Structural characteristics of yeast F1-ATPase before and after 16-degree rotation of the γ subunit: Theoretical analysis focused on the water-entropy effect

We have recently proposed a novel picture of the rotation mechanism for F-1-ATPase [T. Yoshidome, Y. Ito, M. Ikeguchi, and M. Kinoshita, J. Am. Chem. Soc. 133, 4030 (2011)]. In the picture, the asymmetric packing in F-1-ATPase, originating from the water-entropy effect, plays the key role in the rotation. Here, we analyze the differences between the experimentally determined structures of yeast F-1-ATPase before and after 16 degrees rotation of the gamma subunit with the emphasis on the water-entropy effect. For each of these structures, we calculate the hydration entropies of three sub-complexes comprising the gamma subunit, one of the beta subunits, and two alpha subunits adjacent to them. The beta(E), beta(TP), and beta(DP) subunits are involved in sub-complexes I, II, and III, respectively. The calculation is performed using a hybrid of the angle-dependent integral equation theory combined with the molecular model for water and the morphometric approach. The absolute value of the hydration entropy is in the following order: sub-complex I > sub-complex II > sub-complex III. The packing efficiency of the sub-complex follows the opposite order. The rotation gives rise to less efficient packing in sub-complex III and a corresponding water-entropy loss. However, the other two sub-complexes, accompanying water-entropy gains, become more efficiently packed. These results are consistent with our picture of the rotation mechanism, supporting its validity. The water-entropy analysis shows that the interfaces of alpha(DP)-beta(DP) and alpha(E)-beta(E) become more open after the rotation, which is in accord with the experimental observation. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4734298]