Mouse transcription factor PEBP2 (polyomavirus enhancer-binding protein (2) is composed of two distinct subunits α and β. The α subunit has an ability to bind the specific DNA sequences, which is enhanced by formation of a heterodimer with the β subunit. The DNA binding and heterodimerization activities of the α subunit are both localized within a 128-amino-acid (aa) region termed as the Runt domain for its homology to the Drosophila segmentation gene runt. To characterize the molecular determinants for these activities, the Runt domain was randomly mutagenized and produced in E. coli as a secreted form. Using E. coli culture supernatant, the DNA binding and heterodimerization of mutant Runt domains were analyzed by gel retardation assay. Nine randomly picked single-aa substitution mutants showed various functional alterations in DNA binding and heterodimerization either separately or simultaneously. This observation suggests that the structure of Runt domain is highly ordered and is quite sensitive to modulations in its primary structure. The method presented here provides a simple and quick method to characterize a large number of mutant DNA binding proteins.
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