Multiple binding of some sulfonic dyes with trypsin in acidic media was investigated by equilibrium gel filtration. The apparent dissociation constants for the binding of flavianate, orange II, and orange G were, respectively, 46, 6, and 61 mM, reflecting differences in the organic moieties of the dyes. The elution profiles displayed a negative correlation of the eluted volumes between the monophasic trough and the peak with saturation ratios. This correlation was attributed to the outcome of distinct ORDER REPRINTS tautomeric forms of trypsin induced by ligand, together with the role of the dextran polymer and self-association of dye molecules. Protein transconformation was achieved after a lag time-depending on the ligand structure and concentration inside the column.