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Wyniki wyszukiwania dla: CHIMERIC PROTEINS
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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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A cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublikacjaThe 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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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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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
PublikacjaThe 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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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublikacjaDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublikacjaEmrE 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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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublikacjaThe 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 insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublikacjaEmrE 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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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublikacjaMolecular 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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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublikacjaIn 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
PublikacjaA 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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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublikacjaA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
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Human proteinase 3 resistance to inhibition extends to alpha‐2 macroglobulin
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Design of selective substrates of proteinase 3 using combinatorial chemistry methods
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Comparative Proteomic Profiling of Ectosomes Derived from Thyroid Carcinoma and Normal Thyroid Cells Uncovers Multiple Proteins with Functional Implications in Cancer
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The Early Stages of Photosystem II Assembly Monitored by Measurements of Fluorescence Lifetime, Fluorescence Induction and Isoelectric Focusing of Chlorophyll-Proteins in Barley Etiochloroplasts
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Diverse Expression of Selected SMN Complex Proteins in Humans with Sporadic Amyotrophic Lateral Sclerosis and in a Transgenic Rat Model of Familial Form of the Disease
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Meat Proteins as Dipeptidyl Peptidase IV Inhibitors and Glucose Uptake Stimulating Peptides for the Management of a Type 2 Diabetes Mellitus In Silico Study
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Heat shock proteins (HSP 90, 70, 60, and 27) in Galleria mellonella (Lepidoptera) hemolymph are affected by infection with Conidiobolus coronatus (Entomophthorales)
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Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope
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The effect of high pressure at subzero temperature on proteins solubility, drip loss and texture of fish (cod and salmon) and mammal’s (pork and beef) meat
PublikacjaOne of the possibilities of using high pressure technique in inactivation of microorganism is conducting this process at subzero temperature. However, for its practical application in meat preservation the appropriate properties of meat should be kept. Therefore, the aim of this work was to examine the effect of pressure at subzero temperature (without freezing of water) on proteins and texture of mammal’s and cold-adapted fish...
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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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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublikacjaUsing 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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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublikacjaC99 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
PublikacjaWe 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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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublikacjaThe 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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Gene and Protein Accumulation Changes Evoked in Porcine Aorta in Response to Feeding with Two Various Fructan Sources
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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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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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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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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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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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GRA1 protein vaccine confers better immune response compared to codon-optimized GRA1 DNA vaccine
PublikacjaW 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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Electrochemical Synthesis of Polysaccharide-Protein Complexes. Part 1: Preliminary Studies on Apple Pectin-Albumin Complexes
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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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A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.
PublikacjaThe 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...