To test whether long-chain fatty acyl-CoA esters link obesity with type 2 diabetes through inhibition of the mitochondrial adenine nucleotide translocator, we applied a system-biology approach, dual modular kinetic analysis, with mitochondrial membrane potential (⌬) and the fraction of matrix ATP as intermediates. We found that 5 mol/l palmitoyl-CoA inhibited adenine nucleotide translocator, without direct effect on other components of oxidative phosphorylation. Indirect effects depended on how oxidative phosphorylation was regulated. When the electron donor and phosphate acceptor were in excess, and the mitochondrial "work" flux was allowed to vary, palmitoyl-CoA decreased phosphorylation flux by 38% and the fraction of ATP in the medium by 39%. ⌬ increased by 15 mV, and the fraction of matrix ATP increased by 46%. Palmitoyl-CoA had a stronger effect when the flux through the mitochondrial electron transfer chain was maintained constant: ⌬ increased by 27 mV, and the fraction of matrix ATP increased 2.6 times. When oxidative phosphorylation flux was kept constant by adjusting the rate using hexokinase, ⌬ and the fraction of ATP were not affected. Palmitoyl-CoA increased the extramitochondrial AMP concentration significantly. The effects of palmitoyl-CoA in our model system support the proposed mechanism linking obesity and type 2 diabetes through an effect on adenine nucleotide translocator. Diabetes 54:944 -951, 2005 O besity is a common finding in patients with type 2 diabetes (1-3). Numerous studies suggest that the oversupply of lipid to nonadipose tissues might result in lipotoxicity and contribute to the development of the insulin resistance syndrome and type 2 diabetes (4,5). The molecular mechanisms responsible for lipotoxicity, insulin resistance, and -cell dysfunction are not fully understood. It is particularly confusing that so many processes appear to be affected at the same time, but not always to the same extent, and often in paradoxical ways.It has been hypothesized that inhibition of the mitochondrial adenine nucleotide translocator by long-chain fatty acyl-CoA esters, the active form of fatty acids, may be an important link between obesity and type 2 diabetes (6,7). Adenine nucleotide translocator is an enzyme that catalyzes the exchange of mitochondrial ATP for cytosolic ADP (8). It was shown that long-chain fatty acyl-CoA esters are potent inhibitors of adenine nucleotide translocator from both the cytosolic and the matrix side of the inner mitochondrial membrane (9). It was proposed that accumulation of long-chain fatty acyl-CoA esters in the cell and subsequent inhibition of adenine nucleotide translocator could lead to an increase in the matrix ATP-to-ADP ratio, membrane potential (⌬; i.e., electric potential across the inner mitochondrial membrane [out minus in]), and oxygen free radical production. In -cells, like in other cells (10), an initial increase in O 2 ⅐ Ϫ (superoxide anion radical) production could stimulate cell growth and contribute to compensatory hyperinsulinemia. Later ...