SWISS-PROT to assess the current status of the functional annotation of the TM proteomes based on sequence similarity only. More than three-quarters, that is, 75.7% of the TM protein sequences are functionally "unknown," with only 3.8% and 20.5% of them being classified as "known" and "putative," respectively. Using our clustering approach based on TM topology similarity, we succeeded in increasing the rate of TM protein sequences functionally classified and identified from 24.3% to 60.9%. Obtained clusters correspond well to functional superfamilies or families, and the functional classification and identification are successfully achieved by this approach. For example, in an obtained cluster of TM proteins with six TM segments, 109 sequences out of 119 sequences annotated as "ATP-binding cassette transporter" are properly included and 122 "unknown" sequences are also contained.

Algorithms↗
PubMed2004

[Serotypes, genotypes and drug resistance of group A streptococcal strains isolated in 1991, 2001 and 2002 in Tokushima Prefecture--comparison after decade].

Sixty two strains of Group A streptococcus were isolated between August 2001 and June 2002. They were examined for T serotypes, pyrogenic exotoxin genes and resistance against antibiotics. The results were compared with those for 61 isolates of the same species collected between April and December 1991. Among the strains isolated in 1991, T4 was the dominant serotype (18 strains) followed by T12 and T1 (each 15 strains). These three serotypes represented 78.7% of the total number. In contrast, among the strains isolated in 2001 and 2002 T28 (13 strains) was the dominant serotype followed by T1 (12 strains) and T4 (7 strains). Examination of these isolates for pyrogenic exotoxin gene revealed that all carried speB and more than half of the strains isolated in 1991, 2001 and 2002 carried both speB and speC. Regarding the combination of T type and toxin genotype, out of the isolates in 1991 fifteen T4 strains were associated with B and C, eleven T12 types with B and C, and nine T1 strains with A and B, while out of the strains isolated in 2001 and 2002 eleven T28 strains were associated with B and C, six T1 strains with B and C, and both five T4 and T12 types with B and C. Sma I Pulsed-field gel electrophorasis analysis revealed that PFGE patterns of T4:spe B and C and T12:spe B and C strains in 2001 and 2002 are same as one of those in 1991, respectively. On the other hand, during the decade strains resistant to macrolide increased from 1 strain (1.6%) to 11 strains (17.7%) and those to tetracycline increased from 23 strains (37.7%) to 32 strains (41.6%). During the same period the incidence of multiple resistance increased from 9 strains (14.7%) to 14 strains (22.5%).

Drug Resistance, Multiple, Bacterial↗
PubMed2003

Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: "waiting for Godot".

Genome-wide sequence analysis in the invertebrate chordate, Ciona intestinalis, has provided a comprehensive picture of immune-related genes in an organism that occupies a key phylogenetic position in vertebrate evolution. The pivotal genes for adaptive immunity, such as the major histocompatibility complex (MHC) class I and II genes, T-cell receptors, or dimeric immunoglobulin molecules, have not been identified in the Ciona genome. Many genes involved in innate immunity have been identified, including complement components, Toll-like receptors, and the genes involved in intracellular signal transduction of immune responses, and show both expansion and unexpected diversity in comparison with the vertebrates. In addition, a number of genes were identified which predicted integral membrane proteins with extracellular C-type lectin or immunoglobulin domains and intracellular immunoreceptor tyrosine-based inhibitory motifs (ITIMs) and immunoreceptor tyrosine-based activation motifs (ITAMs) (plus their associated signal transduction molecules), suggesting that activating and inhibitory receptors have an MHC-independent function and an early evolutionary origin. A crucial component of vertebrate adaptive immunity is somatic diversification, and the recombination activating genes (RAG) and activation-induced cytidine deaminase (AID) genes responsible for the Generation of diversity are not present in Ciona. However, there are key V regions, the essential feature of an immunoglobulin superfamily VC1-like core, and possible proto-MHC regions scattered throughout the genome waiting for Godot.

Animals↗
PubMed2003

The cooperative binding of large ligands to a one-dimensional lattice: the steric hindrance effect.

The cooperative binding of monomeric ligands to a long lattice of a linear polymer with complete or partial steric hindrance is treated using a matrix method. Results and typical calculations of the model are represented. Non-saturated cooperative binding as well as two-step (biphasic) binding isotherms can be interpreted by the steric hindrance model. This is applicable to the analysis of the binding of surfactants to polymer. The usefulness and the limitation also are discussed.

Binding Sites↗
PubMed2003

Formation and structures of mercury complexes of 18-membered unsaturated and saturated thiacrown ethers.

The complexation of 18-membered unsaturated thiacrown ether, 18-UT-6, with 1 equiv of HgCl(2) in acetone afforded mercury complex Hg(II)(18-UT-6)Cl(2). The complexations of 18-membered saturated thiacrown ether, 18S6, with 1 equiv each of HgCl(2) and CdCl(2) in acetone afforded Hg(II)(18S6)Cl(2) and Cd(II)(18S6)Cl(2), respectively. The crystal structure of Hg(II)(18-UT-6)Cl(2) revealed that the mercury atom was inside the cavity of the macrocycle and the geometry around the mercury atom was an eight-coordinate hexagonal bipyramidal arrangement. ORTEP drawing of Hg(II)(18S6)Cl(2) revealed the existence of the mercury atom outside the cavity of the ring, as well as a polymeric chain structure. (1)H NMR study of Hg(II)(18-UT-6)Cl(2) in acetone-d(6) indicated that the interconversion between free 18-UT-6 and pure complex was slower than the NMR time scale. The titration experiment by (1)H NMR revealed that 18-UT-6 had inclusion selectivity for the number of mercury atoms. The electrochemical behavior of complexes Hg(II)(18-UT-6)Cl(2) and Hg(II)(18S6)Cl(2) was also examined.

Journal Article↗
PubMed2003

Synthesis and structures of 15- and 18-membered unsaturated selenacrown ethers and their complexation with silver trifluoroacetate.

The reaction of Na(2)Se with cis-dichloroethene yielded (Z,Z,Z,Z,Z)-1,4,7,10,13-pentaselenacyclopentadeca-2,5,8,11,14-pentaene (15-US-5) and (Z,Z,Z,Z,Z,Z)-1,4,7,10,13,16-hexaselenacyclooctadeca-2,5,8,11,14,17-hexaene (18-US-6). X-ray crystallographic analysis of 15-US-5 and 18-US-6 revealed an all-cis geometry around the carbon-carbon double bonds, with all of the selenium atoms located on one side of the respective ring planes. 15-US-5 and 18-US-6 were also found to be oxidized more easily than the corresponding sulfur analogues. The complexation of 15-US-5 and 18-US-6 with silver trifluoroacetate afforded Ag(I)(15-US-5)(CF(3)COO) and Ag(I)(5)(18-US-6)(3)(CF(3)COO)(5), respectively. [reaction: see text]

Journal Article↗
PubMed2003

Comprehensive analysis of transmembrane topologies in prokaryotic genomes.

We analysed comprehensively transmembrane (TM) topologies of TM proteins of 50 selected prokaryotic genomes, by discriminating between TM and soluble proteins by using SOSUI, then detecting and removing signal peptides by applying 'DetecSig', and finally predicting TM topologies by employing 'ConPred'. Estimated fraction of TM proteins in proteome averaged over the 50 genomes is approximately 22%. About 13% of TM proteins were predicted to have a signal peptide, and the fraction of soluble proteins with signal peptide (secretory proteins) ranges from 8 to 18% for most majority of the genomes. The N(in)-type TM proteins with 2-, 4-, 6- and 12-tms (number of transmembrane segments) are predominant among multi-spanning TM proteins, and correspondingly, significantly higher fractions of N(out)-type TM proteins with 1-, 3-, 5- and 11-tms have a signal peptide. It is also found that the TM proteins with signal peptide tend to have a long N-tail loop. The averaged sequence length of TM proteins increases linearly with the increase of the number of TM segments, with the increasing rate of about 35 residues, suggesting a possibility that TM topologies might have been evolved by the 'internal gene duplication' mechanism. Datasets of TM topologies predicted in this study are available at http://bioinfo.si.hirosaki-u.ac.jp/ approximately TMPinGS/.

Archaea↗
PubMed2003

TMPDB: a database of experimentally-characterized transmembrane topologies.

TMPDB is a database of experimentally-characterized transmembrane (TM) topologies. TMPDB release 6.2 contains a total of 302 TM protein sequences, in which 276 are alpha-helical sequences, 17 beta-stranded, and 9 alpha-helical sequences with short pore-forming helices buried in the membrane. The TM topologies in TMPDB were determined experimentally by means of X-ray crystallography, NMR, gene fusion technique, substituted cysteine accessibility method, N-linked glycosylation experiment and other biochemical methods. TMPDB would be useful as a test and/or training dataset in improving the proposed TM topology prediction methods or developing novel methods with higher performance, and as a guide for both the bioinformaticians and biologists to better understand TM proteins. TMPDB and its subsets are freely available at the following web site: http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/.

Animals↗
PubMed2003

Identification of transmembrane protein functions by binary topology patterns.

We propose a novel method for identifying and classifying the functions of transmembrane (TM) proteins based on their TM topology [the number of TM segments (tms), the loop length and the N-terminus location]. In this method, the TM topology is expressed as a string of '0' and '1', and this is designated the binary topology pattern (BTP). We focused on TM proteins with up to 12 tms, with the exception of 1 and 9 tms, and classified them into 37 functional groups by the number of tms and the functional annotation. These grouped TM protein sequences were used to determine BTPs which are specific to the individual functional groups. Since the evaluated accuracies (sensitivity, specificity and self-consistency) of these patterns in functional identification were quite high overall, i.e. 0.940, 0.934 and 0.935, respectively, as averaged over the 37 functional groups, we confirmed that TM protein function can be identified by the number of tms and the characteristics of loop lengths, i.e. BTPs.

Data Interpretation, Statistical↗
PubMed2003

[Common toxicity criteria: version 2.0, an improved reference for grading the adverse reaction of cancer treatment].

In 1998, the National Cancer Institute (NCI) made an effort to revise and expand the Common Toxicity Criteria (CTC) in cancer treatment. New CTC version 2.0 includes more than 279 individual adverse events with more than 24 of these applicable to adverse reaction category. The Radiation Therapy Oncology Group(RTOG) Acute Radiation Morbidity Scoring Criteria and BMT Complex/Multi-Component Events were added to New CTC version 2.0. CTC version 2.0 represents an improvement in the evaluation and grading of toxicity for all modalities in cancer treatment.

Antineoplastic Agents↗
PubMed2002

Silver complexes with unsaturated thiacrown ethers: inclusion behavior of conformationally restricted macrocycles.

The reactions of 18- and 21-membered unsaturated thiacrown ethers, 18-UT-6 and 21-UT-7, with CF(3)COOAg in acetone afforded novel silver(I) complexes Ag(I)(18-UT-6)(CF(3)COO) and Ag(I)(2)(21-UT-7)(CF(3)COO)(2), respectively. The crystal structure of Ag(I)(18-UT-6)(CF(3)COO) shows that the silver atom occupies the cavity of the 18-UT-6 and the geometry around the silver atom has a distorted five-coordinate square pyramidal arrangement. The crystal structure of Ag(I)(2)(21-UT-7)(CF(3)COO)(2) shows that the two silver atoms and all sulfur atoms are nearly coplanar and the two trifluoroacetate groups are located at the opposite sides of the plane. The stoichiometry for the complexation of 15-UT-5, 18-UT-6, and 21-UT-7 with CF(3)COOAg in solution was examined by (1)H NMR measurement. The titration plots of 15-UT-5 and 21-UT-7 show a distinct inflection point at 1:1 and 2:1 metal/macrocycle ratios, respectively, whereas the plot of 18-UT-6 gradually changes at the range of 1:1 to 2:1. From these results, 15-UT-5 and 21-UT-7 were found to show inclusion selectivity for number of silver ions, respectively, whereas 18-UT-6 showed low selectivity for the inclusion number of metals. Comparison of the oxidation and reduction potentials of the silver(I) complexes with those of free macrocycles and CF(3)COOAg revealed that unsaturated thiacrown ethers become difficult to be oxidized by complexation with CF(3)COOAg, and CF(3)COOAg becomes difficult to be reduced by complexation with unsaturated thiacrown ethers.

Journal Article↗
PubMed2002

Newly established regulation in Japan: foods with health claims.

The Japanese government enacted a new regulatory system called 'Foods with health claims' in April 2001, which consists of 'Foods for Specified Health Use' (FOSHU) and 'Foods with Nutrient Function Claims' (FNFC). The FOSHU was set up by the Ministry of Health and Welfare in 1991 to approve descriptions on a label regarding an effect of food on the human body. It was enacted as a part of 'food for specified dietary use' under the Nutrition Improvement Law. There are three important requirements for FOSHU approval. The first is scientific evidence of the efficacy, including clinical testing. The second is safety for consumption. The third is analytical determination of the effective component. At present there are 293 items approved as FOSHU. Most of the descriptions of foods under the FOSHU system are similar to the category of enhanced function claims of Codex. Under FNFC, 12 vitamins (vitamin A, B1, B2, B6, B12, C, E, D, biotin, pantothenic acid, folic acid, and niacin) and two minerals (calcium and iron) are standardized. These claims are similar to the nutrient function claims approved by Codex in 1997. It is desirable that the Japanese administration and the food industry cooperate with ASEAN countries to work together in the development and promotion of nutrition and health claims on foods.

Food↗
PubMed2002

Motor cortical disinhibition in the unaffected hemisphere after unilateral cortical stroke.

Following a hemispheric stroke, various degrees of neuronal reorganization around the lesion occur immediately after disease onset and thereafter up to several months. These include transcallosal excitability, changes of the intact motor cortex and ipsilateral motor responses after transcranial magnetic stimulation (TMS) on the intact hemisphere. To elucidate the relationship between lesion localization and motor cortex excitability (intracortical inhibition; ICI) in the intact hemisphere, we applied a paired conditioning-test TMS paradigm in 12 patients with unilateral cortical stroke (cortical group) and nine patients with subcortical stroke caudal to the corpus callosum (subcortical group), with interstimulus intervals varying from 1 to 10 ms. All patients exhibited unilateral complete hand palsy. ICI was significantly less in the cortical group than in age-matched healthy control subjects. It was especially more marked in the cortical group patients with a disease duration of less than 4 months after onset. Patients in the cortical group with a duration longer than 4 months showed a tendency for ICI to be normalized, and there was a significant correlation between ICI and disease duration. Patients in the subcortical group showed normal excitability curves. All patients in the cortical group showed no transcallosal inhibition (TCI) in the active unaffected hand muscle after TMS of the affected motor cortex, whereas all the subcortical patients showed some TCI. No ipsilateral motor responses were elicited in the paretic hand in any of the patients. The reduced ICI in the cortical group might have been a result of disruption of TCI. The normalization of ICI in the patients with longer disease duration and the normal ICI in the subcortical group patients do not support the functional significance of motor cortex hyperexcitability in the unaffected hemisphere, at least in a patient population with poor motor recovery.

Aged↗
PubMed2002

Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies.

We selected 10 transmembrane (TM) prediction methods (KKD, TMpred, TopPred II, DAS, TMAP, MEMSAT 2, SOSUI, PRED-TMR2, TMHMM 2.0 and HMMTOP 2.0) and re-assessed its prediction performance using a reliable dataset with 122 entries of experimentally-characterized TM topologies. Then, we improved prediction performance by a consensus prediction method. Prediction performance during re-assessment and consensus prediction were based on four attributes: (i) the number of transmembrane segments (TMSs), (ii) the number of TMSs plus TMS-position, (iii) N-tail location and (iv) TM topology. We noted that hidden Markov model-based methods dominate over other methods by individual prediction performance for all four attributes. In addition, all top-performing methods generally were model-based. Among prokaryotic sequences, HMMTOP 2.0 solely topped among other methods with prediction accuracies ranging from 64% to 86% across all attributes. However, among eukaryotic sequences, prediction performance for all the attributes was relatively poor compared with prokaryotic ones. On the other hand, our results showed that our proposed consensus prediction method significantly improved prediction performance by, at least, an additional nine percentage points particularly among prokaryotic sequences for the number of TMS (84%), number of TMS and position (80%), and TM topology attributes (74%). Although our consensus prediction method improved also the prediction performance among eukaryotic sequences, the obtained accuracies for all attributes were relatively lower than that obtained by prokaryotic counterparts particularly for TM topology.

Cell Membrane↗