Journal of Biomolecular NMR

, Volume 51, Issue 4, pp 411–424 | Cite as

Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids

  • Wookyung Yu
  • Woonghee Lee
  • Weontae Lee
  • Suhkmann Kim
  • Iksoo Chang
Article
First Online:
Received:
Accepted:

Abstract

Unravelling the complex correlation between chemical shifts of 13 C α, 13 C β, 13 C′, 1 H α, 15 N, 1 H N atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous empirical correlation scores which relate chemical shifts of 13 C α, 13 C β, 13 C′, 1 H α, 15 N, 1 H N atoms to secondary structures resulted in progresses toward assigning secondary structures of proteins. However, the physical-mathematical framework for these was elusive partly due to both the limited and orthogonal exploration of higher-dimensional chemical shifts of hetero-nucleus and the lack of physical-mathematical understanding underlying those correlation scores. Here we present a simple multi-dimensional hetero-nuclear chemical shift score function (MDHN-CSSF) which captures systematically the salient feature of such complex correlations without any references to a random coil state of proteins. We uncover the symmetry-breaking vector and its reliability order not only for distinguishing different secondary structures of proteins but also for capturing the delicate sensitivity interplayed among chemical shifts of 13 C α, 13 C β, 13 C′, 1 H α, 15 N, 1 H N atoms simultaneously, which then provides a straightforward framework toward assigning secondary structures of proteins. MDHN-CSSF could correctly assign secondary structures of training (validating) proteins with the favourable (comparable) Q3 scores in comparison with those from the previous correlation scores. MDHN-CSSF provides a simple and robust strategy for the systematic assignment of secondary structures of proteins and would facilitate the de novo determination of three-dimensional structures of proteins.

Keywords

Assigning secondary structures of proteins NMR chemical shift Complex correlation between chemical shifts and secondary structures of proteins Singular value decomposition analysis 
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Notes

Acknowledgments

This work was supported by the Creative Research Initiative (Center for Proteome Biophysics, Grant No. 2011-0000041 to W.Y. and I.C.) of National Research Foundation/Ministry of Education, Science and Technology, Korea. This research was also supported by World Class University (WCU) program (R33-2009-000-10123-0 to W.L.). Authors would like to thank Prof. Kurt Wuthrich for fruitful discussion and Weonjoong Kim for constructing the web-server for MDHN-CSSF.

Supplementary material

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Supplementary material 1 (PDF 4612 KB)
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Supplementary material 5 (PDF 25 KB)

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Wookyung Yu
    • 1
  • Woonghee Lee
    • 2
  • Weontae Lee
    • 2
  • Suhkmann Kim
    • 3
  • Iksoo Chang
    • 1
  1. 1.Department of Physics, Center for Proteome BiophysicsPusan National UniversityBusanKorea
  2. 2.Department of Biochemistry, Structural Biochemistry and Molecular Biophysics LaboratoryYonsei UniversitySeoulKorea
  3. 3.Department of Chemistry, Biochemistry and Bio-NMR LaboratoryPusan National UniversityBusanKorea

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