The human calmodulin interactome reveals functional diversity linking calcium signaling to transcriptional regulation

Calcium-calmodulin signaling represents a central mechanism through which intracellular calcium fluctuations coordinate diverse cellular processes. Despite the identification of numerous calmodulin binding proteins, a systems level understanding of how these interactions integrate into global signaling networks and influence disease relevant pathways remains incomplete. Here, we constructed a comprehensive human calmodulin interactome by integrating experimentally validated protein-protein interactions from the IntAct and BioGRID databases, identifying 919 calmodulin associated proteins. Network analysis revealed highly connected hub proteins, including SRC and UBC, and delineated three major functional clusters enriched in translational machinery, calcium dependent kinase signaling, and actin cytoskeleton organization. Functional enrichment analyses further highlighted strong associations with phosphosignaling pathways, cytoskeletal dynamics, and hormone mediated signaling processes. Further, classification of interactome into functional categories of interest identified 102 kinases, 16 phosphatases, 24 metabolic enzymes, 29 ion channel proteins, and 56 transcription factors, underscoring the broad regulatory scope of calmodulin signaling. Integration and evaluation of publicly available calcium perturbation proteomics datasets to assess potential Ca²⁺-dependent and Ca²⁺-independent calmodulin interactions identified 43 presumed calmodulin-interacting proteins exhibiting consistent calcium-responsive regulation. Importantly, kinase substrate network mapping revealed that 46 presumed calmodulin interacting kinases phosphorylate 155 human transcription factors, suggesting formation of an extensive calmodulin linked phospho-regulatory transcriptional network. Collectively, these findings establish a systems level framework of the calmodulin signaling axis and highlight its potential relevance in transcriptional regulation, providing a resource for future mechanistic and therapeutic investigations.