Search
Filters
total: 3294
filtered: 1972
displaying 1000 best results Help
Search results for: FREE ENERGIES OF BINDING
-
Independence in uniform linear triangle-free hypergraphs
PublicationThe independence number a(H) of a hypergraph H is the maximum cardinality of a set of vertices of H that does not contain an edge of H. Generalizing Shearer’s classical lower bound on the independence number of triangle-free graphs Shearer (1991), and considerably improving recent results of Li and Zang (2006) and Chishti et al. (2014), we show a new lower bound for a(H) for an r-uniform linear triangle-free hypergraph H with r>=2.
-
DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublicationWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
-
A Highly Selective Biosensor Based on Peptide Directly Derived from the HarmOBP7 Aldehyde Binding Site
PublicationThis paper presents the results of research on determining the optimal length of a peptide chain to eectively bind octanal molecules. Peptides that map the aldehyde binding site in HarmOBP7 were immobilized on piezoelectric transducers. Based on computational studies, four Odorant Binding Protein-derived Peptides (OBPPs) with dierent sequences were selected. Molecular modelling results of ligand docking with selected peptides were...
-
Efficient three-dimensional fluorescence measurements for characterization of binding properties in some plants
PublicationThe main aim of this research was to characterize some plants and to determine their similarities and differences, using spectroscopic methods. The interactions of soluble polyphenols of different plants with human serum albumin (HSA) were investigated by 3D-fluorescence. The obtained fluorescence results allow to classify the investigated plants according to their binding properties. The HSA-binding capacities of these plants...
-
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...
-
Functionalized azobenzocrown ethers as sensor materials—The synthesis and ion binding properties
PublicationNew 13- and 16-membered azobenzocrown ethers with aromatic amino, amide, ether–ester or ether–amide residue in para position to an azo moiety were obtained. Acid–base properties and ion binding ability of the colored compounds were studied by spectroscopic methods: UV–vis, fluorimetry and 1H NMR spectroscopy. Selected azobenzocrowns were tested as ionophores in ion-selective membrane electrodes (ISEs) – classic and miniature all...
-
Decoherence-free communication over multiaccess quantum channels
PublicationIn this paper we consider decoherence-free communication over multiple access and k-user quantum channels. First, we concentrate on a hermitian unitary noise model U for a two-access bi-unitary channel and show that in this case a decoherence-free code exists if the space of Schmidt matrices of an eigensubspace of U exhibits certain properties of decomposability. Then, we show that our technique is also applicable for generic random unitary...
-
Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
-
Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis
PublicationSingle-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNAreplication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-likegene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoal-teromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism.PhaSSB possesses...
-
On the size of identifying codes in triangle-free graphs
PublicationIn an undirected graph G, a subset C⊆V(G) such that C is a dominating set of G, and each vertex in V(G) is dominated by a distinct subset of vertices from C, is called an identifying code of G. The concept of identifying codes was introduced by Karpovsky, Chakrabarty and Levitin in 1998. For a given identifiable graph G, let gammaID(G) be the minimum cardinality of an identifying code in G. In this paper, we show that for any connected...
-
Lefschetz periodic point free self-maps of compact manifolds
PublicationLet f be a self-map of a compact connected manifold M. We characterize Lefschetz periodic point free continuous self-maps of M for several classes of manifolds and generalize the results of Guirao and Llibre [J.L.G. Guirao, J. Llibre, On the Lefschetz periodic point free continuous self-maps on connected compact manifolds,
-
K X-ray line energies as diagnostics of warm dense plasma
Publication -
Continuum models for pantographic blocks with second gradient energies which are incomplete
PublicationWe postulate a deformation energy for describing the mechanical behavior of so called pantographic blocks, that is bodies constituted by stacking of layers of pantographic sheets. We remark that the pantographic effect is limited in the plane of pantographic sheets and therefore only the second derivatives of transverse displacements along the pantographic fibers appear in the chosen deformation energy. We use this novel energy...
-
Surface and Trapping Energies as Predictors for the Photocatalytic Degradation of Aromatic Organic Pollutants
PublicationIn this study, anatase samples enclosed by the majority of three different crystal facets {0 0 1}, {1 0 0}, and {1 0 1} were successfully synthesized. These materials were further studied toward photocatalytic degradation of phenol and toluene as model organic pollutants in water and gas phases. The obtained results were analyzed concerning their surface structure, reaction type, and surface development. Moreover, the regression...
-
Novel single-stranded DNA-binding proteins from extreme psychrophilic bacterium Psychromonas ingrahamii 37
PublicationWe report the identification and characterization of the single-stranded DNA binding protein (SSB) from extreme psychrophilic bacterium Psychromonas ingrahamii 37 (PinSSB) that grows expotentially at -12°C and may well grow at even lower temperatures. PinSSB is one of the largest known bacterial SSB protein consisting 222 amino acid residues with a calculated molecular mass of 25.1 kDa. The analysis by gel filtration chromatography...
-
Structure of liquid gold from tight-binding driven molecular-dynamics
PublicationPraca przedstawia wyniki symulacji ciekłego złota w nadkomórce periodycznej przy użyciu stworzonego przez autorów programu komputerowego, za pomocą połączonych metod dynamiki molekularnej (MD) i ciasnego wiązania (TB). Omówiono strukturę tak symulowanej cieczy, porównując ją z dostępnymi danymi doświadczalnymi oraz wynikami innych symulacji, pod kątem radialnej i kątowej funkcji rozkładu i elektronowej gęstości stanów.A tight-binding...
-
Lefschetz periodic point free self-maps of compact manifolds
PublicationLet f be a self-map of a compact connected manifold M. We characterize Lefschetz periodic point free continuous self-maps of M for several classes of manifolds and generalize the results of Guirao and Llibre [J.L.G. Guirao, J. Llibre, On the Lefschetz periodic point free continuous self-maps on connected compact manifolds, Topology Appl. 158 (16) (2011) 2165-2169].
-
A cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublicationThe 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...
-
Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis
PublicationThe thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular...
-
Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor
PublicationGranulocyte macrophage colony stimulating factor (GMCSF) is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with biologically active compounds is critical...
-
Influence of temperature and interactions with ligands on dissociation of dsDNA and ligand-dsDNA complexes of various types of binding : an electrochemical study.
PublicationSeveral medicinally important compounds that bind to dsDNA strands via intercalation (C-1311, C-1305, EtBr), major groove binding (Hoechst 33258) and covalent binding (cis-Pt) were examined. The obtained results suggest that both the transfer of conformation B to C and the denaturation process, for the ligand-dsDNA complexes, except for covalently bound cis-Pt, took place at higher temperatures compared to the unbound helix. Furthermore,...
-
Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublicationTo study the biochemical properties of SSB from Desulfolatea psychrophila (DpsSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 426 nucleotides encoding SSB protein of 142 amino acids with a calculated molecular mass of 15.6 kDa and it is the smallest known bacterial SSB protein indentified to date. The amino-acid sequence...
-
Correction: Nazir et al. An Inclination in Thermal Energy Using Nanoparticles with Casson Liquid Past an Expanding Porous Surface. Energies 2021, 14, 7328
Publication -
Thermodynamic, Anticoagulant, and Antiproliferative Properties of Thrombin Binding Aptamer Containing Novel UNA Derivative
PublicationThrombin is a serine protease that plays a crucial role in hemostasis, fibrinolysis, cell proliferation, and migration. Thrombin binding aptamer (TBA) is able to inhibit the activity of thrombin molecule via binding to its exosite I. This 15-nt DNA oligonucleotide forms an intramolecular, antiparallel G-quadruplex structure with a chair-like conformation. In this paper, we report on our investigations on the influence of certain...
-
Electron detachment energies in high-symmetry alkali halide solvated-electron anions
Publication -
A dressing of zero-range potentials and electron-molecule scattering problem at low energies
PublicationTechnika ''ubierania'' jest używana do poprawy modelu potencjału zerowego promienia (ZRP). Rozważamy przekształcenia Darboux zaczynające się od ZRP, wynik ''ubierania'' daje potencjał z niezerowym promieniem, który zależy od parametrów rozwiązania.
-
Precise x-ray energies of gadolinium determined by a combined experimental and theoretical approach
Publication -
Low-Barrier Hydrogen Bond Determines Target-Binding Affinity and Specificity of the Antitubercular Drug Bedaquiline
PublicationThe role of short strong hydrogen bonds (SSHB) in ligand-target binding remains largely unexplored, thereby hin- dering a potentially important avenue in the rational drug de- sign. Here, we investigate the interaction between bedaquiline (Bq), a potent anti-tuberculosis drug, and the mycobacterial ATP synthase, to unravel the role of a specific hydrogen bond to a conserved acidic residue in the target affinity and specificity....
-
Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe 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...
-
Quantitative chirality in the binding of androgens to their receptor
Publication -
The influence of combination of binding agents on fatigue properties of deep cold in-place recycled mixtures in Indirect Tensile Fatigue Test (ITFT)
PublicationThe publication presents fatigue properties of cold recycled mixtures for eight combinations of binding agents (cement and bituminous emulsion). Cold recycled mixtures were evaluated in Indirect Tensile Fatigue Test (ITFT) at the temperature of 20 C in controlled stress mode. As a function of horizontal stress, fatigue life is strongly influenced by combination of the binding agents. When fatigue life is analyzed as a function...
-
Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublicationNanoarchaeum 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,...
-
Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana
PublicationBACKGROUND: In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods.RESULTS: We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino...
-
Determination of free tyrosine in equestrian supplements by LC–MS/MS and comparison of its quantity with total free amino acids content in view of doping control
PublicationThe reports on the probable beneficial impact of tyrosine (TYR) supplementation on performance enhancement have contributed to the growth of interest in TYR in equestrian sports field and related industries, such as the manufacture of dietary and nutritional supplements. In this study, the first attempt to the assessment of horses exposure to TYR during nutritional supplementation was demonstrated by quantification of unbound TYR...
-
Free convection of water-Al2O3 nanofluid from horizontal porous coated tube
PublicationThe main aim of the present study was to investigate the influence of nanoparticles on heat transfer coefficients during free convection of water-Al2O3 nanofluid from horizontal porous coated tube under atmospheric pressure for nanoparticle concentration of 0.01% by weight. Contrary to published data present study concerns on free convection of nanofluids in extensive, quiescent fluid.
-
The Opening of Central and Eastern European Countries to Free Trade: A Critical Assessment
PublicationThree decades after the fall of the Berlin wall and one and a half decades after the Big Bang enlargement of the European Union (2004-2007), we revisit contrasting narratives about the benefit of both free trade and the EU enlargement for Central and Eastern European (CEE) countries. We distinguish old, pre-2004 EU countries from CEE countries that joined the EU in 2004-2007, as well as from the CEE countries that have not become...
-
Extending loophole-free nonlocal correlations to arbitrarily large distances
PublicationQuantum theory allows spatially separated observers to share nonlocal correlations, which enable them to accomplish classically inconceivable information processing and cryptographic feats. However, the distances over which nonlocal correlations can be realized remain severely limited due to their high fragility to noise and high threshold detection efficiencies. To enable loophole- free nonlocality across large distances, we introduce...
-
Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
-
Novel Analytic-Numerical Model of Free Convection: with Leading Edge Considered
PublicationA novel solution of the free convection boundary problem is represented in analytical form for velocity and temperature for an isothermal vertical plate, as an example. These fields are built as a Taylor Series in the x coordinate with coefficients as functions of the vertical coordinate (y). We restrict ourselves by cubic approximation for both functions. The basic Navier-Stokes and Fourier-Kirchhoff equations and boundary conditions...
-
Reactive extrusion of biodegradable aliphatic polyesters in the presence of free-radical-initiators: A review
PublicationNowadays, growing attention is being paid to the environment and sustainability, what fully justified research works focused on modification of biodegradable polymers and their composites. In this field of research reactive extrusion seems to be the most promising approach, which fits well to sustainable development strategy. In In the present work, the in-situ modification of biodegradable aliphatic polyesters and the compatibilization...
-
Luminescent collisions of He+ and He++ ions with H2 molecules at energies below 2 keV
PublicationSpectroscopic studies of collisions between He+ and He++ ions with H2 gas target have been performed in the 200–600nm wavelength range. Atomic lines of hydrogen Balmer series and several helium lines were identified and their excitation functions between 50 eV and 1keV (2keV for He++) were determined.
-
Induced-fit binding of laccase to gold and carbon electrodes for the biological fuel cell applications
PublicationAnalogues of laccase natural substrates (syringic, veratric, ferulic, vanillic, isovanillic, 3,5-dimethoxybenzoic aldehydes) were employed to bind and orient laccase molecules in a way which facilitates adsorption of the catalyst molecules and their electrical connection with the conductive support. Laccase was bound efficiently to these substrates both on gold and carbon electrodes forming, respectively, 2D and 3D films sensitive...
-
An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublicationAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
-
An excess electron binding to the `purple' zwitterion quinonoid
Publication -
Taq DNA polymerase fused with DNA binding protein with increased resistance to inhibitors from clinical samples
PublicationNowadays PCR method is commonly used in molecular diagnostic. However, in many cases PCR is limited, by the presence of inhibitory substances in biological, soil or food samples Efficiency and fidelity of amplification is strongly connected with DNA polymerase and reaction conditions. To meet the requirements of modern diagnostic methods it is essential to seeking for new DNA polymerases with better properties useful in these field....
-
Inhibition of the granular anammox process by the high concentration of free ammonia.
PublicationHigh concentrations of ammonia and nitrite, typical for reject water treatment in the anammox process with the use of high temperatures and pH, may cause free ammonia (FA) inhibition. In this study, the inhibitory effect of FA on anammox process rate was investigated in a bench-scale sequencing batch reactor (SBR) with granular anammox biomass. Results of the study present that the anammox process could be successfully operated...
-
Optical fiber aptasensor for label-free bacteria detection in small volumes
PublicationHighly sensitive devices for fast bacteria detection are sought to be developed with the task of quantifying the worldwide problem of pathogenic bacteria and thus helping to take control over spreading bacterial infections. This work concerns a sensing solution based on microcavity in-line Mach-Zehnder interferometer (μIMZI) induced in an optical fiber. Such a device exhibits ultrahigh sensitivity to refractive index changes...
-
Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains
PublicationOkreślono 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.
-
Synthesis, structure, DNA binding and anticancer activity of mixed ligand ruthenium(II) complex
PublicationIn order to obtain a potential chemotherapeutic which is not affected on the normal BALB/3T3 cell line, a new arene ruthenium(II) complex {[RuCl(L1)(η6-p-cymene)]PF6}2 · H2O has been synthesized by a direct reaction of precursor, [{(η6-p-cymene)Ru(μ-Cl)}2Cl2], with N,N-chelating ligand (L1 - 2,2′-bis(4,5-dimethylimidazole). The compound has been fully characterized by elemental analysis, X-ray diffraction, IR, UV–Vis and 1H, 13C...
-
A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublicationWe 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...