GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection

Xue, Yu; Liu, Zexian; Cao, Jun; Ma, Qian; Gao, Xiaolan; Wang, Qingqi; Jin, Changjie; Zhou, Yanhong; Wen, Longping; Ren, Jian

doi:10.1093/protein/gzq094

Cited by 230 publications

(223 citation statements)

References 15 publications

Supporting

Mentioning

220

Contrasting

Unclassified

Order By: Relevance

“…One can see that the PKA phosphorylation of Ser-435 was predicted by all three predictors. Sites Ser-184, Ser-189, and Thr-220 were predicted by Scansite3 (31) and GPS3 (32) but not by Kinasephos2 (33). This limited comparison indicates that Scansite3 and GPS3 can identify the most important PKA phosphorylation sites within the intrinsically disordered protein MAP2c.…”

Section: Sequence-based Prediction Of Phosphorylation Sitesmentioning

confidence: 98%

Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau

Jansen

Melková

Trošanová

et al. 2017

Journal of Biological Chemistry

View full text Add to dashboard Cite

Edited by Norma AllewellMicrotubule-associated protein 2c (MAP2c) is involved in neuronal development and is less characterized than its homolog Tau, which has various roles in neurodegeneration. Using NMR methods providing single-residue resolution and quantitative comparison, we investigated molecular interactions important for the regulatory roles of MAP2c in microtubule dynamics. We found that MAP2c and Tau significantly differ in the position and kinetics of sites that are phosphorylated by cAMP-dependent protein kinase (PKA), even in highly homologous regions. We determined the binding sites of unphosphorylated and phosphorylated MAP2c responsible for interactions with the regulatory protein 14-3-3 . Differences in phosphorylation and in charge distribution between MAP2c and Tau suggested that both MAP2c and Tau respond to the same signal (phosphorylation by PKA) but have different downstream effects, indicating a signaling branch point for controlling microtubule stability. Although the interactions of phosphorylated Tau with 14-3-3 are supposed to be a major factor in microtubule destabilization, the binding of 14-3-3 to MAP2c enhanced by PKA-mediated phosphorylation is likely to influence microtubule-MAP2c binding much less, in agreement with the results of our tubulin co-sedimentation measurements. The specific location of the major MAP2c phosphorylation site in a region homologous to the muscarinic receptor-binding site of Tau suggests that MAP2c also may regulate processes other than microtubule dynamics.Cytoskeletal microtubule-associated proteins (MAPs) 3 are proteins of critical importance for regulating the stability and dynamics of microtubules (1). MAP2 and Tau represent MAP subfamilies expressed in neurons; MAP2 is localized in dendrites, whereas Tau is found mainly in axons (2). Tau and MAP2 belong to the class of intrinsically disordered proteins (IDPs), which lack a unique structure and which exist in multiple, quickly interconverting conformations (3-7). NMR is the method of choice for structural investigation of this type of protein. Tau and MAP2 differ in their N-terminal projection domains, which contain acidic and proline-rich subdomains, whereas the C-terminal parts, containing the microtubulebinding domain (MTBD) and the C-terminal region, are homologous (8). Tau is expressed in several splice variants. The human brain isoforms differ in the number of microtubulebinding regions (MTBRs) in the C-terminal portion and in the presence of two inserts near the N terminus. For the sake of simplicity, only the 441-residue variant lacking exons 6, 8, and 10 (9) is discussed in this paper. This variant has been studied in detail and was shown to form paired helical filaments and neurofibillary tangles in brains of patients suffering from Alzheimer's disease (10). The MAP2 family is composed of two high-molecular-weight proteins, MAP2a and MAP2b, each consisting of 1830 amino acids, and two low-molecular-weight proteins, MAP2c and MAP2d, consisting of 467 and 498 amino acids, respectively. The ...

show abstract

Section: Sequence-based Prediction Of Phosphorylation Sitesmentioning

confidence: 98%

Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau

Jansen

Melková

Trošanová

et al. 2017

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…34,35 We were able to predict a potential kinase group, family and/or subfamily for 30 out of 94 upregulated phosphosites (32%) and 33 out of 126 downregulated phosphosites (26%) (ESI, † Table S3). For the background set, Fig.…”

Section: -Fold Regulated Upon 007-am Stimulationmentioning

confidence: 99%

Quantitative global phosphoproteomics of human umbilical vein endothelial cells after activation of the Rap signaling pathway

et al. 2013

View full text Add to dashboard Cite

The small GTPase Rap1 is required for proper cell-cell junction formation and also plays a key role in mediating cAMP-induced tightening of adherens junctions and subsequent increased barrier function of endothelial cells. To further study how Rap1 controls barrier function, we performed quantitative global phosphoproteomics in human umbilical vein endothelial cells (HUVECs) prior to and after Rap1 activation by the Epac-selective cAMP analog 8-pCPT-2 0 -O-Me-cAMP-AM (007-AM). Tryptic digests were labeled using stable isotope dimethyl labeling, enriched with phosphopeptides by strong cation exchange (SCX), followed by titanium(IV) immobilized metal affinity chromatography (Ti 4+ -IMAC) and analyzed by high resolution mass spectrometry. We identified 19 859 unique phosphopeptides containing 17 278 unique phosphosites on 4594 phosphoproteins, providing the largest HUVEC phosphoproteome to date. Of all identified phosphosites, 220 (B1%) were more than 1.5-fold up-or downregulated upon Rap activation, in two independent experiments. Compatible with the function of Rap1, these alterations were found predominantly in proteins regulating the actin cytoskeleton, cell-cell junctions and cell adhesion.

show abstract

“…A high-level threshold was selected for GPS 3.0. For NetPhos 3.1, serine, threonine and tyrosine residues with a score of 0.5 were considered as phosphorylated [31,32]. The web-server iPTM-mLys, (http://www.jci-bioinfo.cn/iPTM-mLys) the first multi label PTM predictor was used to predict the identifying lysine PTM sites [33,34,35].…”

Section: Prediction Of Post -Translational Modification Sitesmentioning

confidence: 99%

Untitled

2017

RJLBPCS

View full text Add to dashboard Cite

Aim: Proliferating cell nuclear antigen (PCNA) is an ancillary protein that assists in DNA replication and DNA repair process. Detection of mutations in PCNA gene or protein could be helpful to analyze many disorders relating to DNA replication and repair. In the present study, non-synonymous single nucleotide polymorphisms (nsSNPs) generated by missense mutation were studied using different computational methods to evaluate the nsSNPs that may be deleterious to PCNA function.Method: The missense nsSNPs were retrieved from the database of NCBI and subjected to functional prediction by the computational algorithms. The evolutionary conservation data of the PCNA protein was obtained from the ConSurf web server. The protein structural analysis for the variants was performed using I-Mutant, SPDB viewer and YASARA to check their structural variations and energy minimizations. Results: Out of the 42 nsSNPs, 5 nsSNPs namely rs780735449 (Q38R), rs1050525 (S39R), rs781573975 (E104G), rs772308650 (L182W) and rs753494859 (K248N) were identified as deleterious by using different computational algorithms. The evolutionary conservation data revealed that all the high risk nsSNPs positions were highly conserved and were either functional or structural residues in the protein. The I-Mutant tool had showed a decrease in the protein stability for the five high risk nsSNPs. A deviance in the energy minimization was observed for the variants with respect to the native protein. The RMSD (root mean square deviation) and TM (template modeling) values predicted that the mutants were structurally similar to the wild type protein. The PTM (post translational modifications) analysis using various in silico tools showed that S39R and K248N were putative PTM sites and through FTSite it was observed that these two variants were also involved in the ligand binding sites.Conclusion: Through the robust use of various in silico tools, five nsSNPs of PCNA protein were found to deleterious. Out of them two mutations at 39th and 248th positions (S39R & K248N) are to be further validated for their effect on the PCNA protein function.

show abstract

GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection

Cited by 230 publications

References 15 publications

Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau

Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau

Quantitative global phosphoproteomics of human umbilical vein endothelial cells after activation of the Rap signaling pathway

Untitled

Contact Info

Product

Resources

About