Physiochemical properties of DNA binding proteins: gene 32 protein of T4 and Escherichia coli unwinding protein

Abstract

The single-stranded DNA binding protein coded for by gene 32 of bacteriophage T4 and a similar protein isolated from uninfected Escherichia coli both induce characteristic changes in the circular dichroism (CD) of single-stranded nucleic acids. These CD changes have been adapted as an assay of protein-DNA complex formation. Far-ultraviolet CD spectra show the secondary structure of the two proteins to be similar with approximately 20% alpha helix, approximately 20% beta structure, and 60% random coil. Both proteins show prominent Cotton effects arising from their aromatic chromophores. Nitration of five of the nine tyrosyl residues of gene 32 protein prevents DNA binding, while prior formation of the DNA complex protects all tyrosyl residues from nitration. The tyrosyl residues may participate in gene 32 protein-DNA binding by intercalation between bases of the single strand. In contrast, no tyrosyl residues can be nitrated in the E. coli protein suggesting that surface tyrosyls do not play a part in binding of E. coli protein to DNA. Approximately 50 amino acids can be cleaved from the gene 32 protein with trypsin. This cleavage also occurs spontaneously in infected cell extracts. The remaining protein of mol wt 30000 has the same CD spectra and DNA binding properties as the native protein. The physicochemical properties can be correlated with previous work on the structures and functions of the group of DNA "unwinding proteins".