phosphorylation
Definition
Phosphorylation is a post-translational modification where a phosphate group (PO₄³⁻) is enzymatically added to a protein, typically to serine, threonine, or tyrosine residues. This reversible modification is catalyzed by kinases and reversed by phosphatases, serving as a critical regulatory mechanism in cellular signaling. Phosphorylation can alter protein function, localization, stability, and interactions with other molecules. It plays essential roles in signal transduction cascades, cell cycle regulation, metabolism, and cellular responses to environmental stimuli. In proteomics research, phosphorylation site identification and quantification reveal dynamic cellular states and signaling pathway activity, making it a key focus in understanding disease mechanisms, drug responses, and cellular behavior under various conditions.
Visualize phosphorylation in Nodes Bio
Researchers can map phosphorylation events as network edges connecting kinases to substrate proteins, revealing signaling cascades and regulatory hierarchies. Nodes Bio enables visualization of phosphoproteomic datasets where phosphorylation sites become nodes linked to upstream kinases and downstream effectors. Users can overlay quantitative phosphorylation changes across conditions, identify activated pathways, and trace signal propagation through multi-layered protein interaction networks to understand cellular responses.
Visualization Ideas:
- Kinase-substrate networks showing phosphorylation cascades with temporal dynamics
- Differential phosphorylation heatmaps overlaid on signaling pathway networks
- Multi-omics integration connecting phosphoproteomics data with gene expression and protein abundance
Example Use Case
A cancer researcher investigating resistance to tyrosine kinase inhibitors performs phosphoproteomics on drug-sensitive versus resistant cell lines. Mass spectrometry identifies 2,500 differentially phosphorylated sites. By mapping these phosphorylation events onto kinase-substrate networks, the researcher discovers hyperactivation of alternative receptor tyrosine kinases and downstream AKT/mTOR pathway components in resistant cells. Network analysis reveals compensatory signaling mechanisms bypassing the inhibited target, suggesting combination therapy strategies targeting both the original kinase and the newly activated pathways to overcome resistance.