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

Authors: Tjandra, Nico¹; Suzuki, Motoshi; Chang, Shou-Lin²

Source: Journal of Biomolecular NMR, Volume 38, Number 3, July 2007 , pp. 243-253(11)

Publisher: Springer

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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.

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

Document Type: Research article

DOI: http://dx.doi.org/10.1007/s10858-007-9165-7

Affiliations: 1: Email: nico@helix.nih.gov 2: Email: slchang@life.nthu.edu.tw

Publication date: 2007-07-01