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41.
42.
Kazuyuki Nagamatsu 《Journal of biomolecular structure & dynamics》2013,31(4):729-739
Abstract Fluorophore of proflavine was introduced onto the 3′-terminal ribose moiety of yeast tRNAPhe. The distance between the fluorophore and the fluorescent Y base in the anticodon of yeast tRNAPhe was measured by a singlet-singlet energy transfer. Conformational changes of tRNAPhe with binding of tRNAGlu 2, which has the anticodon UUC complementary to the anticodon GAA of tRNAPhe, were investigated. The distance obtained at the ionic strength of 100 mM K+ and 10 mM Mg2+ is very close to the distance from x-ray diffraction, while the distance obtained in the presence of tRNAGlu 2 is significantly smaller. Further, using a fluorescent probe of 4-bromomethl-7-methoxycoumarin introduced onto pseudouridine residue Ψ55 in the TΨC loop of tRNAPhe, Stern-Volmer quenching experiments for the probe with or without added tRNAGlu 2were carried out. The results showed greater access of the probe to the quencher with added tRNAGlu 2. These results suggest that both arms of the L-shaped tRNA structure tend to bend inside with binding of tRNAGlu 2 and some structural collapse occurs at the corner of the L-shaped structure. 相似文献
43.
Gunnar Dick Chin Lik Tan Joao Nuno Alves Erich M. E. Ehlert Gregory M. Miller Linda C. Hsieh-Wilson Kazuyuki Sugahara Arie Oosterhof Toin H. van Kuppevelt Joost Verhaagen James W. Fawcett Jessica C. F. Kwok 《The Journal of biological chemistry》2013,288(38):27384-27395
Chondroitin sulfate (CS) and the CS-rich extracellular matrix structures called perineuronal nets (PNNs) restrict plasticity and regeneration in the CNS. Plasticity is enhanced by chondroitinase ABC treatment that removes CS from its core protein in the chondroitin sulfate proteoglycans or by preventing the formation of PNNs, suggesting that chondroitin sulfate proteoglycans in the PNNs control plasticity. Recently, we have shown that semaphorin3A (Sema3A), a repulsive axon guidance molecule, localizes to the PNNs and is removed by chondroitinase ABC treatment (Vo, T., Carulli, D., Ehlert, E. M., Kwok, J. C., Dick, G., Mecollari, V., Moloney, E. B., Neufeld, G., de Winter, F., Fawcett, J. W., and Verhaagen, J. (2013) Mol. Cell. Neurosci. 56C, 186–200). Sema3A is therefore a candidate for a PNN effector in controlling plasticity. Here, we characterize the interaction of Sema3A with CS of the PNNs. Recombinant Sema3A interacts with CS type E (CS-E), and this interaction is involved in the binding of Sema3A to rat brain-derived PNN glycosaminoglycans, as demonstrated by the use of CS-E blocking antibody GD3G7. In addition, we investigate the release of endogenous Sema3A from rat brain by biochemical and enzymatic extractions. Our results confirm the interaction of Sema3A with CS-E containing glycosaminoglycans in the dense extracellular matrix of rat brain. We also demonstrate that the combination of Sema3A and PNN GAGs is a potent inhibitor of axon growth, and this inhibition is reduced by the CS-E blocking antibody. In conclusion, Sema3A binding to CS-E in the PNNs may be a mechanism whereby PNNs restrict growth and plasticity and may represent a possible point of intervention to facilitate neuronal plasticity. 相似文献
44.
Satomi Nadanaka Shaobo Zhou Shoji Kagiyama Naoko Shoji Kazuyuki Sugahara Kazushi Sugihara Masahide Asano Hiroshi Kitagawa 《The Journal of biological chemistry》2013,288(13):9321-9333
Mutant alleles of EXT1 or EXT2, two members of the EXT gene family, are causative agents in hereditary multiple exostoses, and their gene products function together as a polymerase in the biosynthesis of heparan sulfate. EXTL2, one of three EXT-like genes in the human genome that are homologous to EXT1 and EXT2, encodes a transferase that adds not only GlcNAc but also N-acetylgalactosamine to the glycosaminoglycan (GAG)-protein linkage region via an α1,4-linkage. However, both the role of EXTL2 in the biosynthesis of GAGs and the biological significance of EXTL2 remain unclear. Here we show that EXTL2 transfers a GlcNAc residue to the tetrasaccharide linkage region that is phosphorylated by a xylose kinase 1 (FAM20B) and thereby terminates chain elongation. We isolated an oligosaccharide from the mouse liver, which was not detected in EXTL2 knock-out mice. Based on structural analysis by a combination of glycosidase digestion and 500-MHz 1H NMR spectroscopy, the oligosaccharide was found to be GlcNAcα1-4GlcUAβ1–3Galβ1–3Galβ1–4Xyl(2-O-phosphate), which was considered to be a biosynthetic intermediate of an immature GAG chain. Indeed, EXTL2 specifically transferred a GlcNAc residue to a phosphorylated linkage tetrasaccharide, GlcUAβ1–3Galβ1–3Galβ1–4Xyl(2-O-phosphate). Remarkably, the phosphorylated linkage pentasaccharide generated by EXTL2 was not used as an acceptor for heparan sulfate or chondroitin sulfate polymerases. Moreover, production of GAGs was significantly higher in EXTL2 knock-out mice than in wild-type mice. These results indicate that EXTL2 functions to suppress GAG biosynthesis that is enhanced by a xylose kinase and that the EXTL2-dependent mechanism that regulates GAG biosynthesis might be a “quality control system” for proteoglycans. 相似文献
45.
46.
Kazuyuki Nakamura Hirofumi Kodera Tenpei Akita Masaaki Shiina Mitsuhiro Kato Hideki Hoshino Hiroshi Terashima Hitoshi Osaka Shinichi Nakamura Jun Tohyama Tatsuro Kumada Tomonori Furukawa Satomi Iwata Takashi Shiihara Masaya Kubota Satoko Miyatake Eriko Koshimizu Kiyomi Nishiyama Mitsuko Nakashima Yoshinori Tsurusaki Noriko Miyake Kiyoshi Hayasaka Kazuhiro Ogata Atsuo Fukuda Naomichi Matsumoto Hirotomo Saitsu 《American journal of human genetics》2013
47.
Keisuke Maruyama Masaharu Nakamura Shusuke Tomoshige Kazuyuki Sugita Makoto Makishima Yuichi Hashimoto Minoru Ishikawa 《Bioorganic & medicinal chemistry letters》2013,23(14):4031-4036
Our multi-template approach for drug discovery, focusing on protein targets with similar fold structures, has yielded lead compounds for various targets. We have also shown that a diphenylmethane skeleton can serve as a surrogate for a steroid skeleton. Here, on the basis of those ideas, we hypothesized that the diphenylmethane derivative bisphenol A (BPA) would bind to the ligand-binding domain of estrogen receptors (ERs) in a similar manner to estradiol and act as a steroid surrogate. To test this idea, we synthesized a series of BPA analogs and evaluated their structure-activity relationships, focusing on agonistic/antagonistic activities at ERs and ERα/ERβ subtype selectivity. Among the compounds examined, 18 was found to be a potent ERα-antagonist with high selectivity over ERβ and androgen receptor under our assay conditions. A computational docking study suggested that 18 would bind to the antagonistic conformation of ERα. ERα-selective antagonists, such as 18, are candidate agents for treatment of breast cancer. 相似文献
48.
Nao Kusuhashi Yukiyasu Tsutsumi Haruo Saegusa Kenji Horie Tadahiro Ikeda Kazumi Yokoyama Kazuyuki Shiraishi 《Proceedings. Biological sciences / The Royal Society》2013,280(1759)
We here describe a new Early Cretaceous (early Albian) eutherian mammal, Sasayamamylos kawaii gen. et sp. nov., from the ‘Lower Formation’ of the Sasayama Group, Hyogo Prefecture, Japan. Sasayamamylos kawaii is characterized by a robust dentary, a distinct angle on the ventral margin of the dentary at the posterior end of the mandibular symphysis, a lower dental formula of 3–4 : 1 : 4 : 3, a robust lower canine, a non-molariform lower ultimate premolar, and a secondarily reduced entoconid on the molars. To date, S. kawaii is the earliest known eutherian mammal possessing only four premolars, which demonstrates that the reduction in the premolar count in eutherians started in the late Early Cretaceous. The occurrence of S. kawaii implies that the relatively rapid diversification of eutherians in the mid-Cretaceous had already started by the early Albian. 相似文献
49.
Toshiyuki Ohtsuka Masaya Negishi Kazuyuki Sugita Yasuo Iimura Mitsuru Hirota 《Ecological Research》2013,28(5):855-867
Biometric-based carbon flux measurements were conducted in a pine forest on lava flow of Mt. Fuji, Japan, in order to estimate carbon cycling and sequestration. The forest consists mainly of Japanese red pine (Pinus densiflora) in a canopy layer and Japanese holly (Ilex pedunculosa) in a subtree layer. The lava remains exposed on the ground surface, and the soil on the lava flow is still immature with no mineral soil layer. The results showed that the net primary production (NPP) of the forest was 7.3 ± 0.7 t C ha?1 year?1, of which 1.4 ± 0.4 t C ha?1 year?1 was partitioned to biomass increment, 3.2 ± 0.5 t C ha?1 year?1 to above-ground fine litter production, 1.9 t C ha?1 year?1 to fine root production, and 0.8 ± 0.2 t C ha?1 year?1 to coarse woody debris. The total amount of annual soil surface CO2 efflux was estimated as 6.1 ± 2.9 t C ha?1 year?1, using a closed chamber method. The estimated decomposition rate of soil organic matter, which subtracted annual root respiration from soil respiration, was 4.2 ± 3.1 t C ha?1 year?1. Biometric-based net ecosystem production (NEP) in the pine forest was estimated at 2.9 ± 3.2 t C ha?1 year?1, with high uncertainty due mainly to the model estimation error of annual soil respiration and root respiration. The sequestered carbon being allocated in roughly equal amounts to living biomass (1.4 t C ha?1 year?1) and the non-living C pool (1.5 t C ha?1 year?1). Our estimate of biometric-based NEP was 25 % lower than the eddy covariance-based NEP in this pine forest, due partly to the underestimation of NPP and difficulty of estimation of soil and root respiration in the pine forest on lava flows that have large heterogeneity of soil depth. However, our results indicate that the mature pine forest acted as a significant carbon sink even when established on lava flow with low nutrient content in immature soils, and that sequestration strength, both in biomass and in soil organic matter, is large. 相似文献
50.
Kazuyuki Maekawa Yasutaka Miyoshi Kenshiro Tsuru 《Bioscience, biotechnology, and biochemistry》2013,77(10):1951-1956
Dextran was subjected to oxidative scission by periodate, followed by ring closure with nitromethane to form nitrodextran. The nitro group attached to the ring was reduced by LiAlH4 to yield amino-polysaccharide of which the molecular weight was about 10,000. It became clear that nitrodextran consisted of 3-deoxy-3-nitro-mannopyranoside, -glucopyranoside, -galactopyranoside and -talopyranoside and their molar ratio was 6: 5: 1: 2 as determined by column Chromatographic separation and gas Chromatographic analysis of the methanolyzate of nitro-dextran. 相似文献