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Shizuaki Murata

Publications and source records attributed to Shizuaki Murata.

18 recordsLinked to original sources
PubMed2007

Weak interaction induces an ON/OFF switch, whereas strong interaction causes gradual change: folding transition of a long duplex DNA chain by poly-L-lysine.

A large-scale conformational change in genomic DNA is an essential feature of gene activation in living cells. Considerable effort has been applied to explain the mechanism in terms of key-lock interaction between sequence-specific regulatory proteins and DNA, in addition to the modification of DNA and histones such as methylation and acetylation. However, it is still unclear whether these mechanisms can explain the ON/OFF switching of a large number of genes that accompanies differentiation, carcinogenesis, etc. In this study, using single-molecule observation of DNA molecules by fluorescence microscopy with the addition of poly-L-lysine with different numbers of monomer units (n = 3, 5, 9, and 92), we found that an ON/OFF discrete transition in the higher-order structure of long duplex DNA is induced by short poly-L-lysine, whereas a continuous gradual change is induced by long poly-L-lysine. On the other hand, polycations with a lower positive charge have less potential to induce DNA compaction. Such a drastic difference in the conformational transition of a giant DNA between short and large oligomers is discussed in relation to the mechanisms of gene regulation in a living cell.

Biophysics↗
PubMed2006

Molecular mechanism for pterin-mediated inactivation of tyrosine hydroxylase: formation of insoluble aggregates of tyrosine hydroxylase.

Tyrosine hydroxylase (TH), an iron-containing enzyme, catalyzes the first and rate-limiting step of catecholamine biosynthesis, and requires tetrahydrobiopterin (BH4) as a cofactor. We found that preincubation of recombinant human TH with BH4 results in the irreversible inactivation of the enzyme at a concentration far less than the Km value toward BH4 in spite of its cofactor role, whereas oxidized biopterin, which has no cofactor activity, does not affect the enzyme activity. We show that TH is inactivated by BH4 in competition with the binding of dopamine. The sequential addition of BH4 to TH results in a gradual decrease in the intensity of the fluorescence and CD spectra without changing their overall profiles. Sedimentation velocity analysis demonstrated an association of TH molecules with each other in the presence of BH4, and studies using gel-permeation chromatography, turbidity measurements, and transmission electron microscopy demonstrated the formation of amorphous aggregates with large molecular weights following the association of the TH proteins. These results suggest that BH4 not only acts as a cofactor, but also accelerates the aggregation of TH. We propose a novel mechanism for regulating the amount of TH protein, and discuss its physiological significance.

Biopterins↗
PubMed2005

Specific formation of beads-on-a-chain structures on giant DNA using a designed polyamine derivative.

Fluorescence microscopy was used to study the folding transition of giant DNAs, T4 DNA (ca. 166 kbp), and lambda DNA (ca. 48 kbp), which proceeds through intermediates with intramolecular segregation induced by pteridine-polyamine conjugates, i.e., 2-amino-6,7-dimethyl-4-(4,9,13-triazatridecylamino)pteridine and -4-(3-(aminopropyl)amino)pteridine. According to the results of DNA denaturation, UV and fluorescent spectroscopy, and transmission electron microscopic observations, it became clear that DNA folding induced by the polyamine derivative is not a continuous shrinking process but a combination of discontinuous processes.

Bacteriophage T4↗
PubMed2005

Dramatic change in the tertiary structure of giant DNA without distortion of the secondary structure caused by pteridine-polyamine conjugates.

Pteridine-polyamine conjugates, such as 2-polyamine (1,3-diaminopropane and spermine) substituted 6,7-dimethyl-3H-pteridine-4-one, induce a folding transition of a giant DNA molecule more effectively than the corresponding polyamines. However, since neither a DNA high-temperature shift of denaturation (Tm) curve nor distortion of the UV/fluorescence spectra is observed in a mixture of these compounds with DNA, they do not interact with the DNA duplex strongly.

Bacteriophage T4↗
PubMed2005

Open-cage fullerene derivatives suitable for the encapsulation of a hydrogen molecule.

The encapsulation of molecular hydrogen into an open-cage fullerene having a 16-membered ring orifice has been investigated. It is achieved by the pressurization of H2 at 0.6-13.5 MPa to afford endohedral hydrogen complexes of open-cage fullerenes in up to 83% yield. The efficiency of encapsulation is dominantly dependent on both H2 pressure and temperature. Hydrogen molecules inside the C60 cage are observed in the range of -7.3 to -7.5 ppm in 1H NMR spectra, and the formations of hydrogen complexes are further confirmed by mass spectrometry. The trapped hydrogen is released by heating. The activation energy barriers for this process are determined to be 22-24 kcal/mol. The DSC measurement of the endohedral H2 complex reveals that the escape of H2 from the C60 cage corresponds to an exothermic process, indicating that encapsulated H2 destabilizes the fullerene.

Journal Article↗
PubMed2005

How does DNA compaction favor chiral selectivity with cationic species? Higher selectivity with lower cationic charge.

A single-molecule study on giant DNA compaction by enantiomeric dications and tetracations demonstrates that strong chiral discrimination in DNA compaction is manifested only if the positive charge on enantiomeric multications is relatively low. The increase in cationicity of the chiral compaction agent inevitably leads to an increase in nonspecific electrostatic interactions and quenching of chiral discrimination in the DNA-folding phase transition.

Bacteriophage T4↗
PubMed2004

A bowl-shaped fullerene encapsulates a water into the cage.

The sequential carbon-carbon bond cleaving reactions of the diketone derivative of C60 with o-phenylenediamine give a novel bowl-shaped fullerene bearing a 20-membered ring orifice. The product reversibly encapsulates a water molecule into the fullerene cage for the first time.

Fullerenes↗
PubMed2004

DNA compaction by divalent cations: structural specificity revealed by the potentiality of designed quaternary diammonium salts.

DNA interaction with quaternary diammonium dications, R(CH(3))(2)N(+)(CH(2))(n)N(+)(CH(3))(2)R, having various intercharge distances, lengths, and branching, and the chemical nature of the hydrophobic substituents were investigated by fluorescent microscopy and circular dichroism (CD) spectroscopy to reveal their structural specificity for binding to DNA. The conformational behavior of DNA was found to be highly sensitive to the structure of the dications with separated charges. The distance between two ammonium groups greatly influences the compaction activity of the dications. To explain this situation, we proposed a model that demonstrates that the charge density of the dication and the geometric fit between DNA phosphates and the ammonium groups in the dications play an important role in providing efficient DNA collapse. Elongation of the alkyl substituents (R) in the diammonium salts from ethyl to hexyl did not generate any significant alterations in the compaction activities, whereas the branching of substituents caused a drastic decrease in their compaction ability. Based on the results of CD spectroscopy, it was found that the ability of the dications to provoke a DNA transition from the B-form to A-form was also specific: it depended on their intercharge distances and was independent of the length of alkyl substituents.

Cations, Divalent↗
PubMed2004

Folding transition of DNA depending on ionic environments.

We examined the effect of monovalent salts, NaCl and KCl, on spermidine-induced DNA compaction using fluorescence microscopy. By increasing concentrations of salts, unfolding process of compacted DNAs were observed. It was also shown that NaCl is more effective for unfolding compacted DNAs than KCl.

Bacteriophage T4↗
PubMed2003

Nonspecificity induces chiral specificity in the folding transition of giant DNA.

The all-or-none type DNA folding transition from a coil to globule can be differentiated by the chirality of the triamines. The fluorescent microscope observation on single DNA molecules makes it clear that the tripeptides obtained from naturally occurring basic amino acids (l-lysine or l-arginine) can compact DNA molecules at concentrations lower than those from d-isomers. Nanometer-sized beads are found in the AFM images on the folded DNA molecule.

Bacteriophage T4↗
PubMed2003

Rearrangement of the cyclohexadiene derivatives of C60 to bis(fulleroid) and bis(methano)fullerene: structure, stability, and mechanism.

The cyclohexadiene derivative of C(60) rearranges photochemically to bis(fulleroid) (two [6,5] open structure) and bis(methano)fullerene (two [6,6] closed structure). During this process, a [6,5] open/[6,6] closed intermediate is observed. The isolated intermediate undergoes photochemical rearrangement to bis(fulleroid) and bis(methano)fullerene. On the other side, it undergoes retrorearrangement to the starting material in the dark. The structure and energetics of these C(60) derivatives have been studied at the AM1, PM3, RHF, and B3LYP levels of theory. It is found that bis(fulleroid) bearing four tert-butoxycarbonyl substituents is 5.8 kcal/mol (B3LYP) more stable than the corresponding bis(methano)fullerene. The isolated intermediate having the [6,5] open/[6,6] closed structure is 6.7 kcal/mol more favorable than the previously proposed two [6,5] closed intermediate, and the formation of this compound is well explained by the di-pi-methane rearrangement. (13)C NMR calculation at the B3LYP level reproduced the experimental chemical shifts with very good accuracy for each molecular system. Theoretical studies mainly at the unrestricted B3LYP level on singlet and triplet state potential energy surfaces on fullerene derivatives support the di-pi-methane rearrangement mechanism. The previously proposed symmetrical [4+4]/[2+2+2] and the novel proposed unsymmetrical di-pi-methane pathways may coexist during the reaction.

Journal Article↗
PubMed2003

Controlling the intrachain segregation on a single DNA molecule.

Intrachain segregation in single DNA molecules induced by quaternary ammonium dications was studied. By means of fluorescent and electron microscopy, it was found that variations in the chemical structure of condensing agents provide one with the opportunity to control the average amount of intrachain segregation centers on the DNA single chain. The manner of interaction between the diammonium molecules was considered to be the key factor for controlling the morphology of the partially collapsed DNA molecules.

Bacteriophage T4↗
PubMed2003

Ascorbic acid induces a marked conformational change in long duplex DNA.

Ascorbic acid is often regarded as an antioxidant in vivo, where it protects against cancer by scavenging DNA-damaging reactive oxygen species. However, the detailed mechanism of the action of ascorbic acid on genetic DNA is still unclear. We examined the effect of ascorbic acid on the higher-order structure of DNA through real-time observation by fluorescence microscopy. We found that ascorbic acid generates a pearling structure in single giant DNA molecules, with elongated and compact regions coexisting along a molecular chain. Results from electron microscopy and atomic force microscopy indicate that the compact regions assume a loosely packed conformation. A possible mechanism for the induction of this conformational change is discussed in relation to the interplay between the higher-order and second-order structures of DNA.

Ascorbic Acid↗
PubMed2002

A novel photorearrangement of a cyclohexadiene derivative of C60.

[reaction: see text] Photorearrangement of tetraalkoxycarbonyl-substituted cyclohexadiene derivatives of C(60) yields not only well-known bis(fulleroid) but also bis(methano)fullerene. Existence of a labile and structurally new intermediate is observed in the reaction mixture. The discovery of the compound suggests the existence of another possible pathway giving those two products other than the widely accepted [4 + 4]/[2 + 2 + 2] mechanism.

Journal Article↗
PubMed2002

(6R)-5,6,7,8-tetrahydro-L-monapterin from Escherichia coli, a novel natural unconjugated tetrahydropterin.

The structure of the major tetrahydropterin in Escherichia coli was determined as (6R)-5,6,7,8-tetrahydro-L-monapterin, i. e. (6R)-2-amino-5,6,7,8-tetrahydro-6-[(1S,2S)-1,2,3-trihydroxypropyl]pteridin-4(3H)-one. Although the stereochemical structure of the trihydroxypropyl side chain has been determined previously by fluorescence detected circular dichroism analysis on its aromatic derivative, the most important configuration at C(6) has not been clarified. The major difficulties for the determination of the chirality were instability toward air oxidation and very low concentration of the tetrahydropterin derivative. In the present study, the C(6)-configuration was determined as R by comparing its stable hexaacetyl derivative with authentic (6R)- and (6S)-hexaacetyl-5,6,7,8-tetrahydro-L-monapterins by high performance liquid chromatography (HPLC) and HPLC-mass spectrometry (LC-MS). (6R)-5,6,7,8-Tetrahydro-L-monapterin is a new unconjugated tetrahydropterin from natural sources.

Chromatography, High Pressure Liquid↗