Biomedical subjects

Minoru Sakurai

Publications and source records attributed to Minoru Sakurai.

12 recordsLinked to original sources

PubMed2006

Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method.

Here we improved our hybrid QM/MM methodology (Houjou et al. J Phys Chem B 2001, 105, 867) for evaluating the absorption maxima of photoreceptor proteins. The renewed method was applied to evaluation of the absorption maxima of several retinal proteins and photoactive yellow protein. The calculated absorption maxima were in good agreement with the corresponding experimental data with a computational error of <10 nm. In addition, our calculations reproduced the experimental gas-phase absorption maxima of model chromophores (protonated all-trans retinal Schiff base and deprotonated thiophenyl-p-coumarate) with the same accuracy. It is expected that our methodology allows for definitive interpretation of the spectral tuning mechanism of retinal proteins.

Computer Simulation↗

PubMed2006

Accumulation of theanderose in association with development of freezing tolerance in the moss Physcomitrella patens.

Mosses are known to have the ability to develop high degrees of resistance to desiccation and freezing stress at cellular levels. However, underlying cellular mechanisms leading to the development of stress resistance in mosses are not understood. We previously showed that freezing tolerance in protonema cells of the moss Physcomitrella patens was rapidly increased by exogenous application of the stress hormone abscisic acid (ABA) [Minami, A., Nagao, M., Arakawa, K., Fujikawa, S., Takezawa, D., 2003a. Abscisic acid-induced freezing tolerance in the moss Physcomitrella patens is accompanied by increased expression of stress-related genes. J. Plant Physiol. 160, 475-483]. Herein it is shown that protonema cells with acquired freezing tolerance specifically accumulate low-molecular-weight soluble sugars. Analysis of the most abundant trisaccharide revealed that the cells accumulated theanderose (G6-alpha-glucosyl sucrose) in close association with enhancement of freezing tolerance by ABA treatment. The accumulation of theanderose was inhibited by cycloheximide, an inhibitor of nuclear-encoded protein synthesis, coinciding with a remarkable decrease in freezing tolerance. Furthermore, theanderose accumulation was promoted by cold acclimation and treatment with hyperosmotic solutes, both of which had been shown to enhance cellular freezing tolerance. These results reveal a novel role for theanderose, whose biological function has been obscure, in high freezing tolerance in moss cells.

Abscisic Acid↗

PubMed2006

Linear-scaling molecular orbital calculations for the pKa values of ionizable residues in proteins.

In this report, we present a computational methodology for the pKa prediction of proteins, based on linear-scaling molecular orbital calculations for their solution-conformations obtained from NMR measurements. The method is used to predict the pKa values of five carboxylic acids (Asp7, Glu10, Glu19, Asp27, and Glu43) in turkey ovomucoid third domain (OMTKY3), and six aspartates residues (Asp 22, Asp 44, Asp 54, Asp 75, Asp 83, and Asp 93) in barnase. For OMTKY3, all the predicted pKa values are within 1 pH units from the available experimental ones, except for the case of Glu 43. For barnase, the root-mean-square deviation from experiment is 1.46 pH units. As a result, the proposed pKa calculation method correctly reproduces the relative order of the pKa values among the carboxylic acids located in different sites of the proteins. The calculated pKa values are decomposed into the contributions of short- and long-range structural difference effects. The results indicate that in both proteins the pKa value of the given carboxylic acid is partially influenced by long-range interactions with distant charged residues, which significantly contribute to determining the relative order of the pKa values. The current methodology based on LSMO provides us useful information about the titration behavior in a protein.

Computer Simulation↗

PubMed2005

De- and rehydration behavior of alpha,alpha-trehalose dihydrate under humidity-controlled atmospheres.

Effects of humidity were investigated on de- and rehydration behavior of alpha,alpha-trehalose dihydrate (T(h)) throughout simultaneous measurements of differential scanning calorimetry and X-ray diffractometry (DSC-XRD) and simultaneous thermogravimetry and differential thermal analysis (TG-DTA). When T(h) was heated from room temperature under dry nitrogen atmosphere, a metastable anhydrous crystal (T(alpha)) was formed at 105 degrees C after dehydration of T(h). The resulting T(alpha) melted at 125 degrees C and became amorphous, followed by cold crystallization from 150 degrees C giving rise to a stable anhydrous crystal T(beta). Under a highly humid atmosphere, on the other hand, T(beta) was formed at 90 degrees C directly as a result of T(h) dehydration. T(alpha) was readily rehydrated and turned back to T(h) when nitrogen gas with low water vapor pressure of 2.1kPa was admitted, whereas high water vapor pressure up to 7.4kPa was required for rehydration of T(beta) into T(h). This study provided a picture of pathways that link various solid forms of trehalose, taking into account the effects of a humid environment.

Atmosphere↗

PubMed2005

Combined NMR and quantum chemical studies on the interaction between trehalose and dienes relevant to the antioxidant function of trehalose.

In a previous study (Oku, K.; Watanabe, H.; Kubota, M.; Fukuda, S.; Kurimoto, M.; Tujisaka, Y.; Komori, M.; Inoue, Y.; Sakurai, M. J. Am. Chem. Soc. 2003, 125, 12739), we investigated the mechanism of the antioxidant function of trehalose against unsaturated fatty acids (UFAs) and revealed that the key factor relevant to the function is the formation of OH...pi and CH...O hydrogen bonds between trehalose and the cis double bonds of the UFA. Here, we investigate whether such intriguing interactions also occur between this sugar and cis double bonds in other unsaturated compounds. For this purpose, we selected various diene compounds (1,3-butadiene, 1,3-pentadiene, 1,4-pentadiene, and 2,5-heptadiene) as interaction partners. All NMR experiments performed, including 1H-1H NOESY measurements, indicated that trehalose selectively interacts with the cis-olefin proton pair in the above diene with a 1:1 stoichiometry, and the C-3 (C-3') and C-6' (C-6) sites of the sugar are responsible for the interaction. Similar interactions were not observed for the mixtures of the diene and other saccharides (neotrehalose, kojibiose, nigerose, maltose, isomaltose, sucrose, maltitol, and sorbitol). Quantum chemical calculations revealed that the OH-3 and OH-6 groups bind to the olefin double bonds of the diene through OH...pi and CH...O types of hydrogen bonds, respectively, and the stabilization energy of the resulting complex is 5-6 kcal mol(-1). These results strongly support the above NMR results. Finally, the activation energies were calculated for the hydrogen abstraction reactions from the activated methylene group of heptadiene. In particular, when the reaction was initiated by a methyl radical, the activation energy was only 10 kcal mol(-1) for the free heptadiene, but on complexation with trehalose it drastically increased to ca. 40 kcal mol(-1). This indicates that trehalose has a significant depression effect on the oxidation of the diene compounds. These results strongly support the antioxidant mechanism deduced in the previous study and indicate that the formation of unique multiple hydrogen bonds between trehalose and cis-olefin bonds is rather a general event not confined to the case of UFA.

Antioxidants↗

PubMed2005

A quantum chemical method for rapid optimization of protein structures.

A quantum chemical method for rapid optimization of protein structures is proposed. In this method, a protein structure is treated as an assembly of amino acid units, and the geometry optimization of each unit is performed with taking the effect of its surrounding environment into account. The optimized geometry of a whole protein is obtained by repeated application of such a local optimization procedure over the entire part of the protein. Here, we implemented this method in the MOPAC program and performed geometry optimization for three different sizes of proteins. Consequently, these results demonstrate that the total energies of the proteins are much efficiently minimized compared with the use of conventional optimization methods, including the MOZYME algorithm (a representative linear-scaling method) with the BFGS routine. The proposed method is superior to the conventional methods in both CPU time and memory requirements.

Algorithms↗

PubMed2005

Interaction between trehalose and alkaline-earth metal ions.

We investigated the interaction between trehalose and alkaline-earth metal ions. The nuclear relaxation times of carbon atoms of trehalose were shortened by addition of the alkaline-earth chloride salts, MgCl2, CaCl2, and SrCl2, indicating that trehalose formed metal-complexes with the alkaline-earth metal chlorides. From the data of the 1H-1H coupling constants of trehalose in the presence of the alkaline-earth chlorides, it appeared that trehalose formed complexes with MgCl2, and CaCl2 at the various complexing sites: Mg2+ was coordinated to O-4 and O-4' of trehalose, and Ca2+ to O-2 and O-3. We succeeded in the preparation of two types of crystals of the trehalose/CaCl2. One was a crystal consisting of trehalose, CaCl2, and water in a ratio of 1:1:1. The other was an anhydrous crystal containing trehalose and CaCl2 in a ratio of 1:2. Several applications of the complexing between trehalose and the metal ions for food processing are proposed.

Animals↗

PubMed2003

NMR and quantum chemical study on the OH...pi and CH...O interactions between trehalose and unsaturated fatty acids: implication for the mechanism of antioxidant function of trehalose.

Trehalose is a disaccharide that attracts much attention as a stress protectant. In this study, we investigated the mechanism of the antioxidant function of trehalose. The spin-lattice relaxation times (T(1)) of (1)H and (13)C NMR spectra were measured to investigate the interaction between trehalose and unsaturated fatty acid (UFA). We selected several kinds of UFA that differ in the number of double bonds and in their configurations (cis or trans). Several other disaccharides (sucrose, maltose, neotrehalose, maltitol, and sorbitol) were also analyzed by NMR. The T(1) values for the (1)H and (13)C signals assigned to the olefin double bonds in UFA decrease with increasing concentration of trehalose and the changes reaches plateaus at integer ratios of trehalose to UFA. The characteristic T(1) change is observed only for the combination of trehalose and UFA with cis double bond(s). On the other hand, from the (13)C-T(1) measurements for trehalose, the T(1) values of the C-3 (C-3') and C-6' (C-6) are found to change remarkably by addition of UFA. (1)H[bond](1)H NOESY measurements provide direct evidence for complexation of trehalose with linoleic acid. These results indicate that one trehalose molecule stoichiometrically interacts with one cis-olefin double bond of UFA. Computer modeling study indicates that trehalose forms a stable complex with an olefin double bond through OH...pi and CH...O types of hydrogen bonding. Furthermore, a significant increase in the activation energy is found for hydrogen abstraction reaction from the methylene group located between the double bonds that are both interacting with the trehalose molecules. Therefore, trehalose has a significant depression effect on the oxidation of UFA through the weak interaction with the double bond(s). This is the first study to elucidate the antioxidant function of trehalose.

Antioxidants↗

PubMed2003

Decisive role of electronic polarization of the protein environment in determining the absorption maximum of halorhodopsin.

It is known that the absorption maximum of halorhodopsin is red shifted by 10 nm with the uptake of a chloride ion Cl(-). According to the X-ray structure, the ion is located at the position of the counterion of the chromophore, protonated retinal Schiff base. Thus, the direction of the observed spectral change is opposite to that expected from the pi-electron redistribution (an increase in the bond alternation) induced by the counterion. The physical origin of this abnormal shift is never explained in terms of any simple chemical analogues. We successfully explain this phenomenon by a QM/MM type of excitation energy calculation. The three-dimensional structure of the protein is explicitly taken into account using the X-ray structure. We reveal that the electronic polarization of the protein environment plays an essential role in tuning the absorption maximum of halorhodopsin.

Chlorides↗

PubMed2002

Supercritical CO(2) fluid extraction of crystal water from trehalose dihydrate. Efficient production of form II (T(alpha)) phase.

Form II is a kind of metastable crystalline form of trehalose anhydrate, and it is easily converted to the dihydrate crystal by absorbing water in moist atmosphere at room temperature (Akao et al., Carbohydr. Res. 2001, 334, 233-241). It can be utilized as an edible and nontoxic desiccant, and thus its efficient production from the dihydrate is significant from a viewpoint of industrial applications. In this study, we attempt to extract crystal water from the dihydrate using supercritical CO(2). We examine the dependence of extraction efficiency on the extraction time, the temperature and pressure of the fluid. Then, FTIR measurements are carried out to detect the extracted water and to identify the polymorphic phase of the sugar sample after the extraction treatment. In particular, the so-called first derivative euclidean distance analysis for IR spectra is shown to be quite useful for the structural identification. Consequently, we demonstrate that form II is produced from the dihydrate through supercritical CO(2) fluid extraction if appropriate temperature and pressure conditions (around 80 degrees C and 20 MPa) are maintained.

Carbon Dioxide↗

PubMed2002

[Cardiac pool scintigraphy using the solid-state Digirad 2020tc Imager--comparison with the conventional anger-type gamma camera using moving cardiac phantom].

UNLABELLED: Movable gamma camera, 2020tc Imager, was light miniaturized using Si photodiode as a semiconductor sensor instead of photomultiplier tubes. To validate performance of this new camera in cardiac pool scintigraphy, multigated equilibrium radionuclide ventriculography using the moving cardiac phantom was performed with 2020tc Imager and a conventional Agner-type gamma camera (PRISM 3000). METHOD: Both measured cardiac functional values were compared with the set-up ones for the phantom. Five-, 7.5-, and 10-minute-multigated data were acquired using both cameras under constant contractile condition. Constant 5-minute-multigated data acquisitions using 2020tc Imager were also carried out with varied contractile conditions. RESULTS: Measured ejection fraction (EF) derived from 2020tc Imager and an Anger-type camera were 68.5 +/- 0.6 and 70.3 +/- 1.4%, respectively. Both of these values were absolutely close to the set-up EF value of 70%. Both of end-diastolic volume and EF showed excellent correlation between set-up and measured values with the correlation coefficient of 0.97 and 0.99, respectively. CONCLUSION: This new movable camera could provide comparative cardiac functional values with an Anger-type camera and it can be useful to evaluate acute cardiac function in a coronary care unit.

Gamma Cameras↗

PubMed1996

Increased Deoxycytidine Kinase mRNA Level After Treatment with Interleukin-3.

Pretreatment of IL-3 to Kasumi-1 human acute myeloid leukemia cells enhanced 1-B-D-arabinofuranosyl cytosine (ara-C) cytotoxicity 1.2. to 1.4-fold (median 1.3). To clarify the mechanism of interleukin-3 (IL-3) on ara-C cytotoxicity, we investigated the level of deoxycytidine kinase mRNA with the competitive polymerase chain reaction method and enzyme activities, the incorporation of [(3)H] ara-C into DNA and intracellular ara-cytidine triphosphate (CTP) levels with high-performance liquid chromatography and analyzed cell cycles. The level of deoxycytidine kinase mRNA showed a fourfold increase (88.3 plus minus 4.33 amol &mgr;g of total RNA) at 3 days after treatment with IL-3 compared to control (20.3 plus minus 4.33 amol &mgr;g). After IL-3 treatment, ara-C incorporation into the DNA was increased to 1.33 to 1.83-fold (median, 1.73-fold). The G0/G1 late-phase and S-phase percentages of cells were increased from 28.99 to 78.73% in the IL-3 treatment group as compared to control. These results indicate that IL-3 pretreatment increases the level of deoxycytidine kinase mRNA and ara-C incorporation into the DNA and also increases ratios of G0/G1 late-phase and S-phase subsequent to an enhancement of ara-C cytotoxicity against leukemia cells.

Journal Article↗