The Structural Organization of the HMGB1 Nuclear Protein and Its Effect on the Formation of Ordered Supramolecular Complexes

Biophysics - HMGB1 is one of the key proteins of the cell. HMGB1 performs its main functions predominantly in the cell nucleus, as an essential component of DNA–protein and multiprotein...     

The effect of manganese(II) on DNA structure: electronic and vibrational circular dichroism studies

The interaction of DNA with Mn²⁺ was studied in absorbance and optical activity in the electronic and vibrational regions. Based on the data, several stages of the interaction were identified. Con formational transition towards the C-form of DNA was observed in solution at the molar ratio Mn²⁺/DNA-phosphates between 0.1 and 1.5. The exact ratio depended on the ionic strength and increased with increasing NaCl concentration. Although manganese interacted with the phosphates and bases of DNA at higher metal concentrations, it is unlikely that direct chelation occurred. A model for the interaction between manganese ions and DNA mediated by water is suggested destabilizing the double helix and partially breaking the hydrogen bonds between the base pairs. At high Mn²⁺ concentrations DNA aggregation was observed.     

Linker histones: conformational changes and the role in the structural organization of chromatin

Histones, linker histones of the H1 family, their postsyntetic modifications, DNA-histone H1 interaction are reviewed. A question of protein change in spermatogenesis at the formation of inactive nucleus with high degree of DNA density is considered. Special attention was paid to sperm-specific histones of the H1 family of sperm cells. Their role in organization of high-order chromatin structure of sperm cells is discussed. Also, results of different studies on the structural organization of chromatin (nucleosomes, 30-nm fibers, chromatin loops and metaphase chromosomes) are discussed.     

Conformational properties of nuclear protein HMGB1 and specificity of its interaction with DNA

Changes in secondary structure of DNA and non-histone chromosomal protein HMGB1 during the formation of the complex have been studied by circular dichroism and UV spectroscopy. It was demonstrated that the HMGB1 protein is able to change its secondary structure upon binding to DNA. Based on the assumption that there are two spectroscopically distinguishable forms of the HMGB1 in solution, we estimated the fraction of bound protein. The fraction of bound protein decreases at higher protein to DNA ratios r from 0.48 at r = 0.13 to 0.06 at r = 2.43. It was shown that HMGB1 is able to induce considerable changes in DNA structure, even when the amount of protein actually bound is low.     

Interaction of DNA with sperm-specific histones of the H1 family

Interactions of DNA with sperm-specific histones of the H1 family of sea urchin Strongylocentrotus intermedius, sea star Aphelasterias japonica, and bivalve mollusc Chlamis islandicus were studied using circular dichroism and the DNA melting analysis. Under physiological conditions, the highest DNA compacting ability was found in the echinoderm sperm H1 protein, in which additional α-helical domains are present in their C-terminal sequence. The derivative melting curves have two peaks: the low-temperature peak corresponds to the melting of free DNA, whereas the DNA regions bound to the protein melt at higher temperature. The highest stabilizing ability is characteristic of complexes with the mollusc sperm H1 protein.     

The structure of the complexes of DNA with non-histone chromosomal protein HMGB1 in the presence of manganese ions

The complexes of DNA - HMGB1 protein - manganese ions have been studied using circular dichroism (CD) technique. It was shown that in such three-component system the interactions of both the protein and metal ions with DNA differ from those in two-component complexes. The manganese ions do not affect the CD spectrum of free HMGB1 protein. However, Mn2+ ions induce considerable changes in the CD spectrum of free DNA in the spectral range of 260-290 nm. The presence of Mn2+ ions prevents formation of the ordered supramolecular structures specific for the HMGB1-DNA complexes. The interaction of manganese ions with DNA has a marked influence on the local DNA structure changing the properties of protein-binding sites. This results in the serious decrease in cooperativity of the DNA-protein binding. Such changes in the mode of the DNA-protein interactions occur at concentrations as small as 0.01 mM Mn2+. Moreover, the changes in local DNA structure induced by manganese ions promote the appearance of new HMGB1 binding sites on the DNA double helix. At the same time interactions with HMGB1 protein induce alterations in the structure of the DNA double helix which increase with a growth of the protein/DNA ratio. These alterations make the DNA/protein complex especially sensitive to manganese ions. Under these conditions the Mn2+ ions strongly affect the DNA structure that reflects in abrupt changes of the CD spectra of DNA in the complex in the range of 260-290 nm. Thus, structural changes of the DNA double helix in the three-component DNA-HMGB1-Mn2+ complexes come as a result of the combined and interdependent interactions of DNA with Mn2+ ions and the molecules of HMGB1.     

The effect of manganese(II) on the structure of DNA/HMGB1/H1 complexes: electronic and vibrational circular dichroism studies

The interactions were studied of DNA with the nonhistone chromatin protein HMGB1 and histone H1 in the presence of manganese(II) ions at different protein to DNA and manganese to DNA phosphate ratios by using absorption and optical activity spectroscopy in the electronic [ultraviolet (UV) and electronic circular dichroism ECD)] and vibrational [infrared (IR) and vibrational circular dichroism (VCD)] regions. In the presence of Mn2+, the protein-DNA interactions differ from those without the ions and cause prominent DNA compaction and formation of large intermolecular complexes. At the same time, the presence of HMGB1 and H1 also changed the mode of interaction of Mn2+ with DNA, which now takes place mostly in the major groove of DNA involving N7(G), whereas interactions between Mn2+ and DNA phosphate groups are weakened by histone molecules. Considerable interactions were also detected of Mn2+ ions with aspartic and glutamic amino acid residues of the proteins.