JOPSS - Search Results

Journal Articles

Cross-scale analysis of temperature compensation in the cyanobacterial circadian clock system

Furuike, Yoshihiko*; Ouyang, D.*; Tominaga, Taiki*; Matsuo, Tatsuhito*; Mukaiyama, Atsushi*; Kawakita, Yukinobu; Fujiwara, Satoru*; Akiyama, Shuji*

Communications Physics (Internet), 5(1), p.75_1 - 75_12, 2022/04

https://doi.org/10.1038/s42005-022-00852-z

Times Cited Count：4 Percentile：65.23(Physics, Multidisciplinary)

Journal Articles

Complexation of Eu(III), Pb(II), and U(VI) with a glycoprotein; Microbial transformation of heavy elements in the aquatic environment

Kozai, Naofumi; Sakamoto, Fuminori; Tanaka, Kazuya; Onuki, Toshihiko; Sato, Takahiro*; Kamiya, Tomihiro*; Grambow, B.

Chemosphere, 196, p.135 - 144, 2018/04

https://doi.org/10.1016/j.chemosphere.2017.12.154

Times Cited Count：5 Percentile：17.39(Environmental Sciences)

Transformation of heavy elements by microbes such as bacteria and fungi has been an intense research subject; however, little is known about that of protozoa. This study investigated interaction of a representative protozoa, , with heavy elements (Eu(III), Pb(II), U(VI)). Non-destructive elemental analysis by micro-PIXE hardly detected those elements on living cells after sorption experiments but clearly detected on the cells that were killed with a fixative beforehand. Chromatographic analysis of aquatic species of those heavy elements after the sorption experiments revealed a fraction of those elements bound to a glycoprotein dissolved from the cell surface of living cells to form soluble pseudocolloid. These findings suggest that complexation of heavy elements with the dissolved surface glycoprotein reduced the sorption of those heavy elements on living cells.

Journal Articles

Two protonation states and structural features of a bilin reductase PcyA revealed by neutron crystallography

Unno, Masayoshi*; Sugishima, Masakazu*; Wada, Kei*; Hagiwara, Yoshinori*; Kusaka, Katsuhiro*; Tamada, Taro; Fukuyama, Keiichi*

Nihon Kessho Gakkai-Shi, 57(5), p.297 - 303, 2015/10

https://doi.org/10.5940/jcrsj.57.297

Bilin compounds are fundamentally important for oxygenic photosynthetic organisms, because they are utilized as pigments for photosynthesis (phycobilins) and photoreceptors (phytochromobilin). Phycocyanobilin (PCB), a phycobilin, comprises the chromophore of algal phytochromes and the core phycobiliprotein antennae of cyanobacteria and red algae. PCB is biosynthesized by a member of the ferredoxin-dependent bilin reductase family, phycocyanobilin:ferredoxin oxidoreductase (PcyA). In the present study, we determined the neutron crystal structure of PcyA in complex with its substrate biliverdin (BV). This neutron structure revealed the protonation state of BV and the surrounding residues. We found that two forms of BV, neutral BV and protonated BVH $^{+}$ , were coupled with the two conformation/protonation states of the essential residue Asp105. Further, His88 and His74 near BV were singly protonated and were connected with an intervening hydronium ion. Neutron analysis also revealed how X-ray irradiation of the PcyA-BV crystal altered the structure of the PcyA-BV complex.

Journal Articles

Fabrication of enzyme-degradable and size-controlled protein nanowires using single particle nano-fabrication technique

Omichi, Masaaki*; Asano, Atsushi*; Tsukuda, Satoshi*; Takano, Katsuyoshi*; Sugimoto, Masaki; Saeki, Akinori*; Sakamaki, Daisuke*; Onoda, Akira*; Hayashi, Takashi*; Seki, Shu*

Nature Communications (Internet), 5, p.3718_1 - 3718_8, 2014/04

https://doi.org/10.1038/ncomms4718

Times Cited Count：35 Percentile：77.9(Multidisciplinary Sciences)

Protein nanowires exhibiting specific biological activities hold promise for interacting with living cells and controlling and predicting biological responses such as apoptosis, endocytosis and cell adhesion. Here we report the result of the interaction of a single high-energy charged particle with protein molecules. Degradation of the human serum albumin nanowires was examined using trypsin. The biotinylated human serum albumin nanowires bound avidin, demonstrating the high affinity of the nanowires. Human serum albumin-avidin hybrid nanowires were also fabricated from a solid state mixture and exhibited good mechanical strength. The biotinylated human serum albumin nanowires can be transformed into nanowires exhibiting a biological function such as avidin-biotinyl interactions and peroxidase activity. The present technique is a versatile platform for functionalizing the surface of any protein molecule with an extremely large surface area.

Journal Articles

Protein boson peak originated from hydration-related multiple minima energy landscape

Jochi, Yasumasa*; Kitao, Akio*; Go, Nobuhiro

Journal of the American Chemical Society, 127(24), p.8705 - 8709, 2005/06

https://doi.org/10.1021/ja0425886

Times Cited Count：27 Percentile：61.14(Chemistry, Multidisciplinary)

no abstracts in English

Journal Articles

Electrostatic potential of nucleotide-free protein is sufficient for discrimination between adenine and guanine-specific binding sites

Basu, G.*; Sivanesan, D.*; Kawabata, Takeshi*; Go, Nobuhiro

Journal of Molecular Biology, 342(3), p.1053 - 1066, 2004/09

https://doi.org/10.1016/j.jmb.2004.07.047

Times Cited Count：23 Percentile：35.48(Biochemistry & Molecular Biology)

no abstracts in English

Journal Articles

Hydrogen and hydration in proteins

Niimura, Nobuo; Chatake, Toshiyuki; Kurihara, Kazuo; Maeda, Mitsuru

Cell Biochemistry and Biophysics, 40(3), p.351 - 369, 2004/06

https://doi.org/10.1385/CBB:40:3:351

Times Cited Count：24 Percentile：25.25(Biochemistry & Molecular Biology)

Neutron diffraction provides an experimental method of directly locating hydrogen atoms in proteins. High resolution neutron diffractometers dedicated to biological macromolecules (BIX-type diffractometer) have been constructed at the Japan Atomic Energy Research Institute (JAERI) and they have been used in the 1.5 AA -resolution crystal structure analyses of several proteins.

Journal Articles

PprI: A General switch responsible for extreme radioresistance of

Hua, Y.*; Narumi, Issei; Gao, G.*; Tian, B.*; Sato, Katsuya; Kitayama, Shigeru; Shen, B.*

Biochemical and Biophysical Research Communications, 306(2), p.354 - 360, 2003/06

https://doi.org/10.1016/S0006-291X(03)00965-3

Times Cited Count：152 Percentile：95.76(Biochemistry & Molecular Biology)

We have identified a unique deinococcal gene, , as a general switch for downstream DNA repair and protection pathways, from a natural mutant, in which is disrupted by a transposon. Complete functional disruption of the gene in wild-type leads to dramatic sensitivity to ionizing radiation. Radioresistance of the disruptant could be fully restored by complementation with . In response to radiation stress, PprI can significantly and specifically induce the gene expression of and and enhance the enzyme activities of catalases. These results strongly suggest that PprI plays a crucial role in regulating multiple DNA repair and protection pathways in response to radiation stress.