Structure determination of a protein assembly by amino acid selective cross-saturation

Authors

  • Eiji Kanamori,

    Corresponding author
    1. Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo 135-0064, Japan
    2. Hitachi Software Engineering Co., Ltd., Tsurumi-Ku, Yokohama 230-0045, Japan
    • Japan Biological Informatics Consortium (JBIC), 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
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  • Shunsuke Igarashi,

    1. Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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  • Masanori Osawa,

    1. Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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  • Yoshifumi Fukunishi,

    1. Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
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  • Ichio Shimada,

    1. Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
    2. Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
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  • Haruki Nakamura

    1. Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
    2. Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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Abstract

Amino acid selective cross-saturation (ASCS) method not only provides information about the interface of a protein assembly by the spin relaxation experiment, but also identifies the amino acid residues in the acceptor protein, which are located close to the selectively labeled amino acid residues in the donor protein. Here, a new method was developed to build a precise structural model of a protein assembly, which satisfies the experimental ASCS values, using simulated annealing computation. This method was applied to the ubiquitin–yeast ubiquitin hydrolase 1 (Ub-YUH1) complex to build a precise complex structure compatible with that determined by X-ray crystallography. Proteins 2010. © 2010 Wiley-Liss, Inc.

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