Elucidations of the catalytic cycle of NADH-cytochrome reductase by X-ray crystallography; New insights into regulation of efficient electron transfer

Yamada, Mitsugu*; Tamada, Taro; Takeda, Kazuki*; Matsumoto, Fumiko*; Ono, Hiraku*; Kosugi, Masayuki*; Takaba, Kiyofumi*; Shoyama, Yoshinari*; Kimura, Shigenobu*; Kuroki, Ryota; et al.

Journal of Molecular Biology, 425(22), p.4295 - 4306, 2013/11

https://doi.org/10.1016/j.jmb.2013.06.010

NADH-Cytochrome reductase (b5R), a flavoprotein consisting of NADH and flavin adenine dinucleotide (FAD) binding domains, catalyzes electron transfer from the two-electron carrier NADH to the one-electron carrier cytochrome (Cb5). The crystal structures of both the fully reduced form and the oxidized form of porcine liver b5R were determined. In the reduced b5R structure determined at 1.68 resolution, the relative configuration of the two domains was slightly shifted in comparison with that of the oxidized form. This shift resulted in an increase in the solvent-accessible surface area of FAD and created a new hydrogen-bonding interaction between the N5 atom of the isoalloxazine ring of FAD and the hydroxyl oxygen atom of Thr66, which is considered to be a key residue in the release of a proton from the N5 atom. The isoalloxazine ring of FAD in the reduced form is flat as in the oxidized form and stacked together with the nicotinamide ring of NAD. Determination of the oxidized b5R structure, including the hydrogen atoms, determined at 0.78 resolution revealed the details of a hydrogen-bonding network from the N5 atom of FAD to His49 via Thr66. Both of the reduced and oxidized b5R structures explain how backflow in this catalytic cycle is prevented and the transfer of electrons to one-electron acceptors such as Cb5 is accelerated. Furthermore, crystallographic analysis by the cryo-trapping method suggests that re-oxidation follows a two-step mechanism. These results provide structural insights into the catalytic cycle of b5R.

Detailed design of new material nitric acid recovery evaporator

Yokoyama, Hiroomi*; Kanazawa, Toshio*; Fukuma, Tadashi*; Tamekiyo, Kozo*; Yanagida, Koji*; Furuya, Takashi*; Kono, Hiroshi*; Ito, Keiji*; Shirakura, Takao*; Kashiwara, Shinichiro*; et al.

PNC TN8410 87-086VOL1, 1037 Pages, 1986/09

PNC-TN8410-87-086VOL1.pdf:34.39MB

A detailed design for a New Material Nitric Acid Recovery Evaporator was carried out with a plan to use it to replace an already constructed stainless steel Nitric Acid Recovery Evaporator at the Power Reactor and Nuclear Fuel Development Corporation's Tokai Works. Most of the original Evaporator's conditions such as compliance with applicable laws, standards, structure, treatment performance and operating conditions were maintained when designing the new machine. The material is titanium with the addition of 5% tantalum. The Evaporator was designed with an operational life expectance of 10 years. We have calculated that the new Evaporator will have sufficient strength (including a seismatic design) and have the same evaporative performance as the already constructed one. During design, we referred to the results of already completed basic designs (Phase 1) of New Material Nitric Acid Recovery Evaporators, design and production of small-scale test equipment units, and the development of successful joints between different materials. We also considered manufacturing, installation, trial runs, maintenance, and the specifications for materials used for manufacturing, installation, piping and operation of the new Evaporator.

Analysis of Si(113) surfaces oxidized by a supersonic seeded molecular beam technique

Tanaka, Kazuma*; Ono, Shinya*; Kodama, Hiraku*; Yoshigoe, Akitaka; Teraoka, Yuden; Tanaka, Masatoshi*

no journal, , 

no abstracts in English

Initial oxidation processes on Si(113) surfaces at room temperature

Tanaka, Kazuma*; Ono, Shinya*; Kodama, Hiraku*; Abe, Sosuke*; Miura, Shu*; Narishige, Takuma*; Yoshigoe, Akitaka; Teraoka, Yuden; Tanaka, Masatoshi*

no journal, , 

Structure of hydrogen atoms in high-resolution neutron structure of protein

Hirano, Yu; Tamada, Taro; Kurihara, Kazuo; Kusaka, Katsuhiro*; Ono, Hiraku*; Takeda, Kazuki*; Miki, Kunio*

no journal, , 

Hydrogen atoms are involved in protein folding and enzymatic reaction. Structures of hydrogen atoms in proteins have been discussed based on the ideal bond distances and angles obtained by small molecular crystallography. However, structural information about hydrogen atoms without geometric restraints is important for understanding structures and functions of proteins. High-potential iron-sulfur protein (HiPIP) is an electron carrier protein which functions in photosynthetic electron transfer chain of purple bacteria. In this work, we determined high-resolution neutron structure of HiPIP. The neutron diffraction experiment was performed at the BL03 beamline (iBIX) of J-PARC/MLF. We have collected the highest resolution data at 1.1 angstrom in the protein neutron structures. After structure refinement, we have observed many deviations in positions and bond lengths of hydrogen atoms from the ideal geometries.