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Search results for: MOLECULAR STRUCTURE
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Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”
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Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations
PublicationThis work presents the analysis of the conformation of albumin in the temperature range of 300K – 312K, i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from...
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Molecular dynamics simulations of ultraprecision machining of fcc monocrystals
PublicationArtykuł zawiera wyniki wielkoskalowych symulacji dynamiczno-molekularnych ultraprecyzyjnego skrawania monokryształów metali niedeformowalnym narzędziem. Zmiennymi parametrami symulacji były: szybkość i głębokość skrawania, temperatura, orientacja krystalograficzna skrawanego kryształu oraz kształt narzędzia.Analizie poddano zmiany strukturalne w obrabianym materiale.
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Same but different — Molecular comparison of human KTI12 and PSTK
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Low-Molecular-Weight Aldehyde Inhibitors of Cathepsin G
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Plasma Treatment as an Unconventional Molecular Magnet Engineering Method
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Molecular dynamics of fentanyl bound to μ-opioid receptor
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Molecular diagnosis in type I epithelial ovarian cancer
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Molecular factors involved in the development of diabetic foot syndrome.
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Shape resonance of the ethylene anion stabilized in a molecular trap
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Real-Time PCR: molecular technique of many applications
PublicationReal-Time PCR is a sensitive DNA amplification technique initially applied in genetics and molecular biology. It enables in vivo copying of the selected DNA fragment (flanked by two primers) by the thermostable polymerase (in the presence of magnesium ions and deoxynucleotide triphosphates) and simultaneous measurement of the fluorescence. For one or more specific sequences in a DNA sample, real-time PCR enables both detection...
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Molecular basis of the low activity of antitumor anthracenediones, mitoxantrone and ametantrone, in oxygen radical generation catalyzed by NADH dehydrogenase. Enzymatic and molecular modelling studies
PublicationSyntetyczne antracenodionowe leki przeciwnowotworowe, w przeciwieństwie do antybiotyków antracyklinowych, charakteryzują się słabym wytwarzaniem wolnych rodników w układach z dehydrogenazą NADH. Wyniki prezentowane w artykule wskazują, że ani potencjał redukcyjny, ani konformacja łańcuchów bocznych, ani energie orbitali granicznych (LUMO i HOMO) nie determinują zdolności antracenedionów do stymulacji wytwarzania reaktywnych form...
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Self-assembly, stability and conductance of amphotericin B channels: bridging the gap between structure and function
PublicationAmphotericin B (AmB), one of the most powerful but also toxic drugs used to treat systemic mycoses, is believed to selectively permeabilize fungal cell membranes to ions in a sterol-dependent manner. Unfortunately, the structure of the biologically active AmB channels has long eluded researchers, obstructing the design of safer alternatives. Here, we investigate the structural and thermodynamic aspects of channel formation, stability,...
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Azo group(s) in selected macrocyclic compounds
PublicationAzobenzene derivatives due to their photo- and electroactive properties are an important group of compounds finding applications in diverse fields. Due to the possibility of controlling the trans–cis isomerization, azo-bearing structures are ideal building blocks for development of e.g. nanomaterials, smart polymers, molecular containers, photoswitches, and sensors. Important role play also macrocyclic compounds well known for...
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Mass spectrometry based identification of geometric isomers during metabolic stability study of a new cytotoxic sulfonamide derivatives supported by quantitative structure-retention relationships
PublicationA set of 15 new sulphonamide derivatives, presenting antitumor activity have been subjected to a metabolic stability study. The results showed that besides products of biotransformation, some additional peaks occurred in chromatograms. Tandem mass spectrometry revealed the same mass and fragmentation pathway, suggesting that geometric isomerization occurred. Thus, to support this hypothesis, quantitative structure-retention relationships...
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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublicationPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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Molecular-dynamics simulation of clustering processes in sea-ice floes
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Molecular Determinants of Proton Transfer in ATP Synthase FO Complex
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Current molecular methods for the detection of hepatitis B virus quasispecies
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Current rectification in molecular junctions produced by local potential fields
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Cationic or anionic surfactant oscillators for molecular recognition of taste substances
PublicationOtrzymano krzywe oscylacyjne róznicy potencjału elektrochemicznego miedzy fazami wodnymi oscylatora zawierajacego jonowy surfanktant. Były one analizowane poprzez konsrukcje portretów fazowych uzywając metody opóźnienia czasowego. Kształt portertów fazowych jest rożny dla układów z kationowym lub anionowym surfanktantem. Szeregi wzrostu powierzchni atraktorów dla tych dwoch oscylatorów sa także rózne.
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Oscillators with anionic surfactants as systems for molecular recognition of taste substances
PublicationZaprezentowano, charakterystyki oscylacyjne układów trojfazowych, ktore mogą byc uzyte do rozpoznawania substancji smakowych. Zaobserwowano, że zmiany osylacyjne róznicy potencjału elektrycznego miedzy fazami wodnymi zależą od rodzaju substancji smakowej obecnej w układzie. Ich rózne wartosci poczatkowe są ważną cechą z punktu mozliwości zastosowania tych układów w sensorach smaku. Dla kazdego układu wyznaczono portrety fazowe...
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Molecular modelling of membrane sterols with the use of the GROMOS 96 forcefield
PublicationPodstawowym zadaniem tego projektu było udowodnienie zasadności stosowania pola siłowego GROMOS 96 do symulacji steroli błonowych metodą dynamiki molekularnej. Uzyskane wyniki jasno wskazują, że to pole siłowe bardzo dobrze nadaje się do symulacji silnie lipofilowych układów.
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Molecular modelling of amphotericin B-ergosterol primary complex in water
PublicationBadano właściwości pierwotnego kompleksu amfoterycyny B z ergosterolem przy pomocy symulacji dynamiki molekularnej. Otrzymane w wyniku naszych symulacji rezultaty słabo odpowiadają postulowanym przez innych autorów modelom kompleksu antybiotyk-sterol. Z drugiej strony uzyskane geometrie nie są sprzeczne z wynikami eksperymentów biofizycznych dotyczących powstawania kompleksów w wodzie i w środowisku wodno-alkoholowym.
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New Peptide Based Fluconazole Conjugates with Expanded Molecular Targets
PublicationInfections of Candida spp. etiology are frequently treated with azole drugs. Among azoles, the most widely used in the clinical scenario remains fluconazole (FLC). Promising results in treatment of dangerous, systemic Candida infections demonstrate the advantages of combined therapies carried out with combinations of at least two different antifungal agents. Here, we report five conjugates composed of covalently linked FLC and...
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Molecular Dynamics of a Vasopressin V2 Receptor in a Phospholipid Bilayer Membrane
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Molecular targets for antifungals in amino acid and protein biosynthetic pathways
PublicationFungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems...
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Synthesis and hydrogen evolving catalysis of a panchromatic photochemical molecular device
PublicationA dinuclear hydrogen evolution photocatalyst [(tbbpy)2Os(tpphz)PtI2](PF6)2 (tbbpy = 4,4′-tert-butyl-2,2′-bipyridine; tpphz = tetrapyrido[3,2-a:2′,3′-c:2′′,3′′-h:2′′′,3′′′-j]phenazine) is synthesized in order to make use of the broader range of visible light absorption mitigated by the osmium center. In a first step, the activity of the complex for hydrogen evolution is investigated by evaluating the role of different electron donors...
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Parkinson’s disease: Etiopathogenesis, molecular basis and potential treatment opportunities
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Molecular dynamics-based model of VEGF-A and its heparin interactions
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Slow growth conservation and molecular characterization of Deutzia scabra Thunb
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Molecular Modeling of Interaction of the Vasopressin Analogs with Vasopressin and Oxytocin Receptors
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Molecular Insight into the Self-Assembly Process of Cellulose Iβ Microfibril
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PF5 and PCl5 interacting with water – Comparative study at the molecular level
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublicationThe 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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Functionalized polypyrroles. New molecular materials for electrocatalysis and related applications
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Raman spectroscopy analysis of molecular configuration forms of the macular xanthophylls
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Porphyrazines as Molecular Scaffolds: Flexible Syntheses of Novel Multimetallic Complexes
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ortho-Fluorobenzanilides and ortho-fluorothiobenzanilides: Molecular conformations and crystal packing
PublicationSeries of 2-fluoro and 2,6-difluorobenzanilides and their thiobenzanilide analogs have been synthesized to investigate the influence of the fluorine atom on their crystal structures and self-assembly in the crystal lattice. The X-ray analysis of the single crystal revealed that the synthesized molecules adopt a geometry being deflected from planarity. The deflection was investigated by analysis of dihedral angles between mean planes...
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Evaluating experimental molecular physics studies of radiation damage in DNA*
PublicationThe field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental...
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Capillary Electrophoresis in Determination of Low Molecular Mass Organic Acids
PublicationThis paper presents overviews the capabilities of capillary electrophoretic techniques to determine low molecular mass organic acids in a variety of aqueous, gas and solid samples. It mainly focuses on short - chain carboxylic acids containing one or more carboxylic groups and possibly some other functional groups (hydroxyl, keto-, amino- etc.). Finally the procedures applied to the determine the acids in different matrices are...
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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Molecular Umbrellas Modulate the Selective Toxicity of Polyene Macrolide Antifungals
PublicationAntifungal polyene macrolide antibiotics Amphotericin B (AmB) and Nystatin (NYS) were conjugated through the ω-amino acid linkers with diwalled “molecular umbrellas” composed of spermidine-linked deoxycholic or cholic acids. The presence of “umbrella” substituents modulated biological properties of the antibiotics, especially their selective toxicity. Some of the AmB-umbrella conjugates demonstrated antifungal in vitro activity...
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Positron binding to alkali-metal hydrides: The role of molecular vibrations
PublicationThe bound vibrational levels for J=0 have been computed for the series of alkali-metal hydride molecules from LiH to RbH, including NaH and KH. For all four molecules the corresponding potential-energy curves have been obtained for each isolated species and for its positron-bound complex (e+XH). It is found that the calculated positron affinity values strongly depend on the molecular vibrational state for which they are obtained...
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Electron-impact dissociation of molecular hydrogen: benchmark cross sections
PublicationWe present a joint experimental and theoretical investigation of a fundamental process in atomic and molecular physics: electron impact excitation of molecular hydrogen’s (H2) most dominant transition (X1Σg+ → b3Σu+). Excitation of this state is by far the main channel that causes the dissociation of H2 into H + H atoms at low energies. The Convergent Close-Coupling (CCC) calculations predicted significant, more than factor of...
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Positron scattering on molecular hydrogen: Analysis of experimental and theoretical uncertainties
PublicationExperiments performed in recent years on positron scattering from molecular hydrogen indicated a rise of the total cross section in the limit of zero energy, but essentially disagree on the amplitude of this rise. Mitroy and collaborators [J.-Y. Zhang et al., Phys. Rev. Lett. 103, 223202 (2009)] predicted a scattering length somewhat different from values deduced experimentally. Using a Markov chain Monte Carlo modified effective...
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FT-IR studies of molecular interactions in formamide-methanol mixtures
PublicationTechniką ATR zmierzono widma FT-IR roztworów metanolu(MeOH) i formamidu(FA) w całym zakresie ich składu. Przeprowadzono analizę faktorową widm, która wykazała obecność dwóch kompleksów molekularnych matanolu z formamidem. Na podstawie profilów stężeniowych indywiduów absorbujących wyznaczono średni skład kompleksów w zależności od składu mieszaniny. Przeprowadzono również analizę pasma CO formamidu metodą widm różnicowych. Wyniki...
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Molecular interaction sensors: a new detector platform for separation methods
PublicationPotencjometria jest nową metodą detekcji dla chromatografii cieczowej (LC)i elektroforezy kapilarnej (CE). Zastosowanie potencjometrii dla chromatograficznych technik wynika z faktu, że sygnał z detektora jest zależny od stanu rozdzielenia analitów nad pokryciem sensora i od rodzaju eluentu. Rozdzielenie analitu powoduje zmiany potencjału, a zmiany te można zaklasyfikować jako potencjometryczne. Do opisu ilościowego potrzebny jest...
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Cation diffusion coefficients in CuAgI via molecular dynamics simulations
PublicationPraca prezentuje wyniki analizy strukturalnej otrzymane poprzez symulacje dynamiczno-molekularne (zespół NpT, dwuciałowy potencjał Vashisty-Rahmana) superjonowego związku o składzie (1-x)Cu-xAg-I, x = 0.0, 0.25, 0.5, 0.75, 1.0). Wyznaczono wartość współczynnika dyfuzji kationów i energii aktywacji w funkcji składu szkła i temperatury. Otrzymane rezultaty porównano z danymi literaturowymi.
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Understanding homogenous nucleation: the recent phenomenological and molecular dynamic approaches
PublicationPraca przedstawia dwa podejścia do problemu homogenicznej nukleacji. Pierwsze jest podejściem fenomenologicznym. Nukleacja jest tu rozumiana jako wzrost kropel krytycznych, które po przejściu określonego wymiaru, warunku równowagi termodynamicznej, mają tendencje do wzrostu. W tym podejściu problem wzrostu kropel oraz problem populacji kropel jest określany poprzez parametry makroskopowe. Przedstawiono nowe rozwiązania uzyskane...