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

Research output: Contribution to journalArticle

16 Citations (Scopus)

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 1 Hα, 1HN, 13 Cα, 13Cβ, 13 C′, 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.

Original languageEnglish
Pages (from-to)57-63
Number of pages7
JournalJournal of Biomolecular NMR
Volume38
Issue number1
DOIs
Publication statusPublished - 2007 May 1

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Secondary Protein Structure
Cluster analysis
Chemical shift
Oxidation-Reduction
Cluster Analysis
Nuclear magnetic resonance
Amino Acids
Proteins
Tertiary Protein Structure
Cysteine
Peptides
Scattering

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Spectroscopy

Cite this

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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 1 Hα, 1HN, 13 Cα, 13Cβ, 13 C′, 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.",
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2DCSi : Identification of protein secondary structure and redox state using 2D cluster analysis of NMR chemical shifts. / Wang, Ching Cheng; Chen, Jui Hung; Lai, Wen Chung; Chuang, Woei Jer.

In: Journal of Biomolecular NMR, Vol. 38, No. 1, 01.05.2007, p. 57-63.

Research output: Contribution to journalArticle

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