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Protein structure determination in living cells by in-cell NMR spectroscopy

Author

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  • Daisuke Sakakibara

    (Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
    CREST/Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan)

  • Atsuko Sasaki

    (Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
    CREST/Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan)

  • Teppei Ikeya

    (Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
    Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, J. W. Goethe-University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany)

  • Junpei Hamatsu

    (Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
    CREST/Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan)

  • Tomomi Hanashima

    (Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan)

  • Masaki Mishima

    (Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
    CREST/Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan)

  • Masatoshi Yoshimasu

    (Cellular and Molecular Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan)

  • Nobuhiro Hayashi

    (Institute for Comprehensive Medical Science, Fujita Health University, Toyoake-shi, Aichi 470-1192, Japan
    Present address: Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 B-1, Nagatsuda-chou, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.)

  • Tsutomu Mikawa

    (Research Group for Bio-supramolecular Structure-Function, RIKEN, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan)

  • Markus Wälchli

    (Bruker BioSpin, 3-21-5 Ninomiya, Tsukuba-shi, Ibaraki 305-0051, Japan)

  • Brian O. Smith

    (Faculty of Biomedical and Life Sciences, University of Glasgow)

  • Masahiro Shirakawa

    (CREST/Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
    Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan)

  • Peter Güntert

    (Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
    Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, J. W. Goethe-University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
    Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany)

  • Yutaka Ito

    (Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
    CREST/Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
    Research Group for Bio-supramolecular Structure-Function, RIKEN, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan)

Abstract

In-cell NMR: three-dimensional protein structures Previously, the relatively low sensitivity of spectroscopy and short lifetime of the samples have made it difficult to acquire sufficient structural information to determine protein structures using in-cell NMR spectroscopy. It can take one or two days to collect NMR data, too long for living cells. Sakakibara et al. overcome this limitation by collecting enough data in a few hours; they report the first three-dimensional protein structure determined exclusively on the basis of information obtained in living Escherichia coli. The model protein used in this 'proof of principle' study is the putative heavy metal-binding protein TTHA1718 from Thermus thermophilus.

Suggested Citation

  • Daisuke Sakakibara & Atsuko Sasaki & Teppei Ikeya & Junpei Hamatsu & Tomomi Hanashima & Masaki Mishima & Masatoshi Yoshimasu & Nobuhiro Hayashi & Tsutomu Mikawa & Markus Wälchli & Brian O. Smith & Mas, 2009. "Protein structure determination in living cells by in-cell NMR spectroscopy," Nature, Nature, vol. 458(7234), pages 102-105, March.
    • Handle: RePEc:nat:nature:v:458:y:2009:i:7234:d:10.1038_nature07814
    DOI: 10.1038/nature07814
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    Cited by:

    1. Ahrum Son & Hyunsoo Kim & Jolene K. Diedrich & Casimir Bamberger & Daniel B. McClatchy & Stuart A. Lipton & John R. Yates, 2024. "Using in vivo intact structure for system-wide quantitative analysis of changes in proteins," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. V. S. Manu & Cristina Olivieri & Gianluigi Veglia, 2023. "AI-designed NMR spectroscopy RF pulses for fast acquisition at high and ultra-high magnetic fields," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    3. Piotr Klukowski & Roland Riek & Peter Güntert, 2022. "Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

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