Browsing by Author "Aho, Noora"

Cytochrome bc1, also known as complex III, is the third enzyme of the electron transfer chain in cellular respiration, which is the main process generating energy in living cells. Complex III operates by oxidizing ubiquinol, and transferring two electrons to cytochrome c, while reducing ubiquinone. The electron transfer is coupled to proton translocation across the inner mitochondrial membrane. Thus, complex III contributes to generation of a proton electrochemical gradient, which is required for the function of ATP synthase. Cardiolipins (CLs), constituting up to 20 mol % of lipids in the inner mitochondrial membrane, have an important role in the structure and dynamics of the membrane, as well as in maintaining the correct function of the whole electron transfer chain. Cardiolipins are especially vulnerable to oxidation by reactive oxygen species (ROS) due to their dimeric structure with four doubly unsaturated acyl chains. Cytochrome bc1 is one of the main producers of ROS in mitochondria, increasing the exposure of tightly bound CLs to oxidation. Oxidative stress and CL oxidation have been associated with, for instance, programmed cell death and aging, and developing Alzheimer's and Parkinson's diseases. The objective of this thesis was to build a new computational model of cytochrome bc1 in a membrane, and to study the lipid interactions of complex III using atomistic molecular dynamics simulations. A model system with a high-resolution structure of complex III, embedded in a multicomponent bilayer mimicking the inner mitochondrial membrane was constructed. Four atomistic simulations of 1 μs each were performed to reveal possible cardiolipin binding sites and to examine the effects of CL oxidation on the complex. Altogether, eight CL binding sites on cytochrome bc1 were found, out of which two have not been suggested previously. The key residues of each binding site were listed, to compare with earlier results, and to identify the new binding sites in detail. In order to investigate the effects of CL oxidation, carboxylic acid and hydroperoxyl groups were attached to the acyl chains of three crystallographically resolved CLs. The oxidized region of the CL tails changed the nature of interactions with the protein and the surrounding water. As the tail was oxidized, the results showed an increase in the number of water molecules surrounding it. Additionally, the oxidized tails were found to affect the configuration of CL by bending the tail towards the lipid headgroup, or by reaching out to the water interface of the opposite leaflet. Normally, the acyl chains of CL mostly interact with the nonpolar residues of the protein. After oxidation, the number of polar and charged amino acids in the vicinity of the acyl chain increased.