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Search results for: folded proteins
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Toxoplasma gondii Tetravalent Chimeric Proteins as Novel Antigens for Detection of Specific Immunoglobulin G in Sera of Small Ruminants
PublicationThe detection of Toxoplasma gondii infection in small ruminants has important significance for public health and veterinary medicine. This study, for the first time, describes the reactivity of four tetravalent chimeric proteins (AMA1N-SAG2-GRA1-ROP1, AMA1C-SAG2-GRA1-ROP1, AMA1-SAG2-GRA1-ROP1, and SAG2-GRA1-ROP1-GRA2) containing immunodominant regions from the AMA1 (apical membrane antigen 1), SAG2 (surface antigen 2), GRA1 (dense...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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Hot spot identification by ligand-protein surface interactions mapping – in silico study
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Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field
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Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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Recent improvements in prediction of protein structure by global optimization of a potential energy function
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublicationInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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A comparative study of water distribution and dehydrin protein localization in maturing pea seeds
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Mapping Mechanostable Pulling Geometries of a Therapeutic Anticalin/CTLA-4 Protein Complex
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Molecular dynamics insights into protein‐glycosaminoglycan systems from microsecond‐scale simulations
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Local and long range potentials for heparin‐protein systems for coarse‐grained simulations
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Chromatin-associated microprocessor assembly is regulated by the U1 snRNP auxiliary protein PRP40
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Depression as is Seen by Molecular Spectroscopy. Phospholipid- Protein Balance in Affective Disorders and Dementia
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublicationA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublicationMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...
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Assembly of Lipopolysaccharide in Escherichia coli Requires the Essential LapB Heat Shock Protein
PublicationHere, we describe two new heat shock proteins involved in the assembly of LPS in Escherichia coli, LapA and LapB (lipopolysaccharide assembly protein A and B). lapB mutants were identified based on an increased envelope stress response. Envelope stress responsive pathways control key steps in LPS biogenesis and respond to defects in the LPS assembly. Accordingly, the LPS content in ΔlapB or Δ(lapA lapB) mutants was elevated, with...
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How water mediates the long-range interactions between remote protein molecules
PublicationThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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Justification of quasi-stationary approximation in models of gene expression of a self-regulating protein
PublicationWe analyse a model of Hes1 gene transcription and protein synthesis with a negative feedback loop. The effect of multiple binding sites in the Hes1 promoter as well as the dimer formation process are taken into account. We consider three, possibly different, time scales connected with: (i) the process of binding to/dissolving from a binding site, (ii) formation and dissociation of dimers, (iii) production and degradation of Hes1...
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Determination of viscosity changes of protein hydrolyzate solutions depending on shear rate
Open Research DataRheological characteristics of connective tissue protein solutions were made on the basis of viscosity measurement using a Brookfield viscometer using LV SC4 - 27 spindles and shear rate of 85 s-1 (Fig. 1). Solutions of protein hydrolysates with a concentration of 2% in 0.5M acetic acid were prepared.
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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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A vector-enzymatic DNA fragment amplification-expression technology for construction of artificial, concatemeric DNA, RNA and proteins for novel biomaterials, biomedical and industrial applications
PublicationA DNA fragment amplification/expression technology for the production of new generation biomaterials for scientific, industrial and biomedical applications is described. The technology enables the formation of artificial Open Reading Frames (ORFs) encoding concatemeric RNAs and proteins. It recruits the Type IIS SapI restriction endonuclease (REase) for an assembling of DNA fragments in an ordered head-to-tail-orientation. The...
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Simplified Method of Modelling Behaviour of Ship in Waves with Partially Flooded Compartments
PublicationThis paper contains a description of a numerical model for calculating behaviour of ships in waves. There are many models available, but the one described here can be characterised with a set of parameters that have a decisive impact on the final values of roll motion amplitude and frequency. In this paper, it is shown how a fitting of a standard-shape hull characterised by certain readily available parameters affects...
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Modeling of Passive and Forced Convection Heat Transfer in Channels with Rib Turbulators
PublicationThe main goal of the research presented in this paper was the experimental and numerical analysis of heat enhancement and aerodynamic phenomena during air flow in a channel equipped with flow turbulators in the form of properly configured ribs. The use of ribs intensifies the heat transfer and at the same time increases not only the flow resistance but also the energy costs. Therefore, designing modern heat exchangers with optimal...
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Analysis of pounding between adjacent buildings founded on different soil types
PublicationEarthquake-induced pounding was experienced in many previous earthquakes and it was found to be a critical issue. This study investigates the effect of pounding between buildings founded on the same and different soil types. Three 3-D buildings with 4, 6 and 8 storeys were considered in this study. Three pounding scenarios were taken into account, i.e. pounding between 4-storey and 6-storey buildings, between 4-storey and 8-storey...
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Formulation, characterisation and in vitro studies of doxorubicin-loaded silica–polydimethylsiloxane granules
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Synthesis and in vitro characterization of freeze-dried doxorubicin-loaded silica xerogels
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Chitosan/poly(4-vinylpyridine) coatings formed on AgNPs-decorated titanium
PublicationElectrophoretic deposition (EPD) of chitosan/poly(4-vinylpyridine) (chit/P4VP) coatings on titanium substrates previously decorated with silver nanoparticles (AgNPs) was performed at different content of P4VP in the suspension and different voltage values. The results revealed that the composite coatings were formed, well-adjacent to the titanium substrate, of suitable roughness, hydrophilicity, and corrosion resistance. The voltage...
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Tribological Properties of Thermoplastic Materials Formed by 3D Printing by FDM Process
PublicationThe dataset entitled 3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 019_h_4 contains: the time base (expressed in seconds and minutes), the friction torque for sliding friction, rotational velocity of the counter – specimen (velocity of sliding), friction coefficient, load in the friction contact...
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Analysis of floor-to-column pounding of buildings founded on different soil types
PublicationThe aim of this study is to investigate the effect of the soil type on buildings experiencing floor-to-column pounding during earthquakes. Five buildings with 4-storeys, 6-storeys, and 7-storeys were considered. Three types of the 4-storey building with different total heights were taken into account which leads to floor-to-column pounding at 1/3, 1/2 and 2/3 of the height of the impacted column. Two pounding scenarios were considered,...
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Numerical Modelling of Forced Convection of Nanofluids in Smooth, Round Tubes: A Review
PublicationA comprehensive review of published works dealing with numerical modelling of forced convection heat transfer and hydrodynamics of nanofluids is presented. Due to the extensive literature, the review is limited to straight, smooth, circular tubes, as this is the basic geometry in shell-and-tube exchangers. Works on numerical modelling of forced convection in tubes are presented chronologically in the first part of the article....
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Preparation and Properties of Thermoplastic Polyurethane Composites Filled with Powdered Buckwheat Husks
PublicationBio-based fillers for the polymer composites are still interesting from the scientific and industrial point of view, due to their low cost and renewable nature. In this work partially green composites were obtained by the mixing of thermoplastic poly(ester-urethane) with the unmodified and modified (by acetylation) grinded buckwheat husks. Obtained biocomposites were characterized in the terms of their chemical structure (FTIR),...
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Pounding between high-rise buildings founded on different soil types
PublicationEarthquake-induced pounding is a phenomenon that has been often experienced in previous earthquakes. The aim of this study is to investigate the effect of the soil type on high-rise buildings experiencing earthquake induced-pounding. Pounding between 7-storey and 9-storey buildings is examined under five soil types defined in the ASCE 7-10 code which are hard rock, rock, very dense soil and soft rock, stiff soil and soft clay soil....
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Turbulent flow and heat transfer of a liquid film formed by impinging jet.
PublicationZaproponowano prosty model wymiany ciepła w turbulentnym filmie cieczowym utworzonym przez uderzająca strugę. Rozpatrzono dwa przypadki: przepływ rozwijający się i w pełni rozwinięty filmu cieczowego. W obu przypadkach model wyprowadzono na podstawie zmiany grubości filmu w wyniku działania sił bezwładności i sił tarcia. Wyznaczono profile prędkości w obu zakresach co umożliwia wyznaczenie współczynników wymiany ciepła.
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Evolution of post welded residual stress due multilayer circumferentialweld of tube.
PublicationOpisano sposób wykorzystania polowego efektu Barkhausena do pomiaru rozkładu naprężeń w spawanych rurach. Przedstawiono procedurę kalibracji oraz wyniki pomiaru naprężeń uzyskanych po stopniowym spawaniu rury.
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Evaluation of the Antibacterial Activity of Ag- and Au-Nanoparticles Loaded TiO2 Nanotubes
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Automatic control systems for ships fitted with podded propulsion drive (POD).
PublicationW artykule ukazano celowość i możliwości automatyzacji układów napędowych, zwłaszcza typu POD, przewidzianych do zastosowania na projektowanych w ramach projektu Eureka BALTECOLOGICAL SHIP czterech statkach bałtyckich: kontenerowca, pojazdowa i tankowca oraz statku rzeczno - morskiego. Zawarte w artykule informacje ułatwiają dokonanie wyboru właściwych założeń projektowanego układu sterowania napędem wymienionych wyżej statków.
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Research on deformations of laser-welded joint of a steel sandwich structure model.
PublicationPrzedstawiono problemy związane z zachowaniem złącza laserowego pod obciążeniem zginającym. Pokazano wyniki badań laboratoryjnych dla określenia mechanizmu pracy złącza i przedyskutowano uzyskane rezultaty.
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Investigations of dissimilar stainless steels welded joints for chemical tankers construction
PublicationArtykuł przedstawia właściwości mechaniczne złączy różnoimiennych stali typu duplex oraz austenitycznej typu 316L otrzymanych za pomocą spawania automatycznego łukiem krytym. Wykazano możliwość wykorzystania wysokowydajnej metody SAW w miejsce dotychczas stosowanych metod GTAW i GMAW do spawania blach zbiorników statków do przewozu chemikaliów.
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Stability and limit load analysis of a cold-formed channel section column
PublicationThe paper presents stability and limit load analysis of a steel column 1440 mm high of a cold-formed channel section, subjected to a combination of compression and bending. Experimental results were compared to the resistance of a code procedure and to the outcome of numerical non-linear analysis. Comparison was made of numerical solutions by means of static (Riks) and dynamic (Explicit and Implicit) methods. Perfectly elastic...
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Hybrid technique for the analysis of circular waveguide junctions loaded with ferrite posts
PublicationThis study presents a hybrid technique for the analysis of circular waveguide junctions loaded with axially symmetrical ferrite posts of irregular shape. The method is based on a combination of the finite-difference frequency- domain technique with a mode-matching technique. The proposed approach is validated by comparing the presented results with numerical ones obtained from commercial software. The application of a cylindrical...
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Arc-length Algorithm Efficiency in the Analysis of Thermally Loaded Multilayered Shells
PublicationThis paper concerns the efficiency study of the arc-length algorithm in the geometrically non-linear analysis of thermally loaded multilayered shells. The thermal loading is considered as the one-way thermo-mechanical coupling effect. Two implementations of the arc-length method are examined: the path-following technique available in NX-Nastran and the RiksWempner-Ramm algorithm adopted in the authors’ computer code SHLTH. It is...
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Research on assessment of bolted joint state using elastic wave propagation
PublicationThe work contains results of experimental investigation of elastic wave propagation in a bolted single-lap joint. Tests were carried out for the excitation perpendicular to the connection plane. In experimental studies, PZT transducers were used for both excitation and registration of ultrasonic waves. The analyses took into account varying contact conditions between the elements of the connection depending on the value of the...
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Analysis of a caustic formed by a spherical reflector: Impact of a caustic on architectural acoustics
PublicationFocusing sound in rooms intended for listening to music or speech is an acoustic defect. Design recommendations provide remedial steps to effectively prevent this. However, there is a category of objects of high historical or architectural value in which the sound focus correction is limited or even abandoned. This also applies to indoor or outdoor concert shells, installations for teaching and acoustic presentations, etc. The...
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Nanotubular Oxide Layer Formed on Helix Surfaces of Dental Screw Implants
PublicationSurface modification is used to extend the life of implants. To increase the corrosion resistance and improve the biocompatibility of metal implant materials, oxidation of the Ti-13Nb- 13Zr titanium alloy was used. The samples used for the research had the shape of a helix with a metric thread, with their geometry imitating a dental implant. The oxide layer was produced by a standard electrochemical method in an environment of...
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Reverse flow routing problem solved by the Space-Time Conservation Method
PublicationW artykule rozpatruje się zagadnienie odwrotnej transformacji przepływów dla przypadku przepływu nieustalonego wolno zmiennego w kanałach otwartych, opisanego układem równań de Saint Venanta. Przedstawiono specyficzne dla rozpatrywanego przypadku problemy powstające na etapie jego rozwiązywania oraz zaproponowano efektywny algorytm obliczeniowy, wykorzystujący nową, atrakcyjną metodę czasoprzestrzennych objętości skończonych. Do...
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Coupled - mode design of ferrite loaded coupled microstrip lines section
PublicationMetodę rodzajów sprzężonych zastosowano do analizy i projektowania sekcji ferrytowych mikropaskowych linii sprzężonych magnesowanych podłużnie (FCL). W wyniku analizy określono macierz rozproszenia sekcji oraz warunki umożliwiające jej zastosowanie do realizacji cyrkulatora projetowanego jako połączenie badanej sekcji FCL z mikropaskowym rozgałęzieniem typu T. W oparciu o opracowane oprogramowanie przeprowadzono modelowanie parametrów...
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Effect of electrode waterproof coating on quality of underwater wet welded joints
PublicationIn this paper, the effects of different hydrophobic coatings on the surface of covered electrodes on the quality of wet welded carbon steel joints were discussed. Commonly available hydrophobic substances used in industrial applications were selected for the research. The aim of using waterproof coatings was to check the possibility to decreasing the susceptibility of highstrength low-alloy S460N steel to cold cracking. During...
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Effect of welding conditions on susceptibility to cold cracking of underwater welded joints
PublicationPrzedstawiono wybrane aspekty spawalności stali przy spawaniu pod wodą metodą lokalnej komory suchej. Zwrócono szczególną uwagę na skłonność do tworzenia peknięć zimnych w SWC. Przy pomocy planowania doświadczeń określono ilościowy wpływ parametrów spawania na naprężenia krytyczne z próby implant.
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Investigations into tendency to stress corrosion of joints welded in austenitic and duplex steels
PublicationPrzedstawiono wyniki badań spawanych złączy różnoimiennych wykonanych ze stali austenitycznej oraz typu duplex 2205. Badania podatności do korozji naprężeniowej złączy wykonano metodą odkształcania z małą prędkością. Próby przeprowadzono w środowisku obojętnym oraz agresywnym (MgCl2).