post-translational modification
Definition
Post-translational modifications (PTMs) are chemical alterations that occur to proteins after their synthesis by ribosomes. These modifications, including phosphorylation, acetylation, ubiquitination, methylation, and glycosylation, regulate protein function, localization, stability, and interactions. PTMs are critical for cellular signaling, gene expression, and metabolic regulation. Over 400 types of PTMs have been identified, affecting the majority of proteins in cells. Mass spectrometry-based proteomics has revolutionized PTM detection, enabling researchers to map modification sites and quantify their dynamics. Understanding PTMs is essential for deciphering disease mechanisms, as aberrant modifications are implicated in cancer, neurodegeneration, and metabolic disorders. PTMs create functional diversity from a limited genome, allowing cells to rapidly respond to environmental changes without new protein synthesis.
Visualize post-translational modification in Nodes Bio
Researchers can visualize PTM networks in Nodes Bio by mapping modified proteins as nodes and their regulatory relationships as edges. Network analysis reveals how kinases, phosphatases, and other modifying enzymes control signaling cascades. Users can integrate PTM data from mass spectrometry with protein-protein interaction networks to identify modification-dependent complexes, visualize crosstalk between different PTM types, and discover novel regulatory hubs that coordinate cellular responses to stimuli.
Visualization Ideas:
- Kinase-substrate networks showing phosphorylation cascades and signaling pathways
- PTM crosstalk networks displaying interactions between different modification types on the same proteins
- Temporal PTM dynamics networks tracking modification changes across experimental conditions or disease progression
Example Use Case
A cancer research team investigating drug resistance in melanoma uses phosphoproteomics to identify changes in protein phosphorylation after BRAF inhibitor treatment. They discover that resistant cells exhibit hyperphosphorylation of receptor tyrosine kinases and downstream MAPK pathway components. By visualizing these phosphorylation networks in Nodes Bio, they identify a previously unknown feedback loop involving MEK phosphorylation sites that bypass BRAF inhibition. This network analysis reveals combination therapy targets, leading to a clinical trial testing dual BRAF-MEK inhibition with a third agent targeting the identified resistance node.