Structure of DNA Complexes with Nonhistone Chromosomal Protein HMGB1 in the Presence of Manganese Ions

The complexes of DNA-HMGB1 protein-manganese ions have been studied using the circular dichroism (CD) technique. It was shown that the interactions of both the protein and metal ions with DNA in this three-component system differ from those in two-component complexes. The manganese ions did not affect the CD spectrum of the free HMGB1 protein. However, Mn super(2+) ions induced considerable changes in the CD spectrum of free DNA in the spectral range of 260-290 nm. The presence of Mn super(2+) ions prevented the formation of the ordered supramolecular structures typical of HMGB1-DNA complexes. The interaction of manganese ions with DNA had a marked influence on the local DNA structure, changing the properties of protein-binding sites and resulting in a marked decrease in cooperativity of HMGB1-DNA binding. Such changes in the mode of protein-DNA interactions occurred at concentrations as small as 0.01 mM Mn super(2+). Moreover, the changes in local DNA structure induced by the manganese ions promoted the appearance of new HMGB1 binding sites in the DNA double helix. At the same time, interactions with the HMGB1 protein induced alterations in the structure of the DNA double helix, which increased with an increase in the protein-to-DNA ratio. These alterations made the DNA-protein complex especially sensitive to manganese ions. Under these conditions the Mn super(2+) ions strongly affected the DNA structure, which was reflected in abrupt changes in the CD spectra of DNA in the complex in the range of 260-290 nm. Thus, structural changes in the DNA double helix in three-component DNA-HMGB1-Mn super(2+) complexes result from the combined and interdependent interactions of DNA with Mn super(2+) ions and HMGB1 molecules.