Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts

Ching Cheng Wang, Wen Chung Lai, Woei-Jer Chuang

Research output: Contribution to journalArticle

Abstract

A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine 13C′, 13Cα, 13Cβ, 1Hα, 1HN, and 15NH chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the Cα, Cβ, Hα, and NH chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that HN and C′ chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.

Original languageEnglish
Pages (from-to)55-68
Number of pages14
JournalJournal of Biomolecular NMR
Volume66
Issue number1
DOIs
Publication statusPublished - 2016 Sep 1

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Chemical shift
Oxidation-Reduction
Cysteine
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Libraries
Servers

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Spectroscopy

Cite this

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title = "Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts",
abstract = "A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine 13C′, 13Cα, 13Cβ, 1Hα, 1HN, and 15NH chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the Cα, Cβ, Hα, and NH chemical shifts had the highest prediction accuracy of 100 and 95.9 {\%} for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 {\%}, suggesting that HN and C′ chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.",
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Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts. / Wang, Ching Cheng; Lai, Wen Chung; Chuang, Woei-Jer.

In: Journal of Biomolecular NMR, Vol. 66, No. 1, 01.09.2016, p. 55-68.

Research output: Contribution to journalArticle

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