Cellular function is powered by mitochondria through an energy conversion process known as oxidative phosphorylation. Central to this process is respiratory complex I, an enzyme that couples NADH oxidation with ubiquinone reduction and the pumping of protons across the inner mitochondrial membrane. In this thesis, the mechanistic principles of complex I were investigated using multi-scale simulations, including atomistic molecular dynamics simulations and hybrid quantum/classical mechanics (QM/MM) calculations. We found that complex I drives quinone reduction and proton pumping through a network of buried charged residues. These residues couple protonation changes to conformational shifts, electrostatic interactions, and modulations of the hydration dynamics. Additionally, we expanded the applicability of QM/MM to long-range protonation dynamics by developing a novel sampling scheme. This scheme combines advanced sampling methods with a general reaction coordinate to provide a quantitative description of hydration dynamics and conformational changes during proton transfer reactions, which are indispensable for understanding the function of the respiratory enzymes. We further investigated the molecular details of how and why respiratory complexes cluster together to form supercomplexes. Our findings indicate that membrane proteins alter the membrane properties and introduce strain, which could drive the formation of these assemblies. The combined mechanistic findings of this thesis enhance our understanding of respiratory complex I and supercomplexes and their underlying proton transfer reactions, conformational changes, and enzymatic activity.