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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 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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TiCoCrFeMn (BCC + C14) High-Entropy Alloy Multiphase Structure Analysis Based on the Theory of Molecular Orbitals
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublicationChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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Steroidal Molecular Rotors with 1,4-Diethynylphenylene Rotators: Experimental and Theoretical Investigations Toward Seeking Efficient Properties
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Conformational Studies of Two Bradykinin Antagonists by Using Two-dimensional NMR Techniques and Molecular Dynamics Simulations
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Molecular processes induced in primed seeds—increasing the potential to stabilize crop yields under drought conditions
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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 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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The comparison of semiempirical and ab initio molecular modeling methods in activity and property evaluation of selected antimicrobial sulfonamides
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Investigation of volatile low molecular weight compounds formed during continuous reclaiming of ground tire rubber
PublicationGround tire rubber was thermo-mechanically reclaimed at different temperature conditions (80, 120, 160 °C) using a co-rotating twin screw extruder. The progress of ground tire rubber reclaiming was evaluated with specific mechanical energy, sol fraction and thermogravimetric analysis. Volatile organic compounds (VOCs) including volatile sulfur compounds (VCSs) released from ground tire rubber and ground tire rubber after reclaiming...
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Molecular mobility of water protons under interaction with chemically modified starches. DSC and HMR-relaxation investigations
PublicationThe change of water protons mobility in the system chemically modified starches – water were investigated by DSC and NMR-relaxation methods. The amount of unfrozen water at subzero temperature as well as additional unfrozen water which appears after gelatinization have lower values for chemically modified starches in comparison with the native starch. The proton spin-spin relaxation time Т2 for chemically modified starch samples,...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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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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Docking simulations, Molecular properties and ADMET studies of novel Chromane6,7diol analogues as potential inhibitors of Mushroom tyrosinase
PublicationResearch on inhibition of tyrosinase enzyme has attained significant value, because tyrosinase inhibitors have potential applications in medicine, cosmetics (as whitening agents) and in agriculture (as bioinsecticides). Determination and elucidation of new tyrosinase inhibitors are not only beneficial for medical purposes, but their promising applications in improving food quality and nutritional...
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Investigation of sweet substances of different molecular structure by potentiometric taste sensor with all solid state electrodes
PublicationA five channel potentiometric taste sensor consisting of an array of All Solid State Electrodes (ASSESs) with different lipid-polymer membranes has been developed. The electrodes are constructed of glassy carbon discs with electrochemically deposited poly(3,4-ethylenedioxythiophene) (PEDOT) acting as ion to electron transducer. The outer layer of the electrode is lipid-polymer membrane. Lipid substances immobilized in PVC membranes...
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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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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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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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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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The influence of association of alcohol molecules on their adsorption and desorption heats
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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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Reporter Fluorescent Molecules in Biological Systems: The Current Overview
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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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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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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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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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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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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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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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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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CELLULAR AND MOLECULAR BIOLOGY
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CURRENT MOLECULAR MEDICINE
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International Conference on Computational Molecular Biology
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DEVELOPMENT OF HYDROGEL CAPSULES FOR USE IN DUAL-PHASE TOPICAL PREPARATIONS CONTAINING DIHYDROXYACETONE AND AMINO ACIDS – PRELIMINARY RESULTS
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How Does In Vitro Digestion Change the Amount of Phenolics in Morus alba L. Leaf? Analysis of Preparations and Infusions
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Separation of nitroaromatics and their transformation products in soil around ammunition plants: New high performance liquid chromatographic charge transfer stationary phases
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Separation of nicotinic acid and its structural isomers using 1-ethyl-3-methylimidazolium ionic liquid as a buffer additive by capillary electrophoresis
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The antagonistic role of chaotropic hexafluorophosphate anions and imidazolium cations composing ionic liquids applied as phase additives in the separation of tri-cyclic antidepressants
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Effect of Laminar Pulsatile Fluid Flow on Separation of Volatile Organic Compounds from Aqueous Solution by a Hollow Fiber Membrane-Based Process
PublicationIn this study, a laminar pulsatile fluid flow was used for the separation of benzene, toluene, ethylbenzene, and xylene isomers (BTEX) from aqueous solutions. Polyether sulfone hollow fiber membrane has been applied to this process. The effects of BTEX concentration, and feed and extraction flow rates were examined. It was found that the application of the pulsatile fluid flow with...
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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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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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Kinetics of molecular decomposition under irradiation of gold nanoparticles with nanosecond laser pulses—A 5-Bromouracil case study
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On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...