Evaluation of Protein Phosphorylation Site Predictors

Que, Shufu; Wang, Yong Fei; Chen, Peixiang; Tang, Yurong; Zhang, Ziding; He, Hongwen

doi:10.2174/092986610789909412

Cited by 16 publications

(16 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The use of consensus sites to predict kinase phosphorylation sites is sometimes useful, but often inaccurate (Que et al, 2010). Here we provide evidence for CPKs that predictions are usually wrong when based on consensus sites alone.…”

Section: Discussionmentioning

confidence: 99%

Calcium-Dependent Protein Kinases from Arabidopsis Show Substrate Specificity Differences in an Analysis of 103 Substrates

Curran¹,

Chang²,

Chang³

et al. 2011

Front. Plant Sci.

View full text Add to dashboard Cite

The identification of substrates represents a critical challenge for understanding any protein kinase-based signal transduction pathway. In Arabidopsis, there are more than 1000 different protein kinases, 34 of which belong to a family of Ca2+-dependent protein kinases (CPKs). While CPKs are implicated in regulating diverse aspects of plant biology, from ion transport to transcription, relatively little is known about isoform-specific differences in substrate specificity, or the number of phosphorylation targets. Here, in vitro kinase assays were used to compare phosphorylation targets of four CPKs from Arabidopsis (CPK1, 10, 16, and 34). Significant differences in substrate specificity for each kinase were revealed by assays using 103 different substrates. For example CPK16 phosphorylated Serine 109 in a peptide from the stress-regulated protein, Di19-2 with KM ∼70 μM, but this site was not phosphorylated significantly by CPKs 1, 10, or 34. In contrast, CPKs 1, 10, and 34 phosphorylated 93 other peptide substrates not recognized by CPK16. Examples of substrate specificity differences among all four CPKs were verified by kinetic analyses. To test the correlation between in vivo phosphorylation events and in vitro kinase activities, assays were performed with 274 synthetic peptides that contained phosphorylation sites previously mapped in proteins isolated from plants (in vivo-mapped sites). Of these, 74 (27%) were found to be phosphorylated by at least one of the four CPKs tested. This 27% success rate validates a robust strategy for linking the activities of specific kinases, such as CPKs, to the thousands of in planta phosphorylation sites that are being uncovered by emerging technologies.

show abstract

Section: Discussionmentioning

confidence: 99%

Calcium-Dependent Protein Kinases from Arabidopsis Show Substrate Specificity Differences in an Analysis of 103 Substrates

Curran¹,

Chang²,

Chang³

et al. 2011

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…In the 100 μM Hg/pervanadate experiment, 226 of 943 (24%) had motif assignments (figure 3 B and 4 B). Scansite has high specificity and low sensitivity relative to other phosphosite prediction algorithms and assignment of kinase motifs for less than 50% of the submitted sites is reasonable 42 .…”

Section: Resultsmentioning

confidence: 99%

Mercury Alters B-Cell Protein Phosphorylation Profiles

et al. 2013

View full text Add to dashboard Cite

Environmental exposure to mercury is suggested to contribute to human immune dysfunction. To shed light on the mechanism we identified changes in the phosphoproteomic profile of the WEHI-231 B cell line after intoxication with Hg2+. These changes were compared to changes in the phosphoproteome that were induced by pervanadate or okadaic acid exposure. Both 250 μM HgCl2 and pervanadate, a known phosphotyrosine phosphatase inhibitor, caused an increase in the number of proteins identified after TiO2 affinity selection and LC-MS/MS analysis. Pervanadate treatment had a larger effect than Hg2+ on the number of Scansite motifs which were tyrosine-phosphorylated, 17, and Ingenuity canonical signaling pathways activated, 4 with score > 5.0. However, Hg2+ had a more focused effect, primarily causing tyrosine-phosphorylation in SH2 domains in proteins that are in the B cell receptor signaling pathway. The finding that many of the changes induced by Hg2+ overlap with those of pervanadate, indicates that at high concentrations Hg2+ inhibits protein tyrosine phosphatases.

show abstract

“…, 2011). PTM predictors have been discussed and evaluated (Eisenhaber and Eisenhaber, 2010; Que et al. , 2010).…”

Section: Question 7: What Posttranslational Modifications Have Been Rmentioning

confidence: 99%

What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins

Hutchins

2014

MBoC

View full text Add to dashboard Cite

The genomic era has enabled research projects that use approaches including genome-scale screens, microarray analysis, next-generation sequencing, and mass spectrometry–based proteomics to discover genes and proteins involved in biological processes. Such methods generate data sets of gene, transcript, or protein hits that researchers wish to explore to understand their properties and functions and thus their possible roles in biological systems of interest. Recent years have seen a profusion of Internet-based resources to aid this process. This review takes the viewpoint of the curious biologist wishing to explore the properties of protein-coding genes and their products, identified using genome-based technologies. Ten key questions are asked about each hit, addressing functions, phenotypes, expression, evolutionary conservation, disease association, protein structure, interactors, posttranslational modifications, and inhibitors. Answers are provided by presenting the latest publicly available resources, together with methods for hit-specific and data set–wide information retrieval, suited to any genome-based analytical technique and experimental species. The utility of these resources is demonstrated for 20 factors regulating cell proliferation. Results obtained using some of these are discussed in more depth using the p53 tumor suppressor as an example. This flexible and universally applicable approach for characterizing experimental hits helps researchers to maximize the potential of their projects for biological discovery.

show abstract

Evaluation of Protein Phosphorylation Site Predictors

Cited by 16 publications

References 34 publications

Calcium-Dependent Protein Kinases from Arabidopsis Show Substrate Specificity Differences in an Analysis of 103 Substrates

Calcium-Dependent Protein Kinases from Arabidopsis Show Substrate Specificity Differences in an Analysis of 103 Substrates

Mercury Alters B-Cell Protein Phosphorylation Profiles

What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins

Contact Info

Product

Resources

About