Preparations of coupled mitochondria were labeled with fluorescein isothiocyanate (FITC). Comparison of characteristics of FITC bound to mitochondria versus azolectin liposomes indicates that a significant part of the probe is bound to mitochondrial proteins including proteins of the matrix side of the inner membrane. The experiments with the probe indicate that mitochondrial proteins resemble typical polyelectrolytes with constant of dissociation close to 10(-7).H+ and K+ compete for binding to mitochondrial proteins at neutral pH. The slow deprotonation of matrix proteins is observed during equilibration of matrix protons with medium protons. This process is not restricted to the transmembrane proton transfer. The data are explained by the theory of immobilized buffer. Under certain conditions the extent of dissociation of the matrix immobilized buffer correlates with the rate of mitochondrial respiration in state 3P according to chance.