Ratio of AT and GC Pairs in the Zones of Open States Genesis in DNA Molecules.

Background: There is an assumption about the presence of a specific nucleotides sequence in DNA molecule, which contributes to the genesis of open states (OS). In addition, it would be logical to assume that OS zones should form in DNA regions with a large proportion of Adenine-Thymine (AT) pairs, since they contain fewer hydrogen bonds than Guanine- Cytosine (GC) base pairs. However, studies have shown that in areas rich in AT pairs, the probability of open states will not always be higher.

The Best Material from the VII Congress of Russian Biophysicists.

The purpose of this Special Issue is to demonstrate the current state of research in the field of biophysics in the Russian Federation [...

Structure and Neuroprotector Properties of a Complex Compound of Lithium with Comenic Acid.

The structure, antioxidant and neuroprotective properties of lithium comenate (lithium 5-hydroxy-4-oxo-4H-pyran-2-carboxylate) were studied. Lithium comenate was obtained by reacting comenic acid (HCom) with lithium hydroxide in an aqueous solution. The structure of lithium comenate was confirmed via thermal analysis, mass spectrometry, IR, NMR and UV spectroscopy.

Novel Hydroxamic Acids Containing Aryl-Substituted 1,2,4- or 1,3,4-Oxadiazole Backbones and an Investigation of Their Antibiotic Potentiation Activity.

UDP-3-(-3-hydroxymyristoyl)--acetylglucosamine deacetylase (LpxC) is a zinc amidase that catalyzes the second step of the biosynthesis of lipid A, which is an outer membrane essential structural component of Gram-negative bacteria. Inhibitors of this enzyme can be attributed to two main categories, non-hydroxamate and hydroxamate inhibitors, with the latter being the most effective given the chelation of Zn in the active site. Compounds containing diacetylene or acetylene tails and the sulfonic head, as well as oxazoline derivatives of hydroxamic acids, are among the LpxC inhibitors with the most profound antibacterial activity.

Glutathione Non-Covalent Binding Sites on Hemoglobin and Major Glutathionylation Target betaCys93 Are Conservative among Both Hypoxia-Sensitive and Hypoxia-Tolerant Mammal Species.

Intracellular tripeptide glutathione is an important agent of cell survival under hypoxia. Glutathione covalently binds to SH groups of hemoglobin cysteine residues, protecting them from irreversible oxidation, and changes its affinity to oxygen. Reduced glutathione (GSH) can also form a noncovalent complex with hemoglobin.

VII Congress of Russian Biophysicists-2023, Krasnodar, Russia.

This special issue of Biophysical Reviews contains the materials presented at the VII Congress of Biophysicists of Russia, held from 17 to 23 April in Krasnodar. We believe that we have managed to prepare a selection of articles that well reflects the current state of biophysical science in Russia and its place in the world science. The VII Russian Congress on Biophysics was held in Krasnodar in April 2023, continuing the tradition of the series of biophysics conferences held every 4 years.

Protein-DNA recognition mechanisms and specificity.

The accumulated knowledge about the structure of protein-DNA complexes allowed us to understand the mechanisms of protein-DNA recognition and searching for a specific site on DNA. Obviously, the mechanism of specific DNA recognition by a protein must satisfy two requirements. First, the probability of incorrect binding should be very small.

Changes in Hemoglobin Properties in Complex with Glutathione and after Glutathionylation.

Hemoglobin is the main protein of red blood cells that provides oxygen transport to all cells of the human body. The ability of hemoglobin to bind the main low-molecular-weight thiol of the cell glutathione, both covalently and noncovalently, is not only an important part of the antioxidant protection of red blood cells, but also affects its affinity for oxygen in both cases. In this study, the properties of oxyhemoglobin in complex with reduced glutathione (GSH) and properties of glutathionylated hemoglobin bound to glutathione via an SS bond were characterized.

Research Topics of the Bioinformatics of Gene Regulation.

The study of gene expression regulation raises the challenge of developing bioinformatics tools and algorithms, demanding data integration [...

Hemoglobin is an oxygen-dependent glutathione buffer adapting the intracellular reduced glutathione levels to oxygen availability.

Fast changes in environmental oxygen availability translate into shifts in mitochondrial free radical production. An increase in intraerythrocytic reduced glutathione (GSH) during deoxygenation would support the detoxification of exogenous oxidants released into the circulation from hypoxic peripheral tissues. Although reported, the mechanism behind this acute oxygen-dependent regulation of GSH in red blood cells remains unknown.

An open call for contributions to a special issue of highlighting the research themes of VII Congress of Russian Biophysicists 2023.

We announce a call for contributions to a Special Issue of associated with the VII Congress of Russian Biophysicists (to be held in Krasnodar, Russia, 17-23 April 2023). The Congress is the main biophysical meeting held within Russia and is organized every four years. The Congress will focus on both the physical principles and mechanisms of biological processes occurring at different levels of structural organization, from molecular to cellular to organism and to population levels.

Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters.

Eukaryotic and archaeal RNA polymerase II (POL II) machinery is highly conserved, regardless of the extreme changes in promoter sequences in different organisms. The goal of our work is to find the cause of this conservatism. The representative sets of aligned promoter sequences of fifteen organisms belonging to different evolutional stages were studied.

Na,K-ATPase Acts as a Beta-Amyloid Receptor Triggering Src Kinase Activation.

Beta-amyloid (Aβ) has a dual role, both as an important factor in the pathology of Alzheimer's disease and as a regulator in brain physiology. The inhibitory effect of Aβ oligomers on Na,K-ATPase contributes to neuronal dysfunction in Alzheimer's disease. Still, the physiological role of the monomeric form of Aβ interaction with Na,K-ATPase remains unclear.

CBLRR: a cauchy-based bounded constraint low-rank representation method to cluster single-cell RNA-seq data.

The rapid development of single-cel+l RNA sequencing (scRNA-seq) technology provides unprecedented opportunities for exploring biological phenomena at the single-cell level. The discovery of cell types is one of the major applications for researchers to explore the heterogeneity of cells. Some computational methods have been proposed to solve the problem of scRNA-seq data clustering.

Overview of structural variation calling: Simulation, identification, and visualization.

Structural variation (SV) is a vital part of biological genetic diversity. The simulation and identification with high efficiency and accuracy are considered to be very important. With the continuous development and wide application of various technologies, computer simulation of genomic data has attracted wide attention due to its intuitive and convenient advantages.

MutCov: A pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing an outbreak of coronavirus disease 2019 (COVID-19), is a major threat to public health worldwide. Previous studies have shown that the spike protein of SARS-CoV-2 determines viral infectivity and major antigenicity. However, the spike protein has been undergoing various mutations, which bring a great challenge to the prevention and treatment of COVID-19.

Entropy Analysis of Protein Sequences Reveals a Hierarchical Organization.

Background: Analyzing the local sequence content in proteins, earlier we found that amino acid residue frequencies differ on various distances between amino acid positions in the sequence, assuming the existence of structural units.

Methods: We used informational entropy of protein sequences to find that the structural unit of proteins is a block of adjacent amino acid residues-"information unit". The ANIS (ANalysis of Informational Structure) method uses these information units for revealing hierarchically organized Elements of the Information Structure (ELIS) in amino acid sequences.

Life: Computational Genomics Applications in Life Sciences.

This Special Issue, "Life: Computational Genomics", presents research articles on systems biology applications, computational genomics, and bioinformatics methods in life sciences [...

Recent Trends in Cancer Genomics and Bioinformatics Tools Development.

We overview recent research trends in cancer genomics, bioinformatics tools development and medical genetics, based on results discussed in papers collections "Medical Genetics, Genomics and Bioinformatics" (https://www [...

Biophysical Reviews' "Meet the Councilor"-a profile of Anastasia A. Anashkina.

As one of the twelve Councilors of the International Union of Pure and Applied Biophysics elected in summer 2021, I have been asked to provide this short biographical sketch for the journal readers. I am a new member of the IUPAB Council. I hold a specialist degree in Applied Physics and Mathematics from the Moscow Institute of Physics and Technology and PhD in Biophysics from Moscow State University.

Bioinformatics Applications to Reveal Molecular Mechanisms of Gene Expression Regulation in Model Organisms.

Gene expression regulation at the transcriptome, genome, cell, and tissue levels is a complex phenomenon demanding the development of bioinformatics tools [...