Significance Many functions in the cell are performed by Brownian machines, macromolecular assemblies that use energy from the thermal environment for many of the conformational changes involved in ...their work cycles. Here we present a new approach capable of mapping the continuous motions of such nanomachines along their trajectories in the free-energy landscape and demonstrate this capability in the context of experimental cryogenic electron microscope snapshots of the ribosome, the nanomachine responsible for protein synthesis in all living organisms. We believe our approach constitutes a universal platform for the analysis of free-energy landscapes and conformational motions of molecular nanomachines and their dependencies on temperature, buffer conditions, and regulatory factors.
A Brownian machine, a tiny device buffeted by the random motions of molecules in the environment, is capable of exploiting these thermal motions for many of the conformational changes in its work cycle. Such machines are now thought to be ubiquitous, with the ribosome, a molecular machine responsible for protein synthesis, increasingly regarded as prototypical. Here we present a new analytical approach capable of determining the free-energy landscape and the continuous trajectories of molecular machines from a large number of snapshots obtained by cryogenic electron microscopy. We demonstrate this approach in the context of experimental cryogenic electron microscope images of a large ensemble of nontranslating ribosomes purified from yeast cells. The free-energy landscape is seen to contain a closed path of low energy, along which the ribosome exhibits conformational changes known to be associated with the elongation cycle. Our approach allows model-free quantitative analysis of the degrees of freedom and the energy landscape underlying continuous conformational changes in nanomachines, including those important for biological function.
The lack of standardized language assessment tools in Russian impedes clinical work, evidence-based practice, and research in Russian-speaking clinical populations. To address this gap in assessment ...of neurogenic language disorders, we developed and standardized a new comprehensive assessment instrument-the Russian Aphasia Test (RAT). The principal novelty of the RAT is that each subtest corresponds to a specific level of linguistic processing (phonological, lexical-semantic, syntactic, and discourse) in different domains: auditory comprehension, repetition, and oral production. In designing the test, we took into consideration various (psycho)linguistic factors known to influence language performance, as well as specific properties of Russian. The current paper describes the development of the RAT and reports its psychometric properties. A tablet-based version of the RAT was administered to 85 patients with different types and severity of aphasia and to 106 age-matched neurologically healthy controls. We established cutoff values for each subtest indicating deficit in a given task and cutoff values for aphasia based on the Receiver Operating Characteristic curve analysis of the composite score. The RAT showed very high sensitivity (> .93) and specificity (> .96), substantiating its validity for determining presence of aphasia. The test's high construct validity was evidenced by strong correlations between subtests measuring similar linguistic processes. The concurrent validity of the test was also strong as demonstrated by a high correlation with an existing aphasia battery. Overall high internal, inter-rater, and test-retest reliability were obtained. The RAT is the first comprehensive aphasia language battery in Russian with properly established psychometric properties. It is sensitive to a wide range of language deficits in aphasia and can reliably characterize individual profiles of language impairments. Notably, the RAT is the first comprehensive aphasia test in any language to be fully automatized for administration on a tablet, maximizing further standardization of presentation and scoring procedures.
The effect of a new pyridoxine derivative B6NO on doxorubicin cytotoxicity and Nrf2-dependent cellular processes
in vitro
was studied. Antioxidant B6NO enhances the cytotoxic effect of doxorubicin on ...tumor cells, which is associated with G2/M cell division arrest and an increase in activity of proapoptotic enzyme caspase-3. The antioxidant promotes intracellular accumulation and nuclear translocation of Nrf2 transcription factor in non-tumor and tumor cells. In non-tumor cells, B6NO increases the expression of antioxidant system proteins and reduces ROS generation in the presence of doxorubicin. In tumor cells, no activation of Nrf2-dependent processes occurs under the action of the antioxidant. Our findings demonstrate the prospect of further studies of pyridoxine derivatives as antioxidants to reduce adverse reactions during chemotherapy.
Ribosome recoding is used by RNA viruses for translational readthrough or frameshifting past termination codons for the synthesis of extension products. Recoding sites, along with downstream recoding ...stimulatory elements (RSEs), have long been studied in reporter constructs, because these fragments alone mediate customary levels of recoding and are thus assumed to contain complete instructions for establishment of the proper ratio of termination to recoding. RSEs from the Tombusviridae and Luteoviridae are thought to be exceptions, since they contain a long-distance RNA-RNA connection with the 3' end. This interaction has been suggested to substitute for pseudoknots, thought to be missing in tombusvirid RSEs. We provide evidence that the phylogenetically conserved RSE of the carmovirus Turnip crinkle virus (TCV) adopts an alternative, smaller structure that extends an upstream conserved hairpin and that this alternative structure is the predominant form of the RSE within nascent viral RNA in plant cells and when RNA is synthesized in vitro The TCV RSE also contains an internal pseudoknot along with the long-distance interaction, and the pseudoknot is not compatible with the phylogenetically conserved structure. Conserved residues just past the recoding site are important for recoding, and these residues are also conserved in the RSEs of gammaretroviruses. Our data demonstrate the dynamic nature of the TCV RSE and suggest that studies using reporter constructs may not be effectively recapitulating RSE-mediated recoding within viral genomes.
Ribosome recoding is used by RNA viruses to enable ribosomes to extend translation past termination codons for the synthesis of longer products. Recoding sites and a downstream recoding stimulatory element (RSE) mediate expected levels of recoding when excised and placed in reporter constructs and thus are assumed to contain complete instructions for the establishment of the proper ratio of termination to recoding. We provide evidence that most of the TCV RSE adopts an alternative structure that extends an upstream conserved hairpin and that this alternative structure, and not the phylogenetically conserved structure, is the predominant form of the RSE in RNA synthesized in vitro and in plant cells. The TCV RSE also contains an internal pseudoknot that is not compatible with the phylogenetically conserved structure and an RNA bridge to the 3' end. These data suggest that the TCV RSE is structurally dynamic and that multiple conformations are likely required to regulate ribosomal readthrough.
The implementation of the "Digital transformation in the Russian Federation" program is a national goal, a powerful conglomerate for the development of the Russian economy and is aimed at ...understanding, formulating and implementing strategies and tactics for the development of education, business and society as a whole. In the situation of a high degree of uncertainty caused by external environment and internal problems, universities today, more than ever before, cannot fail to fill in the gaps between the needs of the labor market and the professional competencies formed in the university for it. The university has all the opportunities to increase the human capital of the region, which is defined as the structure of knowledge, skills, and intellectual potential with the ability to apply them in work to create added value and is formed, among other things, by the university education system. The article presents a look at the content of the multicomponent electronic educational environment of the Master's training in the field of Applied Informatics, which is built on the principles of consistency, which takes into account all aspects of the modern educational process: personnel, technology, educational resources.
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