Predicting the oxidation state of cysteines by multiple sequence alignment

Andrés Fiser, I. Simon

Research output: Contribution to journalArticle

74 Citations (Scopus)

Abstract

Motivation: Protein sequences found in databanks usually do not report post translational covalent modifications such as the oxidation state of cystein (Cys) residues. Accurate prediction of whether a functionally or structurally important Cys occurs in the oxidized or thiol form would be helpful for molecular biology experiments and structure prediction. Results: A new method is presented for predicting the oxidation state of Cys residues based on multiple sequence alignments and on the observation that Cys tends to occur in the same oxidation state within the same protein. The prediction of the redox state of Cys performs above 82%. The oxidation state of Cys correlates with the cellular location of the given protein within the cell, but the correlation is not perfect (up to 70%). We also perform a statistical analysis of the different redox states of Cys found in secondary structures and buried positions, and of the secondary structures linked by disulfide bonds. The results suggest that the natural borderline lies between the different oxidation states of Cys rather than between the half cystines and cysteins. Availability: A web server implementing the prediction method is available at http://guitar.rockefeller.edu/~andras/cyspred.html.

Original languageEnglish
Pages (from-to)251-256
Number of pages6
JournalBioinformatics
Volume16
Issue number3
Publication statusPublished - Mar 2000

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Multiple Sequence Alignment
Sequence Alignment
Oxidation
Cysteine
Oxidation-Reduction
Secondary Structure
Proteins
Post Translational Protein Processing
Prediction
Molecular Structure
Sulfhydryl Compounds
Disulfides
Molecular Biology
Cystines
Protein
Molecular biology
Structure Prediction
Databases
Web Server
Protein Sequence

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Predicting the oxidation state of cysteines by multiple sequence alignment. / Fiser, Andrés; Simon, I.

In: Bioinformatics, Vol. 16, No. 3, 03.2000, p. 251-256.

Research output: Contribution to journalArticle

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