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Ikeya T.,Tokyo Metroplitan University
Nature protocols | Year: 2010

The cell is a crowded environment in which proteins interact specifically with other proteins, nucleic acids, cofactors and ligands. Atomic resolution structural explanation of proteins functioning in this environment is a main goal of biochemical research. Recent improvements to nuclear magnetic resonance (NMR) hardware and methodology allow the measurement of high-resolution heteronuclear multidimensional NMR spectra of macromolecules in living cells (in-cell NMR). In this study, we describe a protocol for the stable isotope ((13)C, (15)N and (2)H) labeling and structure determination of proteins overexpressed in Escherichia coli cells exclusively on the basis of information obtained in living cells. The protocol combines the preparation of the protein in E. coli cells, the rapid measurement of the three-dimensional (3D) NMR spectra by nonlinear sampling of the indirectly acquired dimensions, structure calculation and structure refinement. Under favorable circumstances, this in-cell NMR approach can provide high-resolution 3D structures of proteins in living environments. The protocol has been used to solve the first 3D structure of a protein in living cells for the putative heavy metal-binding protein TTHA1718 from Thermus thermophilus HB8 overexpressed in E. coli cells. As no protein purification is necessary, a sample for in-cell NMR measurements can be obtained within 2-3 d. With the nonlinear sampling scheme, the duration of each 3D experiment can be reduced to 2-3 h. Once chemical shift assignments and NOESY peak lists have been prepared, structure calculation with the program CYANA and energy refinement can be completed in less than 1 h on a powerful computer system.

Ito Y.,Tokyo Metroplitan University | Selenko P.,Leibniz Institute for Molecular Pharmacology
Current Opinion in Structural Biology | Year: 2010

While we appreciate the complexity of the intracellular environment as a general property of every living organism, we collectively lack the appropriate tools to analyze protein structures in a cellular context. In-cell NMR spectroscopy represents a novel biophysical tool to investigate the conformational and functional characteristics of biomolecules at the atomic level inside live cells. Here, we review recent in-cell NMR developments and provide an outlook towards future applications in prokaryotic and eukaryotic cells. We hope to thereby emphasize the usefulness of in-cell NMR techniques for cellular studies of complex biological processes and for structural analyses in native environments. © 2010 Elsevier Ltd.

Haruta M.,Tokyo Metroplitan University
Faraday Discussions | Year: 2011

Gold can be deposited as nanoparticles (NPs) of 2 to 5 nm in diameter on a variety of materials such as metal oxides and carbides, carbons, organic polymers and exhibits surprisingly high catalytic activities for many reactions in both gas and liquid phases. The mechanisms for the genesis of catalysis by gold NPs is discussed based on real powder catalysts and model single crystal catalysts for two simple reactions, low-temperature oxidation of CO in which gold NPs catalysts are exceptionally active and for dihydrogen dissociation in which gold NPs catalysts are still poorly active. For both the two reactions, it has been revealed that reactions take place at perimeter interfaces around gold NPs. © 2011 The Royal Society of Chemistry.

Haruta M.,Tokyo Metroplitan University | Haruta M.,CAS Dalian Institute of Chemical Physics
Angewandte Chemie - International Edition | Year: 2014

"Have you tried gold?" This question after a presentation on hydrogen oxidation steered Masatake Haruta's research on heterogeneous catalysis. He found that gold combined with 3d transition metal oxides could exhibit surprisingly high catalytic activity for carbon monoxide oxidation at temperatures as low as 203 K. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kawahara H.,Tokyo Metroplitan University
Astrophysical Journal Letters | Year: 2012

We consider the effect of planetary spin on the planetary radial velocity (PRV) in dayside spectra of exoplanets. To understand the spin effect qualitatively, we derive an analytic formula of the intensity-weighted radial velocity from the planetary surface on the following assumptions: (1) constant and solid rotation without precession, (2) stable and uniform distribution of molecules/atoms, (3) emission models from the dayside hemisphere, and (4) a circular orbit. On these assumptions, we find that the curve of the PRV is distorted by the planetary spin and this anomaly is characterized by the spin radial velocity at the equator and a projected angle on a celestial plane between the spin axis and the axis of orbital motion λp in a manner analogous to the Rossiter-McLaughlin effect. The latter can constrain the planetary obliquity. Creating mock PRV data with 3km s-1 accuracy, we demonstrate how λp and the spin radial velocity at the equator are estimated. We find that the stringent constraint of eccentricity is crucial to detect the spin effect. Though our formula is still qualitative, we conclude that the PRV in the dayside spectra will be a powerful means for constraining the planetary spin. © 2012. The American Astronomical Society. All rights reserved..

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