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CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

Journal of Biomolecular NMR volume 44, pages 185–194 (2009)Cite this article

Abstract

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1Hα and 13C′ chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment.

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Acknowledgments

The facilities provided by NMR Research Centre at IISc supported by Department of Science and Technology (DST), India is gratefully acknowledged. HSA acknowledges support from Department of Atomic Energy (DAE) BRNS, DST-SERC and DST-FAST TRACK research awards. MS acknowledges fellowship from Council of Scientific and Industrial Research (CSIR), India. We thank Dr. John Cort, Pacific Northwest National Laboratory, for providing the Ubiquitin plasmid and B. Krishnarjuna, IISc, for preparing the Ubiquitin sample.

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Affiliations

  1. NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India

    Monalisa Swain & Hanudatta S. Atreya

  2. Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012, India

    Monalisa Swain

Authors
  1. Monalisa Swain
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  2. Hanudatta S. Atreya
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Correspondence to Hanudatta S. Atreya.

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Swain, M., Atreya, H.S. CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts. J Biomol NMR 44, 185–194 (2009). https://doi.org/10.1007/s10858-009-9327-x

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  • DOI: https://doi.org/10.1007/s10858-009-9327-x

Keywords

  • Protein secondary structure
  • CSI
  • GFT NMR
  • Protein folding
  • 3D structure