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Search results for: PROTON AFFINITY
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Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis
PublicationW celu zbadania właściwości biochemicznych białka wiążącego się do jednoniciowego DNA (SSB) pochodzącego z Deinococcus geothermalis (DgeSSB), sklonowano gen ssb otrzymany w reakcji PCR, a następnie uzyskano wydajną biosyntezę białka DgeSSB. Gen składa się z 900 par zasad, kodujących białko złożone z 300 reszt aminokwasowych, o wyliczonej masie molekularnej równej 32.45 kDa. Sekwencja aminokwasowa wykazuje 43, 44% i 75% identyczności...
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
PublicationRNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA....
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Proteolysis of whey protein isolates in nanoemulsion systems: impact of nanoemulsification and additional synthetic emulsifiers
PublicationNanoemulsions are currently of interest in the functional food sector because their small droplet size (100–500 nm) provides a number of potential advantages over conventional emulsions. This study concerned the behavior of nanoemulsions stabilized with whey proteins and two synthetic emulsifiers (Tween 80 and Croduret), and exposed to conditions simulating the human upper gastrointestinal tract. In particular, the effect of synthetic...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Expression of goose parvovirus whole VP3 protein and its epitopes in Escherichia coli cells
PublicationThe aim of this study was the expression of goose parvovirus capsid protein (VP3) and its epitopes in Escherichia coli cells. Expression of the whole VP3 protein provided an insufficient amount of protein. In contrast, the expression of two VP3 epitopes (VP3ep4, VP3ep6) in E. coli, resulted in very high expression levels. This may suggest that smaller parts of the GPV antigenic determinants are more efficiently expressed than the...
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Torsional elasticity and energetics of F1-ATPase
PublicationFoF1-ATPase is a rotary motor protein synthesizing ATP from ADP driven by a cross-membrane proton gradient. The proton flow through the membrane-embedded Fo generates the rotary torque that drives the rotation of the asymmetric shaft of F1. Mechanical energy of the rotating shaft is used by the F1 catalytic subunit to synthesize ATP. It was suggested that elastic power transmission with transient storage of energy in some compliant...
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New photocatalyst for decomposition of humic acids in photocatalysis and photo-Fenton processes
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IPMSM rotor position estimator based on analysis of phase current derivatives
PublicationThis paper describes an algorithm for estimation of IPMSM angular rotor position. The algorithm uses derivatives of motor phase currents resulting from PWM modulation to obtain the rotor position. The presented method is designed for medium- and high-speed range, since it is based on determination of the EMF vector. Algorithm is characterised by a very simple formulae. The calculation of rotor position is performed in every PWM...
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An Innovative Floating System with a Savonius Rotor as a Horizontal-Axis Wind Turbine
PublicationIn this project, an innovative wind turbine was designed for a floating plant. A large Savonius rotor was replaced with a double-rotor wind turbine implemented as a horizontal-axis turbine. This double rotor was positioned on the tip of a thrust plate and fixed to the deck of a catamaran. Simple 2D numerical simulations were performed to confirm the effectiveness of the concept. An analysis of the floating system configuration...
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Impact of rotor geometry optimization on the off-design ORC turbine performance
PublicationThe paper describes the method of CFD based Nelder-Mead optimization of a 10 kW single-stage axial turbine operating in an ORC system working on R7100. The total-to-static isentropic efficiency is defined as an objective function. Multi-point linear regression is carried out to determine the significance of the objective function arguments and to pick up the set of particular variables and characteristic quantities (e.g. flow angles)...
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Rotor-Flux Vector based Observer of Interior Permanent Synchronous Machine
PublicationThe sensorless control system of the interior permanent magnet machine is considered in this paper. The control system is based on classical linear controllers. In the machine, there occurs non-sinusoidal distribution of rotor flux together with the slot harmonics, which are treated as the control system disturbances. In this case, the classical observer structure in the (d-q) is unstable for the low range of rotor speed resulting...
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Management of Dark Fermentation Broth via Bio Refining and Photo Fermentation
PublicationLignocellulose and starch-based raw materials are often applied in the investigations regarding biohydrogen generation using dark fermentation. Management of the arising post-fermentation broth becomes a problem. The Authors proposed sequential processes, to improve the efficiency of both hydrogen generation and by-products management carried under model conditions. During the proposed procedure, the simple sugars remaining in...
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Thermal failure of a second rotor stage in heavy duty gas turbine
PublicationThe impulse mode of operation and the supply of various types of fuels causes frequent failures even in the heavy duty gas turbines. The paper presents the ravages of second rotor stage failure in a gas turbine. The excessive thermal elongation rise caused by fuel change was indicated as the main cause. We applied nonlinear numerical analysis, preceded by thermodynamic calculations of the turbine and visual inspection of the effects...
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Characterization of Bioactivity of Selective Molecules in Fruit Wines by FTIR and NMR Spectroscopies, Fluorescence and Docking Calculations
PublicationFourier transform infrared (FTIR) and proton nuclear magnetic resonance (1H NMR) spectroscopies were applied to characterize and compare the chemical shifts in the polyphenols’ regions of some fruit wines. The obtained results showed that FTIR spectra (1800–900 cm−1) and 1H NMR (δ 6.5–9.3 ppm) of different fruit wines can be used as main indices of the year of vintage and quality of fruit wines. In addition to the classical determination...
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Structure and transport properties of proton-conducting BaSn 0.5 In 0.5 O 2.75 and A-site substituted Ba 0.9 Ln 0.1 Sn 0.5 In 0.5 O 2.8 (Ln = La, Gd) oxides
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Excessive amount of lactose in the diet of two-week-old calves induces urinary protein changes
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The use of Preston equation to determine material removal during lap-grinding with electroplated CBN tools
PublicationGrinding executed in a lapping configuration is an alternative finishing process benefiting from both grinding and free-abrasive machining, while minimizing the heat effect impact. Electroplated tools can be effectively used in different abrasive processes, including high-speed grinding, however, the assessment of machining performance over time is a key factor in their correct use to achieve satisfactory technological results....
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublicationDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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LABORATORY STAND FOR INVESTIGATIONS OF THE QUICK - CHANGING TEMPERATURE OF GAS FLOWING IN THE PISTON COMPRESSOR OUTLET CHANNEL
PublicationThis paper presents a laboratory stand, created as a part of work on the doctor dissertation, intended for investigation of heat and flow processes taking place in the Espholin H3S piston compressor outlet channel. The test stand elements and their configuration within the stand are described. Discussed are also problems connected with the quick-changing measurement technique, solutions which have been proposed so far in that technology...
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Sulforaphane, a cruciferous vegetable-derived isothiocyanate, inhibits protein synthesis in human prostate cancer cells
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Comparison of Antioxidant Activity of Protein Isolates Derived from Selected Dry-Cured Meat Products
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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E2/E3‐independent ubiquitin‐like protein conjugation by Urm1 is directly coupled to cysteine persulfidation
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Post mortem changes in M. iliotibialis lateralis muscle protein profile of emu (Dromaius novaehollandiae)
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CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublicationThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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The Escherichia coli RNA polymerase alpha subunit and transcriptional activation by bacteriophage lambda CII protein.
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Mitogen activated protein kinase 4 (MPK4) influences growth in Populus tremula L.×tremuloides
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Rapeseed Meal Waste Biomass as Single-Cell Protein Substrate for Nutritionally-Enhanced Feed Component
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A cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublicationThe expression of reporter gene may be induced by activation of cryptic signalling sequences, as we found while constructing the mutS-lacZ fusion gene. We cloned the Escherichia coli lacZ gene encoding beta-galactosidase into a plasmid vector carrying the Thermus thermophilus mutS gene. The clones expected to produce beta-galactosidase as the C-terminal fusion were selected for the complementation of beta-galactosidase activity...
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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublicationMolecular dynamics simulations have been performed for a model aqueous solution of mucin. As mucin is a central part of lubricin, a key component of synovial fluid, we investigate its ability to form cross-linked networks. Such network formation could be of major importance for the viscoelastic properties of the soft-matter system and crucial for understanding the lubrication mechanism in articular cartilage. Thus,the inter- and...
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Simulation of fluid structure interaction in a novel design of high pressure axial piston hydraulic pump
PublicationA novel type of an axial, piston-driven high pressure hydraulic pump with variable capacity marks a significant improvement in the area of the hydraulic machinery design. Total discharge from hydrostatic forces eliminates a need for a servomechanism, thus simplifying operation, reducing weight and introducing the possibility of the pump displacement control by computer. PWK-type pumps, invented in the Gdansk University of Technology,...
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublicationThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublicationOxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments...
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Angle Tracking Observer for Filtering Rotor Position Estimates in Sensorless Electric Drives
PublicationSensorless electric drives use measurements of electrical quantities to estimate rotor position and speed. Measurement errors deteriorate the estimation accuracy, thus additional means are necessary to remove high-frequency components from estimated signals. This paper proposes to use an Angle Tracking Observer (ATO) for reducing noise in rotor position estimates, which is related to random errors in the measurements. A simplified,...
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Mechanism of phenol decomposition on FeCTiO2 and FeTiO2 photocatalysts via photo-Fenton process
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Porównanie wydajności modyfikacji algorytmu Proof-number search uwzględniających wartości remisowe
PublicationProof-number search to znana rodzina algorytmów służących do wyznaczania wartości pozycji w nielosowych grach dwóch graczy z pełną informacją. W wersji podstawowej pn-search doskonale radzi sobie z wyszukiwaniem strategii wygrywającej jednego z graczy. Jednak istnieje wiele znanych gier, w których obydwaj gracze posiadają jedynie strategię remisującą (Młynek, Awari, Warcaby). W niniejszej pracy porównano wydajność dwóch modyfikacji...
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Noninvasive method for rotor fault diagnosis in inverter fed induction motor drive
PublicationThis article presents a proposal, simulation and experimental results of a noninvasive rotor fault diagnosis method for the inverter fed induction motor drive. Comparing to reported methods the proposed one does not require any load, rotor brake, slip, mechanical or electrical system physical modification e.g. machine disassembly and can be applied regardless the rotor speed measurement or estimation method.
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Influence of the steam within seals and glands of the turbine on its rotor motion stability.
PublicationPrzedstawiono metodę obliczania charakterystyk dynamicznych wpływu parowych uszczelnień turbin na ich dynamikę i stateczność ruchu wirników. Zarysowano model ''masowy'' uszczelnienia. Podano przykłady zastosowań.
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Unsteady aerodynamic forces acting on the rotor blades in the turbine stagewith steam extraction.
PublicationPrzeprowadzono analizę niestacjonarnych wymuszeń działających na łopatki wirnikowe w stopniu z upustem turbiny 13UC100. Niestacjonarne siły zostały wyznaczone dla 4 punktów pracy upustu. Wskazano na możliwą przyczynę zaistniałego zniszczenia łopatek wirnikowych turbiny.
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Network-assisted processing of advanced IoT applications: challenges and proof-of-concept application
PublicationRecent advances in the area of the Internet of Things shows that devices are usually resource-constrained. To enable advanced applications on these devices, it is necessary to enhance their performance by leveraging external computing resources available in the network. This work presents a study of computational platforms to increase the performance of these devices based on the Mobile Cloud Computing (MCC) paradigm. The main...