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During pregnancy, a woman becomes more susceptible to respiratory and viral diseases, including novel coronavirus infection (COVID-19). Pregnancy exacerbates the acute inflammation typical to COVID-19, elevating a risk of developing cytokine storm, characterized by an avalanche-like spike of inflammation marker concentrations (C-reactive protein, interleukin-1 в, interleukin-6, interferon-Y, ferritin, erythrocyte sedimentation rate etc.). Cytokine storm increases a risk of pregnancy loss and contribute to formation of multiple organ dysfunction syndrome in pregnant women and fetus. In particular, erythrocyte degradation due to acute inflammation leads to hypoxia and uncontrolled inter-tissue iron redistribution. As a result, conditions are created simultaneously for developing pulmonary hemosiderosis and hemosiderosis of other tissues in pregnant woman and fetus, as well as for augmenting iron loss from the body, which exacerbates iron deficiency anemia (IDA). It is important to emphasize that a surge of ferritin level distinctive for severe COVID-19, does not indicate iron overload. Therefore, recommendations to cancel IDA correction and even to use iron chelators in COVID-19 may increase hypoxia and harm the health of pregnant women.

A total of 6,628 PUBMED-registered publications on the relationships between the effects of vaccination and the provision of micronutrients have been studied by methods of topological analysis of text data. In case of insufficient intake of certain micronutrients, the functioning of the acquired immunity is disrupted resulting in an imbalance of populations of T-cells CD4+/CD8+ and of B-lymphocytes. Nutritional supplements of folate, vitamins A, D and B12, which are recognized regulators of cell division, support a wide range of lymphocyte populations. Trace elements zinc, iron, selenium, manganese and omega-3 polyunsaturated fatty acids are also important for supporting the mechanisms of acquired immunity. The data presented show that a course intake of these micronutrients by patients planning vaccination can significantly improve its effectiveness. In particular, these micronutrients can increase the titers of antibodies to pathogens, and to reduce the percentage of patients who still contract infection after vaccination. Supplements of these micronutrients can also contribute to the safety of vaccination: to prevent malaise and, in the unfortunate case of contracting infection despite the vaccine, to reduce the severity of the course and the mortality from the corresponding infection.

Rubella viruses (RV) have been found in an association with granulomas in children with primary immune deficiencies (PID). Here, we report the recovery and characterization of infectious immunodeficiency-related vaccine-derived rubella viruses (iVDRV) from diagnostic skin biopsies of four patients. Sequence evolution within PID hosts was studied by comparison of the complete genomic sequences of the iVDRVs with the genome of the vaccine virus RA27/3. The degree of divergence of each iVDRV correlated with the duration of persistence indicating continuous intrahost evolution. The evolution rates for synonymous and nonsynonymous substitutions were estimated to be 5.7 x 10−3 subs/site/year and 8.9 x 10−4 subs/site/year, respectively. Mutational spectra and signatures indicated a major role for APOBEC cytidine deaminases and a secondary role for ADAR adenosine deaminases in generating diversity of iVDRVs. The distributions of mutations across the genes and 3D hotspots for amino acid substitutions in the E1 glycoprotein identified regions that may be under positive selective pressure. Quasispecies diversity was higher in granulomas than in recovered infectious iVDRVs. Growth properties of iVDRVs were assessed in WI-38 fibroblast cultures. None of the iVDRV isolates showed complete reversion to wild type phenotype but the replicative and persistence characteristics of iVDRVs were different from those of the RA27/3 vaccine strain, making predictions of iVDRV transmissibility and teratogenicity difficult. However, detection of iVDRV RNA in nasopharyngeal specimen and poor neutralization of some iVDRV strains by sera from vaccinated persons suggests possible public health risks associated with iVDRV carriers. Detection of IgM antibody to RV in sera of two out of three patients may be a marker of virus persistence, potentially useful for identifying patients with iVDRV before development of lesions. Studies of the evolutionary dynamics of iVDRV during persistence will contribute to development of infection control strategies and antiviral therapies., Author summary Primary immunodeficiency diseases (PID) are caused by genetic defects and lead to serious problems including chronic granulomas (abnormal collections (nodules) of inflammatory cells), sometimes lasting for decades and sometimes leading to severe ulcers. Initial reports (2014–2016), including our report of a blinded study using ultrasensitive virus detection in biopsies, proved the association between granuloma of the skin in PID patients and rubella virus. The viruses in these reports and the current report were derived from a widely used vaccine strain of the rubella virus. Work reported here shows that these vaccine-derived viruses are biologically different from the vaccine virus and that their genomes have changed. Genomic changes could be analyzed largely because the exact sequence of starting vaccine virus genome was known. These genomic differences are likely generated via mechanisms similar to those occurring during normal circulation of wild type rubella. We present data that newly recognized mechanisms for generation of sequence diversity in viruses (because of cellular deaminases) likely occurs in the generation of these vaccine-derived rubella viruses. Thousands of PID patients in the United States are likely shedding these vaccine-derived rubella viruses. Our work presented here characterizing viruses in diagnostic specimens highlights at least two areas where insufficient work has been done: 1) research on the properties of rubella virus (limited understanding of the antibody binding sites on the virus); 2) controlled research studies to assess the public health impact of viruses in populations with high immunity.

B virus ( Macacine herpesvirus 1 ) can cause deadly zoonotic disease in humans. Molecular mechanisms of B virus cell entry are poorly understood for both macaques and humans. Here we investigated the abilities of clinical B virus isolates to use entry receptors of herpes simplex viruses (HSV). We showed that resistant B78H1 cells became susceptible to B virus clinical strains upon expression of either human nectin-2 or nectin-1. Antibody against glycoprotein D (gD) protected these nectin-bearing cells from B virus infection, and a gD-negative recombinant B virus failed to enter these cells, indicating that the nectin-mediated B virus entry depends on gD. We observed that the infectivity of B virus isolates with a single amino acid substitution (D122N) in the IgV-core of the gD ectodomain was impaired on nectin-1-bearing cells. Computational homology-based modeling of the B virus gD–nectin-1 complex revealed conformational differences between the structures of the gD-122N and gD-122D variants that affected the gD–nectin-1 protein-protein interface and binding affinity. Unlike HSV, B virus clinical strains were unable to use herpesvirus entry mediator (HVEM) as a receptor, regardless of conservation of the gD amino acid residues essential for HSV-1 entry via HVEM. Based on the model of the B virus gD-HVEM interface, we predict that residues R7, R11, and G15 are largely responsible for the inability of B virus to utilize HVEM for entry. The ability of B virus to enter cells of a human host by using a combination of receptors distinct from those for HSV-1 or HSV-2 suggests a possible mechanism of enhanced neuropathogenicity associated with zoonotic infections. IMPORTANCE B virus causes brainstem destruction in infected humans in the absence of timely diagnosis and intervention. Nectins are cell adhesion molecules that are widely expressed in human tissues, including neurons and neuronal synapses. Here we report that human nectin-2 is a target receptor for B virus entry, in addition to the reported receptor human nectin-1. Similar to a B virus lab strain, B virus clinical strains can effectively use both nectin-1 and nectin-2 as cellular receptors for entry into human cells, but unlike HSV-1 and HSV-2, none of the clinical strains uses an HVEM-mediated entry pathway. Ultimately, these differences between B virus and HSV-1 and -2 may provide insight into the neuropathogenicity of B virus during zoonotic infections.

The HIV-1 proteinase (PR) has proved to be a good target for antiretroviral therapy of AIDS, and various PR inhibitors are now in clinical use. However, there is a rapid selection of viral variants bearing mutations in the proteinase that are resistant to clinical inhibitors. Drug resistance also involves mutations of the nucleocapsid/p1 and p1/p6 cleavage sites of Gag, both in vitro and in vivo. Cleavages at these sites have been shown to be rate limiting steps for polyprotein processing and viral maturation. Furthermore, these sites show significant sequence polymorphism, which also may have an impact on virion infectivity. We have studied the hydrolysis of oligopeptides representing these cleavage sites with representative mutations found as natural variations or that arise as resistant mutations. Wild-type and five drug resistant PRs with mutations within or outside the substrate binding site were tested. While the natural variations showed either increased or decreased susceptibility of peptides toward the proteinases, the resistant mutations always had a beneficial effect on catalytic efficiency. Comparison of the specificity changes obtained for the various substrates suggested that the maximization of the van der Waals contacts between substrate and PR is the major determinant of specificity: the same effect is crucial for inhibitor potency. The natural nucleocapsid/p1 and p1/p6 sites do not appear to be optimized for rapid hydrolysis. Hence, mutation of these rate limiting cleavage sites can partly compensate for the reduced catalytic activity of drug resistant mutant HIV-1 proteinases.

During studies of kinase phosphorylation, not all functional kinase phosphorylation may be found using consensus sequence patterns. This type of phosphorylation is termed ‘non-consensus’ or ‘cryptic’ phosphorylation. Results presented here based on molecular dynamics of short peptides show that protein kinases may phosphorylate not only established consensus sequences (reading a sequence from N-terminus to C-terminus) but also reversed consensus sequences (reading from C- to N-terminus). Several protein sequences were analysed and corresponding biochemical data were presented. Similarity of molecular shapes of direct and reversed consensus peptides, and sequence conservation in the regions of reversed sites in the analysed proteins, indicate that at least part of the phosphorylation sites considered as ‘cryptic’ may be explained in terms of reversed consensus pattern occurrences.

METHODS. This presentation introduces a novel method for identification of the folding cores in proteins. Positive and negative charge centers, defined solely from the structure of the folded protein are likely to indicate the protein’s folding core. The residues and sequences, identified by the procedure, are highly consistent with the available biochemical data on folding as seen for a set of about 20 proteins[1]. Here, the folding of chymotrypsin inhibitor-2 (CI2) from barley is analyzed in some detail.

To study the micronutrients that potentiate the action of anticonvulsant drugs, and in particular, of myo-inositol (vitamin B8).An experimental study of neurotrophic and anticonvulsant effects of a preparation based on myo-inositol (inofert) on thiosemicarbazide models of seizures was carried out.Inofert significantly increased the latent time before the first convulsive seizure, reduced the severity of seizures (p0.05) and reduced mortality in the models of thiosemicarbazide seizures. Myo-inositol enhanced anticonvulsant action of gabapentin and sodium valproate; neuroprotective effect of myo-inositol was also confirmed.The Inofert preparation, containing myo-inositol and folic acid, modulates the effects of drugs with both convulsive and anticonvulsive action, reduces the severity and duration of seizures caused by thiosemicarbazide and increases the survival rate of animals.Цель исследования. Изучение микронутриентов, способных потенцировать действие противосудорожных средств, в частности мио-инозитола (витамин В8). Материал и методы. Проведено экспериментальное исследование нейротропных и противосудорожных эффектов препарата на основе мио-инозитола (иноферт) на тиосемикарбазидной модели судорог у животных. Результаты и заключение. Курсовое введение иноферта на модели тиосемикарбазидовых судорог достоверно увеличивало латентное время до первого судорожного приступа, уменьшало тяжесть судорожных приступов (р0,05) и снижало летальность. Было отмечено также усиление противосудорожного действия вальпроата натрия и габапентина; подтвержден нейропротективный эффект препаратов мио-инозитола. Сделан вывод, что иноферт, содержащий мио-инозитол и фолиевую кислоту, модулирует эффекты лекарственных средств, обладающих как проконвульсантным, так и противосудорожным действием.Цель исследования. Изучение микронутриентов, способных потенцировать действие противосудорожных средств, в частности мио-инозитола (витамин В8). Материал и методы. Проведено экспериментальное исследование нейротропных и противосудорожных эффектов препарата на основе мио-инозитола (иноферт) на тиосемикарбазидной модели судорог у животных. Результаты и заключение. Курсовое введение иноферта на модели тиосемикарбазидовых судорог достоверно увеличивало латентное время до первого судорожного приступа, уменьшало тяжесть судорожных приступов (р0,05) и снижало летальность. Было отмечено также усиление противосудорожного действия вальпроата натрия и габапентина; подтвержден нейропротективный эффект препаратов мио-инозитола. Сделан вывод, что иноферт, содержащий мио-инозитол и фолиевую кислоту, модулирует эффекты лекарственных средств, обладающих как проконвульсантным, так и противосудорожным действием.

Ribozymes are functionally diverse RNA molecules with intrinsic catalytic activity. Multiple structural and biochemical studies are required to establish which nucleotide bases are involved in the catalysis. The relative energetic properties of the nucleotide bases have been analyzed in a set of the known ribozyme structures. It was found that many of the known catalytic nucleotides can be identified using only the structure without any additional biochemical data. The results of the calculations compare well with the available biochemical data on RNA stability. Extensivein silicomutagenesis suggests that most of the nucleotides in ribozymes stabilize the RNA. The calculations show that relative contribution of the catalytic bases to RNA stability observably differs from contributions of the noncatalytic bases. Distinction between the concepts of “relative stability” and “mutational stability” is suggested. As results of prediction for several models of ribozymes appear to be in agreement with the published data on the potential active site regions, the method can potentially be used for prediction of functional nucleotides from nucleic sequence.

Regions of rare conformation were located in 300 protein crystal structures represent- ing seven major protein folds. A distance matrix algorithm was used to search rapidly for 9-residue fragments of rare backbone conformation using a comparison to a relational database of encoded fragments derived from the database of nonredun- dant structures. Rare fragments were found in 61% of the analyzed protein structures. Detailed analy- sis was performed for 78 proteins of different folds. The rare fragments were located near functional sites in 72% of the protein structures. The rare fragments often formed parts of ligand-binding sites (59%), protein-protein interfaces (8%), and domain- domain contacts (5%). Of the remaining structures, 5% had a high average B-factor or high local B- factors. Statistical analysis suggests that the associa- tion between ligands and rare regions does not occur by chance alone. The present study is likely to underestimate the number of functional sites, be- cause not all analyzed protein structures contained a ligand. The results suggest that rapid searches for regions with rare local backbone conformations can assist in prediction of functional sites in novel proteins. Proteins 2003;53:872- 879.

Members of the TCL1 family of oncogenes are abnormally expressed in mature T-cell leukemias and B-cell lymphomas. The proteins are involved in the coactivation of protein kinase B (Akt/PKB), a key intracellular kinase. The sequences and crystal structures of three Tcl1 proteins were analyzed in order to understand their interactions with Akt/PKB and the implications for lymphocyte malignancies. Tcl1 proteins are ~15 kD and share 25—80% amino acid sequence identity. The tertiary structures of mouse Tcl1, human Tcl1, and Mtcp1 are very similar. Analysis of the structures revealed conserved semi-planar surfaces that have characteristics of surfaces involved in protein-protein interactions. The Tcl1 proteins show differences in surface charge distribution and oligomeric state suggesting that they do not interact in the same way with Akt/PKB and other cellular protein(s).

To study the synergism between neuropeptides and lithium ions.An experimental model of stroke (chronic bilateral occlusion of the common carotid arteries in rats), neuronal culture studies, histomorphological analyses, determination of micronutrient profile of brain substrates were used.A complex of experimental studies revealed that the effect of cerebrolysin is influenced by the synergism between lithium ions and the neuropeptide contentof this drug. Pharmacokinetic synergism promotes the accumulation of lithium in brain tissues during cerebrolysin treatment. The existence of the pharmacokinetic synergism is evident from the potentiation of neuroprotective effects of the drug under the action of lithium ions established in the model of stroke.Lithium ions potentiate neuroprotective effects of cerebrolysin.Цель исследования. Изучение синергизма между нейропептидами церебролизина и ионами лития. Материал и методы. Экспериментальная модель инсульта (хроническая двусторонняя окклюзия общих сонных артерий у крыс), исследования на нейронах в культуре, гистоморфологические анализы, исследования микроэлементного профиля биосубстратов мозга. Результаты. Проведенный комплекс экспериментальных исследований показал существование синергизма между ионами лития и нейропептидами в составе церебролизина. Фармакокинетический синергизм заключается в ускоренном накоплении лития в тканях головного мозга под воздействием церебролизина. Существование фармакодинамического синергизма между нейропептидами в составе церебролизина и литием следует из установленного нами потенцирования нейропротективных эффектов препарата под воздействием ионов лития на модели инсульта. Заключение. Ионы лития потенцируют нейропротективные эффекты церебролизина.

To establish an approach to obtain the site-specific calcium binding affinity of EF-hand proteins, we have successfully designed a series of model proteins, each containing the EF-hand calcium-binding loop 3 of calmodulin, but with increasing numbers of Gly residues linking the loop to domain 1 of CD2. Structural analyses, using different spectroscopic methods, have shown that the host protein is able to retain its native structure after insertion of the 12-residue calcium-binding loop and retains a native thermal stability and thermal unfolding behavior. In addition, calcium binding to the engineered CD2 variants does not result in a significant change from native CD2 conformation. The CD2 variant with two Gly linkers has been shown to have the strongest metal binding affinity to Ca(II) and La(III). These experimental results are consistent with our molecular modeling studies, which suggest that this protein with the engineered EF-loop has a calmodulin-like calcium binding geometry and backbone conformation. The addition of two Gly linkers increases the flexibility of the inserted EF-loop 3 from calmodulin, which is essential for the proper binding of metal ions.

Structural classes of protein domains correlate with their amino acid compositions. Several successful algorithms (that use only amino acid composition) have been elaborated for the prediction of structural class or potential biochemical significance. This work deals with dynamic classification (clustering) of the domains on the basis of their amino acid composition. Amino acid contents of domains from a non-redundant PDB set were clustered in 20-dimensional space of amino acid contents. Despite the variations of an empirical parameter and non-redundancy of the set, only one large cluster (tens-hundreds of proteins) surrounded by hundreds of small clusters (1-5 proteins), was identified. The core of the largest cluster contains at least 64% DNA (nucleotide)-interacting protein domains from various sources. About 90% of the proteins of the core are intracellular proteins. 83% of the DNA/nucleotide interacting domains in the core belong to the mixed alpha-beta folds (a+b, a/b), 14% are all-alpha (mostly helices) and all-beta (mostly beta-strands) proteins. At the same time, when core domains that belong to one organism (E.coli) are considered, over 80% of them prove to be DNA/nucleotide interacting proteins. The core is compact: amino acid contents of domains from the core lie in relatively narrow and specific ranges. The core also contains several Fe-S cluster-binding domains, amino acid contents of the core overlap with ferredoxin and CO-dehydrogenase clusters, the oldest known proteins. As Fe-S clusters are thought to be the first biocatalysts, the results are discussed in relation to contemporary experiments and models dealing with the origin of biological macromolecules. The origin of most primordial proteins is considered here to be a result of co-adsorption of nucleotides and amino acids on specific clays, followed by en-block polymerization of the adsorbed mixtures of amino acids.

The EF-hand calcium-binding loop III from calmodulin was inserted with glycine linkers into the scaffold protein CD2.D1 at three locations to study site-specific calcium binding properties of EF-hand motifs. After insertion, the host protein retains its native structure and forms a 1:1 metal-protein complex for calcium and its analog, lanthanum. Tyrosine-sensitized Tb 3 + energy transfer exhibits metal binding and La 3 + and Ca 2 + compete for the metal binding site. The grafted EF-loop III in different environments has similar La 3 + binding affinities, suggesting that it is largely solvated and functions independently from the host protein.