NDLI: Identification, analysis, and prediction of protein ubiquitination sites.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Radivojac, Predrag Vacic, Vladimir Haynes, Chad Cocklin, Ross R. Mohan, Amrita Heyen, Joshua W. Goebl, Mark G. Iakoucheva, Lilia M.
Description	Country affiliation: United States Author Affiliation: Radivojac P ( School of Informatics, Indiana University, Bloomington, Indiana 47408, USA.)
Abstract	Ubiquitination plays an important role in many cellular processes and is implicated in many diseases. Experimental identification of ubiquitination sites is challenging due to rapid turnover of ubiquitinated proteins and the large size of the ubiquitin modifier. We identified 141 new ubiquitination sites using a combination of liquid chromatography, mass spectrometry, and mutant yeast strains. Investigation of the sequence biases and structural preferences around known ubiquitination sites indicated that their properties were similar to those of intrinsically disordered protein regions. Using a combined set of new and previously known ubiquitination sites, we developed a random forest predictor of ubiquitination sites, UbPred. The class-balanced accuracy of UbPred reached 72%, with the area under the ROC curve at 80%. The application of UbPred showed that high confidence Rsp5 ubiquitin ligase substrates and proteins with very short half-lives were significantly enriched in the number of predicted ubiquitination sites. Proteome-wide prediction of ubiquitination sites in Saccharomyces cerevisiae indicated that highly ubiquitinated substrates were prevalent among transcription/enzyme regulators and proteins involved in cell cycle control. In the human proteome, cytoskeletal, cell cycle, regulatory, and cancer-associated proteins display higher extent of ubiquitination than proteins from other functional categories. We show that gain and loss of predicted ubiquitination sites may likely represent a molecular mechanism behind a number of disease-associatedmutations. UbPred is available at http://www.ubpred.org.
File Format	HTM / HTML
ISSN	08873585
e-ISSN	10970134
DOI	10.1002/prot.22555
Journal	Proteins: Structure, Function, and Bioinformatics
Issue Number	2
Volume Number	78
Language	English
Publisher	Wiley-Liss
Publisher Date	2010-02-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Research Support, N.i.h., Extramural Research Support, U.s. Gov't, Non-p.h.s. Amino Acid Sequence Saccharomyces Cerevisiae Proteins Endosomal Sorting Complexes Required For Transport Discipline Biochemistry Molecular Sequence Data Proteome Ubiquitinated Proteins Metabolism Saccharomyces Cerevisiae Sequence Analysis, Protein Ubiquitination Databases, Protein Mass Spectrometry Ubiquitin-protein Ligase Complexes
Content Type	Text
Resource Type	Article
Subject	Structural Biology Biochemistry Molecular Biology

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