Cysteine separations profiles on protein sequences infer disulfide connectivity
Open Access
- 7 December 2004
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 21 (8) , 1415-1420
- https://doi.org/10.1093/bioinformatics/bti179
Abstract
Motivation: Disulfide bonds play an important role in protein folding. A precise prediction of disulfide connectivity can strongly reduce the conformational search space and increase the accuracy in protein structure prediction. Conventional disulfide connectivity predictions use sequence information, and prediction accuracy is limited. Here, by using an alternative scheme with global information for disulfide connectivity prediction, higher performance is obtained with respect to other approaches. Result: Cysteine separation profiles have been used to predict the disulfide connectivity of proteins. The separations among oxidized cysteine residues on a protein sequence have been encoded into vectors named cysteine separation profiles (CSPs). Through comparisons of their CSPs, the disulfide connectivity of a test protein is inferred from a non-redundant template set. For non-redundant proteins in SwissProt 39 (SP39) sharing less than 30% sequence identity, the prediction accuracy of a fourfold cross-validation is 49%. The prediction accuracy of disulfide connectivity for proteins in SwissProt 43 (SP43) is even higher (53%). The relationship between the similarity of CSPs and the prediction accuracy is also discussed. The method proposed in this work is relatively simple and can generate higher accuracies compared to conventional methods. It may be also combined with other algorithms for further improvements in protein structure prediction. Availability: The program and datasets are available from the authors upon request. Contact:cykao@csie.ntu.edu.twKeywords
This publication has 19 references indexed in Scilit:
- Prediction of the bonding states of cysteines Using the support vector machines based on multiple feature vectors and cysteine state sequencesProteins-Structure Function and Bioinformatics, 2004
- Prediction of disulfide connectivity in proteinsBioinformatics, 2001
- What can Disulfide Bonds Tell Us about Protein Energetics, Function and Folding: Simulations and Bioninformatics AnalysisJournal of Molecular Biology, 2000
- Predicting the oxidation state of cysteines by multiple sequence alignmentBioinformatics, 2000
- Crystal Structure of Flavocetin-A, a Platelet Glycoprotein Ib-Binding Protein, Reveals a Novel Cyclic Tetramer of C-Type Lectin-like Heterodimers,Biochemistry, 2000
- The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000Nucleic Acids Research, 2000
- Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteinsProteins-Structure Function and Bioinformatics, 1999
- Solution structure of the thermostable sweet-tasting protein brazzein.Nature Structural & Molecular Biology, 1998
- NMR solution structure of the recombinant tick anticoagulant protein (rTAP), a factor Xa inhibitor from the tick Ornithodoros moubataFEBS Letters, 1994
- Solution structure of .gamma.1-H and .gamma.1-P thionins from barley and wheat endosperm determined by proton NMR: a structural motif common to toxic arthropod proteinsBiochemistry, 1993