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Wyniki wyszukiwania dla: folded proteins
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Electrodes Based on a Titanium Dioxide Nanotube–Spherical Silver Nanoparticle Composite for Sensing of Proteins
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Expression of INHβA and INHβB proteins in porcine oocytes cultured in vitro is dependent on the follicle size
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Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals
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Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublikacjaTo study the biochemical properties of SSB from Desulfolatea psychrophila (DpsSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 426 nucleotides encoding SSB protein of 142 amino acids with a calculated molecular mass of 15.6 kDa and it is the smallest known bacterial SSB protein indentified to date. The amino-acid sequence...
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Optimized procedure of extraction, purification and proteomic analysis of nuclear proteins from mouse brain
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The Effect of Hyperbaric Storage on the Nutritional Value and Retention of Certain Bioactive Proteins in Human Milk
PublikacjaHuman milk (HM) contains the essential macronutrients and bioactive compounds necessary for the normal growth and development of newborns. The milk collected by human milk banks is stored frozen and pasteurized, reducing its nutritional and biological value. The purpose of this study was to determine the effect of hyperbaric storage at subzero temperatures (HS-ST) on the macronutrients and bioactive proteins in HM. As control samples,...
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Nanoparticle Tracking Analysis of Urinary Extracellular Vesicle Proteins as a New Challenge in Laboratory Medicine
PublikacjaUrinary extracellular vesicle (uEV) proteins may be used as specific markers of kidney damage in various pathophysiological conditions. The nanoparticle-tracking analysis (NTA) appears to be the most useful method for the analysis of uEVs due to its ability to analyze particles below 300 nm. The NTA method has been used to measure the size and concentration of uEVs and also allows for a deeper analysis of uEVs based on their protein...
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The Impact of the Antigenic Composition of Chimeric Proteins on Their Immunoprotective Activity against Chronic Toxoplasmosis in Mice
PublikacjaToxoplasmosis may pose a serious threat for individuals with weakened or undeveloped immune systems. However, to date, there is no specific immunoprophylaxis for humans. Thus, the aim of this study was to evaluate the immunogenicity of three trivalent—SAG2-GRA1-ROP1L (SGR), SAG1L-MIC1-MAG1 (SMM), and GRA1-GRA2-GRA6 (GGG)—and two tetravalent—SAG2-GRA1-ROP1-GRA2 (SGRG) and SAG1-MIC1-MAG1-GRA2 (SMMG)—chimeric T. gondii proteins, as...
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Two bacterial small heat shock proteins, IbpA and IbpB, form a functional heterodimer
PublikacjaSmall heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones which in stress conditions bind to unfolded protein substrates and prevent their irreversible aggregation. Substrates trapped in sHsps-containing aggregates are efficiently refolded into native structures by ATP-dependent Hsp70 and Hsp100 chaperones. Most γ-proteobacteria possess a single sHsp (IbpA), while in a subset of Enterobacterales, as...
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Effect of urea and glycine betaine on the hydration sphere of model molecules for the surface features of proteins
PublikacjaWater properties may significantly affect protein stability. Osmolytes are compounds that intrinsically affect water in many different ways and thus can influence proteins with this type of indirect mechanism. In this study, we characterize water properties in ternary solutions: model–water–osmolyte, with two model molecules: N-methylacetamide (NMA) and dimethyl sulfoxide (DMSO) and two osmolytes: glycine betaine (TMG)and urea....
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Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface
PublikacjaA mechanism of interactions between the ice-binding surface of a hyperactive antifreeze protein molecule and the ice surface is proposed, involving the influence of water present between the two surfaces on the behavior of the approaching molecule. It is demonstrated that the interfacial water, even before its full solidification, can act as a factor that pushes away or pulls nearer the protein molecule to ensure its proper positioning....
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Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublikacjaTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublikacjaWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublikacjaNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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MutL protein as a constituent of vsp, ner and mmr repair systems
PublikacjaMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mis- match repair system (MMR). However, there is growing evidence that MMR system is not the only field of action for these pro- teins. Moreover, the participation in MMR does not even have to be their primary function. There are some reports indicat- ing involvement of MutL in BER, NER and VSP (very short patch repair)....
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublikacjaAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Nutritional value, protein and peptide composition of edible cricket powders
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Quantitative determination of mechanical stability in the novel coronavirus spike protein
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Software tools for identification, visualization and analysis of protein tunnels and channels
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C-reactive Protein as a Diagnostic and Prognostic Factor of Endometrial Cancer
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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
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C-reactive protein as a diagnostic and prognostic factor of endometrial cancer
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Delay induced oscillations in gene expression of Hes1 protein model
PublikacjaW pracy został omówiony model produkcji białka Hes1. Stężenie Hes1 jest kontrolowane przez ujemne sprzężenie zwrotne wbudowane w białko i jego mRNA. Przeprowadzona analiza potwierdziła znane wyniki numeryczne, że oscylacje wywołane są przez opóźnienie. Pokazaliśmy również, że jeśli współczynnik Hilla jest większy niż 1, to istnieje krytyczna wartość opóźnienia, dla której ma miejsce bifurkacja Hopfa i pojawiają się rozwiązania...
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Structural Analysis of a Peptide Fragment of Transmembrane Transporter Protein Bilitranslocase
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X-ray and UV Radiation Damage of dsDNA/Protein Complexes
PublikacjaRadiation and photodynamic therapies are used for cancer treatment by targeting DNA. However, efficiency is limited due to physico-chemical processes and the insensitivity of native nucleobases to damage. Thus, incorporation of radio- and photosensitizers into these therapies should increase both efficacy and the yield of DNA damage. To date, studies of sensitization processes have been performed on simple model systems, e.g.,...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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Molecular targets for antifungals in amino acid and protein biosynthetic pathways
PublikacjaFungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems...
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MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publikacja—Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence...
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublikacjaIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Use of X-ray radiography in the diagnosis of bonded anchors
PublikacjaKotwy wklejane należą do najbardziej popularnych metod montażu elementów konstrukcyjnych. Promieniowanie rentgenowskie częściowo umożliwia diagnostykę zespolenia lepiszcza z podłożem. W pracy przedstawiono wyniki analizy wpływu parametrów technicznych aparatów rentgenowskich na sposób i dokładność wykonania zdjęć diagnostycznych osadzenia kotew stalowych przy zastosowaniu lepiszcza syntetycznego
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CLASSIFICATION OF RESTRAINTS IN THE OPTIMIZATION PROBLEM OF A COLD-FORMED PROFILE
PublikacjaThis work describes the restraints in the optimization problem. This is an important and complicated issue because it requires taking into account a vast range of information related to the design and production. In order to describe the relations of a specific optimization problem, it is essential to adopt appropriate criteria and to collect information on all kinds of restraints, i.e. boundary conditions. The following paper...
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A large family of filled skutterudites stabilized by electron count
PublikacjaThe Zintl concept is important in solid-state chemistry to explain how some compounds that combine electropositive and main group elements can be stable at formulas that at their simplest level do not make any sense. The electronegative elements in such compounds form a polyatomic electron-accepting molecule inside the solid, a ‘polyanion’, that fills its available energy states with electrons from the electropositive elements...
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POLDER AND CITY: SUSTAINING WATER LANDSCAPES ON AN URBAN EDGE
PublikacjaThe question investigated in this paper is how to maintain the environmental quality of the polder landscape encompassing the city in the condition of urban pressure on this landscape. On the basis of theoretical approaches, historical surveys and introductory study models new ideas are tested on the case study of Gdansk, a city located in the Vistula River delta in northern Poland. Research shows that the city was created as a...
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Environmental costs for exploitation variants of Racibórz dry polder
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Conversion of Potato Industry Waste into Fodder Yeast Biomass
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Heat tint colours on stainless steel and welded joints
PublikacjaSurface layer condition of stainless steels and welded joints influences strongly their corrosion resistance. This problem seems to be underestimated. This current study explains the phenomenon of heat tint forming on welds, the methods of its removal, inspection procedures after heat tint removing and post weld finishing
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Partially prestressed concrete beams with bonded and unbonded strands
PublikacjaThis article relate the tests of partially prestressed concrete beams. There is presented the research programme - geometry of elements, method of loading, the materials and variables. There have been shown preliminary test results of prestressed concrete elements with bonded and unbonded strands, and compared to the test results of R.C. beam.
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Bolted Joint Monitoring Using the Elastic Wave Propagation
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Emulsion-Based Gel Loaded with Ibuprofen and Its Derivatives
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Propagation in Rectangular Waveguides Periodically Loaded with Cylindrical Posts.
PublikacjaAnaliza rozchodzenie się fali elektromagnetycznej w falowodach prostokątnych z okresowo rozmieszczonymi cylindrycznymi obiektami. Wynikiem analizy są stałych rozprzestrzeniania rodzajów Floquet, które uzyskuje się z rozwiązania równania własnego. W artykule przeprowadzone zostało badanie teoretyczne i eksperymentalne struktur prawie-okresowych i ich macierzy rozproszenia. Pokazano również istnienie pasm przewodzących i zaporowych,...
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Fatigue properties of laser welded steel sandwich panel.
PublikacjaPrzedstawiono wyniki badań laboratoryjnych paneli SANDWICH, prowadzonych w Kat. TOiOO Wydz. OiO na konstrukcjach w skali rzeczywistej. Przedstawiono program badań, omówiono założenia procedur badawczych i konstrukcję stanowisk testowych. Dokonano porównania uzyskanych rezultatów z wynikami prezentowanymi w literaturze. Przedstawiono propozycję algorytmu szacowania trwałości zmęczeniowej konstrukcji spawanych laserowo.
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Determination of toluene formed during fermentation of sewage sludge
PublikacjaW pracy przedstawiono wyniki oznaczeń toluenu w próbkach osadów ściekowych przy wykorzystaniu techniki wypłukiwania i jednoczesnego wychwytywania analitów (PT). Badania procesu feremntacji osadów ściekowych doprowadziły do stwierdzenia, że w trakcie tego procesu powstaje toluen. Stwierdzono wzrost stężenia toluenu od poziomu 3 mg/l do ponad 24 mg/l dla próbek osadów ściekowych z Oczyszczalni Gdańsk -Wschód oraz od poziomu 0,6 mg/l...
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Mechanical properties of dissimilar welded joints for chemical tankers
PublikacjaArtykuł 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. Pomimo obawy uzyskania nieodpowiednich struktur złączy okazało się, że spawanie stali...
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Acoustic heating produced in resonators filled by a newtonian fluid
PublikacjaAcoustic heating in resonators is studied. The governing equation of acoustic heating is derived by means of the special linear combination of conservation equations in differential form, allowing the reduction of all acoustic terms in the linear part of the final equation, but preserving terms belonging to the thermal mode responsible for heating. This equation is instantaneous and includes nonlinear acoustic terms that form a...
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Innovative cold-formed GEB section under compression
PublikacjaCold-formed steel sections extensively affect the modern steel construction industry. Not only are they used as secondary elements like purlins or sheeting, but also they can serve as primary load-bearing members in fabricated steel panels and trusses. A new cross-section called shortly a GEB may serve as that member. However, its existence of the metal building structures industry depends on the exact, optimal dimensional parameters...
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Possibilities for assesment of the angular distortion in Welded T-joint
PublikacjaSpawanie jest podstawową techniką łączenia elementów konstrukcji kadłuba statku. Procesowi temu towarzyszą odkształcenia spawalnicze, co przysparza dużo problemów wykonawczych. W pracy przedstawiono wpływ przewymiarowania spoiny pachwinowej na wielkość kątowych odkształceń złącza. Dokonano porównania wartości określonych na podstawie inżynierskich hipotez z wynikami otrzymanymi podczas prób laboratoryjnych.
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Investigations of welded joints of dissimilar heat resistant steels.
PublikacjaPrzeprowadzono badania metalograficzne połączeń spawanych różnorodnych stali żarowytrzymałych rur o przekroju 31,8x7,1 mm ze stali 10H2M z blachą ze stali 20H23N18. Badania makro- i mikrostruktury złączy spawanych wykazały, że istotnym czynnikiem wpływającym na właściwości mechaniczne złącza jest obecność wad takich jak pory lub wtrącenia żużla. Te nieciągłości w materiale powodują koncentrację naprężeń i powstawanie mikropęknięć.
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Iron filled carbon nanostructures from different precursors
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Preparation, characterization and photocatalytic activity of metal-loaded NaNbO3
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Synthesis and characterization of iron-filled multi-walled nanotubes
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