Structure and Functions of HMGB3 Protein.

HMGB3 protein belongs to the group of HMGB proteins from the superfamily of nuclear proteins with high electrophoretic mobility. HMGB proteins play an active part in almost all cellular processes associated with DNA-repair, replication, recombination, and transcription-and, additionally, can act as cytokines during infectious processes, inflammatory responses, and injuries. Although the structure and functions of HMGB1 and HMGB2 proteins have been intensively studied for decades, very little attention has been paid to HMGB3 until recently. In this review, we summarize the currently available data on the molecular structure, post-translational modifications, and biological functions of HMGB3, as well as the possible role of the ubiquitin-proteasome system-dependent HMGB3 degradation in tumor development.

Rapid and selective colorimetric determination of L-DOPA in human serum with silver nanoparticles.

L-DOPA, or l-3,4-dihydroxyphenylalanine is an aromatic amino acid, which plays a significant role in human metabolism as a precursor of important neurotransmitters. We develop a fast and simple colorimetric method for the detection of L-DOPA in biological fluids. The method is based on the reduction of silver ions with L-DOPA and the subsequent formation of L-DOPA stabilized silver nanoparticles (Ag NPs). In this novel approach, L-DOPA works as both reducing and stabilizing agent, which provides selectivity and simplifies the procedure. HR-TEM images show very narrow Ag NPs distribution with an average size of 24 nm. Such sensor design is suggested for the first time. We also calculate vertical ionization potential, vertical electron affinity, and Gibbs free energy change of different ionic forms of L-DOPA and amino acids at the M06-2X/def2-TZVP level for the gas phase in comparison with that of silver. A model of silver ions reduction by aromatic amino acids is proposed: the ionic forms with charge -1 are suggested to reduce silver ions. High selectivity against aromatic amino acids, dopamine and serotonin is achieved by tuning pH and involving two L-DOPA forms with charged both hydroxyphenolate and carboxylate groups in the stabilization of uniform-sized Ag NPs. The method is applicable for the determination of L-DOPA in human serum with the 50 nM limit of detection and the linear range up to 5 µM. Ag NPs formation and coloring the solution proceeds in a few minutes. The suggested colorimetric method has potential application in clinical trials.

Structure and Functions of HMGB2 Protein.

High-Mobility Group (HMG) chromosomal proteins are the most numerous nuclear non-histone proteins. HMGB domain proteins are the most abundant and well-studied HMG proteins. They are involved in variety of biological processes. HMGB1 and HMGB2 were the first members of HMGB-family to be discovered and are found in all studied eukaryotes. Despite the high degree of homology, HMGB1 and HMGB2 proteins differ from each other both in structure and functions. In contrast to HMGB2, there is a large pool of works devoted to the HMGB1 protein whose structure-function properties have been described in detail in our previous review in 2020. In this review, we attempted to bring together diverse data about the structure and functions of the HMGB2 protein. The review also describes post-translational modifications of the HMGB2 protein and its role in the development of a number of diseases. Particular attention is paid to its interaction with various targets, including DNA and protein partners. The influence of the level of HMGB2 expression on various processes associated with cell differentiation and aging and its ability to mediate the differentiation of embryonic and adult stem cells are also discussed.

Quantitative determination of albumin and immunoglobulin in human serum using gold nanoclusters.

In this experimental study, we developed a simple and selective approach to determine the concentrations of human serum albumin (HSA) and total amount of immunoglobulins (Ig) in real human serum (HS) sample using luminescent gold nanoclusters (Au NCs). In doing so, Au NCs were grown directly on the HS proteins without any sample pretreatment. We synthesized Au NCs on HSA and Ig and studied their photophysical properties. Using combined fluorescent and colorimetric assay we were able to obtain protein concentrations with a high degree of accuracy relative to techniques currently used in clinical diagnostics. We used method of standard additions to determine both HSA and Ig concentrations in HS by the Au NCs absorbance and fluorescence signals. A simple and cost-effective method developed in this work represents an excellent alternative to the techniques currently used in clinical diagnostics.

Structural Characteristics of High-Mobility Group Proteins HMGB1 and HMGB2 and Their Interaction with DNA.

Non-histone nuclear proteins HMGB1 and HMGB2 (High Mobility Group) are involved in many biological processes, such as replication, transcription, and repair. The HMGB1 and HMGB2 proteins consist of a short N-terminal region, two DNA-binding domains, A and B, and a C-terminal sequence of glutamic and aspartic acids. In this work, the structural organization of calf thymus HMGB1 and HMGB2 proteins and their complexes with DNA were studied using UV circular dichroism (CD) spectroscopy. Post-translational modifications (PTM) of HMGB1 and HMGB2 proteins were determined with MALDI mass spectrometry. We have shown that despite the similar primary structures of the HMGB1 and HMGB2 proteins, their post-translational modifications (PTMs) demonstrate quite different patterns. The HMGB1 PTMs are located predominantly in the DNA-binding A-domain and linker region connecting the A and B domains. On the contrary, HMGB2 PTMs are found mostly in the B-domain and within the linker region. It was also shown that, despite the high degree of homology between HMGB1 and HMGB2, the secondary structure of these proteins is also slightly different. We believe that the revealed structural properties might determine the difference in the functioning of the HMGB1 and HMGB2 as well as their protein partners.

Functional Diversity of Non-Histone Chromosomal Protein HmgB1.

The functioning of DNA in the cell nucleus is ensured by a multitude of proteins, whose interactions with DNA as well as with other proteins lead to the formation of a complicated, organized, and quite dynamic system known as chromatin. This review is devoted to the description of properties and structure of the progenitors of the most abundant non-histone protein of the HMGB family-the HmgB1 protein. The proteins of the HMGB family are also known as "architectural factors" of chromatin, which play an important role in gene expression, transcription, DNA replication, and repair. However, as soon as HmgB1 goes outside the nucleus, it acquires completely different functions, post-translational modifications, and change of its redox state. Despite a lot of evidence of the functional activity of HmgB1, there are still many issues to be solved related to the mechanisms of the influence of HmgB1 on the development and treatment of different diseases-from oncological and cardiovascular diseases to pathologies during pregnancy and childbirth. Here, we describe molecular structure of the HmgB1 protein and discuss general mechanisms of its interactions with other proteins and DNA in cell.

tRNA as a stabilizing matrix for fluorescent silver clusters: photophysical properties and IR study.

In this experimental study fluorescent silver clusters on a tRNA matrix were synthesized for the first time. Two types of fluorescent complexes emitting in the green (550 nm) and red (635 nm) regions of the visible spectrum were obtained. Using FTIR spectroscopy, we identified possible binding sites for the clusters, which appeared to be within the helical regions of tRNA. It was also shown that tRNA retained its double helical structure after the cluster formation, which is essential for its functionality.

Folding of poly-amino acids and intrinsically disordered proteins in overcrowded milieu induced by pH change.

pH-induced structural changes of the synthetic homopolypeptides poly-E, poly-K, poly-R, and intrinsically disordered proteins (IDPs) prothymosin α (ProTα) and linker histone H1, in concentrated PEG solutions simulating macromolecular crowding conditions within the membrane-less organelles, were characterized. The conformational transitions of the studied poly-amino acids in the concentrated PEG solutions depend on the polymerization degree of these homopolypeptides, the size of their side chains, the charge distribution of the side chains, and the crowding agent concentration. The results obtained for poly-amino acids are valid for IDPs having a significant total charge. The overcrowded conditions promote a significant increase in the cooperativity of the pH-induced coil-α-helix transition of ProTα and provoke histone H1 aggregation. The most favorable conditions for the pH-induced structural transitions in concentrated PEG solutions are realized when the charged residues are grouped in blocks, and when the distance between the end of the side group carrying charge and the backbone is small. Therefore, the block-wise distribution of charged residues within the IDPs not only plays an important role in the liquid-liquid phase transitions, but may also define the expressivity of structural transitions of these proteins in the overcrowded conditions of the membrane-less organelles.

Fourier transform infrared/vibrational circular dichroism spectroscopy as an informative tool for the investigation of large supramolecular complexes of biological macromolecules.

A combination of ultraviolet (UV) and infrared (IR) absorption and circular dichroism (CD) spectroscopy was applied to investigate the structure and formation of large supramolecular DNA-protein complexes. This combination of techniques was used to overcome limitations of UV-CD (electronic, or ECD) spectroscopy due to considerable light scattering in such solutions. Based on the analysis of FTIR and UV-CD spectra, the interaction of DNA with nonhistone chromatin protein HMGB1 and linker histone H1 was studied. The data obtained showed that under the conditions of the experiment (15 mM NaCl, protein/DNA ratio r < 1 w/w) the proteins did not reveal any AT or GC specificity in binding to DNA. In the presence of both proteins, mainly interactions in the DNA minor groove were observed, which were attributed to HMGB1 binding. Histone H1 facilitated binding of HMGB1 to DNA by interacting with the negatively charged groups of the sugar-phosphate backbone and binding of aspartic and glutamic amino acid residues of HMGB1. Acting together, HMGB1 and H1 stimulated the assemblage of supramolecular DNA-protein structures. The structural organization of the ternary complexes depended not only on the properties of the protein-DNA interactions but also on the interactions between HMGB1 and H1 molecules.

The HMG1 ta(i)le.

We have studied structural changes in DNA/protein complexes using the CD spectroscopy, upon the interaction of HMG1-domains with calf thymus DNA at different ionic strengths. HMG1 protein isolated from calf thymus and recombinant HMG1-(A+B) protein were used. Recombinant protein HMG1-(A+B) represents a rat HMG1 lacking C-terminal acidic tail. At low ionic strength (15 mM NaCl) we observed similar behavior of both proteins upon interaction with DNA. Despite this, at higher ionic strength (150 mM NaCl) their interaction with DNA leads to a completely different structure of the complexes. In the case of HMG1-(A+B)/DNA complexes we observed the appearance of DNA fractions possessing very high optical activity. This could be a result of formation of the highly-ordered DNA structures modulated by the interaction with HMG1-domains. Thus the comparison studies of HMG1 and HMG1-(A+B) interaction with DNA show that negatively charged C-terminal tail of HMG1 modulates interaction of the protein with DNA. The striking difference of the behaviour of these two systems allows us to explain the functional role of multiple HMG1 domains in some regulatory and architectural proteins.