[125I]Iodonaphtylazide labeling selectively a cysteine residue in the F0 of the ATP-synthase from E. coli is unsuitable for topographic studies of membrane proteins.

The ATP synthase from E. coli was reacted with the hydrophobic photolabel [125I]iodonaphtylazide. Subunit b in the F0-part was selectively labelled. Label was traced back to the single cysteine21 in subunit b. Thus the reactive intermediate of INA generated by photolysis had a high preference for nucleophiles. Due to this high selectivity the detection of membrane spanning peptide segments by labelling with INA is not reliable.