Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs

Chen, Yongzi; Tang, Yurong; Sheng, Zhi-Ya; Zhang, Ziding

doi:10.1186/1471-2105-9-101

Cited by 145 publications

(109 citation statements)

References 42 publications

(56 reference statements)

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“…The ROC curves are shown in Figure 6. The AUCs reported in the literature 24,26 are displayed for comparison in Figure 7. The results in Figures 6 and 7 illustrate that the performance of our methods is a little better or much better than that of other methods for prediction of mucin-type O-glycosylation sites.…”

Section: Mucin-type O-glycosylation Sites In Mammalian Proteinsmentioning

confidence: 99%

“…ROC curves of AADOGlySite, DOGlySite, and AAOGlySite for mucin-type O-glycosylation site prediction by 10-fold crossvalidation. For comparison, the corresponding performance measures reported in literature are shown: CKSAAPOGlySite, 24 Li et al, 26 EnsembleGly, 27 and NetOGlyc 3.1. 24 Li et al, 26 EnsembleGly, 27 and NetOGlyc 3.1.…”

Section: Kinase-specific Phosphorylation Sitesmentioning

confidence: 99%

“…For comparison, the corresponding performance measures reported in literature are shown: CKSAAPOGlySite, 24 Li et al, 26 EnsembleGly, 27 and NetOGlyc 3.1. 24 Li et al, 26 EnsembleGly, 27 and NetOGlyc 3.1. 25 For other kinase except the above four well-studied ones, the performance of AADphos also outperforms Dphos and AAphos (see Supporting Information).…”

Section: Kinase-specific Phosphorylation Sitesmentioning

confidence: 99%

“…Following the approach used in the articles, [24][25][26] We use the approach similar to the last section to compare our methods with the existing methods. The ROC curves are shown in Figure 6.…”

Section: Mucin-type O-glycosylation Sites In Mammalian Proteinsmentioning

confidence: 99%

“…An ideal solution to perform an unbiased comparison is running crossvalidations on the same datasets. Fortunately, Chen et al 24 make public their training and testing datasets. The size of positive and negative datasets is shown in the Table 4.…”

Section: Mucin-type O-glycosylation Sites In Mammalian Proteinsmentioning

confidence: 99%

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Retracted: Prediction of posttranslational modification sites from sequences with kernel methods

2012

J Comput Chem

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Abstract:Posttranslational modification (PTM) is the chemical modification of a protein after its translation and one of the later steps in protein biosynthesis for many proteins. It plays an important role in modifying the end product of gene expression and contributes toward biological processes and diseased conditions. However, the experimental methods for identifying PTM sites are not only costly but also time consuming. Hence, computational methods are highly desired. In this article, a novel encoding method PSDP (position-specific dipeptide propensity), which is a modified version of position-specific amino acid propensity, is developed. Then, a support vector machine SVM with the kernel matrix computed by PSDP is applied to predict the PTM sites related to serine (S) and threonine (T) residues. The numerical results indicate that the performance of new method is better than the existing methods. Therefore, the new method is a useful computational resource for the identification of PTM sites. As the application, a software PTMPred is developed for predicting phosphorylation and O-glycosylation sites, and available at http://www.aporc.org/doc/wiki/PTMPred.

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Section: Mucin-type O-glycosylation Sites In Mammalian Proteinsmentioning

confidence: 99%

Section: Kinase-specific Phosphorylation Sitesmentioning

confidence: 99%

Section: Kinase-specific Phosphorylation Sitesmentioning

confidence: 99%

Section: Mucin-type O-glycosylation Sites In Mammalian Proteinsmentioning

confidence: 99%

Section: Mucin-type O-glycosylation Sites In Mammalian Proteinsmentioning

confidence: 99%

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Retracted: Prediction of posttranslational modification sites from sequences with kernel methods

2012

J Comput Chem

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Proteomic Analysis of Posttranslational Modifications

Veenstra

2013

Proteomic Applications in Cancer Detection and Discovery

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An Efficient Approach for the Characterization of Mucin‐Type Glycopeptides: The Effect of O‐Glycosylation on the Conformation of Synthetic Mucin Peptides

Hashimoto

Fujitani

Takegawa

et al. 2011

Chemistry A European J

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Despite the growing importance of mucin core O-glycosylation in many biological processes including the protection of epithelial cell surfaces, the immune response, cell adhesion, inflammation, and tumorigenesis/metastasis, the regulation mechanism and conformational significance of the multiple introduction of α-GalNAc residues by UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (ppGalNAcTs) remains unclear. Here we report an efficient approach by combining MS and NMR spectroscopy that allows for the identification of O-glycosylation site(s) and the effect of O-glycosylation on the peptide backbone structures during enzymatic mucin domain assembly by using an isoform UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-T2 (ppGalNAcT2) in vitro. An electron-capture dissociation device in a linear radio-frequency quadrupole ion trap (RFQ-ECD) combined with a time-of-flight (TOF) mass spectrometer was employed for the identification of Thr/Ser residues occupied by α-GalNAc branching among multiple and potential O-glycosylation sites in the tandem repeats of human mucin glycoproteins MUC4 (Thr-Ser-Ser-Ala-Ser-Thr-Gly-His-Ala-Thr-Pro-Leu-Pro-Val-Thr-Asp) and MUC5AC (Pro-Thr-Thr-Val-Gly-Ser-Thr-Thr-Val-Gly). In the present study, O-glycosylation was initiated specifically at Thr10 in naked MUC4 peptide and additional introduction of α-GalNAc proceeded preferentially but randomly at three other Thr residues to afford densely glycosylated MUC4 containing six α-GalNAc residues at Thr1, Ser2, Ser5, Thr6, Thr10, and Thr15. On the contrary, O-glycosylation of naked MUC5AC peptide occurred predominantly at consecutive Thr residues and led to MUC5AC with four α-GalNAc residues at Thr2, Thr3, Thr7, and Thr8. The solution structures determined by NMR spectroscopic studies elicited that the preferential introduction of α-GalNAc at Thr10 of MUC4 stabilizes specifically a β-like extended backbone structure at this area, whereas other synthetic models with a single α-GalNAc residue at Thr1, Thr6, or Thr15 did not exhibit any converged three-dimensional structure at the proximal peptide moiety. Such conformational impact on the underlying peptides was proved to be remarkable in the glycosylation at the consecutive Thr residues of MUC5AC.

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Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs

Cited by 145 publications

References 42 publications

Retracted: Prediction of posttranslational modification sites from sequences with kernel methods

Retracted: Prediction of posttranslational modification sites from sequences with kernel methods

Proteomic Analysis of Posttranslational Modifications

An Efficient Approach for the Characterization of Mucin‐Type Glycopeptides: The Effect of O‐Glycosylation on the Conformation of Synthetic Mucin Peptides

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