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Yumiko Mishima

Publications and source records attributed to Yumiko Mishima.

8 recordsLinked to original sources
PubMed2006

DNA secondary structure forming at minisatellite repeat unit sequences.

The lengths of simple repeat sequences are generally unstable or polymorphic; that is, they are highly variable with respect to the numbers of tandem repeats. To determine the structural features that cause such variability, we examined a minisatellite DNA isolated from the yellow fin sea bream Acanthopagrus latus. Electrophoresis, CD spectra, and calorimetric analyses of oligodeoxyribonucleotides comprised of the minisatellite repeat unit suggest a stable secondary structure is formed within the repeat unit.

Animals↗
PubMed2005

Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm.

A Gram-negative bacterium, Sphingomonas sp. A1, has a macromolecule (alginate) import system consisting of a pit on the cell surface and an alginate-specific ATP-binding cassette importer in the inner membrane. Transport of alginate from the pit to the ABC importer is probably mediated by two periplasmic binding protein homologues (AlgQ1 and AlgQ2). Here we describe characteristics of binding of AlgQ1 and AlgQ2 to alginate and its oligosaccharides through surface plasmon resonance biosensor analysis, UV absorption difference spectroscopy, and X-ray crystallography. Both AlgQ1 and AlgQ2 were inducibly expressed in the periplasm of alginate-grown cells of strain A1. Biosensor analysis indicated that both proteins specifically bind alginate with a high degree of polymerization (>100) and that dissociation constants for alginate with an average molecular mass of 26 kDa are 2.3 x 10(-)(7) M for AlgQ1 and 1.5 x 10(-)(7) M for AlgQ2. An in vitro ATPase assay using the membrane complex, including the alginate ABC importer, suggested that both alginate-bound forms of AlgQ1 and AlgQ2 are closely associated with the importer. X-ray crystallography showed that AlgQ1 consisted of two domains separated by a deep cleft that binds alginate oligosaccharides through a conformational change in the two domains. These results directly show that alginate-binding proteins play an important role in the efficient transport of alginate macromolecules with different degrees of polymerization in the periplasm.

ATP-Binding Cassette Transporters↗
PubMed2005

The 3111T/C polymorphism of hClock is associated with evening preference and delayed sleep timing in a Japanese population sample.

Sleep timing is influenced by the circadian system. Morningness-eveningness (ME) preference in humans is affected by the free-running period, which is determined by circadian clock-relevant genes. In this study, we investigated association between the 3111T/C polymorphism in the 3'-flanking region of hClock (Homo sapiens Clock homolog) and ME preference in 421 Japanese subjects. The Horne-Ostberg ME questionnaire (MEQ) scores showed normal distribution, with mean score of 51.2 +/- 1.4 (range, 25-73), and scores were positively correlated with sleep onset time (r = 0.541, P < 0.001) and wake time (r = 0.513, P < 0.001). MEQ scores were significantly lower in subjects with 3111C/C (n = 12) than in subjects with 3111T/C (n = 106, P < 0.001) or 3111T/T (n = 303, P < 0.001), suggesting a stronger eveningness preference in 3111C/C homozygotes. This group also showed significantly delayed sleep onset (P < 0.001), shorter sleep time (P < 0.001), and greater daytime sleepiness (P < 0.001) in comparison to parameters in the subjects with the 3111T allele. There was no significant difference in any of these parameters between the 3111C/T and 3111T/T genotypes. The influence of the 3111T/C polymorphism on ME preferences in Caucasian populations remains controversial. The present findings in a Japanese population sample, which should have a relatively low risk of population stratification effects, suggest the significance of the association of the 3111C/C allele of hClock with evening preference.

Adult↗
PubMed2005

Passive body heating ameliorates sleep disturbances in patients with vascular dementia without circadian phase-shifting.

OBJECTIVE: This study investigated the sleep-promoting, thermoregulatory, and circadian phase-shifting actions of passive body heating (PBH) in elderly insomniac patients (IPs) with mild-to-moderate vascular dementia. METHODS: Thirteen elderly IPs with vascular dementia (mean age 76.9 years; male/female ratio 2/11) were subjected to a PBH trial session. This session comprised a 3-day baseline period, 2-day PBH period, and 1-day post-PBH period. In the PBH period, the subjects received PBH (immersion in hot water about 40.0 degrees C to mid-thorax level) for 30 minutes beginning 2 hours before bedtime. Sleep-waking, estimated by actigraph, core body temperature (cBT), and heart rate variability were continuously monitored. Dim-light melatonin-onset time (DLMO) was determined in the baseline and post-PBH periods. RESULTS: PBH significantly improved subjects' sleep quality; sleep latency decreased; sleep efficiency increased; and wake time after sleep onset decreased. These trends were more prominent in the latter half of the sleep time. PBH induced a rapid cBT elevation of approximately 0.80 degrees C, on average, followed by enhanced heat loss (DeltacBT: difference in cBT between just after the PBH and bedtime), lasting 1.5 hours before sleep. There was a significantly positive correlation between DeltacBT and sleep latency. PBH induced no significant phase shift in DLMO. Heart-rate variability data showed that PBH induced parasympathomimetic action during sleep time in the subjects. CONCLUSION: PBH may have a sleep-promoting effect by intervening in the thermoregulatory and autonomic systems in elderly IPs with vascular dementia.

Aged↗
PubMed2002

Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1, complexed with an alginate tetrasaccharide at 1.6-A resolution.

Sphingomonas sp. A1 possesses a high molecular weight (HMW) alginate uptake system composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by the periplasmic HMW alginate-binding proteins AlgQ1 and AlgQ2. We determined the crystal structure of AlgQ2 complexed with an alginate tetrasaccharide using an alginate-free (apo) form as a search model and refined it at 1.6-A resolution. One tetrasaccharide was found between the N and C-terminal domains, which are connected by three extended hinge loops. The tetrasaccharide complex took on a closed domain form, in contrast to the open domain form of the apo form. The tetrasaccharide was bound in the cleft between the domains through van der Waals interactions and the formation of hydrogen bonds. Among the four sugar residues, the nonreducing end residue was located at the bottom of the cleft and exhibited the largest number of interactions with the surrounding amino acid residues, suggesting that AlgQ2 mainly recognizes and binds to the nonreducing part of a HMW alginate and delivers the polymer to the ABC transporter through conformational changes (open and closed forms) of the two domains.

Amino Acid Sequence↗
PubMed2002

Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1 at 2.0A resolution.

Sphingomonas sp. A1 possesses a high molecular mass (average 25,700 Da) alginate uptake system mediated by a novel pit-dependent ABC transporter. The X-ray crystallographic structure of AlgQ2 (57,200 Da), an alginate-binding protein in the system, was determined by the multiple isomorphous replacement method and refined at 2.0 A resolution with a final R-factor of 18.3% for 15 to 2.0 A resolution data. The refined structure of AlgQ2 was comprised of 492 amino acid residues, 172 water molecules, and one calcium ion. AlgQ2 was composed of two globular domains with a deep cleft between them, which is expected to be the alginate-binding site. The overall structure is basically similar to that of maltose/maltodextrin-binding protein, except for the presence of an N2-subdomain. The entire calcium ion-binding site is similar to the site in the EF-hand motif, but comprises a ten residue loop. This calcium ion-binding site is about 40 A away from the alginate-binding site.

Alginates↗