Treatment of brown adipose tissue mitochondria with tetranitromethane or N-ethylmaleimide decreases the affinity with which inhibitory nucleotide GDP binds to the tissue-specific uncoupling protein. Both reagents modify cysteine residues which are 'accessible' and 'buried' to 5,5'-dithio-bis(2-nitrobenzoic acid) (Nbs2). Modification of the single Nbs2-accessible residue correlates with the loss of high-affinity binding sites for GDP. Tetranitromethane does not affect the Cl- or H+ permeability of the protein in the absence of nucleotide, while N-ethylmaleimide increases both by 70-80%. Bound GDP is a less effective inhibitor of Cl- permeability after N-ethylmaleimide or tetranitromethane treatment, but retains much of the ability to inhibit H+ permeation.