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More than three thousand five hundred biological properties of vitamin B[Formula: see text] and four of its derivatives (aquacobalamin, cyanoaquacobyrinic acid heptamethyl ester, dicyanocobyrinic acid heptamethyl ester and stable yellow corrinoid) have been assessed by bioinformation analysis. Based on the data obtained (including the assessments of the interaction of molecules with the proteins of rat proteome), conclusions were drawn about the potential effects and safety of the investigated substances. In particular, it has been shown that heptamethyl esters of cyanoaquacobyrinic and dicyanocobyrinic acids, as well as a stable yellow corrinoid (antivitamin), can be recommended for further study as analgesics, anti-inflammatory drugs and, also, antitumor agents aimed at the therapy of glioblastoma, hepatoblastoma and T-cell leukemia. Estimates of the LD50 constants for rats and the TD50 and IC50 constants for rat muscle cells in culture, along with the results of assessments of the interaction of molecules with the rat proteome, showed that all the compounds studied were of low toxicity. At the same time, cyanocobalamin and aquacobalamin are distinguished by the least cumulative properties in comparison with other studied compounds. Chemoneurocytological analysis of compounds showed that cyanocobalamin and aquacobalamin may have the greatest neuroprotective effects: increase in the concentration of the substances by 1 mmol/l causes the estimate of neuronal survival to increase by 25%.

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.

Quantitative estimates of the effect of 7-hydroxymatairesinol (7-HMR) intake on estrogen balance and clinical aspects of the course of fibrocystic mastopathy have been carried out. Aim. Assessment of effects 7-HMR on metabolism of estrogen (16a-OHE1, 2-OHE2, 2-OHE1, 2-OMEE1, 4-OMEE2, 4-OHE1, a ratio 2-OHE1/16a-OHE1, 2-OHE1/2-OMeE1 and 4-OHE1/4-OMeE1) and progesterone in daily urine at patients with fibrous and cystous mastopathy in the post-menopausal period. Materials and methods. The analysis of metabolites of estrogen (16a-OHE1, 2-OHE2, 2-OHE1, 2-OMEE1, 4-OMEE2, 4-OHE1, ratios 2-OHE1/16a-OHE1, 2-OHE1/2-OMeE1 and 4-OHE1/4-OMeE1) and progesterone in daily urine with use of solid-phase immunofermental set (IFA) of Amerscham International on the analyzer of Amerkard by means of standard sets is carried out. Statistical 10.0 and Microsoft Excel spreadsheets were used in statistical material processing. Results. It was found that taking 7-HMR (60 mg/day, 1 month) contributes to normalizing estrogen metabolism (decreasing estradiol, estrone, estriol, 16a-OHE1) and improves the clinical symptoms of mastopathy. Conclusions. In patients with FCM, 7-HMR contributes to a decrease in hyperestrogenia-related tumor risks by lowering estrogen metabolites levels.

D-chiroinositol (DCI) is one of the 9 inositol isomers that forms inositol phosphoglycans, which are mediators of the action of insulin. The metabolism of DCI and myo-inositol (MI) is impaired against the background of insulin resistance, including the patients with polycystic ovary syndrome (PCOS). Aim. Highlight the most characteristic pharmacological properties of DCI. Materials and methods. Systematic computer analysis of 45 600 publications on the biological roles of inositol by methods of the topological theory of pattern recognition and systems biology analysis of human proteome. Results. A complex of interactions between metabolic disorders of DCI, PCOS, ovulation disorders, obesity associated with numerous hormonal disorders is described. Supplements with DCI and MI increase the sensitivity of cells to insulin and normalize the metabolism of androgens. An important difference between DCI and MI is the presence of DCI in the composition of inositol phosphoglycans that mediate the action of insulin on cells, as well as its participation in the realization of the therapeutic effects of metformin. The use of the MI+DCI combination allows achieving positive dynamics in reducing excess body weight, normalizing blood lipids, glucose and insulin levels, restoring the ovulatory menstrual cycle, improving oocyte quality, and helps prevent gestational diabetes in pregnant women and macrosomia of the fetus. DCI is more effective than MI in reducing the risk of folate-resistant neural tube defects. Conclusion. The therapeutic potential of DCI in combination with MI for treating PCOS and hyperandrogenism is evident. Depending on the therapeutic expediency, various ratios of MI:DCI can be used for the treatment of PCOS and disorders of carbohydrate and lipid metabolism.A

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.

The fundamental criteria of the quality of molecular dynamics (MD) simulation represent a pivotal challenge, especially in the case of MD simulations of large systems (in particular, proteins).This work presents a simple theoretical analysis of time reversibility in classical mechanics that has allowed us to formulate a number of constructive criteria for evaluating the quality of the trajectories, generated in MD simulations. The results of testing the criteria on the structures of eight small proteins are presented. The criteria can be useful for solving different MD problems, such as: choosing the most appropriate thermostats for a MD system under study, the methods for sampling conformations, etc. Communicated by Ramaswamy H. Sarma

INTRODUCTION. The structures of members of the Tcl1 oncoprotein family are being studied in order to understand their roles in lymphocyte biology and their development of lymphocytic diseases[1-3]. These ~15 kD proteins share 25–80% sequence identity between the members of the family. No sequence similarity was found with other human genes suggesting a unique cellular role(s). Family members share an uncommon tertiary structure of an eight-stranded beta barrel. Recently, the crystal structure of murine Tcl1 was determined[3]. The three structures were analyzed to reveal conserved features indicative of a potential binding site for an interacting protein.

The structure of the SH3 domain of α-spectrin (PDB code 1SHG) features Asn47 in the II' area of the Ramachandran plot, which as a rule admits only glycine residues, and this phenomenon still awaits its explanation. Here, we undertook a computational study of this particular case by means of molecular dynamics and bioinformatics approaches. We found that the region of the SH3 domain in the vicinity of Asn47 remains relatively stable during denaturing molecular dynamics simulations of the entire domain and of its parts. This increased stability may be connected with the dynamic hydrogen bonding that is susceptible to targeted in silico mutations of Arg49. Bioinformatics analysis indicated that Asn47 is in the β-turn of a distinctive structural fragment we called 'alternatingly twisted β-hairpin.' Fragments of similar conformation are quite abundant in a nonredundant set of PDB chains and are distinguished from ordinary β-hairpins by some surplus of glycine in their β-turns, lack of certain interpeptide hydrogen bonds, and an increased chirality index. Thus, the disallowed conformation of residues other than glycine is realized in the β-turns of alternatingly twisted β-hairpins.

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.

Empirical criteria for identification of hydrogen bonds were analyzed to produce a set of geometrically consistent criteria. For a data set of 30 structures, application of a set of purely geometrical criteria, along with exclusion of abnormal backbone conformations, also excluded a common interaction of Ser/Thr side chains with Asp/Glu side chains ([ST]/[DE] pairs). These interactions were termed "bifurcated hydrogen bonds", which implies delocalization of a positively charged hydrogen of hydroxyl between the two acceptor atoms of the carboxylic group. These "bifurcated" interactions are among the most common packing patterns for [ST]/[DE] pairs of side chains. Therefore, the identification of hydrogen bonds cannot be based on geometrical criteria only and requires introduction of some physico-chemical criteria.

Electrostatic interactions are important for protein folding. At low resolution, the electrostatic field of the whole molecule can be described in terms of charge center(s). To study electrostatic effects, the centers of positive and negative charge were calculated for 20 small proteins of known structure, for which hydrogen exchange cores had been determined experimentally. Two observations seem to be important. First, in all 20 proteins studied 30-100% of the residues forming hydrogen exchange core(s) were clustered around the charge centers. Moreover, in each protein more than half of the core sequences are located near the centers of charge. Second, the general architecture of all-alpha proteins from the set seems to be stabilized by interactions of residues surrounding the charge centers. In most of the alpha-beta proteins, either or both of the centers are located near a pair of consecutive strands, and this is even more characteristic for alpha/Beta and all-beta structures. Consecutive strands are very probable sites of early folding events. These two points lead to the conclusion that charge centers, defined solely from the structure of the folded protein may indicate the location of a protein's hydrogen exchange/folding core. In addition, almost all the proteins contain well-conserved continuous hydrophobic sequences of three or more residues located in the vicinity of the charge centers. These hydrophobic sequences may be primary nucleation sites for protein folding. The results suggest the following scheme for the order of events in folding: local hydrophobic nucleation, electrostatic collapse of the core, global hydrophobic collapse, and slow annealing to the native state. This analysis emphasizes the importance of treating electrostatics during protein-folding simulations.

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.

Membrane protein prediction is a significant classification problem, requiring the integration of data derived from different sources such as protein sequences, gene expression, protein interactions etc. A generalized probabilistic approach for combining different data sources via supervised selective kernel fusion was proposed in our previous papers. It includes, as particular cases, SVM, Lasso SVM, Elastic Net SVM and others. In this paper we apply a further instantiation of this approach, the Supervised Selective Support Kernel SVM and demonstrate that the proposed approach achieves the top-rank position among the selective kernel fusion variants on benchmark data for membrane protein prediction. The method differs from the previous approaches in that it naturally derives a subset of “support kernels” (analogous to support objects within SVMs), thereby allowing the memory-efficient exclusion of significant numbers of irrelevant kernel matrixes from a decision rule in a manner particularly suited to membrane protein prediction.

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.

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.

2'-5' Oligoadenylate synthetases are interferon-induced enzymes important for antiviral cell defense. Tetramer formation of human OAS1 is essential for the catalytic activity of the enzyme. However, no structure of any oligomeric OAS1 protein has yet been solved and the structural organization of the catalytically active tetramers is not known.Using a novel conjunction of comparative modeling, molecular surface analysis, and sequence analysis, high-resolution models of the known isoforms of human OAS1 were prepared.The resulting models suggest different oligomeric states for the p40, p46, and p48 isoforms as well as a significant difference in enzymatic activity between the p46 and p40/p48 isoforms.The differences in enzymatic activity could result in different susceptibility to viral infection in cells expressing individual isoforms. The models are consistent with the published biochemical data on human OAS1. The results also suggest that the structure of the active OAS2 dimers would be equivalent to that of p40 OAS1 tetramers.

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).

Covalent attachment of hydrogen to the donor atom may be not an essential characteristic of stable hydrogen bonds. A positively charged particle (such as a proton), located between the two negatively charged residues, may lead to a stable interaction of the two negative residues. This paper analyzes close Asp–Glu pairs of residues in a large set of protein chains; 840 such pairs of residues were identified, of which 28% were stabilized by a metal ion, 12% by a positive residue nearby and 60% are likely to be stabilized by a proton. The absence of apparent structural constraints, secondary structure preferences, somewhat lower B-factors and a distinct correlation between pH and the minimal O– O distance in carboxylate pairs suggest that most of the abnormally close pairs could indeed be stabilized by a shared proton. Implications for protein stability and modeling are discussed.

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.

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.

Cell adhesion involves interactions of integrins and extracellular proteins, often facilitated by the RGD motif. Only presence of the RGD in a sequence of a protein may be not sufficient for the biological activity (binding to an integrin) and additional biochemical and/or structural studies are essential.Structural criteria that would allow identification biologically active RGD-sites on the base of a spatial structure may assist analysis of function of a protein in the cell. For the first time, computational analysis of RGD-sites in a large non-redundant set of protein structures was done.Out of 3819 protein chains sequences of about 100 contained RGDs. Analysis of the structures of the RGD-'native' proteins has allowed establishing main determinants of the biologically active conformations of the RGD sites: surface accessibility of the whole RGD-sequence and the secondary structure. The criteria, applied to the remaining proteins of the set, identify 23 proteins ( approximately 25%) with potentially active RGD-sites. The results strongly suggest that RGD has a high propensity for being involved in protein-protein interactions and this may explain occurrence of RGDs in intracellular proteins. Results of the analysis suggest (in some cases, confirm) novel integrin-related activities for 7 membrane/extracellular proteins, as well as confirm RGD-facilitated cell attachment for 5 viral proteins.Only presence of RGD in a sequence is not sufficient to propose biological activity of this site. The results also suggest that the method can be used on large scale: for example, for identifying potential integrin-interacting proteins in an animal genome.

Oligomers and separate subunits of the glycolytic enzymes often have different catalytic properties. However, spectral data show an apparent lack of significant conformational changes during oligomerization. Since the conformation of an enzyme determines its catalytic properties, the structural mechanism(s) influencing the activity is of considerable interest.Analysis of the spatial structures of the junctions between interglobular contacts and binding sites may give a clue to the mechanism(s) of the activation. In this work, the problem was studied using available structural and biochemical data for the oligomeric enzymes of glycolysis.Computational analysis of the structures of the junctions has identified three structurally distinct types of junctions: 1. interglobular binding site (2 of 8 enzymes); 2. domain-domain stabilization (5 of 8); and 3. 'sequence overlap' or a local conformational change (all enzymes). Thus the catalytic activity may be influenced through the shifts of the modules of protein structure (types 1, 2) and/or due to a slight change in the local structure (type 3). The more common junctions of types 2 and 3 are well conserved among eukaryotic enzymes, which suggests their biological importance.The results suggest that a profound and a complex change in conformation in subunits of an oligomeric enzyme may not be necessary for a significant change in the catalytic properties. The analysis maps the residues important for the junctions and thus for the link between the catalytic activity and the oligomeric state of the enzymes.

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.

Tcl1 and Mtcp1, members of the Tcl1 family, are implicated in T-cell prolymphocytic leukemia. The crystal structure of a dimer of murine Tcl1 has been determined at 2.5 A resolution with an R factor of 0.225. Murine Tcl1, human Tcl1 and Mtcp1 share very similar subunit structures, with RMS differences of 0.6 and 1.4 A for C(alpha) atoms, respectively, while the sequences share 50 and 36% identity, respectively. These structures fold into an eight-stranded beta-barrel of unique topology and high internal symmetry of 1.1-1.3 A for the two halves of human and murine Tcl1 and 1.7 A for Mtcp1, despite the low 12-13% sequence identity. The molecular surfaces of all three structures showed a common planar region which is likely to be involved in protein-protein interactions.

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.

The aim of the paper is to experimentally examine the plausibility of Relevance Vector Machines (RVM) for protein secondary structure prediction. We restrict our attention to detecting strands which represent an especially problematic element of the secondary structure. The commonly adopted local principle of secondary structure prediction is applied, which implies comparison of a sliding window in the given polypeptide chain with a number of reference amino-acid sequences cut out of the training proteins as benchmarks representing the classes of secondary structure. As distinct from the classical RVM, the novel version applied in this paper allows for selective combination of several tentative window comparison modalities. Experiments on the RS126 data set have shown its ability to essentially decrease the number of reference fragments in the resulting decision rule and to select a subset of the most appropriate comparison modalities within the given set of the tentative ones.