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Search results for: BINDING ANALYSIS
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Modification of quaternary structure of Candida albicans GlcN-6-P synthase and its desensitization to inhibition by UDP-GlcNAc by site-directed mutagenesis
PublicationSite-directed mutagenesis of the CaGFA1 gene encoding glucosamine-6-phosphate synthase from Candida albicans was performed. Desensitization of the enzyme to inhibition by UDPGlcNAc was achieved upon T487I and H492F substitutions at the UDP-GlcNAc binding site, exchange of D524, S525 and S527 for Ala at the dimer:dimer interface and construction of the tail-lock array (L434R and L460A) at the C-tail region. The first two sets if...
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Bacteriophages as Factories for Eu2O3 Nanoparticle Synthesis
PublicationThe use of phage display to identify peptides with an ability to bind and synthesize Eu2O3 nanoparticles is demonstrated in this report. This is the first report of modified phages specifically binding a lanthanide. The peptides exposed on virions revealed very strong binding to Eu2O3 nanoparticles and the ability to catalyze Eu2O3 nanoparticles’ formation from Eu(OH)3 and Eu(NO3)3 solutions. The luminescence emission spectrum...
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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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Mapping the Transglycosylation Relevant Sites of Cold-Adapted β-D-Galactosidase from Arthrobacter sp. 32cB
PublicationB-Galactosidase from Arthrobacter sp. 32cB (ArthbetaDG) is a cold-adapted enzyme able to catalyze hydrolysis of beta-D-galactosides and transglycosylation reaction, where galactosyl moiety is being transferred onto an acceptor larger than a water molecule. Mutants of ArthbetaDG D207A and E517Q were designed to determine the significance of specific residues and to enable formation of complexes with lactulose and sucrose and to...
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The long-term properties of mineral-cement-emulsion mixtures
PublicationThis publication presents evaluation of long-term behavior of mineral-cement-emulsion (MCE) mixtures. MCE mixtures are among the major products of cold recycling of old asphalt pavements. They are composed by binding of the old materials reclaimed from the pavement and new mineral aggregate using two different binding agents – cement and bituminous emulsion. While bituminous emulsion dissolutes and binds materials quite fast, it...
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Selective detection of F- by chromogenic tetrazole receptor
PublicationA chromogenic anion host 4, containing two amide functionalities linked to azo dye and tetrazole rings was synthesized and its complexes with various anions were investigated. The results show that receptor 4 can recognize selectively biologically important F- ion. The binding affinity for F- was investigated by naked-eye colour change, UV-Vis and 1H NMR spectroscopy. Addition F- ion in CH3CN and DMSO to receptor 4 cause a colour...
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The Ellenbogen's "Matter as Software" Concept for Quantum Computer Implementation: II Bonding Between the C60 and X@C60 Molecules as Available Molecular Building Blocks (MBBs) for Tip-Based Nanofabrication (TBN) of Quantum Computing Devices
PublicationThe binding energy, BE of the X@C60-X@C60 homodimer and the X@C60-Y@C60 heterodimer resulting from the bond formation between the occupied X@C60 MBB and the C60 molecule was studied by means of semiempirical PM7 calculations, where X and Y denote atoms from H to Bi, excluding Tc and lanthanides. All possible combinations of N = 68 guest atoms were considered, which resulted in K = 2346 of different calculated dimers of (X@C60-Y@C60)...
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Influence of different cultivation systems on bioactivity of asparagus
PublicationEvaluation of functional and bioactive compounds of Asparagus officinalis L. growing in conventional and organic greenhouse and conventional open –field farming was the aim of this research. Polyphenols in cladodes grown conventionally were higher than organic. Flavonoids and carotenoids were the highest in cladodes in open field. Organic spears were richer in total phenolics (+6.9% and +19.1%) and flavonoids (+4.7% and 16.8%)...
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Deflection measurement of field section with pavement with base course made of Cement Bitumen Treated Material Mixture C3E4 (28, 180, 270, 365 days after compaction)
Open Research DataDataset presents data of deflections determined for pavement with base course made of cold recycled mixture – cement bitumen treated material mixture with following binding agents: 3% cement, 4% emulsion (C3E4). Mixture was designed according to Polish requirements for the base course of pavement. Mixture was mixed in stationary plant and compacted...
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Fatigue data of Cement Bitumen Treated Material Mixture C3E5.5 (Direct tension, over 28 days of curing at 20C)
Open Research DataFatigue data of Cement Bitumen Treated Material Mixture C3E5.5 (Direct tension, over 28 days of curing at 20C)
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Benzonaza(R): możliwości praktycznych zastosowań.
PublicationBenzonaza znajduje zastosowanie w efektywnym obniżaniu lepkości i usuwaniu kwasów nukleinowych z roztworów białkowych. Zbadano w praktyce jej możliwości aplikacyjne w oczyszczaniu białek rekombinantowych wiążących jednoniciowe DNA (ang. SSB - single stranded DNA binding protein).
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NMR-Based Structural Insight into DNA G-Quadruplex
PublicationEmerging as a promising area in anticancer research, noncanonical DNA structures such as G-quadruplexes are studied using NMR spectroscopy. NOESY spectra reveals crucial interactions between ligands and G-quadruplexes, helping to understand non-covalent binding mechanisms. This knowledge is essential for rational drug design targeting these structures.
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublicationWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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What is important for you makes you think about the pandemic differently: moral foundations, pandemic-related fears and convictions (Lo que cada uno consideramos importante nos hace reflexionar sobre la pandemia de forma distinta: fundamentos morales, temores y convicciones sobre la pandemia)
PublicationBuilding on the Moral Foundations Theory and findings regarding the linkage of values, convictions and beliefs, the aim of the study was to compare people displaying various constellations of moral foundations regarding their tolerance of ambiguity, fear of COVID-19 (FCV), endorsement of COVID-19 conspiracy theories and the extent to which they believed in the effectiveness of five COVID-19 preventive measures. This study was...
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The Usefulness of Cyclic Diamidines with Different Core-substituents as Antitumor Agents
PublicationA series of related polycationic compds. has been screened for potential antitumor activity by the NCI's in vitro testing (one dose primary anticancer assay and the NCI-60 full panel screening). The GI50 values of triazines 3 and 4 are on av. 1.9 μM and 2.4 μM, resp. Furan 8 deserves mention too (1.9 μM). The biol. test results showed that carbazole 10 possessed cytotoxic activity in the nanomolar range, much better than...
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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
PublicationIn 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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Properties of Different Varieties of Durian
PublicationDurian (Durio zibethinus Murr.), like many other exotic, tropical, and conventional fruits, is important in the prevention of different diseases. In this study, the characterization of the main bioactive compounds of the most popular cultivars of durian and their properties are described. The changes in the quality indices of the antioxidant status were determined by CUPRAC, ABTS, FRAP, DPPH, and ORAC assays. The profiling of phytochemicals...
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Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5' diphospho N-acetyl-D-glucosamine (UDPGlcNAc), is an essential substrate for assembly of bacterialand fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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A novel analytical approach in the assessment of unprocessed Kaffir lime peel and pulp as potential raw materials for cosmetic applications
PublicationVolatile fraction of fruits is a rich source of bioactive and aroma compounds, which can be used in the cosmetics industry after meeting relevant criteria. This is particularly evident in citrus fruits, especially in Citrus hystrix, in which the headspace consists mainly of terpenes. Due to the insufficient sensitivity of analytical methods, essential oils are used in investigations in contrast to fresh fruits. Therefore, a novel...
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Investigations of the valence state of Co in a MnCoO ceramics
Open Research DataMcCoO ceramics materials were produced by solid state reaction and sintred in a furnance in air atmosphere for 20h. Annealing temperature was 600 Celsius degree. For investigations a series of samples, with a various composition was chosen: MnCoO, Mn, Co2O and Mn2CoO. Chemical behaviour of the Cobaltium was measured by XPS method. The analyses were...
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublicationSurface 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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Phage-Directed Synthesis of Photoluminescent Zinc Oxide Nanoparticles under Benign Conditions
PublicationBiological systems, especially bacteriophages and peptides, are an attractive green alternative to other known methods of nanoparticle synthesis. In this work, for the first time, bacteriophages were employed to synthesize a specific peptide, capable of producing nanoparticles (NPs). Derivatives of M13 bacteriophage exposing a ZnO-binding peptide (TMGA-LGLKWPV) on either pIII or pVIII phage coat protein were constructed and used...
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In silico assessment and sonochemical synthesis of 2-alkynyl 3-chloropyrazines as prospective ligands for SARS-CoV-2
PublicationThe 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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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Problem of aggregation in dye-DNA interaction, calorimetry studies
PublicationNucleic acids are the biological target for many antimicrobial, antitumor and antiviral drugs. Ligand-DNA interactions can be classified into two major categories: 1. covalent binding, which can provide to intermolecular adducts, 2. physico-chemical interactions, which can be divided into intercalation (e.g. adriamycin) or groove binding (e.g. dystamycin). There are several methods to investigate interactions between drug and DNA....
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A strong preference for the TA/TA dinucleotide step discovered for an acridine-based, potent antitumor dsDNA intercalator, C-1305: NMR-driven structural and sequence-specificity studies
PublicationTriazoloacridinone C-1305, a potent antitumor agent recommended for Phase I clinical trials, exhibits high activity towards a wide range of experimental colon carcinomas, in many cases associated with complete tumor regression. C-1305 is a well-established dsDNA intercalator, yet no information on its mode of binding into DNA is available to date. Herein, we present the NMR-driven and MD-refined reconstruction of the 3D structures...
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Small regulatory bacterial RNAs regulating the envelope stress response
PublicationMost bacteria encode a large repertoire of RNA-based regulatory mechanisms. Recent discoveries have revealed that the expression of many genes is controlled by a plethora of base-pairing noncoding small regulatory RNAs (sRNAs), regulatory RNA-binding proteins and RNA-degrading enzymes. Some of these RNA-based regulated processes respond to stress conditions and are involved in the maintenance of cellular homeostasis. They achieve...
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XPS study of the YST ceramics
Open Research DataYttrium-doped strontium titanate was prepared via conventional solid-state reaction method from Y2O3 (Sigma Aldrich, 99,9%), TiO2 (Sigma Aldrich, 99%) and SrCO3 (Sigma Aldrich,98%). For comparision, two other techniques were used for synthesis: Pechini and wet methods. Both kind of samples were measured, after and before reduction process (in a hydrogen)....
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Modeling of the internal combustion engine cooling system
PublicationThe article concerns computer modelling of processes in cooling systems of internal combustion engines. Modelling objectives and existing commercial programs are presented. It also describes Author’s own method of binding graphs used to describe phenomena in the cooling system of a spark ignition engine. The own model has been verified by tests on the engine dynamometer. An example of using a commercial program for experimental...
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The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein
PublicationThe environment has rapidly looked at proven specialist task forces in the aftermath of the COVID-19 pandemic to build public health policies and measures to mitigate the effects of emerging coronaviruses. According to the researchers, taking 10 μg of 25-hydroxy vitamin D daily is recommended to keep us safe. There have been several studies recently indicating that there is a reduced risk of contracting Coronavirus by 25-hydroxy...
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Anion recognition by n,n'-diarylalkanediamides
PublicationThe preparation of N,N'-diarylalkanediamides from respective aliphatic dicarboxylic acidesand 4-nitroaniline via microwave-promoted reactions is presented. The most positive effect of microwave irradiation was observed for N,N'-bis(4-nitrophenyl)butanediamide. Anion binding studies on the obtained diamides were carried out in DMSO and acetonitrile using UV-vis and 1H NMR spectroscopy. A mechanism for selective fluoride recognition...
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublicationThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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Conservation and diversity of MutS proteins
PublicationThe homologues of MutS, mismatch repair protein, exist in all prokaryotes, with the exception of Actinobacteria, Mollicutes and part of the Archaea. Multiple alignments of 316 MutS amino acid sequences from 169 species revealed conserved residues and sequence motifs distinguishing MutS homologues. All MutS homologues show high conservation within the ATPase domain. MutS1, the homologue responsible for DNA mismatch recognition,...
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Comparative assessment of two extraction procedures for determination of bioactive compounds in some berries used for daily food consumption
PublicationTwo extractions with methanol and water were used to determine the antioxidant and binding properties of some berries as a supplement to food. Fluorometry, FTIR spectra and radical scavenging assays were used for characterisation of bioactive compounds (polyphenols, flavonoids, flavanols and tannins) and the levels of their antioxidant activities (AAs). The contents of bioactive compounds and AAs in water and methanol polyphenol...
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Toward Mechanosynthesis of Diamondoid Structures: IX Commercial Capped CNT Scanning Probe Microscopy Tip as Nowadays Available Tool for Silylene Molecule and Silicon Atom Transfer
PublicationAccording to K. E. Drexler, advanced mechanosynthesis will employ advanced nanomachines, but advanced nanomachines will themselves be product of advanced mechanosynthesis. This circular relationship must be broken in SPM technology development. In the article, the possibility of use easy available commercial CNT tips to assembly silicon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target class...
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Fluoroaromatic substituents attached to carbon nanotubes help to increase oxygen concentration on biocathode in biosensors and biofuel cells
PublicationBased on the known ability of perfluorodecalin/perfluorohydrocarbons to enhance oxygen solubility we modified oxygen sensitive biocathode by adding perfluorinated components to the catholite. This procedure improved the efficiency of the oxygen sensitive cathodes. Glassy carbon electrodes covered with single-wall carbon nanotubes (SWCNTs) with covalently bonded perfluoroaromatic groups were shown to be more sensitive to oxygen,...
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Crystal structures of aminotransferases Aro8 and Aro9 from Candida albicans and structural insights into their properties
PublicationAminotransferases catalyze reversibly the transamination reaction by a ping-pong bi-bi mechanism with pyridoxal 5′-phosphate (PLP) as a cofactor. Various aminotransferases acting on a range of substrates have been reported. Aromatic transaminases are able to catalyze the transamination reaction with both aromatic and acidic substrates. Two aminotransferases from C. albicans, Aro8p and Aro9p, have been identified recently, exhibiting...
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Reduction of the strontium titanate doped by Ytrium ceramics observed by X-ray photoemission spectroscopy method
Open Research DataYtrium-doped strontium titanate (YSTF) ceramics materials were manufactured by three various methods: 1) standard solid-state reaction method from Y2O3 (Sigma Aldrich, 99,9%), TiO2 (Sigma Aldrich, 99%) and SrCO3 (Sigma Aldrich,98%), 2) Pechini method, 3) wet method.
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow 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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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublicationMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Thermodynamics aspects of interactions between acridine derivatives and DNA
PublicationDNA is a molecular target for many anticancer and antiviral drugs. Therefore, a clear understanding of the interaction of small molecules with DNA is important in the rational design of ligands that can bind to DNA with high affinity and selectivity. There are several methods to investigate interactions between drug and DNA. Some of them measure changing into DNA structures, such as lengthening and untwisting of helix of DNA. Other...
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Novel primosomal protein B from Clostridium pastuerianum
PublicationPriB 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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Antioxidant activities and bioactive components in some berries
PublicationThe objective of this study was to evaluate the antioxidant and binding effects of gooseberry, a less-stud-ied berry, and to compare with blueberry and cranberry in the model of interaction with human serum albumin (HSA). The relationship between the scavenging properties of dietary polyphenols of the selected berries and their affinities for HSA were investigated by fluorescence anal- ysis. In order to perform the extraction and...
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Toward Mechanosynthesis of Diamondoid Structures: X. Commercial Capped CNT SPM Tip as Nowadays Available C2 Dimer Placement Tool for Tip-Based Nanofabrication
PublicationAccording to Drexler, advanced mechanosynthesis will employ advanced nano-machines, but advanced nano-machines will themselves be products of advanced mechanosynthesis. This circular relationship must be broken via TBN technology development. In this article, the possibility of using easily available commercial CNT tips to assemble carbon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target...
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Novel primosomal protein B from Clostridium pasteurianum
PublicationPriB 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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Immunization with an anti-idiotypic antibody against the broadly lipopolysaccharide-reactive antibody WN1 222-5 induces Escherichia coli R3-core-type specific antibodies in rabbits
PublicationThe mouse monoclonal antibody (mAb) WN1 222-5 recognizes a carbohydrate epitope in the inner core region of LPS that is shared by all strains of Escherichia coli and Salmonella enterica and is able to neutralize their endotoxic activity in vitro and in vivo. Immunization of mice with mAb WN1 222-5 yielded several anti-idiotypic mAbs one of which (mAb S81-19) competitively inhibited binding of mAb WN1 222-5 to E. coli and Salmonella...
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Comparative Study of the Mechanical Behaviour of Bitumen- and Cement-Dominated Mixtures with Reclaimed Asphalt
PublicationThe bitumen emulsion-based recycling is a commonly used maintenance treatment in the rehabilitation of low-and medium-volume roads in Europe. Nevertheless, the wide range of climatic conditions across the continent resulted in the variety of mixture concepts and the requirements being adopted for various local conditions. In this regard, the most commonly used parameter to distinguish between the main mixture concepts is bitumen...