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Wyniki wyszukiwania dla: RNA-PROTEIN INTERACTIONS
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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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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
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Lipid-protein interactions in membranes: a molecular modelling study
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Role of Oligosaccharide Chain Polarity in Protein–Glycosaminoglycan Interactions
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The Escherichia coli RNA polymerase alpha subunit and transcriptional activation by bacteriophage lambda CII protein.
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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...
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Hot spot identification by ligand-protein surface interactions mapping – in silico study
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublikacjaShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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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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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublikacjaRadiotherapy, 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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Understanding the interactions between protein stabilizers and the peptide bond through the analysis of the volumetric and compressibility properties for the model systems
PublikacjaThis work confirms our earlier supposition, that volumetric and acoustic parameters for simple model proposed by us are directly related to stabilizing/destabilizing effect of osmolytes on proteins structure. The apparent molar volumes, V and the apparent molar isentropic compressions, KS,, of glycine and N,N,N –trimethylglycine (betaine) were determined from densities and speed of sound measurements in aqueous solution of N-methylacetamide...
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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Early Stages of RNA-Mediated Conversion of Human Prions
PublikacjaPrion diseases are characterized by the conversion of prion proteins from a PrPC fold into a disease-causing PrPSC form that is self-replicating. A possible agent to trigger this conversion is polyadenosine RNA, but both mechanism and pathways of the conversion are poorly understood. Using coarse-grained molecular dynamic simulations we study the time evolution of PrPC over 600 μs. We find that both the D178N mutation and interacting...
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Adolfo Poma
OsobyDr. Adolfo Poma (see my biosketch) is the group leader of the Multiscale Modelling of Complex Systems divison. In 2008, he got a MSc. degree in computational physics from the State University of Campinas (Brazil). Then he moved to Germany and under the supervision of Prof. Kurt Kremer (head of the polymer theory group, Max Planck Institute for Polymer Research) and Prof. Luigi Delle Site (Frei University of Berlin) got a PhD degree...
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Gracjana Klein-Raina dr hab.
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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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Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours
Dane BadawczeThe aim of this study was to determine molecular defects in mitochondrial DNA with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained...
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Ultrasound assisted synthesis of 3-alkynyl substituted 2-chloroquinoxaline derivatives: Their in silico assessment as potential ligands for N-protein of SARS-CoV-2
PublikacjaIn view of recent global pandemic the 3-alkynyl substituted 2-chloroquinoxaline framework has been explored as a potential template for the design of molecules targeting COVID-19. Initial in silico studies of representative compounds to assess their binding affinities via docking into the N-terminal RNA-binding domain (NTD) of N-protein of SARS-CoV-2 prompted further study of these molecules. Thus building of a small library of...
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Paweł Możejko dr hab.
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In silico assessment and sonochemical synthesis of 2-alkynyl 3-chloropyrazines as prospective ligands for SARS-CoV-2
PublikacjaThe recent global pandemic caused by COVID-19 has triggered an intense effort worldwide towards the development of an effective cure for this disease. In our effort we have explored the 2-alkynyl substituted 3-chloropyrazine framework as a potential template for the design of molecules for this purpose. Our strategy was supported by the in silico studies of representative compounds to assess their binding affinities via docking...
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Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges
PublikacjaStaphylococci are increasingly recognized as etiological agents of many opportunistic human and animal infections, emphasizing the need for a rapid and accurate identification, even to a genotypical level of these bacteria. In the recent years, there has been a significant progress in typing and phylogenetic study of Staphylococcus species. Here, we describe molecular methods used in taxonomy as well as staphylococci characterization....
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-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
PublikacjaSingle-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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Anticancer Imidazoacridinone C-1311 is Effective in Androgen-Dependent and Androgen-Independent Prostate Cancer Cells
PublikacjaAndrogen receptor (AR) plays a crutial role in prostate cancer (PCa) development and metastasis. Here, we reported potent anti-PCa activity of a small molecule imidazoacridinone C-1311. In AR-positive PCa cells, C-1311 was found to inhibit the transcriptional activity of AR uncovering a novel mechanism that may be relevant for its anticancer effect. Mechanistically, C-1311 decreased AR binding to prostate-specific antigen (PSA)...
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Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2
PublikacjaWe combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while...
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Regulated assembly of lipopolysaccharide and sensing of its alterations in Escherichia coli
PublikacjaThis thesis describes mechanism of the regulation of the transcription of the rpoE gene encoding an essential RNA polymerase subunit in Escherichia coli. The RpoE regulates extracytoplasmic stress response regulon and is required to initiate transcription of genes, whose products are involvedin the folding of periplasmic proteins and synthesis and transport of outer membrane components. The transcriptional regulation of the rpoE...
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NASBA – IZOTERMICZNA AMPLIFIKACJA RNA
PublikacjaNASBA (ang. Nucleic Acid Sequence-Based Amplification) jest skuteczną i czułą techniką izotermicznej amplifikacji opartej na transkrypcji, służąca głównie do detekcji cząsteczek RNA. Znalazła ona zastosowanie do wykrywania RNA wirusowego, bakteryjnego i grzybiczego w próbkach klinicznych oraz żywości.
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Two small RNAs conserved in Enterobacteriaceae provide intrinsic resistance to antibiotics targeting the cell wall biosynthesis enzyme glucosamine-6-phosphate synthase
PublikacjaFormation of glucosamine-6-phosphate GlcN6P) by enzyme GlcN6P synthase (GlmS) represents the first step in bacterial cell envelope synthesis. In Escherichia coli, expression of glmS is controlled by small RNAs (sRNAs) GlmY and GlmZ. GlmZ activates the glmS mRNA by base-pairing. When not required, GlmZ is bound by adapter protein RapZ and recruited to cleavage by RNase E inactivating the sRNA. The homologous sRNA GlmY activates...
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SiMiSnoRNA: Collection of siRNA, miRNA, and snoRNA database for RNA Interference
PublikacjaObjective:The discovery of sequence specific gene silencing which occurs due to the presence of double-stranded RNAs has considerable impact on biology, revealing an unknown level of regulation of gene expression. This process is known as RNA interference (RNAi) or RNA silencing in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecule. Two types of small RNA molecules - small...
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EASY ACCESS TOOL FOR SMALL INTERFERING RNA (siRNA) DATA
PublikacjaFor many decades it was an accepted dogma of molecular genetics that the expression of genes is a “one-way-road” leading only in one direction from DNA to RNA to proteins. Recent discoveries in modern molecular genetics have challenged this dogma showing that specific RNA molecules play a central role in controlling the activity of genes by changing the structure of DNA sequences, targeting other RNAs for degradation or blocking...
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Targeting of FLT3-ITD kinase contributes to high selectivity of imidazoacridinone C-1311 against FLT3-activated leukemia cells
PublikacjaDrugs targeting receptor tyrosine kinase FLT3 are of particular interest since activating FLT3-internal tandem duplication (ITD) mutations abundantly occur in fatal acute myeloid leukemias (AMLs). Imidazoacridinone C-1311, a DNA-reactive inhibitor of topoisomerase II, has been previously shown to be a potent and selective inhibitor of recombinant FLT3. Here, we expand those findings by studying its effect on leukemia cells with...
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PROTEIN EXPRESSION AND PURIFICATION
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The effects of RNA editing in cancer tissue at different stages in carcinogenesis
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RNA-A PUBLICATION OF THE RNA SOCIETY
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On the Origin of Protein Superfamilies and Superfolds
PublikacjaDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Cross sections for electron scattering from selected components of DNA and RNA
PublikacjaWykorzystując metodę atomów niezależnych obliczono różniczkowe i całkowite przekroje czynne na sprężyste rozproszenie elektronów na wybranych drobinach, będących analogami składników DNA i RNA. Przekroje te obliczono w zakresie energii zderzenia od 50eV do 200 eV dla następujących drobin: C4H8O, C4H8O2, C5H10O2 oraz H3PO4. Przy użyciu metody BEB (binary-ecounter Bethe method) dla powyższych związków obliczono również przekroje...
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Taurine as a water structure breaker and protein stabilizer
PublikacjaThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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An integrated DNA and RNA variant detector identifies a highly conserved three base exon in the MAP4K5 kinase locus
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Interactions with recognized objects
PublikacjaImplicit interaction combined with object recognition techniques opens a new possibility for gathering data and analyzing user behavior for activity and context recognition. The electronic eyewear platform, eGlasses, is being developed, as an integrated and autonomous system to provide interactions with smart environment. In this paper we present a method for the interactions with the recognized objects that can be used for electronic...
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Hydration of molecules and intermolecular interactions 2023
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Platelet RNA Sequencing Data Through the Lens of Machine Learning
PublikacjaLiquid biopsies offer minimally invasive diagnosis and monitoring of cancer disease. This biosource is often analyzed using sequencing, which generates highly complex data that can be used using machine learning tools. Nevertheless, validating the clinical applications of such methods is challenging. It requires: (a) using data from many patients; (b) verifying potential bias concerning sample collection; and (c) adding interpretability...
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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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Intercultural interactions in multinational subsidiaries
PublikacjaPurpose - Our aim is to show how individuals perceive the quality of intercultural interactions at work in multinational subsidiaries, and to address the question of what actually prevails in their accounts, i.e. ‘the dark side’ or ‘the bright side’. Design/methodology/approach - We report the findings from five subsidiaries located in Poland and interviews with 68 employees of these companies. Findings - The ‘bright side’ dominated...
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Influence of Osmolytes on Protein and Water Structure: A Step To Understanding the Mechanism of Protein Stabilization
PublikacjaResults concerning the thermostability of hen egg white lysozyme in aqueous solutions with stabilizing osmolytes, trimethylamine-N-oxide (TMAO), glycine (Gly), and its N-methyl derivatives, N-methylglycine (NMG), N,N-dimethylglycine (DMG), and N,N,N-trimethylglycine (betaine, TMG), have been presented. The combination of spectroscopic (IR) and calorimetric (DSC) data allowed us to establish a link between osmolytes’ influence on...
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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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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublikacjaIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Interactions of positrons with atoms and molecules
PublikacjaThe positron is the antiparticle of the electron. It has the same mass as the electron, but opposite charge. The understanding of the interactions of positrons with normal matter, like atoms and molecules, is of interest in various scientific fields, like nuclear medicine, plasma physics and astronomy. In this talk we will give a short introduction to some theoretical methods to describe the interactions of positrons with atoms...
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Determination of viscosity changes of protein hydrolyzate solutions depending on shear rate
Dane BadawczeRheological characteristics of connective tissue protein solutions were made on the basis of viscosity measurement using a Brookfield viscometer using LV SC4 - 27 spindles and shear rate of 85 s-1 (Fig. 1). Solutions of protein hydrolysates with a concentration of 2% in 0.5M acetic acid were prepared.
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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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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Protein & Cell
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Earth Interactions
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HYPERFINE INTERACTIONS
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INTERNATIONAL INTERACTIONS
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PROTEIN JOURNAL
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DMSO and TMAO—Differences in Interactions in Aqueous Solutions of the K-Peptide
PublikacjaInteractions between a solvent and their co-solute molecules in solutions of peptides are crucial for their stability and structure. The K-peptide is a synthetic fragment of a larger hen egg white lysozyme protein that is believed to be able to aggregate into amyloid structures. In this study, a complex experimental and theoretical approach is applied to study systems comprising the peptide, water, and two co-solutes: trimethylamide...
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Modelling gene expression of a self-regulating protein
PublikacjaWe analyze a model of gene transcription and protein synthesis. We take into account the number of sites on the protein’s promoter at which the protein’s dimers can bind blocking transcription of protein mRNA.
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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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Non-coding RNA
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Journal of RNA and Genomics
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublikacjaInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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Novel primosomal protein B from Clostridium pastuerianum
PublikacjaPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Novel primosomal protein B from Clostridium pasteurianum
PublikacjaPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublikacjaBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublikacjaBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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Agencja Badań Medycznych – konkurs RNA
WydarzeniaSzkolenie online podzielone na 3 moduły, uwzględniające zasady udziału w konkursie, istotne aspekty pomocy publicznej oraz kwestie związane z kształtem budżetu.
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Individual Resources and Intercultural Interactions
PublikacjaThe work environment in multinational corporations (MNCs) is specific and demanding including intercultural interactions with co-workers and clients and using a foreign language. Some individual resources can help in dealing with these circumstances. Individual resources refer to personal dispositions, competencies and prior experiences. With regard to previous studies, a caravan of personal resources, namely Psychological Capital...
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Intercultural interactions at multinational corporations' workplace: Grounded theory.
Publikacjaenvironments is a new challenge for employees and managers. The aim of the paper is to analyze the social interactions in multicultural environments of multinational corporations (MNCs) as well as to propose a model of intercultural social interactions in MNCs’ specifi c context. Design/methodology/approach: The grounded theory approach was applied to create a model of intercultural interactions in MNCs. The data was obtained during...
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[NCh-bio] Advances in Biotechnology: Protein Folding and Assembly
Kursy Online{mlang pl} Dyscyplina: nauki chemiczne Zajęcia obowiązkowe dla doktorantów I i II roku z obszaru biotechnologii Prowadzący: dr hab. Gracjana Klein-Raina, prof. PG Liczba godzin: 15 Forma zajęć: wykład {mlang} {mlang en} Discipline: chemical sciences Obligatory course for 1st and 2nd-year PhD students from biotechnology area Academic teachers: dr hab. Gracjana Klein-Raina, prof. PG Total hours of training: 15 teaching...
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imPlatelet classifier: image‐converted RNA biomarker profiles enable blood‐based cancer diagnostics
PublikacjaLiquid biopsies offer a minimally invasive sample collection, outperforming traditional biopsies employed for cancer evaluation. The widely used material is blood, which is the source of tumor-educated platelets. Here, we developed the imPlatelet classifier, which converts RNA-sequenced platelet data into images in which each pixel corresponds to the expression level of a certain gene. Biological knowledge from the Kyoto Encyclopedia...
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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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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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The structure and role of mammalian sperm RNA: a review
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SERRATE: a key factor in coordinated RNA processing in plants
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublikacjaThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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Protein thermal stabilization in aqueous solutions of osmolytes
PublikacjaProteins’ thermal stabilization is a significant problem in various biomedical, biotechnological, and technological applications. We investigated thermal stability of hen egg white lysozyme in aqueous solutions of the following stabilizing osmolytes: Glycine (GLY), N-methylglycine (NMG), N,N-dimethylglycine (DMG), N,N,N-trimethylglycine (TMG), and trimethyl-N-oxide (TMAO). Results of CD-UV spectroscopic investigation were compared...
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Discovering interactions between applications with log analysis
PublikacjaApplication logs record the behavior of a system during its runtime and their analysis can provide useful information. In this article, we propose a method of automated log analysis to discover interactions taking place between applications in an enterprise. We believe that such an automated approach can greatly support enterprise architects in building an up-to-date view of a governed system in a modern, fast-paced development...
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The investigation of the effects of counterions in protein dynamics simulations
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Role of the Synergistic Interactions of Environmental Pollutants in the Development of Cancer
PublikacjaThere is a growing awareness that the large number of environmental pollutants we are exposed to on a daily basis are causing major health problems. Compared to traditional studies that focus on individual pollutants, there are relatively few studies on how pollutants mixtures interact. Several studies have reported a relationship between environmental pollutants and the development of cancer, even when pollutant levels are below...
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Construction and purification of his6-Thermus thermophilus MutS protein
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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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PROTEIN SCIENCE
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Interactions in aqueous solutions of K-peptide and DMSO – spectroscopic and calorimetric studies
PublikacjaIntroduction K-peptide (GILQINSRW) – short 9 amino acid fragment of the hen egg white lysozyme has the ability to form amyloid structures. Dimethyl sulfoxide (DMSO) is an osmolyte which can alter this ability. Our goal was to get an insight into the mechanism of Kpeptide-DMSO interactions in aqueous solutions. Such a knowledge can be helpful to understand processes leading to various neurodegenerative diseases. Methods ATR-FTIR...
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Low-energy interactions related to atmospheric and extreme conditions
PublikacjaThis Topical Issue, entitled “Low-Energy Interactions Related to Atmospheric and Extreme Conditions”, showcases a collection of eighteen articles that reported recent theoretical and experimental findings pertaining to the following topics: – low-energy interactions of charged particles (electrons [1–7], protons [8], positrons [9]), and photons [10] with atoms and molecules of biological [1–4,7,8], astrochemical [10], industrial,...
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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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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublikacjaMost 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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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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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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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublikacjaThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
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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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Novel Nuclear Functions of Arabidopsis ARGONAUTE1: Beyond RNA Interference
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Aquaculture Environment Interactions
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ADVANCES IN PROTEIN CHEMISTRY
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Human-Wildlife Interactions
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JOURNAL OF PROTEIN CHEMISTRY
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City and Environment Interactions
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Journal of Plant Interactions
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Arthropod-Plant Interactions
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