Mitochondrial F₀F₁ ATP synthase. Subunit regions on the F₁ motor shielded by F₀, functional significance, and evidence for an involvement of the unique F₀ subunit F₆

Studies reported here were undertaken to gain greater molecular insight into the complex structure of mitochondrial ATP synthase (F₀F₁) and its relationship to the enzyme's function and motor-related properties. Significantly, these studies, which employed N-terminal sequence, mass spectral, proteolytic, immunological, and functional analyses, led to the following novel findings. First, at the top of F₁ within F₀F₁, all six N-terminal regions derived from α + β subunits are shielded, indicating that one or more F₀ subunits forms a 'cap.' Second, at the bottom of F₁ within F₀F₁, the N-terminal region of the single δ subunit and the C-terminal regions of all three α subunits are shielded also by F₀. Third, and in contrast, part of the γ subunit located at the bottom of F₁ is already shielded in F₁, indicating that there is a preferential propensity for interaction with other F₁ subunits, most likely δ and ε. Fourth, and consistent with the first two conclusions above that specific regions at the top and bottom of F₁ are shielded by F₀, further proteolytic shaving of α and β subunits at these locations eliminates the capacity of F₁ to couple a proton gradient to ATP synthesis. Finally, evidence was obtained that the F₀ subunit called 'F₆,' unique to animal ATP synthases, is involved in shielding F₁. The significance of the studies reported here, in relation to current views about ATP synthase structure and function in animal mitochondria, is discussed.