Journal of Biomolecular NMR

, Volume 38, Issue 1, pp 57–63

2DCSi: identification of protein secondary structure and redox state using 2D cluster analysis of NMR chemical shifts

  • Ching-Cheng Wang
  • Jui-Hung Chen
  • Wen-Chung Lai
  • Woei-Jer Chuang
Article

DOI: 10.1007/s10858-007-9146-x

Cite this article as:
Wang, CC., Chen, JH., Lai, WC. et al. J Biomol NMR (2007) 38: 57. doi:10.1007/s10858-007-9146-x

Abstract

Chemical shifts of amino acids in proteins are the most sensitive and easily obtainable NMR parameters that reflect the primary, secondary, and tertiary structures of the protein. In recent years, chemical shifts have been used to identify secondary structure in peptides and proteins, and it has been confirmed that 1Hα, 13Cα, 13Cβ, and 13C′ NMR chemical shifts for all 20 amino acids are sensitive to their secondary structure. Currently, most of the methods are purely based on one-dimensional statistical analyses of various chemical shifts for each residue to identify protein secondary structure. However, it is possible to achieve an increased accuracy from the two-dimensional analyses of these chemical shifts. The 2DCSi approach performs two-dimension cluster analyses of 1Hα, 1HN, 13Cα, 13Cβ, 13C′, and 15NH chemical shifts to identify protein secondary structure and the redox state of cysteine residue. For the analysis of paired chemical shifts of 6 data sets, each of the 20 amino acids has its own 15 two-dimension cluster scattering diagrams. Accordingly, the probabilities for identifying helix and extended structure were calculated by using our scoring matrix. Compared with existing the chemical shift-based methods, it appears to improve the prediction accuracy of secondary structure identification, particularly in the extended structure. In addition, the probability of the given residue to be helix or extended structure is displayed, allows the users to make decisions by themselves.

Keywords

Chemical shift Protein secondary structure identification Two-dimension cluster 

Abbreviations

2D

Two-dimension

BMRB

BioMagResBank

H

α-helix

G

310-helix

I

π-helix

B

β-strand

E

Extended structure

C

Random coil structure

NMR

Nuclear magnetic resonance

PDB

Protein data bank

Supplementary material

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Ching-Cheng Wang
    • 1
  • Jui-Hung Chen
    • 1
  • Wen-Chung Lai
    • 1
  • Woei-Jer Chuang
    • 2
  1. 1.Institute of Manufacturing EngineeringNational Cheng Kung University College of Electrical Engineering and Computer ScienceTainanTaiwan
  2. 2.Department of Biochemistry and Molecular BiologyNational Cheng Kung University College of MedicineTainanTaiwan

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