Phenylglyoxal (PGO), known to cause post-translational modifications of Arg residues, was used to highlight the role of arginine residues of the F 1 F O-ATPase, which may be crucial to yield for the mitochondrial permeability transition pore (mPTP). In swine heart mitochondria PGO inhibits ATP hydrolysis by the F 1 F O-ATPase either sustained by the natural cofactor Mg 2+ or by Ca 2+ by a similar uncompetitive inhibition mechanism, namely the tertiary complex (ESI) only forms when the ATP substrate is already bound to the enzyme, and with similar strength, as shown by the similar K'i values (0.82±0.07 mM in presence of Mg 2+ and 0.64±0.05 mM in the presence of Ca 2+). Multiple inhibitor analysis indicates that features of the F 1 catalytic sites and/or the F O proton binding sites are apparently unaffected by PGO. However, PGO and F 1 or F O inhibitors can bind the enzyme combine simultaneously. However they mutually hinder to bind the Mg 2+-activated F 1 F O-ATPase, whereas they do not mutually exclude to bind for the Ca 2+-activated F 1 F O-ATPase. The putative formation of PGO-arginine adducts, and the consequent spatial rearrangement in the enzyme structure, inhibits the F 1 F O-ATPase activity but, as shown by the calcium retention capacity evaluation in intact mitochondria, apparently favours the mPTP formation.