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Alternative SAIL-Trp for robust aromatic signal assignment and determination of the χ2 conformation by intra-residue NOEs

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Abstract

Tryptophan (Trp) residues are frequently found in the hydrophobic cores of proteins, and therefore, their side-chain conformations, especially the precise locations of the bulky indole rings, are critical for determining structures by NMR. However, when analyzing [U–13C,15N]-proteins, the observation and assignment of the ring signals are often hampered by excessive overlaps and tight spin couplings. These difficulties have been greatly alleviated by using stereo-array isotope labeled (SAIL) proteins, which are composed of isotope-labeled amino acids optimized for unambiguous side-chain NMR assignment, exclusively through the 13C–13C and 13C–1H spin coupling networks (Kainosho et al. in Nature 440:52–57, 2006). In this paper, we propose an alternative type of SAIL-Trp with the [ζ2,ζ3-2H2; δ1,ε3,η2-13C3; ε1-15N]-indole ring ([12C 12γ, Cε2] SAIL-Trp), which provides a more robust way to correlate the 1Hβ, 1Hα, and 1HN to the 1Hδ1 and 1Hε3 through the intra-residue NOEs. The assignment of the 1Hδ1/13Cδ1 and 1Hε3/13Cε3 signals can thus be transferred to the 1Hε1/15Nε1 and 1Hη2/13Cη2 signals, as with the previous type of SAIL-Trp, which has an extra 13C at the Cγ of the ring. By taking advantage of the stereospecific deuteration of one of the prochiral β-methylene protons, which was 1Hβ2 in this experiment, one can determine the side-chain conformation of the Trp residue including the χ2 angle, which is especially important for Trp residues, as they can adopt three preferred conformations. We demonstrated the usefulness of [12Cγ,12Cε2] SAIL-Trp for the 12 kDa DNA binding domain of mouse c-Myb protein (Myb-R2R3), which contains six Trp residues.

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Acknowledgments

We thank Prof. Yoshifumi Nishimura and Dr. Aritaka Nagadoi, of Yokohama City University, for providing the Myb-R2R3 gene, and Dr. Frank Löhr, Institute of Biophysical Chemistry and Center of Biological Magnetic Resonance, Goethe-University, for his kind help in providing the NMR sequence of the 1H–13C TROSY experiments. This work was supported in part by the Targeted Protein Research Program (MEXT) to M.K., a Grant-in-Aid for Young Scientists (B) (23770109) to M.T. and a Grant-in-Aid for Young Scientists (B) (23770111) to Y.M.

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Authors and Affiliations

  1. Graduate School of Science, Structural Biology Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan

    Yohei Miyanoiri, Mitsuhiro Takeda & Masatsune Kainosho

  2. Center for Priority Areas, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan

    JunGoo Jee, Akira M. Ono, Kosuke Okuma, Tsutomu Terauchi & Masatsune Kainosho

  3. SAIL Technologies Co., Inc., 1-40 Suehiro-cho 1-chome, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

    Akira M. Ono, Kosuke Okuma & Tsutomu Terauchi

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  1. Yohei Miyanoiri
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  2. Mitsuhiro Takeda
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Correspondence to Masatsune Kainosho.

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Miyanoiri, Y., Takeda, M., Jee, J. et al. Alternative SAIL-Trp for robust aromatic signal assignment and determination of the χ2 conformation by intra-residue NOEs. J Biomol NMR 51, 425–435 (2011). https://doi.org/10.1007/s10858-011-9568-3

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