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Recent measurements of the flux control exerted by cytochrome c oxidase on the respiratory activity in intact cells have led to a re-appraisal of its regulatory function. We have further extended this in vivo study in the framework of the Metabolic Control Analysis and evaluated the impact of the mitochondrial transmembrane electrochemical potential (Δμ_H⁺) on the control strength of the oxidase. The results indicate that, under conditions mimicking the mitochondrial State 4 of respiration, both the flux control coefficient and the threshold value of cytochrome oxidase are modified with respect to the uncoupled condition. The results obtained are consistent with a model based on changes in the assembly state of the oxidative phosphorylation enzyme complexes and possible implications in the understanding of exercise-intolerance of human neuromuscular degenerative diseases are discussed.