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Why and how does the proton travelling through the stalked particle in the inner mitochondrial membrane, cause a conformational change in the ATPase?

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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)

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For me, ATP synthase is one of the most remarkable features of the cell. Beautiful. –  Poshpaws Feb 16 '13 at 19:48
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