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Spectral fitting for signal assignment and structural analysis of uniformly 13C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics

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Abstract

We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional 13C–13C magic-angle-spinning solid-state NMR spectra of uniformly 13C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent chemical shift obtained with SHIFTX and the cross-peak intensities computed for recoupled dipolar interactions. This method was applied to a membrane-bound 14-residue peptide, mastoparan-X. The obtained C′, Cα and Cβ chemical shifts agreed with those reported previously at the precisions of 0.2, 0.7 and 0.4 ppm, respectively. This spectral fitting program also provides backbone dihedral angles with a precision of about 50° from the spectra even with resonance overlaps. The restraints on the angles were improved by applying protein database program TALOS to the obtained chemical shifts. The peptide structure provided by these restraints was consistent with the reported structure at the backbone RMSD of about 1 Å.

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Acknowledgments

We would like to thank Prof. D. S. Wishart for releasing the source program of SHIFTX to us. We also thank Dr. Y. Todokoro for the sample preparation.

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Authors and Affiliations

  1. Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan

    Yoh Matsuki, Hideo Akutsu & Toshimichi Fujiwara

  2. Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, 5-3 Yonbancho, Chiyoda, Tokyo, 102-8666, Japan

    Yoh Matsuki

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  1. Yoh Matsuki
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  2. Hideo Akutsu
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  3. Toshimichi Fujiwara
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Correspondence to Toshimichi Fujiwara.

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Matsuki, Y., Akutsu, H. & Fujiwara, T. Spectral fitting for signal assignment and structural analysis of uniformly 13C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics. J Biomol NMR 38, 325–339 (2007). https://doi.org/10.1007/s10858-007-9170-x

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