Why and how does the proton travelling through the stalked particle in the inner mitochondrial membrane, cause a conformational change in the ATPase?
The passage of protons through the FO (membrane) portion of the molecule (driven by the electrochemical gradient of protons across the respiratory membrane) generates torque at the interface between the a and c subunits. This mean that the ring of 10 c subunits rotates relative to the a subunit. The γ subunit in the stalk rotates along with the ring of c subunits, while the ring of α and β subunits in F1 is constrained to remain static with respect to the a subunit because of the interaction with the δ and b subunits (forming the peripheral stalk). So we have two portions of the molecule the "static" a-b2-δ-α3β3 part and the rotating c10-γ-ε part. The γ subunit rotates within the α3β3 part of F1 and drives a three-step cycle of conformational changes (via intersubunit interactions) which are linked to the phosphorylation of ADP.
There is a useful animation here illustrating the three step catalytic cycle being driven by the rotation of the γ subunit.
(image from Aksimentiev et al. (2004) Insights into the molecular mechanism of rotation in the FO sector of ATP synthase. Biophys J. 86:1332-44)