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Wyniki wyszukiwania dla: PROTEIN SURFACE
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ANALYSIS OF THE p53 PROTEIN GENE EXPRESSION MODEL
PublikacjaWe study the asymptotic behaviour of the solutions of the p53-Mdm2 model proposed by Monk (2003). The p53 gene is crucial for cellular inhibition of the angiogenesis process, while Mdm2 is a negative regulator of the p53 tumor-suppressor. We investigate the stability of the positive steady state and perform some numerical experiments.
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Zastosowanie addytywów w separacji pianowej białek serwatkowych i białek mlecznych
PublikacjaZaproponowano proces separacji pianowej do wydzielania białek ze strumieni poprodukcyjnych przemysłu mleczarskiego Ponadto zaproponowano zastosowanie w separacji pianowej białek serwatkowych i mlecznych addytywów dopuszczonych ustawą do stosowania w żywności. Jako cel pracy przyjęto uzyskanie wyników uzasadniających wybór takich addytywów, które intensyfikują przebieg i polepszają wynik procesu separacji pianowej białek. W części...
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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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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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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions
PublikacjaThe biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide)...
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Enhancing colloidal stability of nanodiamond via surface modification with dendritic molecules for optical sensing in physiological environments
PublikacjaPre-treatment of diamond surface in low-temperature plasma for oxygenation and in acids for carboxylation was hypothesized to promote the branching density of the hyperbranched glycidol polymer. This was expected to increase the homogeneity of the branching level and suppress interactions with proteins. As a result, composite nanodiamonds with reduced hydrodynamic diameters that are maintained in physiological environments were...
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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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Function and Frustration of Multi-Drug ABC Exporter Protein and Design of Model Proteins for Drug Delivery Using Protein Hydration Thermodynamics
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Monitoring of lysozyme thermal denaturation by volumetric measurements and nanoDSF technique in the presence of N-butylurea
PublikacjaThe results of thermal studies of denaturation of hen egg white lysozyme (HEWL) in water and an aqueous solution of N-butylurea (BU) are presented. High-precision densimetric measurements were used to characterize and analyze the changes of the specific volume, v, during temperature elevation. The temperature of the midpoint of protein denaturation was also determined by nanoDSF technique (differential scanning fluorimetry). The...
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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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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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Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1
PublikacjaIn this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules....
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Protein overproduction alters exosome secretion in Chinese hamster ovary cells
PublikacjaDespite the abundance of available cell lines, nearly 70% of all recombinant therapeutic proteins today are produced in Chi-nese hamster ovary (CHO) cells. The impact of protein overproduction on the secretion of exosomes by CHO cells has been investigated here. Increased secretion of extracellular vesicles (EVs) by protein overexpressing CHO cells was demonstrated with protein content assay, nanoparticle tracking analysis, and...
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Construction and purification of his6-Thermus thermophilus MutS protein.
PublikacjaGen mutS z termofilnej bakterii Thermus thermophilus zamplifikowano przy użyciu PCR, sklonowano i przeprowadzono jego ekspresję w E. coli. Rekombinantowe białko MutS zawierające oligohistydynową domenę na N-końcu oczyszczono w jednoetapowej procedurze przy wykorzystaniu chromatografii powinowactwaNi(2+). Zdolność do rozpoznania niekomplementarności białka his(6)-MutS potwierdzono w eksperymentach ochrony DNA przed trawieniem...
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Construction and purification of his6-Thermus thermophilus MutS protein
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A bifunctional chimeric protein consisting of MutS and beta-galactosidase
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The protein folding problem: global optimization of force fields
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Lipid-protein interactions in membranes: a molecular modelling study
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A bifunctional chimeric protein consisting of MutS and beta-galactoside
PublikacjaPraca pokazuje konstrukcję DNA plazmidowego kodującego bifunkcjonalne białko chimeryczne złożone z MutS Thermus thermophilus i beta-galaktozydazy E.coli, optymalizację jego ekspresji i oczyszczania. Białko to testowano w metodzie wykrywania mutacji punktowych, wykorzystując kolorymetryczne mierzenie aktywności domeny reporterowej beta galaktozydazy.
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
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Role of Oligosaccharide Chain Polarity in Protein–Glycosaminoglycan Interactions
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Effect of increased protein intake on the risk of female infertility
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Copper containing protein sites - structure, properties and models
PublikacjaEnzymy organizmów żywych katalizują wiele reakcji stosowanych w przemyśle chemicznym. Przykładem potencjalnego zastosowania enzymu w produkcji jest synteza L-Dopy przy udziale tyrozynazy. Ze względu na możliwe praktyczne zastosowanie w katalizie, otrzymano i opisano wiele prostych modeli miejsc aktywnych enzymów. W artykule opisano niektóre modele białek zawierających miedź.
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Electrosynthesis of potato starch–whey protein isolate complexes
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublikacjaEfficient brain function requires as much as 20% of the total oxygen intake to support normal neuronal cell function. This level of oxygen usage, however, leads to the generation of free radicals, and thus can lead to oxidative stress and potentially to age-related cognitive decay and even neurodegenerative diseases. The regulation of this system requires a complex monitoring network to maintain proper oxygen homeostasis. Furthermore,...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublikacjaWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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Mathematical analysis of a generalised p53-Mdm2 protein gene expression model
PublikacjaWe propose the generalisation of the p53-Mdm2 protein gene expression model introduced by Monk (2003). We investigate the stability of a unique positive steady state and formulate conditions which guarantee the occurrence of the Hopf bifurcation. We show that oscillatory behaviour can be caused not only by time lag in protein transcription process, but also can be present in the model without time delay. Moreover, we investigate...
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Drop-coating deposition surface-enhanced Raman spectroscopy on silver substrates for biofluid analysis
PublikacjaUtilization of surface-enhanced Raman spectroscopy as a measurement technique is of particular interest in biodetection due to its superb chemical specificity and high sensitivity. The use of SERS substrates further improve this method by massive enhancement of the molecule Raman spectrum, permitting very low levels of detection. Therefore it is important to seek for new ways to develop reliable substrates, which are quickly and...
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Monocyte Chemoattractant Protein-Induced Protein 1 (MCPIP1) Enhances Angiogenic and Cardiomyogenic Potential of Murine Bone Marrow-Derived Mesenchymal Stem Cells
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublikacjaThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface
PublikacjaAlbumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions...
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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Evolution towards simplicity in bacterial small heat shock protein system
PublikacjaEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either two...
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Identification of antigen Ag43 in uropathogenic Escherichia coli Dr+ strains and defining its role in the pathogenesis of urinary tract infections
PublikacjaUrinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are among the most common bacterial infectious diseases in the developed world. The urovirulence of UPEC is mainly associated with the surface-exposed fimbrial adhesins and adhesins of the autotransporter (AT) family. The best studied of theses proteins is antigen 43 (Ag43) mediating cell aggregation, adhesion and biofilm development as the causes of...
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublikacjaA 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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MUTL PROTEIN AS A COMMON CONSTITUENT OF VSP, BER, NER AND MMR REPAIR SYSTEMS
PublikacjaMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mismatch repair system (MMR). However, there is growing evidence that MMR system is not the only field of action of these proteins. Moreover, involvement in MMR does not even have to be their primary function. There are some reports indicating involvement of MutL in BER, NER and VSP (very short patch repair). MutL protein...
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Chitosan-protein scaffolds loaded with lysostaphin as potential antistaphylococcal wound dressing materials.
PublikacjaAIMS: The development of technology for preparing chitosan-protein scaffolds loaded with lysostaphin, which potentially could be used as dressing for wound treatment and soft tissue infections caused by Staphylococcus aureus. METHODS AND RESULTS: The unique technology of chitosan solubilization using gaseous CO(2) instead of organic or inorganic acids was used for the incorporation of lysostaphin, the enzyme that exhibits bactericidal...
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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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Structural Analysis of a Peptide Fragment of Transmembrane Transporter Protein Bilitranslocase
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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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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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Induction of immune responses in sheep by vaccination with liposome-entrapped DNA complexes encoding Toxoplasma gondii MIC3 gene
PublikacjaToxoplasma gondii is a parasite that has been extensively studied due to its medical and veterinary importance in terminating pregnancies. Consequently, a satisfactory vaccine is required to control itsadverse effects on pregnant animals. The microneme protein, MIC3, is a major adhesion protein that binds to the surface of host cells and parasites, and is therefore a potential vaccine against T. gondii.The viability of MIC3 as...
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Justification of quasi-stationary approximation in models of gene expression of a self-regulating protein
PublikacjaWe 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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Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublikacjaWe have reported that the hsp70 chaperone DnaK from Escherichia coli might assist protein folding by catalyzing the cis/trans isomerization of secondary amide peptide bonds in unfolded or partially folded proteins. In this study a series of fatty acylated benzamido inhibitors of the cis/trans isomerase activity of DnaK was developed and tested for antibacterial effects in E. coli MC4100 cells. Nα-[Tetradecanoyl-(4-aminomethylbenzoyl)]-l-asparagine...
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How water mediates the long-range interactions between remote protein molecules
PublikacjaThe 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...