Browsing by Author "Malkamäki, Aapo"

In mitochondria and many bacteria, the electron transport chain produces energy from foodstuff as a part of cell respiration. Complex IV, also known as Cytochrome c Oxidase, is the last protein complex in the electron transport chain. It couples electron transport with the transfer of protons across the inner mitochondrial membrane (or the cell membrane in bacteria). The pumped protons produce a proton-motive force, which drives adenosine triphosphate synthase to generate adenosine triphosphate molecules used as energy currency in many cellular functions. Dysfunction of complex IV may cause myopathies and other mitochondrial malfunctions, and therefore it is important to understand how this enzyme functions and is regulated. The work performed in this Thesis provides novel insights into the intricate function of the enzyme and reveals the importance of lipid-protein interactions that turn out to be critical in the enzyme function. These insights provide new ways to better understand how cardiolipin as a key lipid in mitochondrial membranes participates in proton uptake pathways, and whether cardiolipin also has an important role in complex IV dimerization. Six large-scale atomistic molecular dynamics simulations of complex IV were performed, including simulations of the dimeric as well as the monomeric complex IV. In each simulation, the membrane consisted of three kinds of primary lipids found in the inner mitochondrial membrane. All the simulations were two to three microseconds long, therefore representing the current state-of-the-art in membrane-protein simulations in this context. The simulation data show that the dimeric complex IV is stable. The data also reveal that there are fewer protein-protein ion pairs between complex IV monomers in the presence of cardiolipins at the interface, however cardiolipin could also function as glue forming charge-charge interactions with both of the monomers. Cardiolipin-complex IV interactions seem to have more significance compared to other lipid-complex IV interactions, favoring the earlier proposals that cardiolipins are possibly involved in proton uptake. The monomeric complex IV was observed to tilt 5-10 degrees with respect to the initial position of the protein and membrane normal, while for the dimeric complex IV no tilt was observed. The difference in tilt might work as a free energy barrier in dimerization. It is also suggested that cardiolipins between the monomers could reduce the possible free energy barrier in dimerization. Understanding of these microscopic aspects by means of molecular dynamics simulations may open up new avenues to target mitochondrial dysfunctions.