Data from 31 P-nuclear magnetic resonance spectroscopy of human forearm flexor muscle were analyzed based on a previously developed model of mitochondrial oxidative phosphorylation (PLoS Comp Bio 1: e36, 2005) to test the hypothesis that substrate level (concentrations of ADP and inorganic phosphate) represents the primary signal governing the rate of mitochondrial ATP synthesis and maintaining the cellular ATP hydrolysis potential in skeletal muscle. Model-based predictions of cytoplasmic concentrations of phosphate metabolites (ATP, ADP, and Pi) matched data obtained from 20 healthy volunteers and indicated that as work rate is varied from rest to submaximal exercise commensurate increases in the rate of mitochondrial ATP synthesis are effected by changes in concentrations of available ADP and Pi. Additional data from patients with a defect of complex I of the respiratory chain and a patient with a deficiency in the mitochondrial adenine nucleotide translocase were also predicted the by the model by making the appropriate adjustments to the activities of the affected proteins associates with the defects, providing both further validation of the biophysical model of the control of oxidative phosphorylation and insight into the impact of these diseases on the ability of the cell to maintain its energetic state. computational model; mitochondria; cellular energetics; oxidative phosphorylation; 31 P-NMR spectroscopy MITOCHONDRIAL OXIDATIVE ADP phosphorylation is the primary source of ATP in skeletal muscle during aerobic exercise. Thus, to maintain the free energy state of the cytoplasmic phosphoenergetic compounds ATP, ADP, and P i , oxidative phosphorylation is modulated to match the rate of ATP utilization during exercise. It has recently been shown through computational model-based analysis of data obtained from 31 P-NMR spectroscopy of working in vivo dog hearts that the primary control mechanism operating in cardiomyocytes is feedback of substrate concentrations for ATP synthesis (5). In other words, changes in the concentrations of the products generated by the utilization of ATP in the cell, ADP and P i , effect changes in the rate at which mitochondria utilize those products to resynthesize ATP (5).Here the question of whether this same mechanism can explain the observed data on the control of oxidative metabolism in skeletal muscle is investigated. Previous analyses of 31 P-NMR spectroscopy ( 31 P-MRS) data on energy balance in exercising skeletal muscle have mainly focused on testing ADP feedback control of mitochondrial ATP synthesis using black box descriptions of the mitochondrial ATP synthetic pathway (8, 14 -16, 28), P i acceptor control (7), and thermodynamic control involving quasi-linear relations between cytoplasmic Gibbs free energy of ATP hydrolysis and mitochondrial ATP synthesis flux (13,18, 31). Yet, to date, these 31 P-MRS data have not been adequately explained based on a detailed mechanistic model of oxidative phosphorylation and cellular energetics.To analyze and interpret data from s...