BINDING OF SPXK-PEPTIDE AND APXK-PEPTIDE MOTIFS TO AT-RICH DNA - EXPERIMENTAL AND THEORETICAL-STUDIES

The binding properties of the SPXK- and APXK-type peptides to the AT-r ich DNA fragments of different length were studied by measuring the co mpetition of peptides with Hoechst 33258 dye for DNA binding and by th e gel shift assay analysis. In parallel to the experimental studies, m olecular modeling techniques were used to analyze possible binding mod es of the SPXZ and APXK motifs to the AT-rich DNA. The results of the competition measurements and gel shift assays suggest that serine at t he i-1 position (i is proline) can be replaced by alanine without affe cting the binding properties of the motif. Thus, the presence of the c onserved serine in this motif in many DNA-binding proteins is probably not dictated by structural requirements. Based on the results of mole cular modeling studies we propose that the binding mode of the SPXK-ty pe motifs to the AT-rich DNA resembles closely that between the N-term inal arm of the homeodomain and DNA. This model confirms that serine i n the SPXK motifs is not essential for the DNA binding. The model also indicates that if X in the motif is glutamic acid, this residue is pr obably protonated in the complex with DNA.