Structure and Affinity of Complexes between the DNA-Binding Domain of Swi4 and DNA

Abstract: The work describes the preparation of the recombinant DNA-binding domain of Swi4 protein, which is a component of the SBF transcription factor of the budding yeast Saccharomyces cerevisiae. Circular dichroism spectroscopy data showed that the structure of the domain involves α-helices (29%), β-sheets (22%), β-turns (21%), and disordered structure (28%). We have studied the interaction of the domain with DNA that contains the SBF SCB (Swi4 Cell-cycle Box) binding site. The formation of the complexes is accompanied by a conformational rearrangement in the protein, which affects at least 10 peptide bonds and leads to a 6% increase in the α-helical content and a concomitant decrease in the β-sheet content. Fluorescence spectroscopy revealed that conformational rearrangements and intermolecular interactions do not affect the regions of the Trp68 and Trp112 residues located near the boundaries of the DNA-binding helix-turn-helix motif. It has been found that the dissociation constant of the complex of the DNA-binding domain of the Swi4 protein with DNA is 20 ± 3 nM.