Cyclophilin D reduces Ca2+ sequestration by complement 1q binding protein

Complement 1q binding protein (C1qBP) and cyclophilin D (CypD) are mitochondrial matrix proteins; C1qBP has been implicated in many cellular processes, including the regulation of oxidative phosphorylation, and CypD is widely associated with the regulation of mitochondrial permeability transition pore (mPTP) opening. In this study, C1qBP and CypD were shown, in vitro, to form a stable protein-protein complex. CypD-C1qBP interaction was disrupted by cyclosporin A and compromised by mutations of the CypD active site residues R55 and R82. AlphaFold protein modelling revealed that the large negatively charged surface of C1qBP binds to the positive surface of CypD. This electrostatically driven interaction was confirmed by the pH dependence of the protein-protein interaction, with lower affinities observed at higher pH values. C1qBP was shown to undergo conformational changes when bound to Ca2+ in vitro, conferring multiple Ca2+ interaction sites in a multi-phase process, thereby indicating that C1qBP may act as a Ca2+ sequester. In contrast, CypD binding to C1qBP diminished the Ca2+-induced conformational changes in C1qBP, lowering its Ca2+-binding capacity. Our findings suggest that C1qBP functions as a mitochondrial Ca2+ chelator, with its efficiency reduced by CypD, this most likely due to CypD and Ca2+ both competing for the same negative surface of C1qBP. The parallels between the features of CypD-C1qBP interaction and the regulation of Ca2+-dependent mPTP opening by CypD highlight a possible functional role of CypD which has so far been elusive.