Search Results 1-20 of 600

  • CaMKII-dependent control of sleep duration in mammals  [in Japanese]

    Ode Koji , Ueda Hiroki

    … CaMKIIα/β dodecamer is activated by Ca2+/CaM and undergoes a large scale conformational change. … The conformational change exposing the kinase domain affects the protein-protein interaction between CaMKIIα/β and other binding partners. …

    Proceedings for Annual Meeting of The Japanese Pharmacological Society 93(0), 1-S12-2, 2020


  • Conformational differences among metarhodopsin I, metarhodopsin II, and opsin probed by wide-angle X-ray scattering

    Imamoto Yasushi , Kojima Keiichi , Oka Toshihiko , Maeda Ryo , Shichida Yoshinori

    … The change in the WAXS curve for the formation of Meta-II was characterized by a peak at 0.2 Å⁻¹ and a valley at 0.6 Å⁻¹, which were not observed in metarhodopsin I and opsin. … However, the displaced helices III and V in Meta-II resulting from the disruption of cytoplasmic ionic lock were restored in Opsin*, which is likely to destabilize the G-protein-activating structure of opsin. …

    The Journal of Physical Chemistry B 123(43), 9134-9142, 2019-10-31


  • Identification of inter-residue interactions appeared in the early stage of folding process of β-lactoglobulin and its folding mutant, E44L, by using high-pressure NMR  [in Japanese]

    櫻井 一正

    … According to the previous studies,the following two types of conformational changes of protein occur upon increase in pressure: That is, (ⅰ)mechanical compression and (ⅱ) transition between thermodynamically distinct states.Pressure-dependent chemical shift changes of individual residues can be measured by using high-pressure NMR apparatus. … A principal component analysis can decompose the obtained data into the two types of conformational changes. …

    Memoirs of Institute of Advanced Technology, Kinki University = 近畿大学先端技術総合研究所紀要 (24), 1-10, 2019-03


  • All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins

    Koike Ryotaro , Ota Motonori

    … We previously developed a computational tool, Motion Tree (MT), to compare protein structures and describe structural changes using solely the Cα atoms. …

    Biophysics and Physicobiology 16(0), 280-286, 2019


  • Second harmonic generation polarization microscopy as a tool for protein structure analysis

    Kaneshiro Junichi , Okada Yasushi , Shima Tomohiro , Tsujii Mika , Imada Katsumi , Ichimura Taro , Watanabe Tomonobu M.

    … <p>Cryo-electron microscopy and X-ray crystallography have been the major tools of protein structure analysis for decades and will certainly continue to be essential in the future. … SHG can be expected to probe the structural changes of proteins in the physiological condition, and thus link protein structure and biological function. …

    Biophysics and Physicobiology 16(0), 147-157, 2019


  • Molecular Basis for Allosteric Inhibition of GTP-Bound H-Ras Protein by a Small-Molecule Compound Carrying a Naphthalene Ring

    Matsumoto Shigeyuki , Hiraga Toshiki , Hayashi Yuki , Yoshikawa Yoko , Tsuda Chiemi , Araki Mitsugu , Neya Masahiro , Shima Fumi , Kataoka Tohru

    … The solution structure of its complex with the guanosine 5'-(β,γ-imide) triphosphate-bound form of H-RasT35S (H-RasT35S·GppNHp) indicates that the naphthalene ring of KBFM123 interacts directly with a hydrophobic pocket located between switch I and switch II and allosterically inhibits the effector interaction by inducing conformational changes in switch I and its flanking region in strand β2, which are directly involved in recognition of the effector molecules, including c-Raf-1. …

    Biochemistry 57(36), 5350-5358, 2018-09-11


  • High-level production of valine by expression of the feedback inhibition-insensitive acetohydroxyacid synthase in Saccharomyces cerevisiae.

    Takpho Natthaporn , Watanabe Daisuke , Takagi Hiroshi

    … In this study, to improve the valine productivity of yeast cells, we constructed several variants of Ilv6 by introducing amino acid substitutions based on a protein sequence comparison with the AHAS regulatory subunit of E. … The computational analysis of Ilv6 predicted that Asn86, Gly89 and Asn104 are located in the vicinity of a valine-binding site, suggesting that amino acid substitutions at these positions induce conformational change of the valine-binding site. …




    中野 隆行 , 櫻井 一正

    … kinds of changes in protein conformation occur upon pressure application.One is (ⅰ)mechanical compression and the other is (ⅱ)transition between thermodynamically distinct states.Theconformational change via machanism (ⅰ)corresponds to a change within a thermodynamic subensemble of conformer,and that via mechanism(ⅱ)corresponds to the transistion between different subensembles of conformers.It is suggested that intermediate states of protein accumulating in the …

    Memoirs of Institute of Advanced Technology, Kinki University = 近畿大学先端技術総合研究所紀要 (23), 1-9, 2018-03


  • Remote Coupled Drastic β-Barrel to β-Sheet Transition of the Protein Translocation Motor

    Arata Furukawa , Nakayama Shintaro , Yoshikaie Kunihito , Tanaka Yoshiki , Tsukazaki Tomoya

    … Summary The membrane protein SecDF, belonging to the RNDsuperfamily, enhances protein translocation atthe extracytoplasmic side using a proton gradient.Here, we report the crystal structure of SecDF in a form we named Super-membrane-facing (Super F) form, demonstrating a β-barrel architecture instead of the previously reported β-sheet structure. …



  • Real-time TIRF Observation of Vinculin Reqruitment to Stretched α-catenin by AFM

    Maki Koichiro , Han Sung-Woong , Hirano Yoshinori , Yonemura Shigenobu , Hakoshima Toshio , Adachi Taiji

    … Adherens junctions (AJs) adaptively change their intensities in response to intercellular tension; … therefore, they integrate tension generated by individual cells to drive multicellular dynamics, such as morphogenetic change in embryos. … Under intercellular tension, α-catenin, which is a component protein of AJs, acts as a mechano-chemical transducer to recruit vinculin to promote actin remodeling. …

    Scientific Reports (8), 2018-01-25


  • Crystal structure of a Ca2+-dependent regulator of flagellar motility reveals the open-closed structural transition

    Shojima Tomoki , Hou Feng , Takahashi Yusuke , Matsumura Yoshitaka , Okai Masahiko , Nakamura Akira , Mizuno Katsutoshi , Inaba Kazuo , Kojima Masaki , Miyakawa Takuya , Tanokura Masaru , 稲葉 一男

    … Calaxin, a member of the neuronal calcium sensor protein family, directly acts on outer-arm dynein and regulates specific flagellar movement during sperm chemotaxis of ascidian, Ciona intestinalis. … The crystal structures revealed that three of the four EF-hands of a calaxin molecule bound Ca2+ ions and that EF2 and EF3 played a critical role in the conformational transition between the open and closed states. …

    Scientific reports (8), 2014, 2018-01


  • Visualization of Protein Dynamics using High-Speed Atomic Force Microscopy and Image Analysis  [in Japanese]

    UCHIHASHI Takayuki

    … <p>Recent progress of high-speed atomic force microscopy (HS-AFM) has enabled us to visualize dynamic conformational change and molecular interaction of proteins in realtime under a physiological condition. …

    Journal of Computer Chemistry, Japan 17(1), 20-30, 2018


  • Alternative substrate-bound conformation of bacterial solute-binding protein involved in the import of mammalian host glycosaminoglycans

    Oiki Sayoko , Kamochi Reiko , Mikami Bunzo , Murata Kousaku , Hashimoto Wataru

    … In Gram-negative pathogenic Streptobacillus moniliformis, the solute-binding protein (Smon0123)-dependent ATP-binding cassette (ABC) transporter incorporates unsaturated GAG disaccharides into the cytoplasm after depolymerization by polysaccharide lyase. … Therefore, the two sulfate groups in CΔ4S6S shifted substrate-binding residue arrangements, causing dynamic conformational change. …

    Scientific Reports (7), 2017-12-05


  • Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate

    Shibata Tomonori , Fujita Yoshihiko , Ohno Hirohisa , Suzuki Yuki , Hayashi Karin , Komatsu Kaoru R. , Kawasaki Shunsuke , Hidaka Kumi , Yonehara Shin , Sugiyama Hiroshi , Endo Masayuki , Saito Hirohide

    … However, the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. … Here we design and build protein-driven RNA-nanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA–protein interaction-mediated protein assembly. …

    Nature Communications 8(1), 2017-09-14


  • Bacterial protease uses distinct thermodynamic signatures for substrate recognition

    Bezerra Gustavo Arruda , Ohara-Nemoto Yuko , Cornaciu Irina , Fedosyuk Sofiya , Hoffmann Guillaume , Round Adam , Márquez José A. , Nemoto Takayuki K. , Djinović-Carugo Kristina

    … Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. … We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme ("entropy reservoirs"). …

    Scientific Reports (7), 2848, 2017-06-06


  • Crystal structure of the solute-binding protein BxlE from Streptomyces thermoviolaceus OPC-520 complexed with xylobiose

    Tomoo Koji , Miki Yasuhiro , Morioka Hideaki , Seike Kiho , Ishida Toshimasa , Ikenishi Sadao , Miyamoto Katsushiro , Hasegawa Tomokazu , Yamano Akihito , Hamada Kensaku , Tsujibo Hiroshi

    The journal of biochemistry 161(6), 493-501, 2017-06

    Ichushi Web 

  • Toyocamycin attenuates free fatty acid-induced hepatic steatosis and apoptosis in cultured hepatocytes and ameliorates nonalcoholic fatty liver disease in mice

    Takahara Ikuko , Akazawa Yuko , Tabuchi Maiko , Matsuda Katsuya , Miyaaki Hisamitsu , Kido Youko , Kanda Yasuko , Taura Naota , Ohnita Ken , Takeshima Fuminao , Sakai Yusuke , Eguchi Susumu , Nakashima Masahiro , Nakao Kazuhiko

    … X-box binding protein-1 (XBP-1) is activated by FFA treatment upon splicing. … Toyocamycin was recently reported to attenuate the activation of XBP-1, possibly by inducing a conformational change in IRE1α. …

    PLOS ONE 12(3), e0170591, 2017-03-09


  • Conformational changes in inhibitory PAS domain protein associated with binding of HIF-1α and Bcl-xL in living cells

    Kasai Shuya , Kajimoto Shinji , Ito Yuma , Saito Tomo , Yasumoto Ken-ichi , Tokunaga Makio , Sakata-Sogawa Kumiko , Fukumura Hiroshi , Sogawa Kazuhiro

    The journal of biochemistry 161(3), 291-296, 2017-03

    Ichushi Web 

  • Comparison between conventional, quadratic analysis and chemical-shift-PCA on data of pressure-dependent chemical shift changes  [in Japanese]

    櫻井 一正

    … According to the previous studies, the following two kinds of conformational changes of protein occur upon increase in pressure. … It is suggested that intermediate states accumulating in the pressureinduced conformational change via mechanism(ii) is relevant for its function. …

    Memoirs of Institute of Advanced Technology, Kinki University (22), 1-11, 2017-03


  • Magnetically tunable control of light reflection in an unusual optical protein of squid

    Iwasaka Masakazu , Tagawa Kunifumi , Kikuchi Yutaka

    … In this study, we focused on the magnetically tunable changes in the reflectivity of the protein reflectin, which is generated by squid and used to control their body surface color for camouflage in seawater. …

    AIP Advances 7(5), 056722, 2017-02-14


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