Search results for: MOLECULAR STRUCTURE
-
Molecular dynamics study on the influence of C-terminal sugar substitution on dynamics and conformation of vancomycin derivatives
Publication -
Molecular mechanism(s) of regulation(s) of c-MET/HGF signaling in head and neck cancer
Publication -
Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
Publication -
Classical to Path-Integral Adaptive Resolution in Molecular Simulation: Towards a Smooth Quantum-Classical Coupling
Publication -
Virtual screening for small molecular non-covalent binders of the SARS-CoV-2 main protease
Publication -
Chapter 32. Method to predict the critical micelle concentration of ionic liquids from the molecular volume
PublicationAmfifilowość wielu imidazoliowych cieczy jonowych powoduje, że zjawiska powierzchniowe mają znaczny wpływ na właściwości układów zawierających te związki. Dotychczas przeprowadzono wiele badań w celu wyznaczenia krytycznego stężenia micelizacji cieczy jonowych o różnej budowie. Ze względu na możliwość modyfikacji budowy kationu i wyboru anionu oraz ich kombinacji, podjęto próbę opracowania empirycznego równania pozwalajacego na...
-
The anion [Mg6Cl8Cp*5]-: a final intermediate on the way to the molecular donor-free Grignard compound MgClCp*?
PublicationOtrzymano i scharakteryzowano strukturalnie rzadki przypadek związku Grignarda pozbawionego donora. Struktura krystaliczna [Mg6Cl8Cp*5][AlCp*2] C6H6 zawiera zarówno metallocen (Cp*AlCp*) jak i odwrócony metallocen (MgCp*Mg).
-
Bacterial SSB-like proteins of family Deinococcaceae - indentification, isolation, obtaining, purification and molecular characteristic
PublicationWiększość poznanych białek SSB jest aktywna w formie homotetramerycznej. Od 2002 roku znane są białka organizmów ekstremofilnych. Scharakteryzowano białka mikroorganizmów rodziny Deinococaceae. Uzyskane termostabilne białka stanowią atrakcyjną alternatywę w stosunku do znanych białek SSB w metodach diagnostyki molekularnej, technikach biologii molekularnej i analityce.
-
Solubility of dapsone in deep eutectic solvents: Experimental analysis, molecular insights and machine learning predictions
PublicationBackground. Dapsone (DAP) is an anti-inflammatory and antimicrobial active pharmaceutical ingredient used to treat, e.g., AIDS-related diseases. However, low solubility is a feature hampering its efficient use. Objectives. First, deep eutectic solvents...
-
Molecular dynamics simulation and MM-PBSA analysis of Oxytricha nova TEBP ternary complex with ssDNA
PublicationPraca dotyczy badań metodami chemii obliczeniowej właściwości elektrostatycznych i termodynamicznych kompleksu telomerowego białka TEBP pochodzącego z organizmu Oxytricha z jednoniciowym telomerowym DNA (ssDNA).
-
Chromatic monitoring technique for thickness measurementof thin transparent films.IV Workshopon Atomic and Molecular Physics.
PublicationW pracy opisano nową technikę monitorowania grubości cienkich warstw podczas procesu ich syntezy. Jest to optyczna metoda oparta na zdegenerowanej analizie widmowej tzw. modulacji chromatycznej. Umożliwia ona precyzyjny ciągły pomiar zmian grubości wzrastających warstw stosowanych w optyce.
-
Planar chiral dianthranilide and dithiodianthranilide molecules: optical resolution, chiroptical spectra, and molecular self-assembly.
PublicationChiralny planarnie diantranilid został rozdzielony na enancjomery przy użyciu chlorku (-)-(1S,4R)-kamfanoilu. Konfigurację absolutną (S)-enancjomeru ustalono na podstawie analizy rentgenograficznej monokryształu jego N,N'-dikamfoilopochodnej. Natomiast rozdział ditiodiantranilidu na enancjomery przeprowadzono poprzez tworzenie związków inkluzyjnych z (R,R)-1,2-diaminocykloheksanem. Otrzymanemu w ten sposób enancjomerowi przypisano...
-
Influence of molecular organization of photo-active azo-phanes on thereactivity in monolayers at the air-water interface.
PublicationStwierdzono, że molekularna organizacja monowarstw na granicy powietrze-woda, otrzymanych z amfifilowego azofanu z nierozgałęzionym podstawnikiem n-dodecylowym różni się od tej uzyskanej dla analogu z objętościowym podstawnikiem ''tert''-oktylowym pod względem powierzchni zajmowanej przez cząsteczkę. Kompleksowanie jonów sodu z subfazy wodnej, jak wywnioskowano z pomiaru potencjału powierzchniowego, jest ułatwione w przypadku azofanu...
-
Early stages of condensation from the gaseous phase in a H2O-N2 system: a molecular dynamics study.
PublicationW pracy przedstawiono wyniki symulacji wczesnych etapów kondensacji z fazy gazowej w układzie xH2O (1-x)N2. Przeanalizowano całkowitą liczbę klastrów, średni rozmiar klastra i rozmiar klastra maksymalnego w funkcji czasu.
-
The exposure to UV filters: Prevalence, effects, possible molecular mechanisms of action and interactions within mixtures
PublicationSubstances that can absorb sunlight and harmful UV radiation such as organic UV filters are widely used in cosmetics and other personal care products. Since humans use a wide variety of chemicals for multiple purposes it is common for UV filters to co-occur with other substances either in human originating specimens or in the environment. There is increasing interest in understanding such co-occurrence in form of potential synergy, antagonist,...
-
Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublicationThe use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The...
-
Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
-
New PCR test for detection of Candida glabrata based on the molecular target chosen by the RAPD technique
PublicationRapid, reliable diagnosis is a necessary condition for the successful treatment of infections. Such diagnostic assays are continually being developed. #e paper presents a method for selecting the molecular target for PCR-based diagnostics based on the comparison of RAPD patterns. A sequence encoding Candida glabrata CBS138 hypothetical protein was selected. The limit of detection for PCR and real-time PCR reactions with DNA extracted...
-
Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
-
Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
-
Multi-state multi-reference Møller-Plesset second-order perturbation theory for molecular calculations
PublicationThis work presents multi‐state multi‐reference Møller–Plesset second‐order perturbation theory as a variant of multi‐reference perturbation theory to treat electron correlation in molecules. An effective Hamiltonian is constructed from the first‐order wave operator to treat several strongly interacting electronic states simultaneously. The wave operator is obtained by solving the generalized Bloch equation within the first‐order...
-
Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
-
Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublicationThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
-
Mangiferin Affects Melanin Synthesis by an Influence on Tyrosinase: Inhibition, Mechanism of Action and Molecular Docking Studies
PublicationMangiferin is a strong antioxidant that presents a wide range of biological activities. The aim of this study was to evaluate, for the first time, the influence of mangiferin on tyrosinase, an enzyme responsible for melanin synthesis and the unwanted browning process of food. The research included both the kinetics and molecular interactions between tyrosinase and mangiferin. The research proved that mangiferin inhibits tyrosinase...
-
Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublicationSeveral 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....
-
Topical delivery of pharmaceutical and cosmetic macromolecules using microemulsion systems
PublicationMicroemulsions are transparent, thermodynamically stable colloidal systems. Over the recent years, they have been increasingly investigated due to their potential as skin delivery vehicles for a wide range of drug molecules. The nanoscale particle size and the specificity of microemulsion components are the main features determining the skin permeation process. However, in order to effectively cross the skin barrier, the active...
-
Paweł Możejko dr hab.
People -
Configurations of H 3 + (H2)n clusters and their energies
PublicationThe H-3(+) ion plays an important role in low temperature astrophysical and laboratory plasmas. It is considered as the initiator of many ion-molecule chemistries. Also its clusters with H-2 are quite interesting. We study configurations of the H-3(+)(H-2)(n) clusters for n = 1 up to n = 12 as a simple test system. Total energies for these structures, with zero point vibration corrections have been calculated. Stabilization energies...
-
OBTAINING OF COUMARONE-INDENE RESINS BASED ON LIGHT FRACTION OF COAL TAR 3. COUMARONE-INDENE RESINS WITH METHACRYLIC FRAGMENTS
PublicationThe method for obtaining coumarone-indene resins with methacrylic fragments (CIRM) was developed with the addition of methyl ethacrylate, using a light fraction of coal tar and its fraction boiling within 423–463 К. CIRM was obtained via radical cooligomerization using 2,2'-azobis (2-methyl-propionitrile) as the initiator. The effect of the initiator amount, temperature and reaction time on the yield, softening temperature and...
-
Selection of effective cocrystals former for dissolution rate improvement of active pharmaceutical ingredients based on lipoaffinity index
PublicationNew theoretical screening procedure was proposed for appropriate selection of potential cocrystal formers possessing the ability of enhancing dissolution rates of drugs. The procedure relies on the training set comprising 102 positive and 17 negative cases of cocrystals found in the literature. Despite the fact that the only available data were of qualitative character, performed statistical analysis using binary classification...
-
EASY ACCESS TOOL FOR SMALL INTERFERING RNA (siRNA) DATA
PublicationFor many decades it was an accepted dogma of molecular genetics that the expression of genes is a “one-way-road” leading only in one direction from DNA to RNA to proteins. Recent discoveries in modern molecular genetics have challenged this dogma showing that specific RNA molecules play a central role in controlling the activity of genes by changing the structure of DNA sequences, targeting other RNAs for degradation or blocking...
-
Stability and phase transition investigation of olanzapine polymorphs
PublicationWe use electrical embedded-fragment QM method with both DFT/ωB97XD/6-31G* and MP2/6-31G* to investigate the phase transformations of olanzapine. Gibbs free energy calculations predict that form I is always the most stable structure and form II is the least stable one, while form IV is more stable than form III below about 200 K but less stable above this temperature, implying a polymorphic phase transformation. This may account...
-
Susceptibility to Degradation in Soil of Branched Polyesterurethane Blends with Polylactide and Starch
PublicationA very important method of reducing the amount of polymer waste in the environment is the introduction to the market of polymers susceptible to degradation under the influence of environmental factors. This paper presents the results of testing the susceptibility to degradation in soil of branched polyesterurethane (PUR) based on poly([R,S]-3-hydroxybutyrate) (R,S-PHB), modified with poly([D,L]-lactide) (PLA) and starch (St). Weight...
-
Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublicationSeveral 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...
-
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...
-
Molecular profiles of thyroid cancer subtypes: Classification based on features of tissue revealed by mass spectrometry imaging
Publication -
Adhesion of the genome-sequenced Lactococcus lactis subsp. cremoris IBB477 strain is mediated by specific molecular determinants
Publication -
Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer
Publication -
Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
Publication -
Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate
Publication -
Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides
Publication -
Gluten-Free Bread with Cricket Powder—Mechanical Properties and Molecular Water Dynamics in Dough and Ready Product
Publication -
Biological Activity and Antibiofilm Molecular Profile of Citrus aurantium Essential Oil and Its Application in a Food Model
Publication -
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...
-
Steroidal Molecular Rotors with 1,4-Diethynylphenylene Rotators: Experimental and Theoretical Investigations Toward Seeking Efficient Properties
Publication -
Molecular processes induced in primed seeds—increasing the potential to stabilize crop yields under drought conditions
Publication -
The comparison of semiempirical and ab initio molecular modeling methods in activity and property evaluation of selected antimicrobial sulfonamides
Publication -
Differential cross sections for electron impact vibrational excitation of molecular oxygen in the angular range 15° - 180°.
PublicationZmierzono absolutne różniczkowe przekroje czynne na wzbudzenie drobin tlenu do poziomów oscylacyjnych v=1-4 stanu podstawowego X3 suma g. Pomiary wykonano dla energii elektronów równej 10eV w zakresie kątów rozproszenia od 15° do 180°.
-
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.
-
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...