A Novel Virus Discovered in the Yeast Pichia membranifaciens.

Mycoviruses are widely distributed across fungi, including yeasts of the Saccharomycotina subphylum. It was recently discovered that the yeast species Pichia membranifaciens contained double stranded RNAs (dsRNAs) that were predicted to be of viral origin. The fully sequenced dsRNA is 4,578 bp in length, with RNA secondary structures similar to the packaging, replication, and frameshift signals of totiviruses of the family Totiviridae. This novel virus has been named Pichia membranifaciens virus L-A (PmV-L-A) and is related to other totiviruses previously described within the Saccharomycotina yeasts. PmV-L-A is part of a monophyletic subgroup within the I-A totiviruses, implying a common ancestry between mycoviruses isolated from the Pichiaceae and Saccharomycetaceae yeasts. Energy minimized AlphaFold2 molecular models of the PmV-L-A Gag protein revealed structural conservation with the previously solved structure of the Saccharomyces cerevisiae virus L-A (ScV-L-A) Gag protein. The predicted tertiary structure of the PmV-L-A Pol and its homologs provide details of the potential mechanism of totivirus RNA-dependent RNA polymerases (RdRps) because of structural similarities to the RdRps of mammalian dsRNA viruses. Insights into the structure, function, and evolution of totiviruses gained from yeasts is important because of their parallels with mammalian viruses and the emerging role of totiviruses in animal disease.

Influence of electronic states of nanographs in carbon microcrystallines on surface chemistry of activated charcoal varieties

In this paper, the nature of the chemical activity of pyrolyzed nanostructured carbon materials (PNCM), in particular active carbon (AC), in reactions of electron transfer considered from a single position, reflecting the priority role of paramagnetic centers and edge defunctionaled carbon atoms of carbon microcristallites (CMC) due to pyrolysis of precursors. Clusters in the form of polycyclic aromatic hydrocarbons with open (OES) and closed (CES) electronic shells containing terminal hydrogen atoms (or their vacancies) and different terminal functional groups depending on specific model reactions of radical recombination, combination, replacement and elimination were used to model of nanographenes (NG) and CM. Quantum-chemical calculations of molecular models of NG and CMC and heat effects of model reactions were performed in frames of the density functional theory (DFT) using extended valence-splitted basis 6-31G(d) with full geometry optimization of concrete molecules, ions, radicals and NG models. The energies of boundary orbitals were calculated by means of the restricted Hartry-Fock method for objects with closed (RHF) and open (ROHF) electronic shells. The total energies of small negative ions (HOO-, HO-) and anion-radical О2•‾) were given as the sum of calculated total energies of these compounds and their experimental electron affinities. The estimation of probability of considered chemical transformations was carried out on the base on the well-known Bell-Evans-Polyani principle about the inverse correlation of the thermal effects of reactions and its activation energies. It is shown that the energy gap ΔЕ (energy difference of boundary orbitals levels) in simulated nanographens should depend on a number of factors: the periphery structure of models, its size and shape, the number and nature of various structural defects, electronic states of NG. When considering possible chemical transformations on the AC surface, rectangular models of NG were used, for which the simple classification by type and number of edge structural elements of the carbon lattice was proposed. Quantum chemical calculations of molecular models of NG and CNC and the energy of model reactions in frames of DTF showed that the chemisorption of free radicals (3O2 and N•O), as recombination at free radical centers (FRC), should occur with significant heat effects. Such calculations give reason to believe that FRC play an important role in formation of the functional cover on the periphery of NG in CMC of studied materials. On the base of of cluster models of active carbon with OES new ideas about possible reactions mechanisms of radical-anion О2•‾ formation and decomposition of hydrogen peroxide on the surface of active carbon are offered. Explanation of increased activity of AC reduced by hydrogen in H2O2 decomposition is given. It is shown that these PNCM models, as first of all AC, allow to adequately describe their semiconductor nature and acid-base properties of such materials.

Oxane dendrimers of tetravalent elements as models for their dioxide polymorphs

Oxides of tetravalent elements are well known to have a lot of crystalline modifications. For example, most of silica polymorphs are characterized by tetrahedral coordination environment of silicon atoms. On the contrary, crystals of stishovite and of some silicate minerals have their silicon atoms in octahedral coordination spheres. It has been found experimentally that the phase transitions between silica polymorphs accompanied by a rearrangement of silica-oxygen tetrahedrons into octahedra require an energy income (preference energy) of 54 kJ/mol. When increasing the atomic mass of the oxide forming element, the former decreases extremely and for tin dioxide is equal to -59 kJ/mol. These values can be reproduced in a theoretical way, within the frameworks of modern quantum chemical methods and periodic models. High disperse silica nanoparticles (as well as those for other oxides) have only the nearest order of atomic stationing, so that theoretical approaches developed for crystals cannot be applied to small particles. These particles can be transformed into stishovite form under hydrothermal conditions. Such a process can be simulated within cluster approximation by use of molecular models. This work is devoted to quantum chemical simulation of formation of the fragments with hexa-coordinated atoms of silicon and of its analogs in the structure of oxane dendrimers. A row of high symmetry models was examined containing two, three, five, and seventeen atoms of silicon and of germanium, titanium and tin, terminated with hydroxyl groups. These structures can be rearranged into another ones including oxide forming atoms with elevated (equal to 5 or 6) coordination number, so mimicking the rutile-like structure. Such models let it possible to fulfill the procedure of transformation without rupturing siloxane bonds, so remaining within a deformation approach. Another advantage is the exclusion of the basis set superposition error due to use of molecular models of the same total formula for all the coordination states. All calculations were carried out by Hartree-Fock and density functional theory methods with the all-electron (3-21G*) and valent (SBKJC) basis sets by means of the GAMESS program. Models of various size have been examined, in particular, disiloxane (HO)3Si-O-Si(OH)3 witch can be transformed into a self-coordinated form where one of silicon atoms becomes a five-coordinated; trisiloxane (HO)3Si-O-Si(OH)2-O-Si(OH)3 can be rearranged into symmetric isomer with one hexa-coordinated silicon atom. Pentasiloxane with neo-structure of [(HO)3Si-O]4Si forms three coordination structures, the most stable of them mimicking the stishovite crystal; it contains one 6-coordinated and two 5-coordinated silicon atoms. Siloxane containing 17 silicon atoms has a super-neo-structure of {[(HO)3Si-O]3Si-O}4Si; it includes seven six-coordinated and four five-coordinated silicon atoms. Relative models for silicon analogs have been also examined. When analyzing a dependence of the energy differences between open and coordinated oxane structures on the number of atoms of the oxide forming element in the cluster, one can jump to the conclusion that the specific value of this characteristic monotonously decreases with the increase in the number of atoms of the molecular model, so becoming close to the experimental data.

Mapping the Deformability of Natural and Designed Cellulosomes in solution

Background : Natural cellulosome multi-enzyme complexes, their components, and engineered ‘designer cellulosomes’ (DCs) promise an efficient means of breaking down cellulosic substrates into valuable biofuel products. Their broad uptake in biotechnology relies on boosting proximity-based synergy among the resident enzymes but the modular architecture challenges structure determination and rational design.Results: We used small angle X-ray scattering combined with molecular modeling to study the solution structure of cellulosomal components. These include three dockerin-bearing cellulases with distinct substrate specificities, original scaffoldins from the human gut bacterium Ruminococcus champanellensis (ScaA, ScaH and ScaK) and a trivalent cohesin-bearing designer scaffoldin (Scaf20L), followed by cellulosomal complexes comprising these components, and the nonavalent fully loaded Clostridium thermocellum CipA in complex with Cel8A from the same bacterium. The size analysis of Rg and Dmax values deduced from the scattering curves and corresponding molecular models highlight their variable aspects, depending on composition, size and spatial organization of the objects in solution.Conclusion: Our data quantifies variability of form and compactness of cellulosomal components in water and confirms that this native plasticity may well be related to speciation with respect to the substrate that is targeted. By showing that scaffoldins or components display enhanced compactness compared to the free objects, we provide new routes to rationally enhance their stability and performance in their environment of action.

Bioinformatics Storing Databases

An exceptional branch of data that requires huge databases has been shown lately from genome sequencing projects which is a field that employs computational approaches to answer biological questions. With this huge sequence of information that is available for researchers, bioinformatics plays a big role in studying basic medical-biological problems. The challenge that faces bioinformatical scientists is to help in discovering genes and designing molecular models, site-directed mutagenesis, and other experiments that reveal the unknown relationships concerning the structure and function of genes and proteins. This become a big challenge especially with the huge amount of data that is generated using the human genome and other systematic sequencing efforts up till now. Bioinformatics solves biological problems depending on available data. It is concerned with creating databases and predicting the outcome of lab experiments.

Thermodynamic Scaling of the Shear Viscosity of Lennard-Jones Chains of Variable Rigidity

In this work, the thermodynamic scaling framework has been used to emphasize the limitations of fully flexible coarse grained molecular models to yield shear viscosity of real liquids. In particular, extensive molecular dynamics simulations have confirmed that, while being reasonable to describe the viscosity of short normal alkanes, the fully flexible Lennard-Jones and Mie chains force fields are inadequate to capture the density dependence of shear viscosity of medium to long alkanes. In addition, it is shown that such a weakness in terms of coarse grained molecular models can be readily quantified by using the thermodynamic scaling framework. As a simple alternative to these force fields, it is demonstrated that the insertion of a variable intramolecular rigidity in the Lennard-Jones chains model exhibits promising results to model medium to long chain-like real fluids from both thermodynamic and viscosity points of view.

In the footsteps of Einstein end Wiener

To date the recognition of universal, a priori inherent in them connection between the objects of the world around us is quite rightly considered almost an accomplished fact. But on what laws do these or those sometimes rather variegated systems function in live and inert nature (including - in modern computer clusters)? Where are the origins of their self-organization activity lurked: whether at the level of still hypothetical quantum-molecular models, finite bio-automata or hugely fashionable now artificial neural networks? Answers to all these questions if perhaps will ever appear then certainly not soon. That is why the bold innovative developments presented in following article are capable in something, possibly, even to refresh the database of informatics so familiar to many of us. And moreover, in principle, the pivotal idea developed here, frankly speaking, is quite simple in itself: if, for example, the laws of the universe are one, then all the characteristic differences between any evolving objects should be determined by their outwardly-hidden informative (or, according to author’s terminology - “mental") rationale. By the way, these are not at all empty words, as it might seem at first glance, because they are fully, where possible, supported with the generally accepted physical & mathematical foundation here. So as a result, the reader by himself comes sooner or later to the inevitable conclusion, to wit: only the smallest electron-neutrino ensembles contain everything the most valuable and meaningful for any natural system! At that even no matter, what namely global outlook paradigm we here hold