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Search results for: Prostein 10E3
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The Extracellular Bacterial HtrA Proteins as Potential Therapeutic Targets and Vaccine Candidates
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNA insequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination. Although there are differences in amino...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNAinsequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination.Although there are differences in amino acid...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
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Partial characterization of proteins from mussel Mytilus galloprovincialis as a biomarker of contamination
PublicationPrzedmiotem zainteresowania były:- funkcjonalne i przeciwutleniające właściwości białek małża Mytilus galloprovincialis,- poziom zawartości metali ciężkich (ołów i kadm) w tkankach.Badania przeprowadzono dla małży zebranych zarówno w zanieczyszczonych, jak i w czystych obszarach strefy brzegowej Morza Czarnego w regionie Warny (Bułgaria). W badaniach wykorzystano takie techniki analityczne jak: spektroskopia FTIR, fluorescencja,...
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Hybrid Monte-Carlo simulations of fluorescence anisotropy decay in disordered two-component systems in the presence of forward and back energy transfer
PublicationW pracy przedstawiono hybrydowy algorytm symulacji Monte Carlo zaniku anizotropii emisji fluorescencji w układach dwuskładnikowych z uwzględnieniem prostego i powrotnego transferu energii. Poprawność nowego algorytmu symulacji Monte Carlo zweryfikowano poprzez porównanie z wynikami obliczeń teoretycznych otrzymanymi w ramach modelu SCDM i z wynikami standardowej symulacji Monte Carlo (algorytm 'step by step').
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Toxoplasma gondii Recombinant antigen AMA1: Diagnostic Utility of Protein Fragments for the Detection of IgG and IgM Antibodies
PublicationToxoplasma gondii is an important zoonotic protozoan that infects a wide variety of vertebrates as intermediate hosts. For this reason, the diagnosis of this disease is very important and requires continuous improvement. One possibility is to use recombinant antigens in serological tests. Apical membrane antigen 1 (AMA1), a protein located in specific secretory organelles (micronemes) of T. gondii, is very interesting in regard...
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Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70
PublicationThe J-domain protein Zuotin is a multi-domain eukaryotic Hsp70 co-chaperone. Though it is primarily ribosome-associated, positioned at the exit of the 60S subunit tunnel where it promotes folding of nascent polypeptide chains, Zuotin also has off-ribosome functions. Domains of Zuotin needed for 60S association and interaction with Hsp70 are conserved in eukaryotes. However, whether the 4-helix bundle (4HB) domain is conserved remains...
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Electrochemical Synthesis of Polysaccharide-Protein Complexes. Part 1: Preliminary Studies on Apple Pectin-Albumin Complexes
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The cell surface protein Ag43 facilitates phage infection of Escherichia coli in the presence of bile salts and carbohydrates
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MITOGEN-ACTIVATED PROTEIN KINASE 4 impacts leaf development, temperature, and stomatal movement in hybrid aspen
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Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito
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Hyperosmolarity adversely impacts recombinant protein synthesis by Yarrowia lipolytica—molecular background revealed by quantitative proteomics
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Analysis of the Link between the Redox State and Enzymatic Activity of the HtrA (DegP) Protein from Escherichia coli
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t-SNE Highlights Phylogenetic and Temporal Patterns of SARS-CoV-2 Spike and Nucleocapsid Protein Evolution
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Gene and Protein Accumulation Changes Evoked in Porcine Aorta in Response to Feeding with Two Various Fructan Sources
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Serum Cholesteryl Ester Transfer Protein (CETP) and Sortilin (SORT) in Patients with Psoriasis with Relation to Systemic Treatment
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Liver fatty acid-binding protein might be a predictive marker of clinical response to systemic treatment in psoriasis
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Nanostructured polyethersulfone membranes for dye and protein separation: Exploring antifouling role of holmium (III) molybdate nanosheets
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Least Squares Estimators of Peptide Species Concentrations Based on Gaussian Mixture Decompositions of Protein Mass Spectra
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Influence of one‐night CPAP therapy on the changes of HIF‐1α protein in OSA patients: A pilot study
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GRA1 protein vaccine confers better immune response compared to codon-optimized GRA1 DNA vaccine
PublicationW publikacji oszacowano immunogenność i właściwości protekcyjne szczepionki anty-Toxoplasma gondii opartej na białku rekombinantowym GRA1 oraz dwóch rodzajach szczepionek DNA (plazmidu zawierającego gen kodujący białko GRA1 dzikiego typu oraz modyfikowanego genu kodującego białko GRA1). Uzyskane wyniki sugerują lepsze właściowści immunoprotekcyjne rekombinantowego białka antygenowego niż szczepionek DNA.
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A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.
PublicationThe presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified...
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Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis
PublicationSingle-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNAreplication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-likegene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoal-teromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism.PhaSSB possesses...
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The Role of Matrix Gla Protein (MGP) Expression in Paclitaxel and Topotecan Resistant Ovarian Cancer Cell Lines
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The Influence of the Parameters of a Gold Nanoparticle Deposition Method on Titanium Dioxide Nanotubes, Their Electrochemical Response, and Protein Adsorption
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Protein oligomerization is the biochemical process highly up-regulated in porcine oocytes before in vitro maturation (IVM)
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Real-time proliferation of porcine cumulus cells is related to the protein levels and cellular distribution of Cdk4 and Cx43
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Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
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Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein
PublicationW ostatnich latach zaproponowano szereg modeli typu implicit solvent, ktore bazują na bezpośrednim rozwiązaniu niejednorodnego równania Poissona w przestrzeni rzeczywistej. Modele te charakteryzują się elegancją, ponieważ wnęka, w której umieszczona jest molekuła substancji rozpuszczanej zdefiniowana jest bezpośrednio w funkcji gęstości elektronowej, a rozkład ładunku jest w sposób samouzgodniony polaryzowany dzięki reakcji dielektryka,...
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Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublicationRadiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions,...
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Taq DNA polymerase fused with DNA binding protein with increased resistance to inhibitors from clinical samples
PublicationNowadays PCR method is commonly used in molecular diagnostic. However, in many cases PCR is limited, by the presence of inhibitory substances in biological, soil or food samples Efficiency and fidelity of amplification is strongly connected with DNA polymerase and reaction conditions. To meet the requirements of modern diagnostic methods it is essential to seeking for new DNA polymerases with better properties useful in these field....
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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t-SNE Highlights Phylogenetic and Temporal Patterns of SARS-CoV-2 Spike and Nucleocapsid Protein Evolution
PublicationWe propose applying t-distributed stochastic neighbor embedding to protein sequences of SARS-CoV-2 to construct, visualize and study the evolutionary space of the coronavirus. The basic idea is to explore the COVID-19 evolution space by using modern manifold learning techniques applied to evolutionary distances between variants. Evolutionary distances have been calculated based on the structures of the nucleocapsid and spike proteins.
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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublicationUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublicationMost protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent...
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FT-Raman Spectroscopy as a Tool to Study the Secondary Structures of Wheat Gliadin Proteins
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Does Nitrogen Fertilization Affect the Secondary Structures of Gliadin Proteins in Hypoallergenic Wheat?
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The Characteristics of New SSB Proteins from Metagenomic Libraries and Their Use in Biotech Applications
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Differentially expressed proteins in the blood serum of piglets in response to a diet supplemented with inulin
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Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS
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Proteins Structure Models in the Evaluation of Novel Variant (C.472_477del) in the MOCS2 Gene
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Why the Solvation Water around Proteins Is More Dense than Bulk Water
PublicationThe main aim of this work is to propose a rational explanation of the commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that the geometry of the water–water hydrogen bond network within solvation layer differs from the one in bulk water, and it is the result of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the...
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Cadmium tri-tert-butoxysilanethiolates. Structural and spectroscopic models of metal sites in proteins.
PublicationW publikacji opisano syntezy i struktury dla dwóch heteroleptycznych kompleksów kadmu z rdzeniem CdS2NO2 i CdS2N2. Bis(tri-tert-butoksysilanotiolato)(1-metyloimidazol)kadmu(II) oraz bis(tri-tert-butoksysilanotiolato)bis(1-metyloimidazol)kadmu(II) współistnieją w roztworze chloroformu przy różnych stężeniach Bis(tri-tert-butoksysilanotiolanu) kadmu(II) i 1 metyloimidazolu. Rotzwór ten został scharakteryzowany za pomocą analizy spektralnej...
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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
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