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Refinement of protein structure against non-redundant carbonyl 13C NMR relaxation

Journal of Biomolecular NMR volume 38, pages 243–253 (2007)Cite this article

Abstract

Carbonyl 13C′ relaxation is dominated by the contribution from the 13C′ chemical shift anisotropy (CSA). The relaxation rates provide useful and non-redundant structural information in addition to dynamic parameters. It is straightforward to acquire, and offers complimentary structural information to the 15N relaxation data. Furthermore, the non-axial nature of the 13C′ CSA tensor results in a T1/T2 value that depends on an additional angular variable even when the diffusion tensor of the protein molecule is axially symmetric. This dependence on an extra degree of freedom provides new geometrical information that is not available from the NH dipolar relaxation. A protocol that incorporates such structural restraints into NMR structure calculation was developed within the program Xplor-NIH. Its application was illustrated with the yeast Fis1 NMR structure. Refinement against the 13C′ T1/T2 improved the overall quality of the structure, as evaluated by cross-validation against the residual dipolar coupling as well as the 15N relaxation data. In addition, possible variations of the CSA tensor were addressed.

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Acknowledgments

Part of this work was supported by the Intramural Research Program of the NIH, National Heart, Lung, and Blood Institute to N.T.

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Affiliations

  1. Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Room 3503, Bethesda, MD, 20892, USA

    Nico Tjandra & Motoshi Suzuki

  2. Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, Life Science Building II, Room 338, 101, Sec. 2 Kuang Fu Rd, HsinChu, 30055, Taiwan

    Shou-Lin Chang

Authors
  1. Nico Tjandra
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  2. Motoshi Suzuki
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  3. Shou-Lin Chang
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Correspondence to Nico Tjandra or Shou-Lin Chang.

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Tjandra, N., Suzuki, M. & Chang, SL. Refinement of protein structure against non-redundant carbonyl 13C NMR relaxation. J Biomol NMR 38, 243–253 (2007). https://doi.org/10.1007/s10858-007-9165-7

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  • DOI: https://doi.org/10.1007/s10858-007-9165-7

Keywords

  • Protein structure refinement
  • NMR
  • 15N relaxation
  • 13C′ relaxation
  • Xplor-NIH
  • Yeast Fis1 protein