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The $\alpha$ and $\beta$ subunits comprising the hexameric assembly ofF1-ATPase share a high degree of structural identity, though low primaryidentity. Each subunit binds nucleotide in similar pockets, yet only $\beta$subunits are catalytically active. Why? We re-examine their internal symmetryaxes and observe interesting differences. Dividing each chain into anN-terminal head region, a C-terminal foot region, and a central torso, weobserve (1) that while the foot and head regions in all chains obtain high andsimilar mobility, the torsos obtain different mobility profiles, with the$\beta$ subunits exhibiting a higher motility compared to the $\alpha$subunits, a trend supported by the crystallographic B-factors. The $\beta$subunits have greater torso mobility by having fewer distributed, nonlocalpacking interactions providing a spacious and soft connectivity, and offsettingthe resultant softness with local stiffness elements, including an additional$\beta$ sheet. (2) A loop near the nucleotide binding-domain of the $\beta$subunits, absent in the $\alpha$ subunits, swings to create a large variationin the occlusion of the nucleotide binding region. (3) A combination of thesoftest three eigenmodes significantly reduces the RMSD between the open andclosed conformations of the $\beta$ subnits. (4) Comparisons of computed andobserved crystallographic B-factors suggest a suppression of a particularsymmetry axis in an $\alpha$ subunit. (5) Unexpectedly, the soft intra-monomeroscillations pertain to distortions that do not create inter-monomer stericclashes in the assembly, suggesting that structural optimization of theassembly evolved at all levels of complexity.

structural dynamics

A comparison of the innate flexibilities of six chains in F$_1$-ATPase  with identical secondary and tertiary folds; 3 active enzymes and 3  structural proteins