EARLY NEOPROTEROZOIC CRUST FORMATON IN THE DZABKHAN MICROCONTINENT, CENTRAL ASIAN OROGENIC BELT

The Dzabkhan microcontinent was defined by [Mossakovsky et al., 1994] as a cratonic terrane with an early Precambrian basement that combines highgrade metamorphic complexes of the Songino, Dzabkhan, Otgon, Baidarik, Ider and Jargalant Blocks. However, early Precambrian ages have so far only been recognized in the Baidarik and Ider blocks [Kozakov et al., 2007, 2011; Kröner et al., 2015].The Dzabkhan microcontinent was defined by [Mossakovsky et al., 1994] as a cratonic terrane with an early Precambrian basement that combines highgrade metamorphic complexes of the Songino, Dzabkhan, Otgon, Baidarik, Ider and Jargalant Blocks. However, early Precambrian ages have so far only been recognized in the Baidarik and Ider blocks [Kozakov et al., 2007, 2011; Kröner et al., 2015]

Statistical method of finding quality indicators distribution of surfaces treated in thickness of gas-thermal coatings in various depths

Проаналізовано статистичну залежність показників якості (на прикладі параметрів шорсткості та мікротвердості) оброблених поверхонь деталей з порошковими газотермічними покриттями системи Ni-Cr-B-Si у діапазоні товщин 0,6…2,4 мм, нанесеними газополуменевим напилюванням, від глибини розташування цих поверхонь (від величини прийнятого припуску). Результати дослідження є основою для визначення припуску на обробку покриттів за допомогою ймовірнісно-статистичного методу, вирішують проблему визначення припусків на оброблення газотермічних порошкових покриттів системи Ni-Cr-B-Si та дозволяють під час механічного оброблення забезпечити найвищі показники якості обробленої поверхні.A gas-thermal coatings application in production is not widely spread. The reasons are those, that they have three thickness zones, which differ in quality, and while processing the working surfaces are often formed in areas with worse quality and results in shortening of the parts operating life. It is caused by the fact that the information in technical reference literature on the depth of processing in the coating thickness is not available (in other words, in mechanical engineering production regulations on the fixed allowances for surfaces machining are not available). In monolithic materials processing technologists provide the necessary quality indicators by choosing the optimal values of machining allowances, varying cutting modes and geometric parameters of the instrument. When processing the coatings, which are heterogeneous and differ in great quality indicators dispersion in their volume, to provide the quality only by selection of modes and processing parameters is not possible. It is necessary, first of all, to form a work surface in the most qualitative coating layer. It is obligatory to know the location of this layer in the coating. Due to the heterogeneity of coatings to determine the location of the most qualitative coating layer is possible only by mathematical statistics methods, which allow to process a large amount of experimental data. The article analyzes the statistical relationship of quality indicators (for example, roughness parameters and microhardness) of treated surfaces with sintered gas-thermal coatings of Ni-Cr-B-Si system in the thicknesses range 0,6...2,4 mm, coated with gas-flamed spraying, with location depth of these surfaces (the value of standard allowance). The results of research are the basis for determining an allowance for coatings processing using probabilistic-statistical method. They solve the problem of determining allowances for processing sintered gas-thermal coatings of Ni-Cr-B-Si system and they allow to receive the best indicators of the treated surface, when machining, provide economy of powders and reduce the costs of gases

SUMOylation of nuclear actin

Actin, a major component of the cytoplasm, is also abundant in the nucleus. Nuclear actin is involved in a variety of nuclear processes including transcription, chromatin remodeling, and intranuclear transport. Nevertheless, the regulation of nuclear actin by posttranslational modifications has not been investigated. We now show that nuclear actin is modified by SUMO2 and SUMO3 and that computational modeling and site-directed mutagenesis identified K68 and K284 as critical sites for SUMOylating actin. We also present a model for the actin–SUMO complex and show that SUMOylation is required for the nuclear localization of actin

Component Interactions and Electron Transfer in Toluene/o-Xylene Monooxygenase

The multicomponent protein toluene/o-xylene monooxygenase (ToMO) activates molecular oxygen to oxidize aromatic hydrocarbons. Prior to dioxygen activation, two electrons are injected into each of two diiron(III) units of the hydroxylase, a process that involves three redox active proteins: the ToMO hydroxylase (ToMOH), Rieske protein (ToMOC), and an NADH oxidoreductase (ToMOF). In addition to these three proteins, a small regulatory protein is essential for catalysis (ToMOD). Through steady state and pre-steady state kinetics studies, we show that ToMOD attenuates electron transfer from ToMOC to ToMOH in a concentration-dependent manner. At substoichiometric concentrations, ToMOD increases the rate of turnover, which we interpret to be a consequence of opening a pathway for oxygen transport to the catalytic diiron center in ToMOH. Excess ToMOD inhibits steady state catalysis in a manner that depends on ToMOC concentration. Through rapid kinetic assays, we demonstrate that ToMOD attenuates formation of the ToMOC–ToMOH complex. These data, coupled with protein docking studies, support a competitive model in which ToMOD and ToMOC compete for the same binding site on the hydroxylase. These results are discussed in the context of other studies of additional proteins in the superfamily of bacterial multicomponent monooxygenases.National Institute of General Medical Sciences (U.S.) (5-R01-GM032134)United States. National Institutes of Health (T32GM008334

Combination of scoring schemes for protein docking

<p>Abstract</p> <p>Background</p> <p>Docking algorithms are developed to predict in which orientation two proteins are likely to bind under natural conditions. The currently used methods usually consist of a sampling step followed by a scoring step. We developed a weighted geometric correlation based on optimised atom specific weighting factors and combined them with our previously published amino acid specific scoring and with a comprehensive SVM-based scoring function.</p> <p>Results</p> <p>The scoring with the atom specific weighting factors yields better results than the amino acid specific scoring. In combination with SVM-based scoring functions the percentage of complexes for which a near native structure can be predicted within the top 100 ranks increased from 14% with the geometric scoring to 54% with the combination of all scoring functions. Especially for the enzyme-inhibitor complexes the results of the ranking are excellent. For half of these complexes a near-native structure can be predicted within the first 10 proposed structures and for more than 86% of all enzyme-inhibitor complexes within the first 50 predicted structures.</p> <p>Conclusion</p> <p>We were able to develop a combination of different scoring schemes which considers a series of previously described and some new scoring criteria yielding a remarkable improvement of prediction quality.</p

Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions are fundamental for the majority of cellular processes and their study is of enormous biotechnological and therapeutic interest. In recent years, a variety of computational approaches to the protein-protein docking problem have been reported, with encouraging results. Most of the currently available protein-protein docking algorithms are composed of two clearly defined parts: the sampling of the rotational and translational space of the interacting molecules, and the scoring and clustering of the resulting orientations. Although this kind of strategy has shown some of the most successful results in the CAPRI blind test <url>http://www.ebi.ac.uk/msd-srv/capri</url>, more efforts need to be applied. Thus, the sampling protocol should generate a pool of conformations that include a sufficient number of near-native ones, while the scoring function should discriminate between near-native and non-near-native proposed conformations. On the other hand, protocols to efficiently include full flexibility on the protein structures are increasingly needed.</p> <p>Results</p> <p>In these work we present new computational tools for protein-protein docking. We describe here the RotBUS (Rotation-Based Uniform Sampling) method to generate uniformly distributed sets of rigid-body docking poses, with a new fast calculation of the optimal contacting distance between molecules. We have tested the method on a standard benchmark of unbound structures and we can find near-native solutions in 100% of the cases. After applying a new fast filtering scheme based on residue-based desolvation, in combination with FTDock plus pyDock scoring, near-native solutions are found with rank ≤ 50 in 39% of the cases. Knowledge-based experimental restraints can be easily included to reduce computational times during sampling and improve success rates, and the method can be extended in the future to include flexibility of the side-chains.</p> <p>Conclusions</p> <p>This new sampling algorithm has the advantage of its high speed achieved by fast computing of the intermolecular distance based on a coarse representation of the interacting surfaces. In addition, a fast desolvation scoring permits the screening of millions of conformations at low computational cost, without compromising accuracy. The protocol presented here can be used as a framework to include restraints, flexibility and ensemble docking approaches.</p

Allostery in Its Many Disguises: From Theory to Applications.

Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts