Publikacje
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wszystkich: 371
Katalog Publikacji
Rok 2018
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublikacjaAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Ludzkość-technologia: organizm symbiotyczny
PublikacjaFelieton popularnonaukowy dotyczący filozofii techniki.
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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublikacjaAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublikacjaUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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New data acquisition system for birch sap concentrate production using the reverse osmosis technology
PublikacjaThe work presents a simple electronic device that helps to monitor the basic parameters of the reverse osmosis (RO) system during the concentration of birch tree sap. The construction costs are low (around 150 Euro) but the functionality of the device is high. It has an in-build two channel conductometer and can measure the volumetric flow rate of two streams of liquids. The collected data are transmitted wirelessly via Bluetooth...
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Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies
PublikacjaA series of novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(6-substituted-4-chloro-1,3,5-triazin-2-ylamino)guanidine derivatives 9–20 have been synthesized by substitution of chlorine atom at the 1,3,5-triazine ring in compounds 5–8 with 3- or 4-aminobenzenesulfonamide and 4-(aminomethyl)benzenesulfonamide hydrochloride. All the synthesized compounds were evaluated for their inhibitory activity toward hCA I, II,...
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On the relationship between the structural and volumetric properties of solvated metal ions in O-donor solvents using new structural data in amide solvents
PublikacjaThe structures of the N,N-dimethylformamide (dmf), N,N-dimethylacetamide (dma), and N,N-dimethylpropionamide (dmp) solvated strontium and barium ions have been determined in solution using large angle X-ray scattering and EXAFS spectroscopy. The strontium ion has a mean coordination number (CN) between 6.2 and 6.8, and the barium ion has a mean CN between 7.1 and 7.8 in these amide solvents. The non-integer numbers indicates that...
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Preparation and characterization of dummy-template molecularly imprinted polymers as potential sorbents for the recognition of selected polybrominated diphenyl ethers
PublikacjaThe main aim of this work was to conduct the preliminary/basic research concerning the preparation process of a new dummy molecularly imprinted polymer (DMIP) materials. Developed DMIPs were proposed as a sorption material in solid-phase extraction (SPE) technique for recognition of selected low mass polybrominated diphenyl ethers (PBDEs) e PBDE-47 and PBDE-99. Four new DMIPs were synthesized employing bulky polymerization technique...
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Solvation of ionic liquids based on N -methyl- N -alkylmorpholinium cations in N,N -dimethylformamide and N,N -dimethylacetamide – Volumetric and compressibility studies
PublikacjaDensity and sound velocity of the solutions of ionic liquids based on N-alkyl-N-methyl- morpholinium cations: N-ethyl- -methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-butyl-Nmethylmorpholinium bis(trifluoromethanesulfonyl)imide, N-octyl-N-methyl -morpholinium bis(trifluor omethanesulfonyl)imide and N-decyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide in N, N-dimethylformamide and N,N-dimethylacetamide were...
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Structural changes of water caused by non-electrolytes: Volumetric and compressibility approach for urea-like analogues
PublikacjaHydration of thiourea (TU), hydroxyurea (HU, hydroxycarbamide), acetone (AC, 2-propanone) and dimethyl sulfoxide (DMSO) has been investigated with the help of the volumetric and compression measurement. The apparent molar volumes and the apparent molar isentropic (adiabatic) compression have been calculated from the density and speed of sound data at temperatures ranging from 288.15 to 308.15 K at atmospheric pressure (0.1 MPa)....
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Taurine as a water structure breaker and protein stabilizer
PublikacjaThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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The energy consumption during the birch tree sap concentration process using the reverse osmosis system
PublikacjaBirch tree sap was concentrated by mens of the reversed osmosis technique. The energy consumption in a small-scale pilot apparatus was estimated. The threshold value for the water removal above which the specific energy consumption significantly increased was identified. Below the threshold value the reversed osmosis had low energy demand and could be an attractive method for the production of birch tree sap-based beverages.
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The relationship between standard reduction potentials of catechins and biological activities involved in redox control
PublikacjaRedox homeostasis involves factors that ensure proper function of cells. The excess reactive oxygen species (ROS) leads to oxidative stress and increased risk of oxidative damage to cellular components. In contrast, upon reductive stress, insufficient ROS abundance may result in faulty cell signalling. It may be expected that dietary antioxidants, depending on their standard reduction potentials (E°), will affect both scenarios....
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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublikacjaExplicit 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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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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Wpływ osmolitów na stabilność białek w oparciu o metodę dynamiki molekularnej
PublikacjaCelem niniejszej pracy było zbadanie molekularnego mechanizmu wpływu biologicznie znaczących związków, tzw. osmolitów na stabilność białek. Aby zweryfikować istniejące hipotezy i dostarczyć spójnego obrazu działania osmolitów na poziomie molekularnym, wykorzystano metodę dynamiki molekularnej do zasymulowania mechanicznej denaturacji modelowych białek – lizozymu i ubikwityny. W tym podejściu odtworzony został efekt stabilizujący...
Rok 2019
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A Three-Step Approach to Estimation of Reduction Potentials of Natural Mixtures of Antioxidants Based on DPPH Test; Illustration for Catechins and Cocoa
PublikacjaThe aim of this study is to propose a methodology to assess electrochemical properties of complex mixtures of antioxidants, such as plant extracts, based on the results of simple and popular DPPH test. The first, most difficult step, involves determinations of standard reduction potentials (E0) for the series of purified compounds (here catechins). The next step is the calculation of stoichiometric values (n10) based on the results...
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Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures
PublikacjaInteractions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions. In this paper, the influence of NMA and N,N-dimethylacetamide...
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Amyloid fibril formation in the presence of water structure-affecting solutes
PublikacjaThe 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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Analytical applications and physicochemical properties of ionic liquid-based hybrid materials: A review
PublikacjaIonic liquids with their unique properties found so far numerous analytical applications. Among them ionic liquids immobilized on the surface or within the pores of a solid support were successfully utilized in extraction techniques dedicated to preconcentration of the analytes from food, environmental and biological samples. In this review we focus on comprehensive summarizing of available literature data on the examples of ionic...
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ANTIOXIDANT POWER SERIES (APS) AS A TOOL FOR RATIONAL DESIGN AND ASSESSMENT OF HEALTH PROMOTING PROPERTIES OF FUNCTONAL FOODS BASED ON ANTIOXIDANT PHYTOCHEMICALS
PublikacjaOver past decades, plantborne antioxidants dominated so called "translational research" in the area of food, nutrition, and disease prevention. Among consumers and producers, such phytochemicals are synonyms of nutriceuticals. Popularity and commercial success of antioxidants stems from mechanistic studies suggesting the involvement of reactive oxygen species in etiology of chronic diseases. However, epidemiology failed to provide...
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Application of ionic liquids in microextraction techniques: Current trends and future perspectives
PublikacjaIonic liquids (ILs) with their unique properties found so far numerous analytical applications. Among them ILs both in their liquid form and immobilized on the surface or within the pores of a solid support were successfully utilized in microextraction techniques. The scope of this review will cover a comprehensive summarizing of available literature data on selected properties of ILs playing a key role in analytical purposes,...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublikacjaShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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"Big data" i Wielki Brat
PublikacjaFelieton popularnonaukowy dotyczący ochrony prywatności danych.
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Ciecze jonowe jako medium sorpcyjne w mikroekstrakcji do pojedynczej kropli Cz. I. Podstawy teoretyczne zagadnienia
PublikacjaTechnika mikroekstrakcji do pojedynczej kropli stanowi sztandarowy przykład rozwiązania technicznego spełniającego wymogi stawiane przez ideę zielonej chemii analitycznej.
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Ciecze jonowe jako medium sorpcyjne w mikroekstrakcji do pojedynczej kropli. Cz.II. Praktyka analityczna
PublikacjaPomimo rosnącego zainteresowania metodami analitycznymi opartymi na użyciu cieczy jonowych ich sprzężenie wraz z techniką mikroekstrakcji do pojedynczej kropli nie osiągnęło zadowalającej popularności oraz akceptacji ze strony środowiska naukowego.
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Density, sound velocity, viscosity, and refractive index of new morpholinium ionic liquids with amino acid-based anions: Effect of temperature, alkyl chain length, and anion
PublikacjaIn this work, room temperature synthesis of twenty new ionic liquids (ILs) based on the N-alkyl-N-methylmorpholinium ([Mor1,R], R = 2, 3, 4, 6, 8) cation and N-acetyl-L-amino acid anions (L-alaninate, L-valinate, L-leucinate, L-isoleucinate) was described. The synthesized ILs were characterized by various spectroscopic techniques and high-resolution mass spectrometry. Furthermore, density (ρ), sound velocity (v), viscosity (η)...
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Determination of Antioxidant Activity of Vitamin C by Voltammetric Methods
PublikacjaVoltammetric methods—cyclic (CV) and differential pulse voltammetry (DPV) are considered the most appropriate way to evaluate antioxidant activity of redox active compounds. They provide information about both mechanism and kinetics of electrochemical oxidation of antioxidants as well as their physical and chemical properties such as the redox potential or the number of electrons transferred. These methods are helpful for understanding...
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Development and validation of a model that includes two ultrasound parameters and the plasma D-dimer level for predicting malignancy in adnexal masses: an observational study
PublikacjaBackground: Pre-operative discrimination of malignant from benign adnexal masses is crucial for planning additional imaging, preparation, surgery and postoperative care. This study aimed to define key ultrasound and clinical variables and develop a predictive model for calculating preoperative ovarian tumor malignancy risk in a gynecologic oncology referral center. We compared our model to a subjective ultrasound assessment (SUA)...
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DMSO hydration redefined: Unraveling the hydrophobic hydration of solutes with a mixed hydrophilic–hydrophobic characteristic
PublikacjaHydrophobic hydration of solutes with a mixed hydrophilic--hydrophobic characteristics is still poorly understood. This is because both experimental and theoretical methods find it difficult to see the ice-like water structure around the nonpolar solute groups, unlike hydrogen bonds with the hydrophilic groups. In order to unravel this problem, we have investigated DMSO hydration by means of infrared spectroscopy and theoretical...
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Ewolucja od węgla do krzemu
PublikacjaFelieton popularnonaukowy dotyczący filozofii techniki.
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General, Mild, and Metal-Free Functionalization of Indole and Its Derivatives Through Direct C3-Selenylation
PublikacjaA very mild method for the introduction of functionalized alkylselenyl group at C-3 position of the indole ring was developed. The proposed procedure consists of an electrophilic substitution of indole and its derivatives with bis(O,O-diisopropoxyphosphorothioyl) diselenide and subsequent cleavage of the P–Se bond with tetrabutylammonium fluoride in the presence of various electrophilic reagents. This method can be successfully...
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How green are ionic liquids? – A multicriteria decision analysis approach
PublikacjaDue to various desirable physicochemical properties, ionic liquids (ILs) are still gaining in popularity. ILs have been recurrently considered green solvents. However, environmental, health and safety assessments of ILs have raised certain doubts about their benignness, and their greenness status is currently unclear. To clarify the situation on their greenness, we perform a comprehensive assessment of more than 300 commercially...
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How to stop salami science: promotion of healthy trends in publishing behavior
PublikacjaThe career of scientists often depends on the number of their published works. This fact leads to the overproduction of low quality papers burying the important articles and making the knowledge less accessible. One of the methods to counteract these negative aspects might lie in the promotion of healthy trends in publishing behavior. In the present work, the theoretical analysis of a new bibliometric measure is presented, and...
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Influence of the ionic strength on the amyloid fibrillogenesis of hen egg white lysozyme
PublikacjaThe study investigates the role of the electrostatic interactions in the fibrillation of the hen egg white lysozyme (HEWL). In order to achieve this aim the influence of the cations Na+, Mg2+ and Al3+ on the amyloid fibril formation and amorphous aggregation was tested. The amyloids are formed in the solution without added salt but the Thioflavin T fluorescence gives the false-negative result. In these conditions, the HEWL fibrils...
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Interactions of N-alkyl-N-methylmorpholinium based ionic liquids with acetonitrile studied by density and velocity of sound measurements and molecular dynamics simulations
PublikacjaMorpholinium-based ionic liquids (ILs) and their mixtures with polar co-solvents are an interesting class of emerging electrolytes in electrochemistry that is relatively poorly studied. In this work, densities and sound velocities of four ILs, N-ethyl-N-methylmorpholinium tetrafluoroborate, N-butyl-N-methylmorpholinium tetrafluoroborate, N-octyl-N-methylmorpho-linium tetrafluoroborate and N-decyl-N-methylmorpholinium tetrafluoroborate...
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Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublikacjaTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
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Medium-sized cyclic bis(anisylphosphonothioyl)- disulfanes and their corresponding cyclic sulfane-structures and most characteristic reactions
PublikacjaCyclic 8-, 9-, 10-, and 12-membered bis(anisylphosphonothioyl)disulfanes were synthesized. Next, structurally related 7 to 9-membered cis and trans sulfanes were isolated as a result of sulfur atom extrusion from the parent cyclic disulfanes. The results of the desulfurization of the disulfanes were compared to the results obtained for desulfurization of the respective bis(anisylphosphodithioates). Cyclic disulfanes predominantly...
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Monitoring of lysozyme thermal denaturation by volumetric measurements and nanoDSF technique in the presence of N-butylurea
PublikacjaThe results of thermal studies of denaturation of hen egg white lysozyme (HEWL) in water and an aqueous solution of N-butylurea (BU) are presented. High-precision densimetric measurements were used to characterize and analyze the changes of the specific volume, v, during temperature elevation. The temperature of the midpoint of protein denaturation was also determined by nanoDSF technique (differential scanning fluorimetry). The...
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Nanoconfined Ionic Liquids. Properties and analytical applications
PublikacjaThe synergistic combination of ionic liquids (ILs) and solid‐like matrices involves a powerful coupling towards the development of new sustainable analytical methodologies. Here we survey the literature regarding such ionic liquid‐based hybrid materials, including a database on relevant physicochemical properties of ionic liquids confined in a solid network. Furthermore, this chapter presents the strategies implemented to combine...
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Obtaining of Coumarone-Indene Resins Based on Light Fraction of Coal Tar. 4. Bitumen-Polymer Blends with Participation of Coumarone-Indene Resins with Epoxy Groups
PublikacjaUsing light fraction of coal tar (5.75 wt % of coumarone and 44.45 wt % of indene), glycidyl methacrylate and styrene, the coumarone-indene resin with epoxy groups (CIRE) has been synthesized. Monoperoxy derivative of diglycidyl ether Bisphenol A (PO) was used as an initiator. The possible formation of CIRE has been studied on the model systems consisting of PO, glycidyl methacrylate, indene or coumarone, or styrene, or mixture...
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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublikacjaMost protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent...
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Strach przed nieznanym błędem
PublikacjaFelieton popularnonaukowy dotyczący algorytmu genetycznego.
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Structural changes of a simple peptide—Trpzip-1—in aqueous solutions and the corresponding hydration phenomena under the influence of temperature
PublikacjaTrpzip-1, a simple β-hairpin, is a rare example of peptide with stable secondary structure and can be a convenient model to study temperature-related processes that potential prion or amyloid proteins undergo. Although its sequence is simple, the exact processes which the peptide undergoes in aqueous solutions are quite complex and not well understood. The selection of well-established experimental (DSC, FTIR) and theoretical methods...
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Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70
PublikacjaThe J-domain protein Zuotin is a multi-domain eukaryotic Hsp70 co-chaperone. Though it is primarily ribosome-associated, positioned at the exit of the 60S subunit tunnel where it promotes folding of nascent polypeptide chains, Zuotin also has off-ribosome functions. Domains of Zuotin needed for 60S association and interaction with Hsp70 are conserved in eukaryotes. However, whether the 4-helix bundle (4HB) domain is conserved remains...
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Symulacje biomolekularne jako narzędzie do badania mechanizmów rozpoznania i wiązania pomiędzy białkami
PublikacjaBiałka pełnią wielorakie funkcje w organizmach żywych, jednak rzadko działają samodzielnie. W zdecydowanej większości przypadków współpracują one między sobą tworząc makrokompleksy o precyzyjnie zorientowanych podjednostkach. Oddziaływania międzybiałkowe wzbudzają więc duże zainteresowanie, jako że w istotny sposób odpowiadają za aktywność biologiczną białek. Choć do tej pory opracowano wiele metod doświadczalnych badania oddziaływań...
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Termodynamika oddziaływań i przejść strukturalnych DNA w układach wodnych na podstawie symulacji metodą dynamiki molekularnej
PublikacjaKwas deoksyrybonukleinowy jest jednym z najistotniejszych elementów każdej żywej komórki ze względu na rolę głównego nośnika informacji genetycznej. Posiada on instrukcje potrzebne do wzrostu, budowy, funkcjonowania oraz namnażania się wielu żywych organizmów, w tym także wirusów. Okazuje się, że w zależności od warunków środowiskowych, DNA może przyjmować wiele różnych struktur drugorzędowych, z których większość stanowi formy...
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Termodynamika oddziaływań substancji tetrafenylowych z wodą w świetle teorii funkcjonału gęstości
PublikacjaW termodynamice roztworów elektrolitów istotne jest zagadnienie podziału eksperymentalnie wyznaczanych wielkości termodynamicznych na udziały jonowe. Z uwagi na niemożność niezależnego wyznaczenia jonowych wielkości cząstkowych, podział wielkości charakteryzujących elektrolit musi być z konieczności dokonany w oparciu o założenie pozatermodynamiczne. Obecnie przyjmuje się, że najbardziej uzasadnionym teoretycznie i eksperymentalnie...
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The hydration of selected biologically relevant molecules – the temperature effect on apparent molar volume and compression
PublikacjaThe densities and sound velocities at T = (288.15, 293.15, 298.15, 303.15 and 308.15) K were measured for aqueous solutions of glycine, trimethylamine-N-oxide, taurine and N-methylacetamide. From these data, the apparent molar volumes, V the apparent molar isentropic compressions, KS,, and the Passynski hydration numbers of solutes were determined. The concentration dependencies of the calculated quantities, their limiting values...
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The interpretation of the parameters of the equation used for the extrapolation of apparent molar volumes of the non-electrolyte (solutes) to the infinite dilution
PublikacjaThe paper discusses how to interpret the parameters of the basic equation used for the extrapolation of the apparent molar volume of the solute to infinite dilution. The common misunderstandings and oversimplifications have been pointed out. We present the alternative ways of the data interpretation that can be used to eliminate these obvious but frequent mistakes.