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Wyniki wyszukiwania dla: DSB PROTEINS
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Excess production of phage λ delayed early proteins under conditions supporting high Escherichia coli growth rates
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Characterization of the interactions between human high-molecular-mass kininogen and cell wall proteins of pathogenic yeasts, Candida tropicalis
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Prenatal stress leads to changes in IGF-1 binding proteins network in the hippocampus and frontal cortex of adult male rat
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Epitope Mapping of BmpA and BBK32 Borrelia burgdorferi Sensu Stricto Antigens for the Design of Chimeric Proteins with Potential Diagnostic Value
PublikacjaLyme disease is a tick-borne zoonosis caused by Gramnegative bacteria belonging to the Borrelia burgdorferi sensu lato (s.l.) group. In this study, IgM- and IgG-specific linear epitopes of two B. burgdorferi sensu stricto (s.s.) antigens BmpA and BBK32 were mapped using a polypeptide array. Subsequently, two chimeric proteins BmpABBK32-M and BmpA-BBK32-G were designed to validate the construction of chimeras using the identified...
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Novel monovalent and multivalent recombinant proteins of Borrelia burgdorferi sensu lato with potential diagnostic value – construction and biotechnological production
PublikacjaThe diverse antigenic structure of Borrelia burgdorferi sensu lato (s.l.) and the low degree of protein sequence conservation between genospecies causes many limitations in serodiagnosis of Lyme disease (LD). Using expression systems based on Escherichia coli, five monovalent B. burgdorferi s.l. recombinant proteins were produced. i.e., BB0108, BB0126, BB0298, BB0323, BB0689 (each in three variants derived from Borrelia afzelii,...
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DSC measurments of ammonium vanadate nanocrystals
Dane BadawczeThe DataSet contains the thermal behavior of the ammonium vanadate nanostructures obtained by the hydrothermal method with different conditions. Differential scanning calorimetry (DSC) measurement was carried out under an argon atmosphere from 40C to 560C (with a heating rate of 10 C/min) using Netzsch STA 449 F1. The results reveal the differences...
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Stability of oil‐in‐water emulsions as influenced by thermal treatment of whey protein dispersions or emulsions
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Genetic and structural characterization of the growth hormone gene and protein from tench, Tinca tinca
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Adipocyte Fatty Acid‐Binding Protein as a Novel Marker of Psoriasis and Clinical Response to Acitretin
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Novel Drying Methods for Sustainable Upcycling of Brewers’ Spent Grains as a Plant Protein Source
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The effect of topical treatment and psoriasis severity on serum retinol-binding protein-4 levels
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Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein
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Comparison of protein precipitation methods for various rat brain structures prior to proteomic analysis
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Similarities and Differences in the Protein Composition of Cutaneous Melanoma Cells and Their Exosomes Identified by Mass Spectrometry
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
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Patients with obstructive sleep apnea present with chronic upregulation of serum HIF-1α protein
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Expression profiles and genomic organisation of group A protein phosphatase 2C genes inBrassica oleracea
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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
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A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublikacjaWe report the identification and characterization of the single-stranded DNA-binding protein (SSB) from the mesophile and highly radiation-resistant Deinococcus radiopugnans (DrpSSB). PCR-derived DNA fragment containing the complete structural gene for DrpSSB protein was cloned and expressed in Escherichia coli. The gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublikacjaPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublikacjaOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublikacjaThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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The plasma concentration of advanced oxidation protein products and arterial stiffness in apparently healthy adults
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Blood plasma protein and lipid profile changes in calves during the first week of life
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MIC1-MAG1-SAG1 chimeric protein, a most effective antigen for detection of human toxoplasmosis
PublikacjaThis study describes a Toxoplasma gondii IgG ELISA test based on a new chimeric antigen containing three immunodominant regions from MIC1, MAG1 and SAG1 proteins of a parasite and shows that this test is useful for diagnostic purposes and may replace the lysed and whole-cell antigens.
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Expression of goose parvovirus whole VP3 protein and its epitopes in Escherichia coli cells
PublikacjaThe aim of this study was the expression of goose parvovirus capsid protein (VP3) and its epitopes in Escherichia coli cells. Expression of the whole VP3 protein provided an insufficient amount of protein. In contrast, the expression of two VP3 epitopes (VP3ep4, VP3ep6) in E. coli, resulted in very high expression levels. This may suggest that smaller parts of the GPV antigenic determinants are more efficiently expressed than the...
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublikacjaSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublikacjaLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublikacjaPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Statistical Method for Analysis of Interactions Between Chosen Protein and Chondroitin Sulfate in an Aqueous Environment
PublikacjaWe present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of univariate time series of chosen features of the dynamics of mucin, which interact with chondroitin sulfate (4 and 6) in four different saline solutions. Our statistical approach is based on recurrence...
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
PublikacjaRNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA....
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Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems
PublikacjaGraphical Processor Units (GPUs) are nowadays widely used in all-atom molecular simulations because of the advantage of efficient partitioning of atom pairs between the kernels to compute the contributions to energy and forces, thus enabling the treatment of very large systems. Extension of time- and size-scale of computations is also sought through the development of coarse-grained (CG) models, in which atoms are merged into extended...
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A 3-dB coupler with UC-PBG structure
PublikacjaPrzedstawiono nową konstrukcję sprzęgacza z liniami paskowymi sprzężonymi szerokim bokiem oraz zmodyfikowaną warstwą metalizacji masy. Modyfikacja metalizacji polega na periodycznym wytrawieniu dwuwymiarowej struktury szczelin, nazywanej strukturą uniplanarnej zwartej przerwy fotonicznej (UC-PBG: Uniplanar Compact Photonic BandGap). Potwierdzono przewidywane wcześniej zjawisko spowolnienia fali oraz powiększenia wielkości sprzężenia...
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DSC Melting Profile of Cold-Pressed Hemp Seed Oil as an Authenticity Fingerprint Influenced by Scanning Rate
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DSC and thermal stability investigation of novel poly(ester-ether) glycolsand poly(ester-ether)urethanes.
PublikacjaOtrzymano serie nowych poli(estro-etero)dioli z kwasu adypinowgo.........
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Western blot analysis of DDR- and apoptosis-related proteins of A549 and H460 cells after exposure to TXT2 and TXT4
Dane BadawczeThe data set contains full-length blot images of DDR- and apoptosis-related proteins of A549 and H460 cells after exposure to TXT2 and TXT4.
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Satish Raina prof. dr
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Comparison of mass spectrometry data and bioinformatics predictions to assess the bona fide localization of proteins identified in cell wall proteomics studies
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins
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Evaluation of long‑term immunity and protection against T. gondii after immunization with multivalent recombinant chimeric T. gondii proteins
PublikacjaToxoplasmosis caused by the opportunistic, cosmopolitan protozoan Toxoplasma gondii is one of the most common parasitoses in the world. Although it may prove dangerous or even fatal for immunocompromised individuals, immunoprophylaxis for humans is still nonexistent. Thus, the aim of the current work was to assess the ability of two immunogenic recombinant chimeric T. gondii proteins, SAG2-GRA1-ROP1 (SGR) and SAG1-MIC1-MAG1-GRA2...
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Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains
PublikacjaOkreślono molekularne właściwości białek SSB-podobnych z Thermus thermophi-lus i T. aquaticus. Zbadano aktywność białek oraz termostabilność. Ponadto, dowiedziono homodimeryczność obu białek i ustalono minimalną sekwencję wiążącą ssDNA.
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Investigation of interaction between xanthene dye rhodamine B and metagenomic-derivated methylthioadenosine phosphorylase RSFP
PublikacjaIn the previous study we found that the expression of the metagenomic - derived methylthioadenosine phosphorylase gene (rsfp) in E. coli cells and the presence of rhodamine B in the growth medium were crucial for the pink fluorescence of one E. coli colony from Antarctic soil metagenomic library (Cieśliński et al., 2009). In this study, rsfp gene expression was induced by an arabinose promoter in an LMG194 E. coli strain and the...
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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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Sulforaphane, a cruciferous vegetable-derived isothiocyanate, inhibits protein synthesis in human prostate cancer cells
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