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T Hirokawa

Publications and source records attributed to T Hirokawa.

At least 19 recordsLinked to original sources
PubMed2000

New method for standardization of electropherograms obtained in capillary zone electrophoresis.

A new method for standardization of electropherograms obtained by capillary zone electrophoresis was proposed, where the migration time axis was replaced by the effective mobility axis. The mobility increase due to temperature increase by Joule heating and the relaxation effect of the potential gradient were eliminated successfully by introducing a temperature coefficient for mobility expression and a delay time, respectively. The precision of the mobility evaluated by the proposed conversion methods was evaluated for a model sample. By using the conversion method, almost the same electropherograms could be obtained even from the electropherograms originally obtained by using different hardware conditions.

Electrophoresis, Capillary↗
PubMed2000

Standardization of capillary zone electropherograms obtained by using field enhanced sample stacking.

Migration times in a capillary zone electropherogram obtained by using the field enhanced sample stacking technique are strongly affected by the injected sample volume. That is, the migration times significantly decrease with the increase of the sample volume. To avoid inaccurate qualitative analysis due to the above phenomena, the time axis of the electropherograms was converted into an effective mobility axis using our conversion method taking account of the temperature increase in the separation tube and relaxation of the potential gradient of the separation field. After the conversion, accurate qualitative analysis was possible in spite of drastic change of the migration time, suggesting our conversion method could be successfully used for the standardization of electropherograms obtained even by using the stacking effect. The cause of the decrease of the migration time in the stacking process was briefly discussed.

Electrophoresis, Capillary↗
PubMed2000

Electropherogram of capillary zone electrophoresis with effective mobility axis as a transverse axis and its analytical utility. I. Transformation applying the hypothetical electroosmotic flow.

For capillary zone electrophoresis, a new method of transformation from migration time to effective mobility was proposed, in which the mobility increase due to Joule heating and the relaxation effect of the potential gradient were eliminated successfully. The precision of the mobility evaluated by the proposed transformation was discussed in relation to the analysis of rare earth ions. By using the transformation, almost the same pherograms could be obtained even from the pherograms obtained originally at different applied voltages.

Animals↗
PubMed2000

A triangle lattice model that predicts transmembrane helix configuration using a polar jigsaw puzzle.

We developed a method of predicting the tertiary structures of seven transmembrane helical proteins in triangle lattice models, assuming that the configuration of helices is stabilized by polar interactions. Triangle lattice models having 12 or 11 nearest neighbor pairs were used as general templates of a seven-helix system, then the orientation angles of all helices were varied at intervals of 15 degrees. The polar interaction energy for all possible positions of each helix was estimated using the calculated polar indices of transmembrane helices. An automated system was constructed and applied to bacteriorhodopsin, a typical membrane protein with seven transmembrane helices. The predicted optimal and actual structures were similar. The top 100 predicted helical configurations indicated that the helix-triangle, CFG, occurred at the highest frequency. In fact, this helix-triangle of bacteriorhodopsin forms an active proton-pumping site, suggesting that the present method can identify functionally important helices in membrane proteins. The possibility of studying the structure change of bacteriorhodopsin during the functional process by this method is discussed, and may serve to explain the experimental structures of photointermediate states.

Algorithms↗
PubMed1999

Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system.

A software system, SOSUI, was previously developed for discriminating between soluble and membrane proteins and predicting transmembrane regions (Hirokawa et al., Bioinformatics, 14 (1998) 378-379). The performance of the system was 99% for the discrimination between two types of proteins and 96% for the prediction of transmembrane helices. When all of the amino acid sequences from 15 single-cell organisms were analyzed by SOSUI, the proportion of predicted polytopic membrane proteins showed an almost constant value of 15-20%, irrespective of the total genome size. However, single-cell organisms appeared to be categorized in terms of the preference of the number of transmembrane segments: species with small genomes were characterized by a significant peak at a helix number of approximately six or seven; species with large genomes showed a peak at 10 or 11 helices; and species with intermediate genome sizes showed a monotonous decrease of the population of membrane proteins against the number of transmembrane helices.

Archaea↗
PubMed1999

Physicochemical factors for discriminating between soluble and membrane proteins: hydrophobicity of helical segments and protein length.

The average hydrophobicity of a polypeptide segment is considered to be the most important factor in the formation of transmembrane helices, and the partitioning of the most hydrophobic (MH) segment into the alternative nonpolar environment, a membrane or hydrophobic core of a globular protein may determine the type of protein produced. In order to elucidate the importance of the MH segment in determining which of the two types of protein results from a given amino acid sequence, we statistically studied the characteristics of MH helices, longer than 19 residues in length, in 97 membrane proteins whose three-dimensional structure or topology is known, as well as 397 soluble proteins selected from the Protein Data Bank. The average hydrophobicity of MH helices in membrane proteins had a characteristic relationship with the length of the protein. All MH helices in membrane proteins that were longer than 500 residues had a hydrophobicity greater than 1.75 (Kyte and Doolittle scale), while the MH helices in membrane proteins smaller than 100 residues could be as hydrophilic as 0.1. The possibility of developing a method to discriminate membrane proteins from soluble ones, based on the effect of size on the type of protein produced, is discussed.

Databases, Factual↗
PubMed1998

SOSUI: classification and secondary structure prediction system for membrane proteins.

UNLABELLED: The system SOSUI for the discrimination of membrane proteins and soluble ones together with the prediction of transmembrane helices was developed, in which the accuracy of the classification of proteins was 99% and the corresponding value for the transmembrane helix prediction was 97%. AVAILABILITY: The system SOSUI is available through internet access: http://www.tuat.ac.jp/mitaku/sosui/. CONTACT: sosui@biophys.bio.tuat. ac.jp.

Computer Communication Networks↗
PubMed1995

A continuum theory for the prediction of lateral and rotational positioning of alpha-helices in membrane proteins: bacteriorhodopsin.

We have developed a new method for the prediction of the lateral and the rotational positioning of transmembrane helices, based upon the present status of knowledge about the dominant interaction of the tertiary structure formation. The basic assumption about the interaction is that the interhelix binding is due to the polar interactions and that very short extramembrane loop segments restrict the relative position of the helices. Another assumption is made for the simplification of the prediction that a helix may be regarded as a continuum rod having polar interaction fields around it. The polar interaction field is calculated by a probe helix method, using a copolymer of serine and alanine as probe helices. The lateral position of helices is determined by the strength of the interhelix binding estimated from the polar interaction field together with the length of linking loop segments. The rotational positioning is determined by the polar interaction field, assuming the optimum lateral configuration. The structural change due to the binding of a prosthetic group is calculated, fixing the rotational freedom of a helix that is connected to the prosthetic group. Applying this method to bacteriorhodopsin, the optimum lateral and rotational positioning of transmembrane helices that are very similar to the experimental configuration was obtained. This method was implemented by a software system, which was developed for this work, and automatic calculation became possible for membrane proteins comprised of several transmembrane helices.

Amino Acid Sequence↗
PubMed1994

[The effects of fresh gas flow rate on the work of breathing during semi-closed circuit anesthesia].

To evaluate the effects of fresh gas flow rate on the work of breathing during semi-closed circuit anesthesia, we measured respiratory frequency, tidal volume, inspiratory work of breathing, peak inspiratory and expiratory flow rate and fluctuations in airway pressure during breathing with fresh gas flow of 6 l.min-1, 3 l.min-1 and 1.5 l.min-1. There was no significant difference among three flow rates in terms of tidal volume, respiratory frequency, inspiratory work of breathing, peak inspiratory flow rate and fluctuation in airway pressure at inspiration. On the other hand, in the expiratory phase, peak expiratory flow rate was lower and fluctuation in airway pressure at expiration was higher at 6 l.min-1 than those at 3 l.min-1 and 1.5 l.min-1, which may be indicative of increased expiratory work of breathing. The present study shows that low fresh gas flow rate does not increase the inspiratory work of breathing and high fresh gas flow rate may increase the expiratory work of breathing, implying that lowering the fresh gas flow is profitable for the work of breathing during semi-closed circuit anesthesia.

Adult↗
PubMed1993

Simulated quantitative and qualitative isotachophoretic indices of 73 amino acids and peptides in the pH range 6.4-10.

Qualitative and quantitative isotachophoretic indices of 73 amino acids, dipeptides and tripeptides were simulated under 24 leading electrolyte conditions covering the pH range 6.4-10. The RE values and time-based zone lengths are tabulated together with the absolute mobility (m0) and pKa values used. The leading electrolyte used was 10 mM HCl and the pH buffers were imidazole, tris(hydroxymethylamino)methane, 2-amino-2-methyl-1,3-propanediol and ethanolamine. The simulated indices will be useful in the assessment of the separability and determination of the listed and related compounds.

Amino Acid Sequence↗
PubMed1993

Protein phosphatase type 2B (calcineurin)-mediated, FK506-sensitive regulation of intracellular ions in yeast is an important determinant for adaptation to high salt stress conditions.

To assess the physiological function of Ca(2+)-dependent protein phosphatase (PP2B) in the yeast Saccharomyces cerevisiae, the phenotypes of PP2B-deficient mutants were investigated. Although PP2B was dispensable for growth under normal conditions, the mutations did, however, cause growth inhibition under certain stress circumstances. The growth of the mutants was inhibited by NaCl and LiCl, but not by KCl, CaCl2, MgCl2 or nonspecific osmotic stresses. Upon shift to high NaCl medium, intracellular Na+ levels of both wild type yeast and the mutants initially increased at a comparable rate. However, internal Na+ in wild type cells started to decline more rapidly than the mutant cells during cultivation in high NaCl medium, indicating that PP2B is important in maintaining a gradient across the membrane. The protection against salt stress was achieved, at least in part, by the stimulation of Na+ export. The maintenance of a high level of internal K+ in high NaCl medium was also PP2B-dependent. In the presence of the immunosuppressant FK506, the growth behaviour and intracellular Na+ and K+ of wild type cells in high NaCl medium became very similar to those of the PP2B-deficient mutant in a manner dependent on the presence of the FK506 binding protein.

Adaptation, Physiological↗
PubMed1992

Determination of limiting ionic mobilities and dissociation constants of some local anaesthetics.

The limiting ionic mobilities and thermodynamic acid dissociation constants were calculated from isotachophoretic experiments for the local anaesthetics procaine, tetracaine, lidocaine, trimecaine, bupivacaine, cinchocaine, diperodone, diocaine, cocaine, psicaine-neu, tropacocaine, amylocaine, beta-eucaine and leucinocaine. The pH values at which the local anaesthetics with very similar limiting ionic mobilities can be isotachophoretically separated were determined from simulated mobility curves. The measuring apparatus employed a high-frequency contactless conductivity detector.

Anesthetics, Local↗
PubMed1992

Relative humidity, not absolute humidity, is of great importance when using a humidifier with a heating wire.

OBJECTIVES: Since the introduction of a humidifier with a heating wire, we have frequently experienced severe upper airway obstruction from consolidation of secretions, previously unencountered when a humidifier without a heating wire was used. Such problems led to the suspicion that the heating wire incorporated into the breathing circuit of the heated humidifier might be the cause. Therefore, we scheduled an experiment to assess the hypothesis that relative humidity, rather than absolute humidity, is a dominant factor in the case of drying secretions in the upper airway when using such a humidifier. DESIGN: Three clinical case reports and an experiment with a tracheal model. SETTING: Intensive care units at Saitama Medical Center, Saitama Medical School, Saitama, Japan. PATIENTS: Three intubated patients. MEASUREMENTS AND MAIN RESULTS: An experiment with a tracheal model showed that gas with a higher temperature and lower relative humidity (35 degrees C, 48%) deprived the tracheal model of significantly more water (5.9 +/- 0.2 [SD] g) than gas with a lower temperature and higher relative humidity (24 degrees C, 87%) (2.9 +/- 0.4 g; p less than .01), even though the gases contained the same amount of water vapor (19 mg H2O/L) minus the same absolute humidity. CONCLUSIONS: A heated humidifier with a heating wire incorporated into the breathing circuit may be dangerous when only temperature is monitored and controlled. Relative humidity, rather than absolute humidity, is a dominant factor in the case of drying secretions in the upper airway when using such a humidifier.

Aged↗
PubMed1991

Electrophoretic mobility and dissociation constants of tripeptides evaluated by isotachophoresis.

Ionic mobilities and dissociation constants of twenty peptides (seventeen tripeptides and a few oligoglycines) were evaluated on the basis of the observed isotachophoretic qualitative indices RE in the pH range 8.1-9.5 by the use of a least-squares method. Good correlation was obtained among the mobilities of amino acids, dipeptides and tripeptides when the clay ball model and the conventional formula weight were adopted.

Amino Acid Sequence↗
PubMed1987

Isotachophoretic determination of mobility and pKa by means of computer simulation. V. Evaluation of mo and pKa of twenty-eight dipeptides and assessment of separability.

Isotachophoretic qualitative indices, RE, for twenty-eight dipeptides were measured in the range pH 7.4-9.6. The absolute mobility, mo, and pKa values were evaluated by the use of the least-squares method, utilizing a simulation of the isotachophoretic steady state. The mo values were newly evaluated and the pKa values were in good agreement with literature values. By comparison of the evaluated mo and pKa values of the dipeptides with those of the constituent amino acids, simple relationships were found which may be used to estimate the mo and pKa values of other dipeptides. The separability of the dipeptides was also evaluated by considering the differences between their simulated effective mobilities. It is concluded that isotachophoresis is very convenient for the separation of dipeptides and their constituent amino acids.

Amino Acids↗