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Search results for: MOLECULAR UMBRELLA
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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
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Molecular characterization of drug-resistant Mycobacterium tuberculosis strains from Poland by use of multiple genetic markers
PublicationW pracy przedstawiono wyniki genotypowania wielolekoopornych szczepów Mycobacterium tuberculosis, izolowanych od pacjentów z Polski.
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Molecular and chemical monitoring of growth and Ochratoxin A biosynthesis of P. verrucosum in wheat stored at different moisture conditions
PublicationDoświadczenie polegało na obserwacji wzrostu P. verrucosum na ziarnach pszenicy, składowanej w różnych warunkach (wilgotność, temperatura) oraz zdolności do produkcji Ochratoksyny A (OTA) przez tę pleśń. Wzrost mierzony był w jednostkach tworzących kolonie (cfu colony forming units). Biosynteza OTA kontrolowana była przy pomocy HPLC, a ekspresja genu otapksPV syntetazy OTA mierzona w czasie przy pomocy odwrotnej transkryptazy...
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Molecular basis for the bifunctional Uba4–Urm1 sulfur‐relay system in tRNA thiolation and ubiquitin‐like conjugation
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Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito
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Hyperosmolarity adversely impacts recombinant protein synthesis by Yarrowia lipolytica—molecular background revealed by quantitative proteomics
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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The molecular function of kallikrein‐related peptidase 14 demonstrates a key modulatory role in advanced prostate cancer
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Graph Neural Networks and Structural Information on Ionic Liquids: A Cheminformatics Study on Molecular Physicochemical Property Prediction
PublicationIonic liquids (ILs) provide a promising solution in many industrial applications, such as solvents, absorbents, electrolytes, catalysts, lubricants, and many others. However, due to the enormous variety of their structures, uncovering or designing those with optimal attributes requires expensive and exhaustive simulations and experiments. For these reasons, searching for an efficient theoretical tool for finding the relationship...
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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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Born-Oppenheimer potential energy curves of the NaK molecule
Open Research DataAdiabatic potential energy curves (APEC) of the singlet (s) and triplet (t) Sigma+, Pi, and Delta electronic states have been calculated for the NaK molecule. All results of the presented molecular states have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Electron collisions with tetrafluoroethylene (C2F4) and ethylene (C2H4) molecules.
PublicationStosując liniową metodę transmisyjną zmierzono całkowite przekroje czynne(TCS) na zderzenie elektronów z drobinami C2F4 w zakresie energii 0.6-370eV.Stwierdzono obecność szerokiego maksimum przy ok. 30eV. Dla porównania zmierzono TCS dla C2H4. Przedyskutowano wpływ podstawienia atomu fluoru w miejsce wodoru.
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Electron impact ionization and cationic fragmentation of the pyridazine molecules
PublicationElectron impact mass spectroscopy was used to investigate ionization and cationic fragmentation of the pyridazine (1,2 diazine), C4H4N2, molecules in the gas phase. The mass spectra were measured and the observed mass peaks assigned to the corresponding cations. The appearance energies of most of the cationic fragments were determined and the possible fragmentation processes are discussed. The total cross section for electron...
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The influence of association of alcohol molecules on their adsorption and desorption heats
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Electronic states of tetrahydrofuran molecules studied by electron collisions
PublicationElectronic states of tetrahydrofuran molecules were studied in the excitation energy range 5.5-10 eV using the technique of electron energy loss spectroscopy in the gas phase. Excitation from the two conformations, C2 and Cs, of the ground state of the molecule are observed in the measured energy loss spectra. The vertical excitation energies of the 3(no3s) triplet state from the C2 and Cs conformations of the ground state of the...
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Ionization and ionic fragmentation of tetrahydrofuran molecules by electron collisions
PublicationElectron impact ionization and ionic fragmentation of tetrahydrofuran molecules in the gas phase were studied in the energy range from ionization threshold up to 150 eV using the technique of mass spectrometry. The cation mass spectra, ionization and ionic fragmentation efficiencies were measured over this energy range. Well-resolved mass peaks were detected in the mass range 10-72 amu and assigned to corresponding ionic molecular...
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Superexcited states in the vacuum-ultraviolet photofragmentation of isoxazole molecules
PublicationThe photofragmentation of isoxazole molecules producing excited atomic and molecular fragments has been investigated over the energy range 16-50 eV, using photon-induced fluorescence spectroscopy. The following fragments have been identified by their fluorescence: the excited hydrogen atoms H(n), n = 3-7 and the diatomic CH(A2Δ, B2Σ−), CN(B2Σ+) and C2(d3Πg) fragments. The diatomic fragments are vibrationally and highly rotationally...
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Collisions of electrons with trimethylphosphine [P(CH3)3] molecules
PublicationPrzedstawiono wyniki pomiarów całkowitych przekrojów czynnych na rozpraszanie elektronów na molekułach P(CH3)3. Pomiary przeprowadzono w przedziale energii od 0,4 do 400eV. Obliczono przekroje czynne na rozpraszanie sprężyste i na jonizację. Wyniki porównano z przekrojami czynnymi dla innych związków zawierających fosfor jako atom centralny oraz grupę metylową.
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Collisions of electrons with trimethylamine N(CH3)3 molecules
PublicationPrzedstawiono całkowite przekroje czynne na rozpraszanie elektronów na drobinach N(CH3)3, zmierzone dla niskich i średnich energii zderzenia. Wyniki porównano z elastycznymi i jonizacyjnymi przekrojami czynnymi, obliczonymi dla tej drobiny, dla średnich energii zderzenia. Porównano i przedyskutowano przekroje czynne dla drobin zawierających azot jako atom centralny.
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Reporter Fluorescent Molecules in Biological Systems: The Current Overview
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Electron scattering from tin tetrachloride (SnCl4) molecules
PublicationAbsolute grand-total cross section (TCS) for electron scattering from a tin tetrachloride, SnCl4, molecule was measured at electron-impact energies ranging from 0.6 to 300 eV, in the linear electron-transmission experiment. The measured TCS energy dependence shows two very pronounced enhancements peaking near 1.2 eV and around 9.5 eV, separated with a deep minimum centered close to 3 eV. The low energy structure is attributed to...
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Vacuum ultraviolet photoionization and ionic fragmentation of the isoxazole molecules
PublicationThe photofragmentation of the isoxazole molecules producing ionized atomic and molecular fragments was investigated in the photon energy range of 9e32 eV, using synchrotron radiation excitation combined with ion time-of-flight spectrometry. Twenty-one well resolved cations were identified in the mass spectra of the isoxazole, and their appearance energies were determined. The yield curves of these cations were obtained in the photon...
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublicationIntermolecular interactions such as those present in molecule···water complexes may profoundly influence the physicochemical properties of molecules. Here, we carried out an experimental–computational study on doubly deprotonated guanosine monophosphate···water clusters, [dGMP – 2H]2–·nH2O (n = 1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations....
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Potential Energy Curves of Diatomic Alkali Molecules Datasets
PublicationThe datasets described in this article contain potential energy curves for several diatomic systems. The data was obtained via high-performance computing using MOLPRO, a system of ab initio programs for advanced molecular electronic structure calculations. The datasets allow to model bond lengths, energy levels, spectra and time-evolution of molecular dimers for which the data are presented.
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Application of nonmetallic frustrated cations in the activation of small molecules
PublicationThe concept of nonmetallic frustrated cations has been used in small molecule activation. The in situ generated ambiphilic phosphinoborinium cation activated phenyl isocyanate, diisopropylcarbodiimide, and acetonitrile under very mild conditions without any catalyst, yielding single-, double-, or mixed-activation products. Furthermore, the mechanisms of the reactions of the phosphinoborinium cation with small molecules were elucidated...
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International Conference on Computational Molecular Biology
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CELLULAR AND MOLECULAR BIOLOGY
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CURRENT MOLECULAR MEDICINE
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Nuclear Magnetic Resonance data for the synthesis of esterase cleavable antifungal conjugates containing fatty acids as molecular carriers
Open Research DataNMR data for novel organic compounds - conjugates composed of C2-18 fatty acid (FA) residues as a molecular carrier and 5-fluorocytosine (5-FC) as an active agent, released upon the action of intracellular esterases on the ester bond between FA and “trimethyl lock” intramolecular linker.
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Data on hydrogen migration in cation-induced dissociation of furan molecules
Open Research DataThe data include furan luminescence spectra obtained in collisions with H3+ and C+ cations and theoretical spectra of OH and CH radicals published in [1].
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THE EFFECTS OF APPLYING CHITOSAN OF DIFFERENT MOLECULAR WEIGHTS ON THE QUALITY OF KAMCHATKA BERRIES (LONICERA CAERULEA L.): PART 2
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Formation, crystal and molecular structures of heteroleptic zinc(II) tri-tert-butoxysilanethiolates with ZnNO2S2 and ZnN2S2 coordination pattern.
PublicationZsyntetyzowano pięć tri-tert-butoksysilanotiolanów cynku zawierających jako dodatkowe ligandy heterocykliczne, zasady azotowe. Wzór ogólny tych kompleksów to Zn(SSi(OBut)3)2L, gdzie L=alfa-pikolina, 2,4-lutydyna, N-metyloimidazol lub Zn(SSiOBut)3)2L2, gdzie L=N-metyloimidazol lub pirydyna. Określono strukturę krystaliczną otrzymanych związków oraz zmierzono widma IR i NMR.
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublicationPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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Molecular modelling of transition state analogue inhibitors of glucosamine-6-P synthase and glucose-6-P isomerase.
PublicationStruktura kompleksu 2-amino-2-deoksy-D-glucitolo-6-P (ADGP) z centrum aktywnym syntazy GlcN-6-P z E. coli została wykorzystAna jako punkt wyjścia do modelowania molekularnego analogów ADGP. Używając programu GROMOS96 wygenerowano konformacje analogów o najniższych energiach wewnętrznych, które następnie ''dokowano'' w centrum aktywnym enzymu. Dokonano syntezy wybranych związków i określono parametry kinetyczne i termodynamiczne...
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Oscillating water-oil-water liquid membrane systems for molecular recognition of substances belonging to diferent taste classes
PublicationBadano oscylacje róznicy potencjału elektrochemicznego miedzy fazami wodnymi. Jedna faza wodna zawiera kationowy lub anionowy surfaktant podczas gdy w drugiej fazie wodnej znajduje sie substancja odpowiedzialna za smak. Dwie fazy wodne sa rozdzielone faza olejową. Oscylacje były analizowane poprzez konstrukcje portretów fazowych uzywając metody opoznienia czasowego. Kształt portretów fazowych jest rozny dla oscylatorów z kationowym...
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Kinetics of molecular decomposition under irradiation of gold nanoparticles with nanosecond laser pulses—A 5-Bromouracil case study
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Virulence, antifungal susceptibility and molecular mechanisms of echinocandin resistance among Candida isolates recovered from clinical specimens
PublicationFungi of the genus Candida belong to the natural microflora of healthy individuals. However, they can also be a cause of opportunistic infections especially among patients with an impaired immune system. The first line therapy of Candida infections is based on triazoles. However, in recent years there an increase of azole resistant Candida spp., in particular C. glabrata and C. krusei, has been observed. For this reason, echinocandin...
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Kinetics of molecular decomposition under irradiation of gold nanoparticles with nanosecond laser pulses—A 5-Bromouracil case study
PublicationABSTRACT Laser illuminated gold nanoparticles (AuNPs) efficiently absorb light and heat up the surrounding medium, leading to versatile applications ranging from plasmonic catalysis to cancer photothermal therapy. Therefore, an in-depth understanding of the thermal, optical, and electron induced reaction pathways is required. Here, the electrophilic DNA nucleobase analog 5-Bromouracil (BrU) has been used as a model compound to...
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Molecular Response in Intestinal and Immune Tissues to in Ovo Administration of Inulin and the Combination of Inulin and Lactobacillus lactis Subsp. cremoris
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Electron-Induced Decomposition of Uracil-5-yl O-(N,N-dimethylsulfamate): Role of Methylation in Molecular Stability
PublicationThe incorporation of modified uracil derivatives into DNA leads to the formation of radical species that induce DNA damage. Molecules of this class have been suggested as radiosensitizers and are still under investigation. In this study, we present the results of dissociative electron attachment to uracil-5-yl O-(N,N-dimethylsulfamate) in the gas phase. We observed the formation of 10 fragment anions in the studied range of electron...
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Interactions of vasopressin and oxytocin receptors with vasopressin analogues substituted in position 2 with 3,3′-diphenylalanine - a molecular docking study
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Micelle-bound conformations of neurohypophyseal hormone analogues modified with a Cα-disubstituted residue: NMR and molecular modelling studies
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Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part I: studies in water
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Self-assembly and interactions of short antimicrobial cationic lipopeptides with membrane lipids: ITC, FTIR and molecular dynamics studies
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Palladium versus Platinum: The Metal in the Catalytic Center of a Molecular Photocatalyst Determines the Mechanism of the Hydrogen Production with Visible Light
PublicationTo develop highly efficient molecular photocatalysts for visible light-driven hydrogen production, a thorough understanding of the photophysical and chemical processes in the photocatalyst is of vital importance. In this context, in situ X-ray absorption spectroscopic (XAS) investigations show that the nature of the catalytically active metal center in a (N^N)MCl2 (M=Pd or Pt) coordination sphere has a significant impact on the...
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Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state
PublicationHuman immunodeficiency virus type 1 protease (HIV-1 PR) is a viral-encoded enzyme that forms a homodimer. HIV-1 PR is essential for replication and assembly of the virus and inactivation of HIV-1 PR enzyme causes production of immature, noninfectious viral particles and thus HIV-1 PR is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different...
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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High- and low-Molecular Weight oat Beta-Glucan Reveals Antitumor Activity in Human Epithelial Lung Cancer
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Molecular organization of antifungal antibiotic amphotericin B in lipid monolayers studied by means of Fluorescence Lifetime Imaging Microscopy
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