Mapping contacts of the S12–S7 intercistronic region of str operon mRNA with ribosomal protein S7 of E. coli

AbstractIn E. coli, S7 initiates 30S ribosome assembly by binding to 16S rRNA. It also regulates translation of the S12 and S7 cistrons of the ‘streptomycin’ operon transcript by binding to the S12–S7 intercistronic region. Here, we describe the contacts of N-terminally His6-tagged S7 with this region as mapped by UV-induced cross-linking. The cross-links are located at U(−34), U(−35), quite distant from the start codons of the two cistrons. In order to explain the mechanism of translational repression of S12–S7, we consider a possible conformational rearrangement of the intercistronic RNA structure induced by S7 binding

The use of the digital twin in the design of a prefabricated product

This paper discusses the process of creating a digital twin of a product, which is a virtual model of a mechanical connection. The modeling was carried out using the Pro/ENGINEER software, which allows building a three-dimensional model of the product assembly process, which is a set of three-dimensional electronic models of the product, equipment and tools. The models include a mathematical description of the geometric, physical-mechanical and technical parameters of the objects under consideration. It is shown that it is the formation of a triad of electronic models: product-man-equipment in the considered area of computer-aided design of technological processes for the implementation of mechanical connections that allows modeling with the necessary accuracy and adequacy

QM/MM Description of Newly Selected Catalytic Bioscavengers Against Organophosphorus Compounds Revealed Reactivation Stimulus Mediated by Histidine Residue in the Acyl-Binding Loop

Butyrylcholinesterase (BChE) is considered as an efficient stoichiometric antidote against organophosphorus (OP) poisons. Recently we utilized combination of calculations and ultrahigh-throughput screening (uHTS) to select BChE variants capable of catalytic destruction of OP pesticide paraoxon. The purpose of this study was to elucidate the molecular mechanism underlying enzymatic hydrolysis of paraoxon by BChE variants using hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. Detailed analysis of accomplished QM/MM runs revealed that histidine residues introduced into the acyl-binding loop are always located in close proximity with aspartate residue at position 70. Histidine residue acts as general base thus leading to attacking water molecule activation and subsequent SN2 inline hydrolysis resulting in BChE reactivation. This combination resembles canonical catalytic triad found in active centers of various proteases. Carboxyl group activates histidine residue by altering its pKa, which in turn promotes the activation of water molecule in terms of its nucleophilicity. Observed re-protonation of catalytic serine residue at position 198 from histidine residue at position 438 recovers initial configuration of the enzyme’s active center, facilitating next catalytic cycle. We therefore suggest that utilization of uHTS platform in combination with deciphering of molecular mechanisms by QM/MM calculations may significantly improve our knowledge of enzyme function, propose new strategies for enzyme design and open new horizons in generation of catalytic bioscavengers against OP poisons

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange

INCREASING EFFICIENCY OF CONTAINER MOVEMENT CONTROL IN RIVER PORT

The aim is to ground and develop the basic principles, methods and mathematical models of making decisions at functioning of the computer-aided container movement control in the river port. The methods and mathematical models for optimum ship loading and container arrangement in the port stockhouse, determination of the container platform capacity and conducting dynamical model "stockhouse", developing operational moving-in and removal planes of container by an automobile transport and freight treatment of the ships have been developed. The problem complex for PC "Computer-aided container movement control in port" has been developed. The investigation results have been introduced in the Perm and Tyumen portsAvailable from VNTIC / VNTIC - Scientific & Technical Information Centre of RussiaSIGLERURussian Federatio

On Modelling the Reliability of Concrete Support for Underground Construction Considering the Impact of Chemical Erosion

Ensuring the reliability of support in mine workings has always been one of the most important scientific and technical problems in mining. To ensure the normal operation of underground structures, it is necessary to apply special measures to maintain the support, providing increased stability of rock array. To one of the most important measures is to maintain the reliability of the supports in underground workings and objects of underground construction. The main method of research in this area is the modeling of the reliability of concrete support, as applied to various exogenous and endogenous factors of disturbance. The article provides theoretical provisions of research in physico-chemical processes of corrosion in reinforced concrete for modelling the reliability of structural elements of supports for underground construction objects

Dynamic Interchange Between Two Protonation States is Characteristic of Active Sites of Cholinesterases

Cholinesterases are well-known and widely studied enzymes crucial to human health and involved in neurology, Alzheimer, and lipid metabolism. The protonation pattern of cholinesterases’ active sites influences all the chemical processes within, including reaction, covalent inhibition by nerve agents, and reactivation. Our understanding of it is, however, limited. In this study, we used enhanced-sampling quantum-mechanical/molecular-mechanical calculations to show that cholinesterases mostly function as dynamical mixtures of two protonation states. Proton transfer between two non-catalytic glutamate residues occurs by Grotthuss mechanism via a mediator water molecule. We show that this uncovered complexity of active sites presents a challenge for classical molecular dynamics simulations that calls for special treatment. The proton transfer barrier of 1.65 kcal/mol opens the discussion on potential existence of two conjugated low barrier hydrogen bonds in the inhibited form of butyrylcholinesterase. These findings expand our understanding of structural features expressed by highly evolved enzymes and guide future advances in cholinesterase-related protein- and drug design studies

The Issues of Cryojet Technology Application for Rock Cutting

Water-jet technologies, based on the use of high-speed jets as cutting tools, are one of the promising directions of the destruction technologies for various materials. Jets’ capability to cut even very strong, anisotropic and composite materials, as well as their high cutting speed, that can be reached without workpiece reaction occurring on the tool, make them attractive from the point of view of their implementation as cutting tools. This paper outlines the methods of materials destruction by means of high-speed cryojet and discusses future areas of its application. The research reveals the main factors and criteria for evaluating the effectiveness of cryojet cutting. Experimental studies of the main factors affecting the cryojet cutting parameters were carried out using a bench unit. As a result of the experimental data analysis, we found the correspondences that can be used for calculating the cryojet cutting of various materials

Functional Status of Neuronal Calcium Sensor-1 Is Modulated by Zinc Binding

International audienceNeuronal calcium sensor-1 (NCS-1) protein is abundantly expressed in the central nervous system and retinal neurons, where it regulates many vital processes such as synaptic transmission. It coordinates three calcium ions by EF-hands 2-4, thereby transducing Ca 2+ signals to a wide range of protein targets, including G protein-coupled receptors and their kinases. Here, we demonstrate that NCS-1 also has Zn 2+-binding sites, which affect its structural and functional properties upon filling. Fluorescence and circular dichroism experiments reveal the impact of Zn 2+ binding on NCS-1 secondary and tertiary structure. According to atomic absorption spectroscopy and isothermal titration calorimetry studies, apo-NCS-1 has two high-affinity (4 × 10 6 M −1) and one low-affinity (2 × 10 5 M −1) Zn 2+-binding sites, whereas Mg 2+-loaded and Ca 2+-loaded forms (which dominate under physiological conditions) bind two zinc ions with submicromolar affinity. Metal competition analysis and circular dichroism studies suggest that Zn 2+-binding sites of apo-and Mg 2+-loaded NCS-1 overlap with functional EF-hands of the protein. Consistently, high Zn 2+ concentrations displace Mg 2+ from the EF-hands and decrease the stoichiometry of Ca 2+ binding. Meanwhile, one of the EF-hands of Zn 2+-saturated NCS-1 exhibits a 14-fold higher calcium affinity, which increases the overall calcium sensitivity of the protein. Based on QM/MM molecular dynamics simulations, Zn 2+ binding to Ca 2+-loaded NCS-1 could occur at EF-hands 2 and 4. The high-affinity zinc binding increases the thermal stability of Ca 2+-free NCS-1 and favours the interaction of its Ca 2+-loaded form with target proteins, such as dopamine receptor D2R and GRK1. In contrast, low-affinity zinc binding Frontiers in Molecular Neuroscience | www.frontiersin.org