Molecular dynamics reveals a novel Regulatory Ca²⁺-Binding Site in the Mitochondrial Calcium Uniporter

The mitochondrial Ca²⁺uniporter (MCU) plays essential roles in energy production, cytosolic Ca²⁺signaling, and regulation of cell death. The activity of this channel complex is modulated by Mitochondrial Calcium Uptake 1 (MICU1) and Mitochondrial Calcium Uptake 2 (MICU2) proteins in response to Ca²⁺levels. In cardiomyocytes, MICU1 inhibits the uniporter in resting cells while it activates it during contraction when bound to Ca²⁺. Despite its importance, the structural mechanisms driving MICU1’s open-close switch remain unclear.

In this study, we used structural modeling combined with molecular dynamics simulations to investigate MICU1’s conformational dynamics under varying Ca²⁺concentrations. Our analysis identified a previously uncharacterized pseudo-EF-hand motif (pEF-h) that acts as an early calcium sensor, initiating conformational transitions that prime canonical EF-hand sites for subsequent calcium binding. Calcium binding induces substantial structural changes in MICU1, including a decrease in isoelectric point, shifts in surface charge distribution, and significant reductions in cavity volume, length, and hydrophobicity. Notably, a 53.4% reduction in intermolecular distances between key domains was observed during the transition from the apo to the Ca²⁺-bound state.

These findings uncover a previously overlooked hierarchical activation of MICU1’s calcium-binding sites and provide new mechanistic insights into the regulation of MCU. This enhanced understanding of mitochondrial calcium signaling paves new ways to potential novel therapeutic strategies targeting calcium dysregulation in metabolic, cardiovascular, and neurodegenerative diseases.