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.

Currently, there is an increase in the number of oncohematological diseases. Simple and reliable screening methods are required for their effective diagnosis. One of the promising and rapidly developing approaches is IR spectroscopy of various samples of biomaterials. In this work, we analyzed the IR spectra of blood serum from patients with multiple myeloma, chronic lymphocytic leukemia and healthy donors.

Data are accumulating on the hydrolytic activity of serum albumin towards esters and organophosphates. Previously, with the help of the technology of proton nuclear magnetic resonance (1H NMR) spectroscopy, we observed the yield of acetate in the solution of bovine serum albumin and p-nitrophenyl acetate (NPA). Thus, we showed that albumin possesses true esterase activity towards NPA. Then, using the methods of molecular docking and molecular dynamics, we established site Sudlow I as the catalytic center of true esterase activity of albumin. In the present work, to expand our understanding of the molecular mechanisms of albumin pseudoesterase and true esterase activity, we investigated—in experiments in vitro and in silico—the interaction of anticoagulant warfarin (WRF, specific ligand of site Sudlow I) and benzodiazepine diazepam (DIA, specific ligand of site Sudlow II) with albumins of different species, and determined how the binding of WRF and DIA affects the hydrolysis of NPA by albumin. It was found that the characteristics of the binding modes of WRF in site Sudlow I and DIA in site Sudlow II of human (HSA), bovine (BSA), and rat (RSA) albumins have species differences, which are more pronounced for site Sudlow I compared to site Sudlow II, and less pronounced between HSA and RSA compared to BSA. WRF competitively inhibits true esterase activity of site Sudlow I towards NPA and does not affect the functioning of site Sudlow II. Diazepam can slow down true esterase activity of site Sudlow I in noncompetitive manner. It was concluded that site Sudlow I is more receptive to allosteric modulation compared to site Sudlow II.

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.

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.

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.

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.

The nonhistone chromosomal protein HMGB1 and histone H1 are chromatin linker proteins. The functions of linker proteins are closely related to their conformational state. The structure of proteins that play a key role in the formation of higher levels of chromatin structural organization is being actively studied. In this study, a comparative analysis of the secondary structure of the linker histone H1 and the nonhistone protein HMGB1 was carried out. Using circular dichroism in the UV region and FTIR spectroscopy, it was shown that positively charged histone H1 binds to the C-terminal fragment of HMGB1, stabilizing the resulting complex and inducing the formation of additional α-helical regions in both proteins.

Multiple myeloma and chronic lymphocytic leukemia are oncological diseases of the blood, which remain incurable today. The paper proposes a method for classifying blood serum samples from patients with multiple myeloma, chronic lymphocytic leukemia and healthy donors based on the analysis of their spectra in the mid-infrared (IR) range. IR spectra of blood serum were recorded using a Tensor 27 IR Fourier spectrometer in D2O solution. To analyze the obtained spectra in this work, a machine learning algorithm was implemented – the principal component analysis. The use of the principal component analysis made it possible to significantly simplify the representation of the array of spectral data. 45 samples of blood serum were analyzed in the work. As a result of applying this approach, the studied set of samples is divided into three disjoint sets corresponding to blood serum samples of patients with multiple myeloma, chronic lymphocytic leukemia and healthy donors. Thus, the principal component method can be successfully applied to classify blood serum samples of patients with diagnoses of multiple myeloma and chronic lymphocytic leukemia. The universality of the proposed algorithm allows us to expect that in the future it is possible to apply a similar approach for other oncohematological diseases.

Features of charge transfer and dielectric relaxation processes in blood serum samples of patients with oncohematological diseases and healthy donors were investigated by dielectric spectroscopy method. The observed features of the dielectric spectra for donors and patients, namely the decrease in conductivity in the high frequency region, the correlation between the degree indicator s and the total protein content, as well as changes in the spectrum of relaxation complexes indicate a change in the quantitative ratios of blood components in the presence of disease. This system rearrangement is the result of the fact that conformation of proteins (albumins and immunoglobulins) for patients is change. Keywords: Dielectric spectroscopy, serum, chronic lymphocytic leukemia, multiple myeloma, charge transfer, dielectric relaxation.

Abstract —A systematic assignment of bands observed in the range of 1800–800 –1 cm when measuring samples in KBr pellets based on the example of the analysis of infrared spectra of DNA complexes with dichlorodiammineplatinum(II) was performed. Based on the performed decomposition of the spectra of DNA and its complexes with dichlorodiammineplatinum(II), it was shown that the results are in good agreement with the direct structural data, as well as with previous measurements in solution. It was also shown that markers of the A- and B-forms of DNA are simultaneously observed in the DNA spectra in KBr pellets.

Multiple myeloma (MM) is a serious disease that is difficult to diagnose especially at early stage. Infrared spectroscopy is a promising approach for diagnosing MM. The principal component analysis (PCA) allows us to reduce the dimension of the data and keep only the important variables. In this study, we apply principal components analysis to infrared (IR) spectra of blood serum from healthy donors and multiple myeloma patients. As a result of the analysis by PCA, it was possible to visualize the separation of patient’s and donor’s samples into two clusters. The result indicates that this method is potentially applicable for diagnosis of multiple myeloma.

One of the promising approaches for diagnosing oncohematological diseases is infrared spectroscopy of blood serum. In this work secondary structure of blood serum proteins of patients with multiple myeloma, chronic lymphocytic leukemia and healthy donors was studied using IR spectroscopy. As a result of the study, it was found that the secondary structure of blood serum proteins in patients with chronic lymphocytic leukemia does not change in comparison with healthy donors. In contrast, patients with multiple myeloma have significant differences in the secondary structure composition of serum proteins compared to healthy donors. We conclude, that IR spectroscopy makes it possible to distinguish serum of healthy donors and patients with multiple myeloma, leading to the potential applicability of this approach to the diagnosis of multiple myeloma.

The non-histone chromosomal proteins HMGB1 and HMGB2 were found in the cells of all studied eukaryotes. They are involved in cell decision and many biological processes such as replication, transcription, repair, etc. In this work, the secondary structure of the HMGB1 and HMGB2 proteins was studied by the circular dichroism method. It was shown that, despite the high homology between them, the secondary structure of these proteins is different. The revealed structural features, most likely, should influence their functions in the cell nucleus, in particular, the interaction with DNA and other proteins.

In this study, we compared the effects of gamma and high-energy proton radiation (1000 MeV) on DNA in aqueous saline solutions (5 and 150 mM NaCl) at doses of 30 and 50 Gy. We used spectral methods (the ultraviolet absorption method, spectrophotometric methods for nucleic acid quantification, spectrophotometric DNA melting, and circular dichroism) for the estimation of the number of damaged nitrogenous bases and damage of the secondary DNA structure. It was found that under these conditions, proton radiation causes more severe destruction of nitrogenous bases and the secondary DNA structure than exposure to gamma rays at the same dose. In DNA irradiated with protons, the formation of crosslinks is possible and the probability for crosslinking increases with the increase of the ionic strength of the irradiated solution.

In this work we designed, synthesized and characterized luminescent metal nanoclusters (NCs) on human serum albumin (HSA) and immunoglobulins (Ig). We demonstrate that the approach developed allows one to determine the relative content of albumins and immunoglobulins in biologically relevant protein mixtures based on the luminescent properties of the NCs. Fast and inexpensive approach which allows to determine concentrations of immunoglobulins (Ig) and serum albumin (HSA) in blood serum might be useful in clinical diagnostics.

Abstract—In the first part of this review (Biophysics, 63, 858 (2018)), the structure of H1 family linker histones, their posttranslational modifications, as well as the role of H1 histone in the formation of compact transcriptionally inactive chromatin, were considered. The second part is devoted to the role of H1 family linker histones in the structural organization of chromatin at different levels: from nucleosomes to metaphase chromosomes. The mechanisms of interaction of H1 histone with other elements of chromatin, including with DNA and nuclear proteins, are discussed.

Abstract The structural organization of DNA in complex with linker histone H1 and non-histone chromosomal protein HMGB1 in presence of calcium and manganese ions have been studied using FTIR and UV circular dichroism spectroscopy. We have demonstrated that the presence of calcium ions leads to the formation of highly ordered DNA-H1-HMGB1 structures, while manganese ions decrease the order in the earlier reported nanoscale complexes.

Using UV absorption spectroscopy and circular dichroism, we studied the interaction of DNA-cisplatin complexes with nonhistone chromosomal proteins HMGB1 and HMGB2. It was shown that the presence of platinum ions affected the ability of HMGB2 to form large supramolecular complexes with DNA. The role of C-terminal domain of the HMGB1/2 proteins is discussed.

E. V. Chikhirzhina1, A. D. Garifullin2, A. Yu. Kuvshinov2, L. V. Plotnikova3, A. M. Polyanichko1,3, E. A. Telnaya3, S. V. Voloshin2,4,5 1 Institute of Cytology of the Russian Academy of Sciences, 4, Tikhoretsky pr., St. Petersburg, 194064, Russian Federation 2 Russian Scientific Research Institute of Hematology and Transfusiology, 16, 2-ya Sovetskaya ul., St. Petersburg, 191024, Russian Federation 3 St. Petersburg State University, 7–9, Universitetskaya nab., St. Petersburg, 199034, Russian Federation 4 North-Western State Medical University named after I. I. Mechnikov, 41, Kirochnaya ul., St. Petersburg, 191015, Russian Federation 5 S. M. Kirov Military Medical Academy, 6, ul. Akademika Lebedeva, St. Petersburg, 194044, Russian Federation