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Journal Articles

X-ray diffraction recording from single axonemes of eukaryotic flagella

Nishiura, Masaya*; Toba, Shiori*; Takao, Daisuke*; Miyashiro, Daisuke*; Sakakibara, Hitoshi*; Matsuo, Tatsuhito; Kamimura, Shinji*; Oiwa, Kazuhiro*; Yagi, Naoto*; Iwamoto, Hiroyuki*

Journal of Structural Biology, 178(3), p.329 - 337, 2012/06

 Times Cited Count:3 Percentile:10.38(Biochemistry & Molecular Biology)

We report the first X-ray diffraction patterns recorded from single axonemes of eukaryotic flagella with a diameter of only $$<$$0.2 $$mu$$m, by using the technique of cryomicrodiffraction. A spermatozoon isolated from Drosophila melanogaster, was mounted straight in a glass capillary, quickly frozen and its 800-$$mu$$m segment was irradiated end-on with intense synchrotron radiation X-ray microbeams (diameter, 2 $$mu$$m) at 74 K. Well-defined diffraction patterns were recorded, consisting of a large number of isolated reflection spots. The patterns had features of an 18-fold rotational symmetry as expected from the axonemal structure. The diffraction patterns were compared with the results of model calculations based on a published electron micrograph of the Drosophila axoneme. The comparison provided information on the native state of axoneme, including estimates of axonemal diameter and interdoublet spacing.

Journal Articles

Hydrogen-bond network and pH sensitivity in transthyretin; Neutron crystal structure of human transthyretin

Yokoyama, Takeshi*; Mizuguchi, Mineyuki*; Nabeshima, Yuko*; Kusaka, Katsuhiro*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi*; Kurihara, Kazuo; Tomoyori, Katsuaki*; Tanaka, Ichiro*; et al.

Journal of Structural Biology, 177(2), p.283 - 290, 2012/02

 Times Cited Count:40 Percentile:83.32(Biochemistry & Molecular Biology)

Journal Articles

Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding

Higuchi, Mariko; Fujii, Jumpei*; Yonetani, Yoshiteru; Kitao, Akio*; Go, Nobuhiro*

Journal of Structural Biology, 173(1), p.20 - 28, 2011/01

 Times Cited Count:2 Percentile:6.99(Biochemistry & Molecular Biology)

MutT distinguishes substrate 8-oxo-dGTP from dGTP and also 8-oxo-dGMP from dGMP despite small differences of chemical structures between them. In this paper we show by the method of molecular dynamics simulation that the transition between conformational substates of MutT is a key mechanism for a high resolution molecular recognition of the differences between the very similar chemical compounds. The native state MutT has two conformational substates with similar free energies, each characterized by either open or close of two loops surrounding the substrate binding active site. Between the two substates, the open substate is more stable in free MutT and in dGMP-MutT complex, and the closed substate is more stable in 8-oxo-dGMP-MutT complex. A hydrogen bond between H7 atom of 8-oxo-dGMP and the sidechain of Asn119 plays a crucial role for maintaining the closed substate in 8-oxo-dGMP-MutT complex.

Journal Articles

Neutron diffraction measurements of skeletal muscle using the contrast variation technique; Analysis of the equatorial diffraction patterns

Fujiwara, Satoru; Takezawa, Yasunori*; Sugimoto, Yasunobu*; Wakabayashi, Katsuzo*

Journal of Structural Biology, 167(1), p.25 - 35, 2009/07

 Times Cited Count:2 Percentile:5.84(Biochemistry & Molecular Biology)

In neutron scattering and diffraction, information on variations of scattering length density of molecules of interest can be extracted by the contrast variation technique. In order to explore the possibilities of this contrast variation technique in neutron fiber diffraction, neutron diffraction measurements of skeletal muscles were performed. The neutron fiber diffraction patterns of frog sartorius muscles were measured in the relaxed state and the rigor state, in various D$$_{2}$$O concentrations. It was shown that there were variations in the scattering length density of the protein regions in the unit cell of the muscle structure. Analysis of the equatorial reflections showed that the phase information of these reflections is obtained, that the scattering length density is different between the thick filament region and the thin filament region, and that the density of the thick filament changes as the state of muscle changes from the relaxed state to the rigor state.

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