Pan-Cancer Landscape of Spatial PTM and Mutation Clusters Reveals Allosteric Regulation of Protein–Protein Interactions

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Abstract
Post-translational modifications (PTMs) and somatic mutations are pervasive in cancer, yet their three-dimensional organization and coordinated regulatory mechanisms within protein–protein interactions (PPIs) remain poorly understood. Here we develop ClusTar, a structural framework that systematically identifies spatial clusters of PTMs and mutations within PPIs and links them to protein dynamics and functional regulation. Integrating TCGA genomics, CPTAC proteomics, and structural PPI data across ten cancer types, we identify 3,966 high-confidence PTM–mutation clusters that are enriched in functional residues and frequently overlap with ligand-binding pockets. Dynamics analyses reveal that many clusters are mechanically coupled to PPI interfaces and mediate long-range allosteric communications. In RhoA complexes, glutamine substitutions at acetylated lysine sites (K7Q, K18Q, K104Q and K118Q/K162Q) have been observed to redistribute key network hubs and rewire allosteric communication pathways among clustered residues. Experimental validation demonstrates that these mutations strengthen protein interactions and promote breast cancer cell migration, highlighting their potential as allosteric hotspots. Together, our results establish a pan-cancer structural atlas of PTM–mutation clusters and highlight allosteric hotspots as potential targets for modulating PPIs.
Funding Information
  • Priority Academic Program Development of Jiangsu Higher Education Institutions
  • Natural Science Foundation for Higher Education Institutions of Jiangsu Province, China
  • National Natural Science Foundation of China
  • Natural Science Foundation of Jiangsu Province, China
  • Basic research program of Jiangsu (BK20255001)

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