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Search results for: protein folding
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Oxidative Modification of Proteins in Pediatric Cystic Fibrosis with Bacterial Infections
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Bean seed proteins digestibility affected by pressure and microwave cooking
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Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants
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Carotenoid binding to proteins: Modeling pigment transport to lipid membranes
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Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants
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Immunogenic and protective activity of recombinant chimeric Toxoplasma gondii proteins
PublicationToxoplasmosis, one of the most common parasitic invasions worldwide, may pose a great threat for individuals with weakened immune system. The parasite also causes considerable economic losses due to infection of livestock. To date there is no efficient immunoprophylaxis for humans and animals, which would provide long-lasting protection against T. gondii invasion. Chimeric proteins, containing several selected fragments of parasite...
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Fragmentomic analysis of biopeptides in silico released from milk proteins
PublicationThe fragmentomic-assisted method was employed to predict the biological potential of peptides derived from milk proteins hydrolyzed by papain and bromelain. Firstly, protein sequences were acquired from the BIOPEP-UWM database and then hydrolyzed by the above enzymes using a BIOPEP-UWM tool called “Enzyme(s) action”. The released peptides were defined as parent peptides and further analyzed for the presence of shorter peptidic...
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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Analysis of the Factors Affecting Static In Vitro Pepsinolysis of Food Proteins
PublicationIn this meta-analysis, we collected 58 publications spanning the last seven decades that reported static in vitro protein gastric digestion results. A number of descriptors of the pepsinolysis process were extracted, including protein type; pepsin activity and concentration; protein concentration; pH; additives; protein form (e.g., ‘native’, ‘emulsion’, ‘gel’, etc.); molecular weight of the protein; treatment; temperature; and...
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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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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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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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Sulforaphane, a cruciferous vegetable-derived isothiocyanate, inhibits protein synthesis in human prostate cancer cells
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Post mortem changes in M. iliotibialis lateralis muscle protein profile of emu (Dromaius novaehollandiae)
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Excessive amount of lactose in the diet of two-week-old calves induces urinary protein changes
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Comparison of Antioxidant Activity of Protein Isolates Derived from Selected Dry-Cured Meat Products
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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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E2/E3‐independent ubiquitin‐like protein conjugation by Urm1 is directly coupled to cysteine persulfidation
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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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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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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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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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Rotational molding of polylactide (PLA) composites filled with copper slag as a waste filler from metallurgical industry
PublicationThe research work carried out so far indicates the ever wider possibilities and demand for shaping composite products in the rotational molding technology. This trend was the main reason to use waste-based filler from the metallurgical process as a filler for manufacturing polylactide (PLA)-based remolded composites. Copper slag (CS) was introduced in the single-step processing method to PLA matrix at 5, 10, 20, and 35 wt%. The...
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Adaptive resolution-constrained scalar multiple-description coding
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Frequency bands selection of the Portevin-LeChatelier
PublicationEfekt Portevina-LeChateliera ujawnia się w postaci skokowych zmian naprężenia w trakcie procesu odkształcenia próbek pewnych stopów. Zjawisko PLC występuje w kilku odmianach charakteryzujących się istotnymi różnicami zarówno w przestrzennym rozkładzie pasm odkształcenia jak też przebiegu krzywej naprężeniowej. Przebiegi odpowiadające różnym odmianom serration charakteryzują się odmiennymi właściwościami rozkładu energetycznego...
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Właściwości i zastosowanie termostabilnych proteaz
PublicationProteazy stanowią największą grupę enzymów spośród dostępnych i wykorzystywanych przemysłowo biokatalizatorów. Wynika to z ważnej roli jaką odgrywają w wielu procesach technologicznych. Obecnie na rynku dostępnych jest wiele preparatów przeznaczonych głównie dla przemysłu żywnościowego, farmaceutycznego, tekstylnego,garbarniczego czy produkcji detergentów.
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The concept of a new two-stage fuse for high power pulse forming
PublicationThis manuscript introduces the concept, physical operating principle and studies on a new and unique two stage forming fuse (TSFF) with interstage spark gap commutation and presents its application for forming high power pulses of extreme parameters. The paper classifies TSFF performance and compares it with conventional single-stage forming fuses. The conclusions are supported by analytical and experimental studies in laboratory...
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Effect of bulk solid on strength of cylindrical corrugated silos during filling.
PublicationW artykule przedstawiono wyniki MES dla metalowych silosów z blachy falistej o kształcie cylindrycznym. Obliczenia wykonano podczas stanu napełnienia silosów z uwzględnieniem materiału sypkiego. Materiały sypki został opisany hipoplastycznym modelem konstytutywnym. W obliczeniach wzięto pod uwagę wstępne imperfekcje geometryczne. Wyniki porównano dla silosów pustych. Zaobserwowano pozytywny efekt obecności materiału sypkiego.
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Use of Neural Networks in Diagnostics of Rolling-Element Bearing of the Induction Motor
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Modeling of Heat Source Based on Parameters of Electron Beam Welding Process
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Numerical Simulation of Electron Beam Welding Process of Inconel 706 Sheets
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An Approximate Linear Analysis of Structures Utilizing Incremental Loading of Force Method
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Interplay of hydrogen bonding and aryl-perfluoroaryl interactions in construction of supramolecular aggregates
PublicationThe stacking between aryl and perfluoroaryl units is an important class of the aromatic – aromatic interactions that has attracted rapidly growing interest in recent years. Continuing interest of our group in this subject it had been prepared three new complexes of pentafluorobenzoic acid with benzyl alcohol, 4-methylbenzyl alcohol and 4-tert-butylbenzyl alcohol and in the next step investigated their self-assembly modes by...
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Impact of intense rains and flooding on mercury riverine input to the coastal zone
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The effect of disturbance caused by rivers flooding on ground beetles (Coleoptera: Carabidae)
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Welding Distortion Characteristics of Door Openings According to Changing Shape of Stiffener
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POPULATION-BASED MULTI-AGENT APPROACH TO SOLVING MACHINE LEARNING PROBLEMS
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Influence of the substrate loading on the quality and diameter distribution of SWCNT in alcohol‐CVD
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Nanotubular Ti Oxide Layers for Enhancement of Bone-Implant Bonding and Bioactivity
PublicationAbstrakt artykułu pt. ''Nanotubular Ti Oxide Layers for Enhancement of Bone-Implant Bonding and Bioactivity''. The paper describes techniques to improve the bioactivity of titanium and ehnahnce the bone-implant bonding ability by the electrochemical anodization to fabricate titania nanotubular oxide layer.
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Tribological performance of PTFE-metal binary coatings in rolling/sliding contact
PublicationTribological performance of surface coatings with embedded PTFE reservoirs in rolling/sliding contact is reported. Using two different coating materials and two shapes and patterns of PTFE reservoirs test samples in the form of discs were prepared and tested in a four-ball contact configuration under loads corresponding to nominal contact pressure of 0.5 and 1.0 GPa. It was found that one coating, namely aluminium-bronze with embedded...
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Determining diffusible hydrogen amounts using the mercury method. Welding International
PublicationW artykule przedstawiono szczegółową charakterystykę procedury oznaczania ilości wodoru dyfundującego metodą rtęciową na tle innych metod badawczych i aktualnego stanu wiedzy dotyczącego rozpatrywanego zagadnienia. Omówiono klasyfikację wodoru występującego w złączu spawanym oraz metody oznaczania ilości wodoru dyfundującego w stopiwie ze zwróceniem szczególnej uwagi na metodę rtęciową jako metodę podstawową. Zestawiono zależności...
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Mersenne Number Finding and Collatz Hypothesis Verification in the Comcute Grid System
PublicationIn this chapter, some mathematic applications have been described to test scalability of the Comcute grid system. Especially, a verification of the Collatz hypothesis and finding Mersenne numbers were applied to prove the scalability and high performance of this grid system. Results were compared with outcomes obtained by the other grid systems.
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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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Interlayer defect evolution in an coating system on steel under hydromechanical loading
PublicationZaprezentowano wyniki pomiarów impedancyjnych obszaru międzywarstwowego w systemie powłokowym poddanym naprężeniom. Przedstawiono nowy sensor który jest zdolny do detekcji defektów w obszarze międzywarstwowym. Dwuwarstwowy system powłokowy przeznacziony do zastosowań morskich zbadano w celu określenia jego odporności na oddziaływanie cyklicznych naprężeń i zanurzeń w 3% roztworze NaCl.