[Analysis of the secondary structure of linker histone H1 based on IR absorption spectra].

This work was carried out to compare the effectiveness of the methods of infrared spectroscopy in the amide I region and UV circular dichroism to the analyze the protein secondary structure by the example of linker histone H1 and bovine serum albumin (BSA). It has been shown that the application of a diamond ATR cell quantifies the proportion of α-helices and ß-structures in a good agreement with UV circular dichroism spectroscopy. It has been shown that histone H1 is able to aggregate, which results in considerable changes in its secondary structure.

[The structure of the complexes of DNA with nonhistone chromosomal protein HMGB1 and the histone H1 in the presence of manganese ions. II. Vibrational circular dichroism spectroscopy].

Complexes of DNA with nonhistone chromosomal protein HMGB1 and histone H1 in the presence of manganese ions were studied using absorption and circular dichroism spectroscopy in infrared region. It was shown that the approach provides good results for solutions containing large particles, which cause light scattering in UV region. It was also shown that the manganese ions are able to coordinate to the chemical groups of DNA as well as to the carboxylic amino acid residues of the protein HMGB1. The latter stimulates DNA condensation and slightly weakens DNA-protein interactions in the complex.

[The structure of the complexes of DNA with chromosomal protein HMGB1 and histone H1 in the presence of manganese ions. I. Circular dicroism spectroscopy].

The mechanisms of interaction of the non-histone chromosomal protein HMGB1 and linker histone H1 with DNA have been studied using circular dichroism and absorption spectroscopy. Both of the proteins are located in the inter-nucleosomal regions of chromatin. It was demonstrated that properties of the DNA-protein complexes depend on the protein content and can not be considered as a simple summing up of the effects of individual protein components. Interaction of HMGB1 and H1 proteins is shown to be co-operative rather than competitive. Lysine-rich histone H1 facilitates the binding of the HMGB1 with DNA by screening the negatively charged groups of the sugar-phosphate backbone of DNA and dicarboxylic amino-acid residues in the C-terminal domain of the HMGB1 protein. The observed joint action of the and H1 proteins stimulates DNA condensation with formation of the anisotropic DNA-protein complexes with typical psi-type CD spectra. Structural organization of the complexes depends not only on the DNA-protein interactions, but also on the interaction between HMGB1 and H1 protein molecules bound to DNA. Manganese ions significantly modify the character of interactions between the components in the triple DNA-HMGB1-H1 complex. Binding of Mn2+ ions causes the weakening of the DNA-protein interactions and strengthening the protein-protein interactions, which promote DNA condensation and formation of large DNA-protein particles in solution.

[Conformational peculiarities of nuclear protein HMGB1 and specificity of its interaction with DNA].

Changes in the secondary structure of DNA and non-histone chromosomal protein HMGB1 were studied by circular dichroism and UV spectroscopy. We have demonstrated that the HMGBI protein is able to change its secondary structure upon binding to DNA. We estimated the proportion of bound protein on the assumption that there were two spectrally distinguishable forms of the HMGB1 in solution. The bound protein fraction decreases with increasing protein to DNA ratios (r) from 0.48 at r = 0.13 to 0.06 at r = 2.43. It has been shown that HMGB1 is able to induce considerable changes in DNA structure even when the amount of the protein directly associated with DNA is low.

[The interaction of DNA with sperm-specific histones of the H1 family].

We have studied the interactions of DNA with sperm-specific histones of the H1 family of sea urchin Strongylocentrotus intermedius, sea starfish Aphelasterias japonica and bivalve mollusk Chlamis islandicus using circular dichroism and DNA melting analysis. It was shown that echinoderm's sperm H1 protein has additional alpha-helical domains in its C-terminus and it demonstrates stronger DNA compaction. The differential melting curves of DNA-protein complexes have two peaks. The low temperature peak characterized the melting temperature of free DNA within the complex. The higher temperature peak characterizes the melting temperature of DNA bond to protein. DNA is found to be in the most stable state in the complexes with mollusk sperm H1 protein.

[Structural organization of DNA complexes with proteins HMGB1 and HMGB1-(A+B)].

The interaction between DNA and the nonhistone proteins HMGB1 and HMGB1-(A+B) has been studied using circular dichroism and scanning force microscopy. The recombinant protein HMGB1-(A+B) has no negatively charged C-terminal domain characteristic for HMGB1. Our earlier suggestion about the structural interaction of tandem HMGB1-domains of the recombinant protein with DNA was confirmed. It was shown that the C-terminal part modulates the interactions of HMGB1-domains with DNA. Without the C-terminal sequence, the HMGB1-(A+B) protein forms DNA-protein complexes with the ordered supramolecular structure.

[The structure of the complexes of DNA with non-histone chromosomal protein HMGB1 in the presence of manganese ions]. / Struktura kompleksov DNK s negistonovym khromosomnym belkom HMGB1 v prisutstvii ionov margantsa.

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 Ca2+ ions on DNA compaction in the complex with non-histone chromosomal protein HMGB1]. / Vliianie ionov Ca2+ na kompaktizatsiiu DNK v komplekse s negistonovym khromosomnym belkov HMGB1.

The analysis of absorption and circular dichroism spectra in UV and IR regions showed that Ca2+ ions interact both with the phosphate groups of DNA and with the HMGB1 protein. Not only negatively charged C-terminal part of the protein molecule participates in interaction with metal ions but also its DNA-binding domains. The latter fact leads to the change of the mode of protein-DNA interaction. The presence of Ca2+ ions prevents formation of ordered supramolecular structures, specific for the HMGB1-DNA complexes, though promotes intermolecular aggregation. The structure of the complexes between DNA and the protein HMGB1 lacking C-terminal tail appears to be the most sensitive to the presence of Ca2+ ions. The data obtained allow to conclude that Ca2+ ions do not play a structural role in the HMGB1/DNA complexes and the presence of these ions is not necessary to DNA compaction in such systems.

[HMG1 domains: the victims of circumstance]. / HMG1-domeny: zalozhniki obstoiatel'stv.

The method of circular dichroism (CD) was used to compare DNA behavior during its interaction with linker histone H1 and with non-histone chromosomal protein HMG1 at different ionic strength and at different protein content in the system. The role of negatively charged C-terminal fragment of HMG1 was analyzed using recombinant protein HMG1-(A + B), which lacks the C terminal amino acid sequence. The psi-type CD spectra were common for DNA interaction with histone H1, but no spectra of this type were observed in HMG1-DNA systems even at high ionic strength. The CD spectrum of the truncated recombinant protein at high salt concentration somewhat resembled the psi-type spectrum. Two very intense positive bands were located near 215 nm and near 273 nm, and the whole CD spectrum was positive. The role of C-terminal tail of HMG1 in formation of the ordered DNA-protein complexes is discussed.

[Interaction of superhelical DNA with the nonhistone protein HMG1]. / Vzaimodeistvie superspiral'noi DNK s negistonovym belkom HMG1.

The interaction between nonhistone chromosomal protein HMG1 and plasmid DNA was studied by optical and hydrodynamical methods. The recombinant protein HMG1 produced by yeast Pichia pastoris strain was used. We have shown that according to the CD spectra local conformational changes in DNA helix occur in the region of DNA-protein interaction. These changes are most significant at r < 3 (w/w). Both gel-shift assay and ultracentrifugation, as well as CD data, indicate that protein-protein interactions between HMG1 molecules play a major role in the formation of DNA-protein complexes. It is suggested that the protein C-terminus may affect HMG1-DNA binding not only by a direct interaction with DNA helix, but also by protein-protein interactions.