Structural-functional Features Research Articles

Comparative Characterization of Plasmodium falciparum Hsp70-1 Relative to E. coli DnaK Reveals the Functional Specificity of the Parasite Chaperone

Hsp70 is a conserved molecular chaperone. How Hsp70 exhibits specialized functions across species remains to be understood. Plasmodium falciparum Hsp70-1 (PfHsp70-1) and Escherichia coli DnaK are cytosol localized molecular chaperones that are important for the survival of these two organisms. In the current study, we investigated comparative structure-function features of PfHsp70-1 relative to DnaK and a chimeric protein, KPf, constituted by the ATPase domain of DnaK and the substrate binding domain (SBD) of PfHsp70-1. Recombinant forms of the three Hsp70s exhibited similar secondary and tertiary structural folds. However, compared to DnaK, both KPf and PfHsp70-1 were more stable to heat stress and exhibited higher basal ATPase activity. In addition, PfHsp70-1 preferentially bound to asparagine rich peptide substrates, as opposed to DnaK. Recombinant P. falciparum adenosylmethionine decarboxylase (PfAdoMetDC) co-expressed in E. coli with either KPf or PfHsp70-1 was produced as a fully folded product. Co-expression of PfAdoMetDC with heterologous DnaK in E. coli did not promote folding of the former. However, a combination of supplementary GroEL plus DnaK improved folding of PfAdoMetDC. These findings demonstrated that the SBD of PfHsp70-1 regulates several functional features of the protein and that this molecular chaperone is tailored to facilitate folding of plasmodial proteins.

SUN-138 Functional Characterization of Tumor-Associated Germline TMEM127 Variants Reveals Novel Insights into Membrane Topology and Protein Trafficking

TMEM127, a tumor suppressor gene in hereditary pheochromocytomas and paragangliomas, encodes for a poorly characterized, ubiquitous, transmembrane (TM) protein with no substantial identity to any other protein and no identifiable functional domains other than putative TM domains. The function and regulation of TMEM127 remain poorly defined which limits prediction of pathogenicity of germline TMEM127 variants. Characterizing structure-function features of TMEM127 is relevant for understanding how dysfunction of this tumor suppressor can lead to inherited tumors. Moreover, a better understanding of TMEM127 functional domains and critical residues will increase our ability to identify pathogenic variants which will improve interpretation of genetic screening results and help guide clinical decisions for patients and their families. In this study, we investigated subcellular localization and steady-state levels of patient-derived, tumor-associated, germline TMEM127 variants (n=21; 16 missense and 5 truncating/frameshift/indel variants). We used confocal immunofluorescence and immunoblot analysis of GFP-TMEM127 constructs expressed in HEK293T cells. Wild-type (WT) TMEM127 localized predominantly to endo-lysosomal vesicles (punctate) with some plasma membrane localization. The localization of variant TMEM127 proteins displayed three distinct patterns: punctate (similar to WT), diffuse (cytoplasmic), and plasma membrane only. All diffuse proteins, and a few punctate proteins, decreased at a faster rate than the WT suggesting instability. Variants resulting in diffuse proteins occurred within TM domains and indicated that membrane binding ability was lost. This observation, supported by in silico analysis and selective permeability assays, led us to conclude that TMEM127 is a four-TM protein, not a three-TM protein, as previously predicted, with a novel TM domain in the N-terminus. One variant with predominantly plasma membrane localization indicated that membrane binding ability was maintained but internalization capability was lost. We identified an atypical, extended acidic dileucine motif in the C-terminal which is responsible for TMEM127 internalization and showed that it is mediated by clathrin. Our findings provide novel insights into structure-function features of TMEM127 which will allow for better understanding of its physiological role and improved prediction of pathogenic variants.

A pluralistic theory of wordhood

What are words and how should we individuate them? There are two main answers on the philosophical market. For some, words are bundles of structural–functional features defining a unique performance profile. For others, words are noneternal continuants individuated by their causal‐historical ancestry. These conceptions offer competing views of the nature of words, and it seems natural to assume that at most one of them can capture the essence of wordhood. This paper makes a case for pluralism about wordhood: The view that there is a plurality of acceptable conceptions of the nature of words, none of which is uniquely entitled to inform us as to what wordhood consists in.

Kinetic improvement of an algal diacylglycerol acyltransferase 1 via fusion with an acyl-CoA binding protein.

Microalgal oils in the form of triacylglycerols (TAGs) are broadly used as nutritional supplements and biofuels. Diacylglycerol acyltransferase (DGAT) catalyzes the final step of acyl-CoA-dependent biosynthesis of TAG, and is considered a key target for manipulating oil production. Although a growing number of DGAT1s have been identified and over-expressed in some algal species, the detailed structure-function relationship, as well as the improvement of DGAT1 performance via protein engineering, remain largely untapped. Here, we explored the structure-function features of the hydrophilic N-terminal domain of DGAT1 from the green microalga Chromochloris zofingiensis (CzDGAT1). The results indicated that the N-terminal domain of CzDGAT1 was less disordered than those of the higher eukaryotic enzymes and its partial truncation or complete removal could substantially decrease enzyme activity, suggesting its possible role in maintaining enzyme performance. Although the N-terminal domains of animal and plant DGAT1s were previously found to bind acyl-CoAs, replacement of CzDGAT1 N-terminus by an acyl-CoA binding protein (ACBP) could not restore enzyme activity. Interestingly, the fusion of ACBP to the N-terminus of the full-length CzDGAT1 could enhance the enzyme affinity for acyl-CoAs and augment protein accumulation levels, which ultimately drove oil accumulation in yeast cells and tobacco leaves to higher levels than the full-length CzDGAT1. Overall, our findings unravel the distinct features of the N-terminus of algal DGAT1 and provide a strategy to engineer enhanced performance in DGAT1 via protein fusion, which may open a vista in generating improved membrane-bound acyl-CoA-dependent enzymes and boosting oil biosynthesis in plants and oleaginous microorganisms.

Food sovereignty and education: A Japanese type of harmonization

Every civilization has specific social-cultural rituals for eating, and contemporary Japan is a particularly interesting case. The architects of the Japanese food policy use a special respect for food in two ways: first, as a tool of soft power to spread Japanese influence worldwide; second, as an effective way to ensure food security. It is the second component that interests the authors. The article identifies key issues of Japan’s food policy. Based on the institutional analysis and the food regime theory, the authors identify the structural nature of food import dependency of the Land of the Rising Sun. The combination of the comparative approach and retrospective analysis allowed to discover a number of elements that are closely connected with the idea of food sovereignty, especially the concept of shokuiku (food education). Based on the historical-genetic method, the authors suggest a cognitive route of the terminological unit “from the component of folklore to the legislative act” and identify structural-functional features of the Basic Law ( Shokuiku Kihon-ho ). The analysis of three Basic Plans for promotion of Shokuiku proved the institutional reorientation of Japan to collectivism, healthy lifestyle and dietetics of younger generations. Despite the fact that effectiveness of re-profiling was verified by empirical data, the article provides a critical analysis of shokuiku as well. The state monopoly on food knowledge and risk discourse legitimize ideologies, generate alarmist feelings and lead to food nationalism.

Plasmodium falciparum R2TP complex: driver of parasite Hsp90 function.

Heat shock protein 90 (Hsp90) is essential for the development of the main malaria agent, Plasmodium falciparum. Inhibitors that target Hsp90 function are known to not only kill the parasite, but also reverse resistance of the parasite to traditional antimalarials such as chloroquine. For this reason, Hsp90 has been tagged as a promising antimalarial drug target. As a molecular chaperone, Hsp90 facilitates folding of proteins such as steroid hormone receptors and kinases implicated in cell cycle and development. Central to Hsp90 function is its regulation by several co-chaperones. Various co-chaperones interact with Hsp90 to modulate its co-operation with other molecular chaperones such as Hsp70 and to regulate its interaction with substrates. The role of Hsp90 in the development of malaria parasites continues to receive research attention, and several Hsp90 co-chaperones have been mapped out. Recently, focus has shifted to P. falciparum R2TP proteins, which are thought to couple Hsp90 to a diverse set of client proteins. R2TP proteins are generally known to form a complex with Hsp90, and this complex drives multiple cellular processes central to signal transduction and cell division. Given the central role that the R2TP complex may play, the current review highlights the structure-function features of Hsp90 relative to R2TPs of P. falciparum.

Fine Tuning of Translation: A Complex Web of Mechanisms and Its Relevance to Plant Functional Genomics and Biotechnology

The paradox of misfit between the levels of mRNAs and their protein products in the eukaryotic cells, including plant cells, encountered by researchers, direct their efforts towards the study into fine mechanisms of translation. Translation is an intricate biological process with numerous players, including mRNAs, tRNAs, ribosomes, and manifold protein factors. Certainly, each of them is important for efficient translation. However, the mRNAs itself contain numerous regulatory elements, such as 5'UTR, the context around the AUG start codon, and codon composition; each element separately or in combination can determine the fate of an individual mRNA in translational process. The previous reviews mainly focus on individual key stages in translation or the aspects of its control. Our goal here is (i) to summarize the recent data on the specific structure–function features of plant mRNAs and their correlation with translational efficiency; (ii) to brief new experimental and theoretical approaches to gaining the insight into the complex network of translation; and (iii) to assess the relevance of this knowledge to both the plant functional genomics and biotechnological application.

The Link That Binds: The Linker of Hsp70 as a Helm of the Protein's Function.

The heat shock 70 (Hsp70) family of molecular chaperones plays a central role in maintaining cellular proteostasis. Structurally, Hsp70s are composed of an N-terminal nucleotide binding domain (NBD) which exhibits ATPase activity, and a C-terminal substrate binding domain (SBD). The binding of ATP at the NBD and its subsequent hydrolysis influences the substrate binding affinity of the SBD through allostery. Similarly, peptide binding at the C-terminal SBD stimulates ATP hydrolysis by the N-terminal NBD. Interdomain communication between the NBD and SBD is facilitated by a conserved linker segment. Hsp70s form two main subgroups. Canonical Hsp70 members generally suppress protein aggregation and are also capable of refolding misfolded proteins. Hsp110 members are characterized by an extended lid segment and their function tends to be largely restricted to suppression of protein aggregation. In addition, the latter serve as nucleotide exchange factors (NEFs) of canonical Hsp70s. The linker of the Hsp110 family is less conserved compared to that of the canonical Hsp70 group. In addition, the linker plays a crucial role in defining the functional features of these two groups of Hsp70. Generally, the linker of Hsp70 is quite small and varies in size from seven to thirteen residues. Due to its small size, any sequence variation that Hsp70 exhibits in this motif has a major and unique influence on the function of the protein. Based on sequence data, we observed that canonical Hsp70s possess a linker that is distinct from similar segments present in Hsp110 proteins. In addition, Hsp110 linker motifs from various genera are distinct suggesting that their unique features regulate the flexibility with which the NBD and SBD of these proteins communicate via allostery. The Hsp70 linker modulates various structure-function features of Hsp70 such as its global conformation, affinity for peptide substrate and interaction with co-chaperones. The current review discusses how the unique features of the Hsp70 linker accounts for the functional specialization of this group of molecular chaperones.

Exploring Chemical and Biological Space of Terpenoids.

Terpenoids represent the largest family of natural products (NPs) with dramatically chemical and structural diversity, which makes terpenoids the important compound resources of drug discovery. However, comprehensive understanding on the structure-function features for terpenoid NPs is limited. In this work, we have systematically explored the chemical and biological space of terpenoid NPs, including their distribution, physicochemical properties, scaffold features, and functional applications, by utilizing various cheminformatics and bioinformatics approaches. We have not only confirmed that terpenoid NPs have good drug-likeness and great potential for drug discovery but, more importantly, illuminated the uniqueness of cyclic scaffold diversity in different species (plants, fungi, bacteria, and animals) and the specificity of biological function for the dominant fused-ring scaffolds of terpenoids. The present work supplies a valuable reference for identifying the new structure and unknown function of terpenoid NPs.

Structural-functional features of the heart in patients with acute Q-myocardial infarction of the anterior wall of the left ventricle in the presence of pulmonary hypertension

The aim was to evaluate the structural and functional features of the heart in the acute myocardial infarction (AMI) of the anterior wall of the left ventricle (LV) in the presence of pulmonary hypertension (PH) for the development of more informative diagnostic markers, forecast predictors and improved treatment of patients.Materials and methods. A total of 90 patients (53 men and 37 women) with acute myocardial infarction of the anterior wall of the LV (AMI AV) were examined in the intensive care unit for acute coronary insufficiency of the Communal Non-profit Enterprise "City Emergency and Ambulance Hospital" of the Zaporizhzhya City Council. Patients were divided into two groups: 55 patients with AMI AV with PH (mean age 70.65±1.83 years), 35 patients with AMI AV without HD (mean age 66.80±2.02 years). For all patients in the first three days after hospitalization, two-dimensional echocardiography was performed on the device "MyLab50" ("Esaote", Italy) according to the recommendations of the American Society of Echocardiography. For statistical data processing, statistical software package "Statistica 6.0 for Windows" (StatSoft Inc., № AXXR712D833214FAN5) was used. The reliability of the differences in the groups was evaluated using the dual t-criterion of the Student for independent samples. To assess the convergence of the indicators, the χ2 criterion, corrected by Yeats, was determined. The reliability of the differences between the indices was confirmed at p<0.05.Results. In patients with AMI AV with PH in comparison with patients with AMI AV without РH, there was a significant decrease in ejection fraction (22.3 %; p<0.05), increase in myocardial mass index (by 18.3 %, p<0.05) and end systolic diameter of left ventricle (12.4 %; p<0.05), dilatation of left atrium (by 11.6 % (p<0.05), right ventricle (by 27.3 %, p<0.05) and right atrium (by 20, 9 %; p<0.05). In assessing the types of remodeling of the of left ventricle, it was found that in patients with AMI AV with PH was predominantly eccentric hypertrophy (90.9 %), which is significantly higher in comparison with the AMI AV without PH.Patients with AMI AV and PH have a significant acceleration peak E of mitral valve (by 34.4 %; p<0.05), an increase in the ratio E/A of mitral valve (by 61.1 %, p <0.05), the time of isovolumetric relaxation LV extension (on 13.9 %; p<0.05) and acceleration peak E of tricuspidal valve E (by 28.3 %, p<0.05) in comparison with patients without PH. According to the data of tissue dopplerography, patients with AMI AV and PH showed an increasing ratio E/E' of mitral valve (MV E/E') (by 46.5 %; p<0.05) and ratio E/E' of tricuspidal valve (TV E/E') (by 39.3 %; p<0.05 ) compared with patients without PH. In patients with AMI AV and PH there was a predominant type of diastolic dysfunction (40 % of cases), type of diastolic dysfunction with disturbance of relaxation (71.4 %) predominated in the group of AMI AV without PH.Conclusions. In patients with AMI AV pulmonary hypertension develops against the background of dilation of the left chambers of the heart with the formation of eccentric hypertrophy and systolic dysfunction of the left ventricle, overloading of the right chambers of the heart with an increase in the size of the right atrium and left ventricle. Patients with AMI AV with PH had a predominantly pseudonormal type of LV diastolic dysfunction with an increase in MV E/E' ratio and diastolic dysfunction of right ventricle, as evidenced by an increase in the ratio of TV E/E'

Computational and Experimental Tools to Monitor the Changes in Translation Efficiency of Plant mRNA on a Genome-Wide Scale: Advantages, Limitations, and Solutions.

The control of translation in the course of gene expression regulation plays a crucial role in plants’ cellular events and, particularly, in responses to environmental factors. The paradox of the great variance between levels of mRNAs and their protein products in eukaryotic cells, including plants, requires thorough investigation of the regulatory mechanisms of translation. A wide and amazingly complex network of mechanisms decoding the plant genome into proteome challenges researchers to design new methods for genome-wide analysis of translational control, develop computational algorithms detecting regulatory mRNA contexts, and to establish rules underlying differential translation. The aims of this review are to (i) describe the experimental approaches for investigation of differential translation in plants on a genome-wide scale; (ii) summarize the current data on computational algorithms for detection of specific structure–function features and key determinants in plant mRNAs and their correlation with translation efficiency; (iii) highlight the methods for experimental verification of existed and theoretically predicted features within plant mRNAs important for their differential translation; and finally (iv) to discuss the perspectives of discovering the specific structural features of plant mRNA that mediate differential translation control by the combination of computational and experimental approaches.

Структурно-функциональные и гемодинамические особенности у пациентов с простой первичной и псевдоэксфолиативной открытоугольной глаукомой и офтальмогипертензией

Структурно-функциональные и гемодинамические особенности у пациентов с простой первичной и псевдоэксфолиативной открытоугольной глаукомой и офтальмогипертензией

Social Media Content in Journalists Articles

The Internet anonymity for a long time made it difficult for journalists to use the content presented in it. Now, thanks to the convergence of the "virtual" personality and the "real" one, this problem has been mitigated. Journalists begin to perceive social networks as sources of information, and they start to interpret what is published in them as reliable data or public statements. This research shows the extent of penetration of social networks information to the media, characterizes structural-functional features of this recent journalism tool. This work shows how often, when and for which purposes Media uses the social networks and how does this situation influences the articles. The continuous selection from RIA Novosti, Life.ru and Lenta.ru (683 articles) allowed us to examine features of representation of information from social networks. It was found that journalists use social media materials to confirm some fact or position of a person, as an information guide, they borrow there photos or videos, and, analyzing the comments, reproduce the "opinion of the audience". In general, it is shown that social networks have already secured the place of information providers for the media. The media began to trust this information, learned how to work with it, to process it for certain genres. There are even special software tools that allow Internet media to integrate very organically posts from social networks into their pages with publications when creating a site. The identical virtual personality of a real person, created now in social media, increasingly brings communication within the network closer to communication in real life, which expands the professional journalistic toolkit.

The right to a fair trial and a modern civil procedure model

In the article the author tries to depart from the previous conventional approach according to which the model of civil procedure is characterized only as adversarial one. The author’s approach to the definition of model of civil procedure is based on the requirements of art. 6 (1) ECHR and the judgments of the Court, where the content and the scope of the right to a fair trial are determined. Abovementioned has allowed to conduct a complex study and to analyze the institutional, structural-functional, substantive, and procedural features of such model. From the institutional point of view c ivil procedure should involve the judicial activity of courts directly integrated into the Judicial System of Ukraine, other jurisdictional bodies as well as enforcement bodies. This order is internally structured and covers both disputable and “conditionally” disputable proceedings and law-enforcement procedures, as well as stages of logical and functional character. In this regard, despite the existence of three procedural codes in Ukraine civil, economic and administrative proceedings should be included to a single civil procedure and, accordingly, be carried out in compliance with the fundamental principles of fair trial. The latter provide, firstly, that the access to jurisdictional and enforcement bodies should not be burdened by excessive legal or economic obstacles. Secondly, the case hearing should occur in compliance with the due (fair) procedure. Thirdly, the hearing should be public. Fourthly, there should be reasonable time of a trial and execution. Fifthly, the jurisdictional body should be independent, unbiased and established by law. Sixthly, enforcement of decisions of jurisdictional bodies should be carried out without undue delay. Civil procedure is considered to be the order for resolving civil cases according to the fundamental principles of fair trial, which is taken by courts in civil, economic and in certain occasions, administrative proceedings as well as, jurisdictional bodies and execution of court decisions by bailiffs and other authorities which make an execution of court judgments and decision of other authorities.

Структурно-функциональные и гемодинамические характеристики при простой первичной и псевдоэксфолиативной открытоугольной глаукоме и офтальмогипертензии

Структурно-функциональные и гемодинамические характеристики при простой первичной и псевдоэксфолиативной открытоугольной глаукоме и офтальмогипертензии

Структурно-функциональные особенности слизистой оболочки желудка у больных с HBV- и HCV-инфекцией

Структурно-функциональные особенности слизистой оболочки желудка у больных с HBV- и HCV-инфекцией

STRUCTURAL-FUNCTIONAL FEATURES OF MEDIA MASS MEDIA TEXTS

STRUCTURAL-FUNCTIONAL FEATURES OF MEDIA MASS MEDIA TEXTS

Properties of Bacterial and Archaeal Branched-Chain Amino Acid Aminotransferases.

Branched-chain amino acid aminotransferases (BCATs) catalyze reversible stereoselective transamination of branched-chain amino acids (BCAAs) L-leucine, L-isoleucine, and L-valine. BCATs are the key enzymes of BCAA metabolism in all organisms. The catalysis proceeds through the ping-pong mechanism with the assistance of the cofactor pyridoxal 5'-phosphate (PLP). BCATs differ from other (S)-selective transaminases (TAs) in 3D-structure and organization of the PLP-binding domain. Unlike other (S)-selective TAs, BCATs belong to the PLP fold type IV and are characterized by the proton transfer on the re-face of PLP, in contrast to the si-specificity of proton transfer in fold type I (S)-selective TAs. Moreover, BCATs are the only (S)-selective enzymes within fold type IV TAs. Dual substrate recognition in BCATs is implemented via the "lock and key" mechanism without side-chain rearrangements of the active site residues. Another feature of the active site organization in BCATs is the binding of the substrate α-COOH group on the P-side of the active site near the PLP phosphate group. Close localization of two charged groups seems to increase the effectiveness of external aldimine formation in BCAT catalysis. In this review, the structure-function features and the substrate specificity of bacterial and archaeal BCATs are analyzed. These BCATs differ from eukaryotic ones in the wide substrate specificity, optimal temperature, and reactivity toward pyruvate as the second substrate. The prospects of biotechnological application of BCATs in stereoselective synthesis are discussed.

Polymyxin B inhibits the chaperone activity of Plasmodium falciparum Hsp70.

Heat shock protein 70 (Hsp70) is a molecular chaperone that plays an important role in cellular proteostasis. Hsp70s are also implicated in the survival and pathogenicity of malaria parasites. The main agent of malaria, Plasmodium falciparum, expresses six Hsp70s. Of these, two (PfHsp70-1 and PfHsp70-z) localize to the parasite cytosol. Previously conducted gene knockout studies suggested that PfHsp70-z is essential, and it has been demonstrated that small-molecule inhibitors targeting PfHsp70-1 cause parasite death. For this reason, both PfHsp70-1 and PfHsp70-z are potential antimalarial targets. Two cyclic lipopeptides, colistin and polymyxin B (PMB), have been shown to bind another heat shock protein, Hsp90, inhibiting its chaperone function. In the current study, we investigated the effect of PMB on the structure-function features of PfHsp70-1 and PfHsp70-z. Using surface plasmon resonance analysis, we observed that PMB directly interacts with both PfHsp70-1 and PfHsp70-z. In addition, using circular dichroism spectrometric analysis combined with tryptophan fluorescence measurements, we observed that PMB modulated the secondary and tertiary structures of Hsp70. Furthermore, PMB inhibited the basal ATPase activity and chaperone function of the two Hsp70s. Our findings suggest that PMB associates with Hsp70 to inhibit its function. In light of the central role of Hsp70 in cellular proteostasis and its essential role in the development of malaria parasites in particular, our findings expand the library of small-molecule inhibitors that target this medically important class of molecular chaperones.

Structural-Functional Features of the Thyrotropin Receptor: A Class A G-Protein-Coupled Receptor at Work.

The thyroid-stimulating hormone receptor (TSHR) is a member of the glycoprotein hormone receptors, a sub-group of class A G-protein-coupled receptors (GPCRs). TSHR and its endogenous ligand thyrotropin (TSH) are of essential importance for growth and function of the thyroid gland and proper function of the TSH/TSHR system is pivotal for production and release of thyroid hormones. This receptor is also important with respect to pathophysiology, such as autoimmune (including ophthalmopathy) or non-autoimmune thyroid dysfunctions and cancer development. Pharmacological interventions directly targeting the TSHR should provide benefits to disease treatment compared to currently available therapies of dysfunctions associated with the TSHR or the thyroid gland. Upon TSHR activation, the molecular events conveying conformational changes from the extra- to the intracellular side of the cell across the membrane comprise reception, conversion, and amplification of the signal. These steps are highly dependent on structural features of this receptor and its intermolecular interaction partners, e.g., TSH, antibodies, small molecules, G-proteins, or arrestin. For better understanding of signal transduction, pathogenic mechanisms such as autoantibody action and mutational modifications or for developing new pharmacological strategies, it is essential to combine available structural data with functional information to generate homology models of the entire receptor. Although so far these insights are fragmental, in the past few decades essential contributions have been made to investigate in-depth the involved determinants, such as by structure determination via X-ray crystallography. This review summarizes available knowledge (as of December 2016) concerning the TSHR protein structure, associated functional aspects, and based on these insights we suggest several receptor complex models. Moreover, distinct TSHR properties will be highlighted in comparison to other class A GPCRs to understand the molecular activation mechanisms of this receptor comprehensively. Finally, limitations of current knowledge and lack of information are discussed highlighting the need for intensified efforts toward TSHR structure elucidation.