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Wyniki wyszukiwania dla: MOLECULAR DYNAMICS,OSMOLITY,PROTEIN FOLDING,ZWIJANIE BIAŁEK,OSMOLYTES
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In silico assessment and sonochemical synthesis of 2-alkynyl 3-chloropyrazines as prospective ligands for SARS-CoV-2
PublikacjaThe recent global pandemic caused by COVID-19 has triggered an intense effort worldwide towards the development of an effective cure for this disease. In our effort we have explored the 2-alkynyl substituted 3-chloropyrazine framework as a potential template for the design of molecules for this purpose. Our strategy was supported by the in silico studies of representative compounds to assess their binding affinities via docking...
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Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublikacjaSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighbouring space around these molecules were investigated. It was found, that water forms a well-defined layer - the first solvation shell - around the peptide molecule, and thickness of this layer is independent of the peptide structure, and it equals to approximately 0.28 nm....
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THE GENE CLONING, OVEREXPRESSION, PURIFICATION AND BIOCHEMICAL CHARACTERISATION OF A NEW COLD-ADAPTED β–GALACTOSIDASE FROM ARTHROBACTER SP. VII-4
PublikacjaINTRODUCTION. β-Galactosidase [EC 3.2.1.23] is an enzyme that catalyzes the hydrolysis of O-glycosidic linkages in galactosides. It is commercially used in dairy industry for the production of milk with reduced lactose content. Potentially, the best method for lactose removal under cooling conditions should be carried out with a cold-adapted enzyme. AIM. The aim of this study was to determine the taxonomic affiliation of the isolate...
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Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water
PublikacjaInfrared (IR) spectroscopy is a commonly used and invaluable tool in the studies of solvation phenomena in aqueous solutions. Concurrently, ab initio molecular dynamics (AIMD) simulations deliver the solvation shell picture at a molecular detail level and allow for a consistent decomposition of the theoretical IR spectrum into underlying spatial correlations. Here, we demonstrate how the novel spectral decomposition techniques...
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Refined theoretical study of radiative association: Cross sections and rate constants for the formation of SiN
PublikacjaRadiative association of silicon mononitride (SiN) in its two lowest molecular electronic states is studied through quantum and classical dynamics. Special attention is paid to the behavior of the cross section at high collision energies. A modified expression for the semiclassical cross section is presented which excludes transitions to continuum states. This gives improved agreement with quantum mechanical perturbation theory...
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublikacjaDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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Study of Icosahedral Clusters in Close-packed Simple Liquids
PublikacjaThe local structure of liquid copper was determined using Steinhardt order parameters, with particular attention paid to icosahedral clusters. The positions of atoms were obtained from three sets of molecular dynamics simulations, with the forces obtained from: the Sutton-Chen (SC) potential, the Naval Research Laboratory total energy tight-binding (NRL-TB) method and the divide-and-conquer learn-on-the-fly (DCLOTF) method, respectively....
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Why is TASK Quarterly a Significant Journal to Publish Your Article? —A Bibliometric Analysis of a Scientific and Technical Journal
PublikacjaA bibliometric analysis of TASK Quarterly in the years 1997-2021 in terms of various bibliometric indicators was performed to celebrate the 25th anniversary of the publication of the first issue of the journal. The number of publications and citations increased over the mentioned span of years. The leading countries in terms of the greatest number of papers published in TASK Quarterly are Poland, Italy, Germany, Ukraine, USA and...
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A novel hierarchically-porous diamondized polyacrylonitrile sponge-like electrodes for acetaminophen electrochemical detection
PublikacjaA novel composite electrode material consisting of tangled fibrous polyacrylonitrile-based hierarchically-struc- tured nanocomposites has been produced by wet-spinning, carbonized and decorated with a carbon nano- architecture by microwave plasma-enhanced chemical vapor deposition and investigated as a metal-free electrode for the enhanced electrochemical detection of acetaminophen. Surprisingly, the hierarchical fiber ar- chitecture...
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Characterization of two aminotransferases from Candida albicans
PublikacjaAminoadipate aminotransferase (AmAA) is an enzyme of α-aminoadipate pathway (AAP) for l-lysine biosynthesis. AmAA may also participated in biosynthesis or degradation of aromatic amino acids and in d-tryptophan based pigment production. The AAP is unique for fungal microorganisms. Enzymes involved in this pathway have specific structures and properties. These features can be used as potential molecular markers. Enzymes catalyzing...
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Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublikacjaSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer—the first solvation shell—around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within...
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Hybrid quantum-classical approach for atomistic simulation of metallic systems
PublikacjaThe learn-on-the-fly (LOTF) method [G. Csanyi et al., Phys. Rev. Lett. 93, 175503 (2004)] serves to seamlessly embed quantum-mechanical computations within a molecular-dynamics framework by continual local retuning of the potential's parameters so that it reproduces the quantum-mechanical forces. In its current formulation, it is suitable for systems where the interaction is short-ranged, such as covalently bonded semiconductors....
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Theoretical studies of fragmentation processes of neutral and ionized furan molecule
PublikacjaThis PhD thesis focuses on the fragmentation mechanism of the furan molecule in the gas phase. The approach taken in this work comprised of three theoretical methodologies considering the dynamical, energetical and entropic aspects of the studied process. First, molecular dynamics simulations were performed. Next, the potential energy surfaces were explored at the DFT/B3LYP level of theory. Finally, a new statistical Microcanonical...
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The influence of intermolecular correlations on the infrared spectrum of liquid dimethyl sulfoxide
PublikacjaDimethyl sulfoxide (DMSO) is routinely applied as an excellent, water-miscible solvent and chemical reagent. Some of the most important data concerning its liquid structure were obtained using infrared (IR) spectroscopy. However, the actual extent of intermolecular correlations that connect the isolated monomer spectrum to the IR response of the bulk liquid is poorly studied thus far. Using ab initio molecular dynamics (AIMD) simulations,...
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Thermophysical study of the binary mixtures of triethyl phosphate with N-methylformamide, N,N-dimethylformamide and N,N-dimethylacetamide – Experimental and theoretical approach
PublikacjaDensities at (293.15, 298.15, 303.15 and 308.15) K, and viscosities and ultrasonic velocities at 298.15 K of binary liquid mixtures of triethyl phosphate with N-methylformamide, N,N-dimethylformamide and N,N-dimethylacetamide have been measured over the entire range of composition at p = 0.1 MPa. From the experimental data, values of excess molar volume, excess isentropic compressibility, viscosity deviation and excess Gibbs energy...
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Low-Barrier Hydrogen Bond Determines Target-Binding Affinity and Specificity of the Antitubercular Drug Bedaquiline
PublikacjaThe 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....
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Unveiling the electron-induced ionization cross sections and fragmentation mechanisms of 3,4-dihydro-2H-pyran
PublikacjaThe interactions of electrons with molecular systems under various conditions are essential to interdisciplinary research fields extending over the fundamental and applied sciences. In particular, investigating electron-induced ionization and dissociation of molecules may shed light on the radiation damage to living cells, the physicochemical processes in interstellar environments, and reaction mechanisms occurring in combustion...
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The ONETEP linear-scaling density functional theory program
PublikacjaWe present an overview of the ONETEP program for linear-scaling density functional theory (DFT) calculations with large basis set (planewave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
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The Development of Toxoplasma gondii Recombinant Trivalent Chimeric Proteins as an Alternative to Toxoplasma Lysate Antigen (TLA) in Enzyme-Linked Immunosorbent Assay (ELISA) for the Detection of Immunoglobulin G (IgG) in Small Ruminants
PublikacjaThis study presents an evaluation of seventeen newly produced recombinant trivalent chimeric proteins (containing the same immunodominant fragment of SAG1 and SAG2 of Toxoplasma gondii antigens, and an additional immunodominant fragment of one of the parasite antigens, such as AMA1, GRA1, GRA2, GRA5, GRA6, GRA7, GRA9, LDH2, MAG1, MIC1, MIC3, P35, and ROP1) as a potential alternative to the whole-cell tachyzoite lysate (TLA) used...
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Texture or Linker? Competitive Patterning of Receptor Assembly toward Ultra-Sensitive Impedimetric Detection of Viral Species at Gold-Nanotextured Titanium Surfaces
PublikacjaIn this work, we study the electrodes with a periodic matrix of gold particles pattered by titanium dimples and modified by 3-mercaptopropionic acid (MPA) followed by CD147 receptor grafting for specific impedimetric detection of SARS-CoV-2 viral spike proteins. The synergistic DFT and MM/MD modeling revealed that MPA adsorption geometries on the Au–Ti surface have preferential and stronger binding patterns through the carboxyl...
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublikacjaIntermolecular 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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Closer look into the structures of tetrabutylammonium bromide–glycerol-based deep eutectic solvents and their mixtures with water
PublikacjaIn recent years, deep eutectic solvents (DES) and it’s mixture with water have become more and more attention as green solvents used in chemistry. However, there are only a few theoretical studies on the mechanisms of pure DES and DES-water complex formation. Therefore, the structural properties of tetrabutylammonium bromide–glycerol-based deep eutectic solvents and their mixtures with water have been investigated by means of Molecular...
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Utilizing pulse dynamics for non-invasive Raman spectroscopy of blood analytes
PublikacjaNon-invasive measurement methods offer great benefits in the field of medical diagnostics with molecular-specific techniques such as Raman spectroscopy which is increasingly being used for quantitative measurements of tissue biochemistry in vivo. However, some important challenges still remain for label-free optical spectroscopy to be incorporated into the clinical laboratory for routine testing. In particular, non-analyte-specific...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublikacjaMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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Torsional elasticity and energetics of F1-ATPase
PublikacjaFoF1-ATPase is a rotary motor protein synthesizing ATP from ADP driven by a cross-membrane proton gradient. The proton flow through the membrane-embedded Fo generates the rotary torque that drives the rotation of the asymmetric shaft of F1. Mechanical energy of the rotating shaft is used by the F1 catalytic subunit to synthesize ATP. It was suggested that elastic power transmission with transient storage of energy in some compliant...
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublikacjaThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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Novel molecules containing structural features of NSAIDs and 1,2,3-triazole ring: Design, synthesis and evaluation as potential cytotoxic agents
PublikacjaFor the first time the template containing structural features of more than one NSAIDs and the 1,2,3-triazole ring was explored for the identification of potential cytotoxic agents. These new and complex molecules were predicted to be effective inhibitors of PDE4B by molecular modelling studies in silico. The multi-step synthesis of these compounds were carried out starting from the well-known drug nimesulide and involved the use...
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A review on computer‐aided chemogenomics and drug repositioning for rational COVID ‐19 drug discovery
PublikacjaApplication of materials capable of energy harvesting to increase the efficiency and environmental adaptability is sometimes reflected in the ability of discovery of some traces in an environment―either experimentally or computationally―to enlarge practical application window. The emergence of computational methods, particularly computer-aided drug discovery (CADD), provides ample opportunities for the rapid discovery and development...
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Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublikacjaDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
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Molecular hydrogen solvated in water – A computational study
PublikacjaThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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Deep eutectic solvents – Ideal solution for clean air or hidden danger?
PublikacjaThe industrial sector is one of the fastest-growing sources of greenhouse gases, due to its excessive energy consumption to meet the rapidly growing demand for energy-intensive products. The use of deep eutectic solvents (DESs) has been studied extensively in order to cope with these harmful gases, but their usage can be an issue in respect to ecological reasons. Do deep eutectic solvents harm the atmosphere? Yes, these solvents...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNA insequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination. Although there are differences in amino...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNAinsequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination.Although there are differences in amino acid...
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Communication: Inside the water wheel: Intrinsic differences between hydrated tetraphenylphosphonium and tetraphenylborate ions
PublikacjaTetraphenylphosphonium tetraphenylborate (TPTB) is a common reference electrolyte in physical chemistry of solutions allowing for a convenient partitioning of thermodynamic properties into single-ion contributions. Here, we compute on the basis of ab initio molecular dynamics simulations the infrared (IR) spectra for hydrated constituent ions of the TPTB assumption. Using spectral decomposition techniques, we extract important...
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Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids
PublikacjaACCEPTED MAIonic liquids (ILs) have attracted much attention for their unique physicochemical properties, which can be designed as needed by altering the ion combinations. Besides experimental work, numerous computational studies have been concerned with prediction of physical properties of ILs. The results of molecular dynamics simulations of ILs depend strongly on the proper force field parameterization. Classical force fields...
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Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublikacjaInfrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently,...
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Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
PublikacjaAmphotericin B (AmB) is a potent but toxic drug commonly used to treat systemic mycoses. Its efficiency as a therapeutic agent depends on its ability to discriminate between mammalian and fungal cell membranes. The association of AmB monomers in an aqueous environment plays an important role in drug selectivity, as oligomers formed prior to membrane insertion – presumably dimers – are believed to act differently on fungal (ergosterol-rich)...
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Laser-Induced Graphitization of Polydopamine on Titania Nanotubes
PublikacjaSince the discovery of laser-induced graphite/graphene, there has been a notable surge of scientific interest in advancing diverse methodologies for their synthesis and applications. This study focuses on the utilization of a pulsed Nd:YAG laser to achieve graphitization of polydopamine (PDA) deposited on the surface of titania nanotubes. The partial graphitization is corroborated through Raman and XPS spectroscopies and supported...
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Investigating the disease- modifying properties of sclerotiorin in Alzheimer's therapy using acetylcholinesterase inhibition
PublikacjaAlzheimer's disease (AD) is a progressive neurodegenerative disorder caused due to the damage and loss of neurons in specific brain regions. It is the most common form of dementia observed in older people. The symptoms start with memory loss and gradually cause the inability to speak and do day-to-day activities. The cost of caring for those affected individuals is huge and is probably beyond most developing countries capability....
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Molecularly targeted nanoparticles: an emerging tool for evaluation of expression of the receptor for advanced glycation end products in a murine model of peripheral artery disease
PublikacjaAbstract Background: Molecular imaging with molecularly targeted probes is a powerful tool for studying the spatio-temporal interactions between complex biological processes. The pivotal role of the receptor for advanced glycation end products (RAGE) in numerous pathological processes, aroused the demand for RAGE targeted imaging in various diseases. In the study, we evaluated the use of a diagnostic imaging agent for RAGE quantification...
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Intercalation complex of imidazoacridinone C-1311, a potential anticancer drug, with DNA helix d(CGATCG)2: stereostructural studies by 2D NMR spectroscopy.
PublikacjaImidazoacridinone C-1311 (Symadex®) is a powerful antitumor agent, which successfully made its way through the Phase I clinical trials and has been recommended for Phase II few a years ago. It has been shown experimentally that during the initial stage of its action C-1311 forms a relatively stable intercalation complex with DNA, yet it has shown no base-sequence specificity while binding to DNA. In this paper, the d(CGATCG)2:C-1311...
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PTD4 Peptide Increases Neural Viability in an In Vitro Model of Acute Ischemic Stroke
PublikacjaIschemic stroke is a disturbance in cerebral blood flow caused by brain tissue ischemia and hypoxia. We optimized a multifactorial in vitro model of acute ischemic stroke using rat primary neural cultures. This model was exploited to investigate the pro-viable activity of cell-penetrating peptides: arginine-rich Tat(49–57)-NH2 (R49KKRRQRRR57-amide) and its less basic analogue, PTD4 (Y47ARAAARQARA57-amide). Our model included glucose...
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Theoretical examination of the fracture behavior of BC3 polycrystalline nanosheets: Effect of crack size and temperature
Publikacja2D carbon graphene nanostructures are elements of advanced materials and systems. This theoretical survey provides explanation to the mechanical and fracture behavior of mono- and polycrystalline BC3 nanosheets (denoted as MC- and PCBC3NS, respectively) as a function of temperature and the type of crack defects. The mechanical performance of PCBC3NS at elevated temperatures was monitored varying the number of grain boundaries (the...
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A novel one-variable first-order shear deformation theory for biaxial buckling of a size-dependent plate based on Eringen’s nonlocal differential law
PublikacjaPurpose – This paper aims to present a new one-variable first-order shear deformation theory (OVFSDT) using nonlocal elasticity concepts for buckling of graphene sheets. Design/methodology/approach – The FSDT had errors in its assumptions owing to the assumption of constant shear stress distribution along the thickness of the plate, even though by using the shear correction factor (SCF), it has been slightly corrected, the errors...
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Continuum contact model for friction between graphene sheets that accounts for surface anisotropy and curvature
PublikacjaUnderstanding the interaction mechanics between graphene layers and co-axial carbon nanotubes (CNTs) is essential for modeling graphene and CNT-based nanoelectromechanical systems. This work proposes a new continuum contact model to study interlayer interactions between curved graphene sheets. The continuum model is calibrated and validated using molecular dynamics (MD) simulations. These are carried out employing the reactive...
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Binding modes of a new epoxysuccinyl–peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?
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Glucosamine-6-phosphate synthase - the multi-facets enzyme
PublikacjaAmidotransferaza L-glutamina: D-frukozo-6-fosforan, nazywana zwyczajowo syntazą glukozamino-6-fosforanu, jako jedyny enzym należący do grupy amidotransferaz, nie wykazuje aktywności amoniakozależnej. Enzym ten, katalizujący pierwszy wyjątkowy etap w szlaku metabolicznym prowadzącym do ostatecznego wytworzenia 5´difosfourydyno-N-acetylo-D-glukozaminy (UDG-GlcNAc) stanowi ważny punkt kontroli metabolicznej biosyntezy makromolekuł...
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Degradation of a nano-cutting tool: an MD simulation
PublikacjaW pracy przedstawiono wyniki symulacji wielokrotnego oddziaływania realistycznie ukształtowanego ostrza tnącego z modelowym, nieskończenie twardym ziarnem, przy zastosowaniu metody dynamiki molekularnej. Ostrze składało się z kilkuset tysięcy atomów metalu fcc, traktowanego za pomocą potencjału Suttona-Chena, przesuwane było ze stałą prędkością 20 m/s. Obserwowane deformacje plastyczne pojawiające się na skutek kontaktu ostrza...
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A Novel Cryptic Clostridial Peptide That Kills Bacteria by a Cell Membrane Permeabilization Mechanism
PublikacjaThis work reports detailed characteristics of the antimicrobial peptide Intestinalin (P30), which is derived from the LysC enzyme of Clostridium intestinale strain URNW. The peptide shows a broader antibacterial spectrum than the parental enzyme, showing potent antimicrobial activity against clinical strains of Gram-positive staphylococci and Gram-negative pathogens and causing between 3.04 ± 0.12 log kill for Pseudomonas aeruginosa...
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Understanding the Electronic Structure and Optical Properties of Vacancy-Ordered Double Perovskite A2BX6 for Optoelectronic Applications
PublikacjaOver the past few years, metal halide perovskite solar cells have made significant advances. Currently, the single-junction perovskite solar cells reach a conversion efficiency of 25.7%. Perovskite solar cells with a wide band gap can also be used as top absorber layers in multi-junction tandem solar cells. We examined the dynamical and thermal stability, electronic structure, and optical features of In2PtX 6 (X = Cl, Br, and I)...