We have recently proposed the "packing exchange mechanism" for F-1-ATPase, wherein the perturbation by a substrate binding/release or an ATP hydrolysis is followed by the reorganization of the asymmetric packing structure of the alpha(3)beta(3) complex, accompanying the gamma subunit rotation. As part of a further investigation of this rotational mechanism, we performed all-atom molecular dynamics simulations for yeast F-1-ATPase both before and after a 16 degrees rotation of the gamma subunit triggered by a Pi release. We analyzed the structural fluctuations, the subunit interface interactions, and the dynamics of the relative subunit arrangements before and after the rotation. We found that with the Pi release the alpha(E)beta(E) subunit interface becomes looser, which also allosterically makes the alpha(DP)beta(DP) subunit interface looser. This structural communication between these interfaces takes place through a tightening of the alpha(TP)beta(TP) subunit interface. The gamma subunit interacts less strongly with alpha(DP) and beta(DP) and more strongly with alpha(TP) and beta(TP). After the Pi release, the tightly packed interfaces are reorganized from the interfaces around beta(DP) to those around beta(TP), inducing the 16 degrees rotation. These results, which are consistent with the packing exchange mechanism, allow us to deduce a view of the structural change during the 40 degrees rotation.