Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks

@article{Olsen2006GlobalIV,
  title={Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks},
  author={Jesper V. Olsen and Blagoy S. Blagoev and Florian Gnad and Boris Ma{\vc}ek and Chanchal Kumar and Peter Mortensen and Matthias Mann},
  journal={Cell},
  year={2006},
  volume={127},
  pages={635-648}
}

Figures and Tables from this paper

Systematic Discovery of In Vivo Phosphorylation Networks
Monitoring Cellular Phosphorylation Signaling Pathways into Chromatin and Down to the Gene Level*
TLDR
The results showed that PS-ChAP offers a new strategy for studying cellular signaling and chromatin biology, allowing us to directly and comprehensively investigate phosphorylation signaling into chromatin to investigate if these pathways are involved in altering gene expression.
Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins
TLDR
This work combines for the first time dynamic properties of the phosphoproteome with protein structural features and suggests that the structural organization of the region in which a phosphorylation site resides may serve as an additional control mechanism.
Quantitative Site-specific Phosphorylation Dynamics of Human Protein Kinases during Mitotic Progression*
TLDR
The data cover most of the already known mitotic kinases and identify attractive candidates for future studies of phosphorylation-based mitotic signaling and provide insight into the system properties of the mitotic phosphokinome.
Multisite Phosphorylation Provides an Effective and Flexible Mechanism for Switch-Like Protein Degradation
TLDR
This model explains the role of multiple phosphorylation sites, compared to a single site, in the regulation of protein degradation and suggests design principles for protein degradation switches which might be a widespread mechanism for precise regulation of cellular processes such as cell cycle progression.
The regulation of protein phosphorylation.
  • L. Johnson
  • Biology
    Biochemical Society transactions
  • 2009
TLDR
The structural consequences of protein phosphorylation are reviewed using the authors' work on glycogen phosphorylase to illustrate one of the more dramatic consequences of phosphorylate, and recent advances on protein kinases as drug targets are considered.
Physicochemical mechanisms of protein regulation by phosphorylation
TLDR
The effects of phosphorylation on protein stability, dynamics, and binding are focused on and several physico-chemical mechanisms of protein regulation through phosphorylate are described and paid particular attention to phosphorylations in protein complexes and phosphorylated in the context of disorder–order and order–disorder transitions.
Structural characterizations of phosphorylatable residues in transmembrane proteins from Arabidopsis thaliana
TLDR
The previously established conclusion that phosphorylation sites are closely associated with intrinsic disorder is found to be confirmed, and it is found that theosphorylation process may also be affected by solvent accessibility of phosphorylated sites and further promoted by neighboring modification events.
...
...

References

SHOWING 1-10 OF 66 REFERENCES
Time-resolved Mass Spectrometry of Tyrosine Phosphorylation Sites in the Epidermal Growth Factor Receptor Signaling Network Reveals Dynamic Modules*S
TLDR
A method enabling the simultaneous quantification of tyrosine phosphorylation of specific residues on dozens of key proteins in a time-resolved manner, downstream of epidermal growth factor receptor (EGFR) activation is developed.
Global analysis of protein phosphorylation in yeast
TLDR
The in vitro substrates recognized by most yeast protein kinases are described, with the use of proteome chip technology, and these results will provide insights into the mechanisms and roles of protein phosphorylation in many eukaryotes.
Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics
TLDR
A mass spectrometric method is developed that converts temporal changes to differences in peptide isotopic abundance and provides an informative perspective on cell signaling and will be crucial to modeling signaling networks in a systems biology approach.
Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry
TLDR
A sensitive approach based on multidimensional liquid chromatography/mass spectrometry is described that enables the rapid identification of numerous sites of tyrosine phosphorylation on a number of different proteins from human whole cell lysates to enable the rapid generation of new insights into signaling pathways as they occur in states of health and disease.
Immunoaffinity profiling of tyrosine phosphorylation in cancer cells
TLDR
Applying this approach to several cell systems, including cancer cell lines, shows it can be used to identify activated protein kinases and their phosphorylated substrates without prior knowledge of the signaling networks that are activated, a first step in profiling normal and oncogenic signaling networks.
The role of STATs in transcriptional control and their impact on cellular function
TLDR
The importance of STAT activation to growth control in experiments using anti-sense molecules or dominant negative STAT protein encoding constructs performed in cell lines or studies in animals lacking specific STATs strongly indicate that STATs play an important role in controlling cell cycle progression and apoptosis.
Large-scale characterization of HeLa cell nuclear phosphoproteins.
TLDR
Using a strategy based on strong cation exchange chromatography, phosphopeptides were enriched from the nuclear fraction of HeLa cell lysate and determined 2,002 phosphorylation sites, an unprecedented large collection of sites permitted a detailed accounting of known and unknown kinase motifs and substrates.
Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins
TLDR
This work states that Phospho.ELM will be a valuable tool both for molecular biologists working on protein phosphorylation sites and for bioinformaticians developing computational predictions on the specificity of phosphorylated reactions.
The ubiquitin-proteasome system and cancer.
TLDR
The ubiquitin proteasome system has emerged from obscurity to be seen as a major player in all regulatory processes in the cell and is expected to be central to cell transformation and cancer progression.
Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway*S
TLDR
Of more than 700 identified phosphopeptides, 139 were differentially regulated at least 2-fold in response to mating pheromone and among these regulated proteins were components belonging to the mitogen-activated protein kinase signaling pathway and to downstream processes including transcriptional regulation, the establishment of polarized growth, and the regulation of the cell cycle.
...
...