Search results for: biophysics
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Two-electron reduction of quinones by Enterobacter cloacae NAD(P)H:nitroreductase: quantitative structure-activity relationships
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Blood free Radicals Concentration Determined by Electron Paramagnetic Resonance Spectroscopy and Delayed Cerebral Ischemia Occurrence in Patients with Aneurysmal Subarachnoid Hemorrhage
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Structural analogues of reactive intermediates as inhibitors of glucosamine-6-phosphate synthase and phosphoglucose isomerase
PublicationCentra aktywne izomerazy fosfoglukozowej (PGI) oraz domeny izomerazowej (HPI) syntazy glukozamino-6-fosforanu (GlcN-6-P), wykazują podobieństwo ułożenia przestrzennego kluczowych reszt aminokwasowych, z wyjątkiem reszty Arg272 PGI i reszt Lys603 i Lys485 HPI. Dziesięć pochodnych D-heksitolo-6-P, kwasu 5-fosfoarabonowego i kwasu 6-fosfoglukonowego, strukturalnych analogów cis-enolaminy lub cis-enolanu, przypuszczalnych stanów przejściowych...
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The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2
PublicationThe telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1TRFH and TRF2TRFH in the presence/absence of the TIN2TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results...
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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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Is mesh fixation necessary in laparoendoscopic techniques for M3 inguinal defects? An experimental study.
Publicationrepairs, in case of large direct hernias (M3) mesh fixation is recommended to reduce recurrence risk. Despite lack of highquality evidence, the recommendation was upgraded to strong by expert panel. The authors conducted a research experiment to verify the hypothesis that it is possible to preserve the mesh in the operating field in large direct hernias (M3) without the need to use fixing materials. Method The authors conducted...
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Limitations of WSSUS modeling of stationary underwater acoustic communication channel
PublicationPerformances of underwater acoustic communication (UAC) systems are strongly related to specific propagation conditions of the underwater channel. Due to their large variability, there is a need for adaptive matching of the UAC systems signaling to the transmission properties of the channel. This requires a knowledge of instantaneous channel characteristics, in terms of the specific parameters of stochastic models. The wide-sense...
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Extension of the Force Matching Method to Anisotropic Coarse-Grained Transferable Force Fields: Application to the Unres Model of Proteins
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Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
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Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles
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Erratum to “Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles” [Biophys. Chem. 105 (2003) 339–359]
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NMR studies of new arginine vasopressin analogs modified with α-2-indanylglycine enantiomers at position 2 bound to sodium dodecyl sulfate micelles
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Molecular Determinants of Proton Transfer in ATP Synthase FO Complex
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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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Lateral diffusion coefficients in membranes measured by resonance energy transfer and a new algorithm for diffusion in two dimentions
PublicationOpisano wyniki pomiarów współczynników dyfuzji w membranach przy wykorzystaniu rezonansowego przekazywania energii wzbudzania. Donorem był kompleks metaloorganiczny renu o czasie życia ok. 3ćs, co pozwalało na pomiary współczynników dyfuzji mniejszych od 10 cm2/s. Zmierzono współczynniki dyfuzji w membranach typu DMPG i DOPC w różnych temperaturach.
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Climatology of Transient Luminous Events and Lightning Observed Above Europe and the Mediterranean Sea
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Recent Results from Studies of Electric Discharges in the Mesosphere
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Protochlorophyllide in model systems — An approach to in vivo conditions
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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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Syntheses and DNA binding of new cationic porphyrin–tetrapeptide conjugates
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Binding of new cationic porphyrin–tetrapeptide conjugates to nucleoprotein complexes
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Arbidol targeting influenza virus A Hemagglutinin; A comparative study
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Molecular modeling of amphotericin B - ergosterol primary complex in water II
PublicationPrezentowane badania dotyczą oddziaływania antybiotyku polienowego anfoterycyny B (AmB) i ergosterolu (ERG) (typowego sterolu błonowego komórek grzybowych) na poziomie molekularnym. W odróżnieniu od badanego poprzednio kompleksu binarnego analizowany obecnie kompleks AnB/ERG/AmB charakteryzuje się zdecydowanie wiekszą stabilnością i wzglednie sztywną, sandwiczową geometrią. Za trwałość i geometrie kompleksu odpowiedzialne są oddziaływania...
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Generalization of the Elastic Network Model for the Study of Large Conformational Changes in Proteins
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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On the mechanism of nitrobenzene liquid membrane oscillators containing hexadecyltrimethylammonium bromide
PublicationBadano oscylacje różnicy potencjałów elektrycznych między fazami wodnymi oscylatora z membraną ciekłą, zawierającego kwas pikrynowy rozpuszczony w nitrobezenie. Wodnej fazie donorowej znajdował się kationowy surfaktant, zaś faza akceptorowa składała się z wodnego roztworu sacharozy. Zaproponowano mechanizm oscylacji składajacy się z trzech etapów. Zaproponowano procesy zachodzące w każdym etapie. Stwierdzono, że procesy adsorpcji...
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublicationAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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Amyloid fibril formation in the presence of water structure-affecting solutes
PublicationThe impact of the differently hydrated non-electrolytes (protein structure destabilizers) on the fibrillation of hen egg white lysozyme (HEWL) was investigated. Two isomeric urea derivatives i.e. butylurea (BU) and N,N,N′,N′-tetramethylurea (TMU) were chosen as a tested compounds. The obtained results show that butylurea exerts greater impact on HEWL and its fibrillation than tetramethylurea. Both substances decrease the time of...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublicationThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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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...
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Multimodal analysis of traction forces and the temperature dynamics of living cells with a diamond-embedded substrate
PublicationCells and tissues are constantly exposed to chemical and physical signals that regulate physiological and pathological processes. This study explores the integration of two biophysical methods: traction force microscopy (TFM) and optically detected magnetic resonance (ODMR) to concurrently assess cellular traction forces and the local relative temperature. We present a novel elastic substrate with embedded nitrogen-vacancy microdiamonds...
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Polyacrylamide substrate viscosity impact on temozolomide activity in glioblastoma cells by flow cytometry and rheological measurements
Open Research DataDataset includes raw data on cell lines LN-229 and LN-18 treated with temozolomide measured by flow cytometry, rheometry and cell projections. It also includes calculations necessary for creation of figures and conclusions based on those figures in the publication titiled: "Substrate viscosity impairs temozolomide-mediated inhibition of glioblastoma...
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Comparison of direct and inverse methods of satellite observations downscaling for the coastal zone area
PublicationThe Earth observation satellite imaging systems have known limitations, especially regarding their spatial and temporal resolution. Therefore, approaches which aim to combine data retrieved from sensors of higher temporal and lower spatial resolution with the data characterized by lower temporal but higher spatial resolution are of high interest. This allows for joint utilization of the advantages of both these types of sensors....
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Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor
PublicationGranulocyte macrophage colony stimulating factor (GMCSF) is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with biologically active compounds is critical...
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PUBLICATIONS OF THE INSTITUTE OF GEOPHYSICS POLISH ACADEMY OF SCIENCES - Serie E Water Resources
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Binary Mixtures of Selected Bisphenols in the Environment: Their Toxicity in Relationship to Individual Constituents
PublicationBisphenol A (BPA) is one of the most popular and commonly used plasticizer in the industry. Over the past decade, new chemicals that belong to the bisphenol group have increasingly been used in industrial applications as alternatives to BPA. Nevertheless, information on the combined effects of bisphenol (BP) analogues is insufficient. Therefore, our current study aimed to find the biological response modulations induced by the...
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1,4-DHP-lipid parameters and rod like micellae
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Environmental Role of Rime Chemistry at Selected Mountain Sites in Poland
PublicationThe results of field experiments on fog pollutantdeposition enhanced by local mountain climate, completed by thedendrochronological analysis of the forest response, are presentedin this paper. In spite of their low absolute altitude (1,000-1,600 ma.s.l), the Sudetes and the Silesian Beskid form a noticeable orographicbarrier for the airflow of the humid Atlantic air masses.This results in the increase of cloudiness and fog frequency...
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Water and chemical properties of hydrometeors over central european mountains
PublicationAtmospheric pollutants are transferred to the groundby the contribution of various types of hydrometeors. Because ofthe different techniques of measurement, comparative analysesbetween them are often neglected. Hence, the main goal is tocompare water volume and chemistry of different types ofhydrometeors and their role in both: water balance and pollutantsdeposition. The results of water input and atmospheric depositschemistry...
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Dew Formation and Chemistry Near a Motorway in Poland
PublicationIn this study, the influence of traffic intensity on dewformation efficiency and chemistry is presented. The measurementswere conducted near the A4 motorway in SW Poland in almost flatland relief with intense agricultural activity. The dew/hoarfrost wascollected by means of insulated plain passive radiative condensersat three sites: AN and AS located in the close vicinity of themotorway (30 m) on the opposite sides of the road,...
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GPR investigation of the strengthening system of a historic masonry tower
PublicationIn this paper the condition assessment of the strengthening system of a masonry tower was carried out by the GPR method. The study provided unique experimental data acquired during measurements of the reinforced concrete frame embedded in masonry walls. Conducted numerical and experimental investigations were focused on the phenomenon of the diffraction-refraction scattering of the electromagnetic energy. A hyperbola resulting...
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An analysis of solar energy conversion systems based on photon and thermal processes
PublicationSolar spectral irradiance covers a fairly broad wavelength range. Solar radiation is part of the electromagnetic spectrum which is described by the concept of wave-particle duality. The corpuscular theory of electromagnetic radiation states that energy is transmitted by photons. Photons carry specific amounts of energy which can be used to convert solar energy into other types of energy, in particular electricity. The internal...
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Investigations of Energy Conversion and Surface Effect for Laser-Illuminated Gold Nanorod Platforms
PublicationAchieving a quick temperature increase is a burning issue for biophysical applications, like germ inactivation and tumor ablation, and for energy performances, like solar collectors and steam generators. Based on the plasmon resonance phenomenon, noble metallic nanoparticles have emerged as promising weapons due to their very high biocompatibility, optical properties, and high surface-to-volume ratio, increasing energy conversion...
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Activation Energy and Inclination Magnetic Dipole Influences on Carreau Nanofluid Flowing via Cylindrical Channel with an Infinite Shearing Rate
PublicationThe infinite shear viscosity model of Carreau fluid characterizes the attitude of fluid flow at a very high/very low shear rate. This model has the capacity for interpretation of fluid at both extreme levels, and an inclined magnetic dipole in fluid mechanics has its valuable applications such as magnetic drug engineering, cold treatments to destroy tumors, drug targeting, bio preservation, cryosurgery, astrophysics, reaction kinetics,...
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Interactions of amphotericin B derivatives with lipid membranes - a molecular dynamics study
PublicationW pracy analizowano oddziaływanie dwóch nisko-toksycznych pochodnych amfoterycyny B (związki SAmE i PAmE) z modelami błon lipidowych. Badania wykonane zostały za pomocą dynamiki molekularnej. Modele błon oprócz fosfolipidów DMPC zawierały odpowiednio cholesterol (model błony zwierzęcej) lub ertosterol (model błony grzybowej). Analiza wyników wykazała, że obie pochodne amfoterycyny B zachowują się inaczej w błonie cholesterolowej...
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Polar localization of new flavonoids from aerial parts of Scleranthus perennis and Hottonia palustris and their modulatory action on lipid membranes properties
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Comparative molecular dynamics simulations of amphotericin B-cholesterol/ergosterol membrane channels
PublicationBadania polegały na przeprowadzeniu porównawczej dynamiki molekularnej dla dwóch typów kanałów amfoterycyny B. Obie symulacje różniły się rodzajem sterolu (cholesterol lub ergosterol). Na podstawie wyników przeprowadzonych prac ustalono jakie elementy strukturalne badanych kanałów mogą być odpowiedzialne za selektywne działanie amfoterycyny B.
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Excitation energy transport and trapping in concentrated solid solutions offlavomononucleotide.
PublicationPraca dotyczy właściwości transportu i pułapkowania energii wzbudzenia w układzie monomer dimer dla flawomononukleotydu rozpuszczonego w filmach alkoholu poliwinylowego. Pokazano, że w tym przypadku wydajność kwantowa i depolaryzacja nie dają się opisać w ramach teorii nie uwzględniającej powrotnego przekazywania energii i że znacznie lepsza zgodność uzyskanych wyników doświadczalnych zachodzi z teorią, w której fluoryzujące...
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Understanding chlorophylls: Central magnesium ion and phytyl as structural determinants
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