I) 1 is a large enzyme that catalyzes the oxidation of NADH by ubiquinone coupled to proton translocation across the inner membrane (1, 2). There are a variety of inhibitors of mitochondrial complex I and with the exception of a few inhibitors which inhibit electron input into the enzyme (3, 4), all inhibitors act at or close to the ubiquinone reduction site (5). Among the inhibitors, positively charged neurotoxic N-methyl-4-phenylpyridinium (MPP ϩ ) and its alkyl analogues exhibit unique inhibitory behavior with bovine heart mitochondrial complex I (6). A series of studies of the inhibition mechanism of MPP ϩ analogues by Singer and colleagues (6 -10) have suggested that MPP ϩ analogues are bound at two sites in the enzyme, one accessible to relatively hydrophilic inhibitors (termed the "hydrophilic site") and one shielded by a hydrophobic barrier on the enzyme (the "hydrophobic site"), and that occupation of both sites is required for complete inhibition. This concept may be helpful in elucidating the terminal electron transfer step in complex I and seems to be consistent with the existence of two EPR-detectable species of complex I-associated ubisemiquinones (11,12). Some experimental results with ordinary complex I inhibitors (13-16) can be explained by assuming the existence of more than one inhibitor (or ubiquinone) binding site.In the previous study (17), we synthesized a series of MPP ϩ analogues which are much more potent than the original MPP ϩ and demonstrated that the presence of hydrophobic counteranion tetraphenylboron (TPB Ϫ ) potentiates the inhibition by MPP ϩ analogues differently depending upon the molar ratio of TPB Ϫ to the inhibitors. In the presence of a catalytic amount of TPB Ϫ , the inhibitory potency of MPP ϩ analogues was markedly enhanced, and the extent of inhibition was almost complete. The presence of an excess amount of TPB Ϫ partially reactivated the enzyme activity, and the inhibition was partly saturated (ϳ50%). This complicated inhibitory behavior could be explained by the dual binding sites model mentioned above (6), which supposes quite different hydrophobic natures of the two sites and/or their environments.If there are indeed two distinct binding sites of MPP ϩ analogues in bovine complex I, there should be specific inhibitors which act selectively at one of the two proposed binding sites since it is unlikely that the structural properties of the two sites are completely identical. We have synthesized such a selective inhibitor, MP-6 (N-methyl-4-[2-(p-tert-butylbenzyl)-propyl]pyridinium, Fig. 1) (17). In the absence of TPB Ϫ , this inhibitor showed approximately 50% inhibition at 5 M in NADH-Q 1 oxidoreductase assay, but the inhibition reached a plateau at this level over a wide range of concentrations. Weak inhibition was again observed above ϳ80 M, and maximum inhibition (Ͼ90%) was obtained only when the concentration of the inhibitor was increased to ϳ250 M. Such a marked biphasic nature of the does-response curve has not been reported previously for usual complex I i...