We have investigated the role of arginine residues in the regulation of the mitochondrial permeability transition pore, a cyclosporin A-sensitive inner membrane channel. Isolated rat liver mitochondria were treated with the arginine-specific chemical reagent 2,3-butanedione or phenylglyoxal, followed by removal of excess free reagent. After this treatment, mitochondria accumulated Ca 2؉ normally, but did not undergo permeability transition following depolarization, a condition that normally triggers opening of the permeability transition pore. Inhibition by 2,3-butanedione and phenylglyoxal correlated with matrix pH, suggesting that the relevant arginine(s) are exposed to the matrix aqueous phase. Inhibition by 2,3-butanedione was potentiated by borate and was reversed upon its removal, whereas inhibition by phenylglyoxal was irreversible. Treatment with 2,3-butanedione or phenylglyoxal after induction of the permeability transition by Ca 2؉ overload resulted in pore closure despite the presence of 0.5 mM Ca
2؉. At concentrations that were fully effective at inhibiting the permeability transition, these arginine reagents (i) had no effect on the isomerase activity of cyclophilin D and (ii) did not affect the rate of ATP translocation and hydrolysis, as measured by the production of a membrane potential upon ATP addition in the presence of rotenone. We conclude that reaction with 2,3-butanedione and phenylglyoxal results in a stable chemical modification of critical arginine residue(s) located on the matrix side of the inner membrane, which, in turn, strongly favors a closed state of the pore.Mammalian mitochondria contain an inner membrane channel, the permeability transition pore (PTP) 1 , that, when fully open, permits free diffusion of solutes with a molecular mass of up to ϳ1500 Da (1, 2). The PTP is controlled by several ligands as well as by the ⌬⌿ across the inner membrane; high values of ⌬⌿ favor the closed state, whereas a decrease in ⌬⌿ may increase the open probability (3). High matrix Ca 2ϩ concentrations, P i , and oxidation of intramitochondrial pyridine nucleotides promote pore opening, whereas ADP, H ϩ , and CsA cause inhibition (1, 2). CsA binds to mitochondrial matrix CyP-D (4), which may cause pore inhibition by releasing CyP-D from its putative binding sites on the pore (5, 6). Based on the effect of atractyloside and bongkrekate on the permeability transition (7) and based on the finding that the ANT may form a Ca 2ϩ -dependent large conductance channel in phospholipid bilayers (8), it has been suggested that the pore may be formed by the ANT (7).The physiological function of the permeability transition is not known, but circumstantial evidence suggests that it is involved in Ca 2ϩ homeostasis (9, 10) and linked to cell death. This notion has gained momentum with the findings that (i) Bax and Bcl-XL , two channel-forming proteins of the Bcl-2 superfamily localized mainly to mitochondria (11,12), may affect the PTP and therefore release of the apoptosis-inducing factor, a mitochondrial caspa...