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Wyniki wyszukiwania dla: molecular interactions
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Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology
PublikacjaLignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization...
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Novel tetrahedral cobalt(II) silanethiolates: structures and magnetism
PublikacjaThree heteroleptic complexes of Co(II) tri-tert-butoxysilanethiolates have been synthesized with piperidine [Co{SSi(OtBu)3}2(ppd)2] 1, piperazine [Co{SSi(OtBu)3}2(NH3)]2(μ-ppz)·2CH3CN 2, and N-ethylimidazole [Co{SSi(OtBu)3}2(etim)2] 3. The complexes have been characterized by a single-crystal X-ray, revealing their tetrahedral geometry on Co(II) coordinated by two nitrogen and two sulfur atoms. Complexes 1 and 3 are mononuclear,...
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Synthesis, Structure, and Spectroscopic Properties of Calcium Thiophenecarboxylate Polymers. Structural Comparison with Analogous Lead Complexes
PublikacjaThree novel calcium coordination polymers [Ca(2tpCOO)2(2mpa)(H2O)]n (1), [Ca(3tpCOO)2(2mpa)(H2O)]n (2), and {[Ca(3tpacCOO)2(H2O)2]⋅⋅⋅H2O}n (3) (2tpCOO− or 3tpCOO− – thiophene-2- or thiophene-3-carboxylate, 3tpacCOO− – thiophene-3-acetate, 2mpa – 2-methylpropanal), were synthesised using a self-assembly method. The obtained polymers were characterised using SC-XRD, FTIR, UV-Vis DRS, thermogravimetric and luminescence analyses. The...
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How Do Intermolecular Interactions Evolve at the Nematic to Twist–Bent Phase Transition?
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Quantitative fluorescent determination of DNA – Ochratoxin a interactions supported by nitrogen-vacancy rich nanodiamonds
PublikacjaOchratoxin A (OTA) is a hazardous contaminant of a large variety of plant and animal originated food. Herein, we report an interaction of OTA with calf thymus DNA (ct DNA) on the nanodiamond surface. We employed multispectroscopic techniques to elucidate the binding mechanism of OTA with ct DNA. The fluorescence and UV–Vis spectroscopy results show that OTA binds to ds ct DNA and forms complexes. We obtained the binding constants...
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Deep Eutectic Solvents as Agents for Improving the Solubility of Edaravone: Experimental and Theoretical Considerations
PublikacjaIn this study, both practical and theoretical aspects of the solubility of edaravone (EDA) in Deep Eutectic Solvents (DESs) were considered. The solubility of edaravone in some media, including water, can be limited, which creates the need for new efficient and environmentally safe solvents. The solubility of EDA was measured spectrophotometrically and the complex intermolecular interactions within the systems were studied with...
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Deep Eutectic Solvents as Agents for Improving the Solubility of Edaravone: Experimental and Theoretical Considerations
PublikacjaIn this study, both practical and theoretical aspects of the solubility of edaravone (EDA) in Deep Eutectic Solvents (DESs) were considered. The solubility of edaravone in some media, including water, can be limited, which creates the need for new efficient and environmentally safe solvents. The solubility of EDA was measured spectrophotometrically and the complex intermolecular interactions within the systems were studied with...
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The influence of reactions conditions on aggregation of dyes used in biochemistry
PublikacjaSelf-association of dyes and related substances is a very important phenomenon in many fields of applied chemistry. It is also fundamental model reaction of many kinds of molecular interactions such as the micelle formation of amphiphilic substances and the binding of small organic molecules to macromolecules. In spite of many studies concerning the dimerization equilibria of dyes and related substances, the mechanism seems not...
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublikacjaHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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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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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublikacjaIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Cobalt(II) tri-tert-butoxysialanethiolates.Synthesis, properties, crystal and molecular structures of [Co{SSi(OtBu)3}2(L)] and[Co{SSi(OtBu)3}2(L)2] type complexes with monodentate nitrogen ligands.
PublikacjaThe title heteroleptic neutral cobalt(II) tri-tert-butoxysilanethiolate complexes with monodentate nitrogen bases (L) as additional ligands have been prepared by the reactions of [Co{μ-SSi(OtBu)3}{SSi(OtBu)3}(NH3)]2 (1) with respective bases. For pyridine both types have been prepared...
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Removal of diphenols using pine biochar. Kinetics, equilibrium, thermodynamics, and mechanism of uptake
PublikacjaThermal pyrolysis synthesized activated biochar from the Pinus elliottii sawdust (PS) at 600° C. The obtained activated biochar (PB600) was used for the removal of three diphenols, catechol (CAT), resorcinol (RES), and hydroquinone (HYD), which are utilized mainly in different industries. The PB600 was characterized by several analytical techniques. The BET surface area of 1473 m2.g−1 and a total pore volume of 0.707 cm3 g−1 was...
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A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublikacjaIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Theoretical investigation of the structural insights of the interactions of γ-Fe2O3 nanoparticle with (EMIM TFSI) ionic liquid
PublikacjaOne of the possible applications of ionic liquids is to produce electricity from heat. The iron oxide nanoparticle is a potent electrical particle, which is expected to improve the heat’s efficiency to electricity conversion, however, it is prone to aggregation and sedimentation, which hamper its application. One of the methods to enhance the nanoparticle’s solubility and electrical properties is the use of a stabilizing component...
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Interactions in Ternary Aqueous Solutions of NMA and Osmolytes—PARAFAC Decomposition of FTIR Spectra Series
PublikacjaIntermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel...
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Dipole-driven dynamics for near-threshold electron/positron interactions with pyrimidinic DNA bases: a path to compound formations
PublikacjaCalculations are reported for electron and positron scattering from isolated cytosine and thymine, where the two pyrimidinic single-ring DNA bases, in the gas-phase at energies near the elastic threshold, they reveal the special features of the dipole-driven scattering states. All molecules examined exhibit, in fact, supercritical (>1.67 D) permanent dipoles which can therefore also support, below threshold, excited bound compound...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublikacjaLow 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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Synthesis of green benzamide-decorated UiO-66-NH2 for biomedical applications
PublikacjaMetal-organic frameworks (MOFs) biocompatible systems can host enzymes/bacteria/viruses. Herein we synthesized a series of fatty acid amide hydrolase (FAAH)-decorated UiO-66-NH2 based on Citrus tangerine leaf extract for drug delivery and biosensor applications. Five chemically manipulated FAAH-like benzamides were localized on the UiO-66-NH2 surface with physical interactions. Comprehensive cellular and molecular analyses were...
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Structure-property relationships disclosed in the family of acridinium esters – chemiluminogenic molecules of great practical importance
PublikacjaAcridinium esters (AE), since their introduction to the analytics 30 years ago, make one of the most important groups of chemiluminogenic (CL) systems, that have been employed in medical diagnostics and environmental analysis today. So far, however, no systematic studies on the structureproperty relationships were carried out in this family of compounds. The latter features likely determine their practical utility and facilitate...
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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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Superconducting SrSnP with Strong Sn–P Antibonding Interaction: Is the Sn Atom Single or Mixed Valent?
PublikacjaThe large single crystals of SrSnP were prepared using Sn self-flux method. The superconductivity in the tetragonal SrSnP is observed with the critical temperature of ∼2.3 K. The results of a crystallographic analysis, superconducting characterization, and theoretical assessment of tetragonal SrSnP are presented. The SrSnP crystallizes in the CaGaN structure type with space group P4/nmm (S.G. 129, Pearson symbol tP6) according...
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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublikacjaWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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(4-(Bis(4-Fluorophenyl)Methyl)Piperazin-1-yl)(Cyclohexyl)Methanone Hydrochloride (LDK1229): A New Cannabinoid CB1 Receptor Inverse Agonist from the Class of Benzhydryl Piperazine Analogs
PublikacjaSome inverse agonists of cannabinoid receptor type 1 (CB1) have been demonstrated to be anorectic antiobesity drug candidates. However, the first generation of CB1 inverse agonists, represented by rimonabant (SR141716A), otenabant, and taranabant, are centrally active, with a high level of psychiatric side effects. Hence, the discovery of CB1 inverse agonists with a chemical scaffold distinct from these holds promise for developing...
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Assessing the Interactions of Statins with Human Adenylate Kinase Isoenzyme 1: Fluorescence and Enzyme Kinetic Studies
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Interactions of fish gelatin and chitosan in uncrosslinked and crosslinked with EDC films: FT-IR study
PublikacjaFilms based on fish gelatin, chitosan and blend of fish gelatin and chitosan before and after cross-linking with EDC have been characterized by FT-IR spectroscopy. The FT-IR spectrum of fish gelatin film showed the characteristic amide I, amide II and amide III bands, and the FT-IR spectrum of chitosan film confirmed that the polymer was only a partially deacetylated product, and included CH3-C=O and NH2 groups, the latter both...
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Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain Serratia quinivorans KP32 to Fungal Phytopathogens
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Antibiotic-sterol interactions provide insight into the selectivity of natural aromatic analogues of amphotericin B and their photoisomers
PublikacjaAromatic heptaene macrolides (AHMs) belong to the group of polyene macrolide antifungal antibiotics. Members of this group were the first to be used in the treatment of systemic fungal infections. Amphotericin B (AmB), a non-aromatic representative of heptaene macrolides, is of significant clinical importance in the treatment of internal mycoses. It includes the all-trans heptaene chromophore, whereas the native AHMs contain two...
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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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Nanofiltration-Assisted Concentration Processes of Phenolic Fractions and Carotenoids from Natural Food Matrices
PublikacjaIn new food formulations, carotenoids and phenolic compounds are likely to be the most sought after food ingredients according to their bioactivity, nutraceutical, nutritional value, and compatibility properties once incorporated into food formulations. Such solutes are naturally present in many plant-based sources, and some portions are directly consumed when enriching food products and formulations; however, some portions, which...
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Copper(I) iodide ribbons coordinated with thiourea derivatives
PublikacjaTwo products of the reactions of CuI with 1-benzoyl-3-(4-bromophenyl)thiourea and with 1-benzoyl-3-(2-iodophenyl)thiourea have been obtained and characterized, namely poly[[[1-benzoyl-3-(4-bromophenyl)thiourea-κS]-µ3-iodidocopper(I)] acetone hemisolvate], {[CuI(C₁₄H₁₁BrN₂OS)]‧0.5C₃H₆O}ₙ, and poly-[µ₄-iodido-µ₃-iodido-[N-(benzo[d]thiazol-2-yl)benzamide-κN]dicopper(I)], [Cu₂I₂(C₁₄H₁₀N₂OS)]ₙ. Their structures, determined by single-crystal...
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Synthesis and biological evaluation of fluorinated N-benzoyl and N-phenylacetoyl derivatives of 3-(4-aminophenyl)-coumarin-7-O-sulfamate as steroid sulfatase inhibitors
PublikacjaIn the present work, we report convenient methods for the synthesis of 3-(4-aminophenyl)-coumarin-7-O-sulfamate derivatives N-acylated with fluorinated analogues of benzoic or phenylacetic acid as steroid sulfatase (STS) inhibitors. The design of these potential STS inhibitors was supported by molecular modeling techniques. Additionally, computational docking methods were used to determine the binding modes of the synthesized inhibitors...
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Engineering boron and nitrogen codoped carbon nanoarchitectures to tailor molecularly imprinted polymers for PFOS determination
PublikacjaPer- and polyfluoroalkyl substances (PFAS) have gained significant attention as emerging contaminants due to their persistence, abundance, and adverse health effects. Consequently, the urgent need for ubiquitous and effective sensors capable of detecting and quantifying PFAS in complex environmental samples has become a priority. In this study, we present the development of an ultrasensitive molecularly imprinted polymer (MIP)...
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The interactions of monomeric acridines and unsymmetrical bisacridines (UAs) with DNA duplexes: an insight provided by NMR and MD studies
PublikacjaMembers of a novel class of anticancer compounds, exhibiting high antitumor activity, i.e. the unsymmetrical bisacridines (UAs), consist of two heteroaromatic ring systems. One of the ring systems is an imidazoacridinone moiety, with the skeleton identical to the structural base of Symadex. The second one is a 1-nitroacridine moiety, hence it may be regarded as Nitracrine’s structural basis. These monoacridine units are connected...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublikacjaOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Thermodynamics and Intermolecular Interactions of Nicotinamide in Neat and Binary Solutions: Experimental Measurements and COSMO-RS Concentration Dependent Reactions Investigations
PublikacjaIn this study, the temperature-dependent solubility of nicotinamide (niacin) was measured in six neat solvents and five aqueous-organic binary mixtures (methanol, 1,4-dioxane, acetonitrile, DMSO and DMF). It was discovered that the selected set of organic solvents offer all sorts of solvent effects, including co-solvent, synergistic, and anti-solvent features, enabling flexible tuning of niacin solubility. In addition, differential...
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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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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublikacjaAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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Structural, spectral and magnetic properties of Ni(II), Co(II) and Cd(II) compounds with imidazole derivatives and silanethiolate ligands
PublikacjaA series of new metal heteroleptic complexes have been obtained in simple reactions of 1-(3-aminopropyl)-imidazole (api) and 1,4-bis(imidazol-1-yl)-butane (bbi) ligands with metal silanethiolates or acetylacetonates. The obtained complexes are the coordination polymers [Ni{SSi(tBuO)3}2(μ-api)]n1, [Co{SSi(tBuO)3}2(μ-api)]n2, [Cd{SSi(tBuO)3}2(μ-api)·2CH3OH]n3, [Cd{SSi(tBuO)3}2(μ-bbi)·CHCl3]n4 and the dimer [Co{SSi(tBuO)3}2(μ-bbi)·3CH3OH]25....
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublikacjaF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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Novel Cell Permeable Polymers of N-Substituted L-2,3-Diaminopropionic Acid (DAPEGs) and Cellular Consequences of Their Interactions with Nucleic Acids
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Interactions between hydration spheres of two different solutes in solution: The least squares fitting with constraints as a tool to determine water properties in ternary systems
PublikacjaBiological systems are complex and the problem of their description lies in mutual interactions between their components. This paper is focused on model experiment-based studies which can reduce these difficulties. The ternary aqueous N-methylacetamide (NMA)–Na2HPO4 system has been studied by means of the FTIR spectroscopy. A novel difference spectra method aimed to extract the spectral contribution of water affected simultaneously...
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Nonlocal Models of Plates and Shells with Applications in Micro- and Nanomechanics
PublikacjaNowadays, the use of small-scale structures in micro/nanomachines has become more and more widespread. The most important applications of such small-sized parts are in micro-electro-mechanical systems (MEMS) as well as nano-electro-mechanical systems (NEMS) as actuators, sensors, energy harvesters. For example, nanosensors are nanoscale devices that measure physical quantities and convert these to signals that can be detected and...
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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublikacjaWe extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
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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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Polarisation effects in low-energy positron–molecule scattering
PublikacjaThe UK molecular R-matrix method has been adapted to treat positron collisions from polyatomic targets. A simple empirical enhancement factor which corrects for the underestimation of electron–positron polarisation and correlation effects in the calculations performed with the static-plus-polarization model at low scattering energies is presented. Application of this model to positron scattering from carbon dioxide at energies...
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Electrochemical simulation of enzymatic transformations studied for the selected antitumor acridine derivatives
PublikacjaThe elucidation of the metabolic pathways and the biotransformation mechanisms of potential drugs is a crucial point in drug development. It allows to know the activation routes of the new biologically active compounds, especially in respect to their possible toxicity. Generally, in vivo or in vitro experiments with liver microsomes or hepatocytes are performed. However, these testing schemes are tedious, time consuming and of...
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Protective effect of Aronia melanocarpa polyphenols against cadmium-induced disorders in bone metabolism: A study in a rat model of lifetime human exposure to this heavy metal
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Cellular uptake of biotransformed graphene oxide into lung cells
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