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Wyniki wyszukiwania dla: MOLECULAR DYNAMICS,OSMOLITY,PROTEIN FOLDING,ZWIJANIE BIAŁEK,OSMOLYTES
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Improvements to the two-phase sandwich method for calculating the melting points of pure metals
PublikacjaThe thermophysical properties of metal alloys are often investigated via molecular dynamics (MD) simulations.An exact and reliable estimation of the thermophysical parameters from the MD data requires a properly and carefullyelaborated methodology. In this paper, an improved two-phase sandwich method for the determination of the metal meltingtemperature is proposed, based on the solid-liquid equilibrium theory. The new method was...
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Excited-state proton transfer and geminate recombination in the molecular cage of β-cyclodextrin
PublikacjaExcited-state proton transfer and geminate recombination in aqueous heptakis(2,6-di-O-methyl)-β-cyclodextrin have been compared with those in water by monitoring the photoinduced prototropic tautomerization of 6-hydroxyquinoline, which occurs via forming anionic intermediate. Enol deprotonation decelerates by 18 times whereas its reverse process accelerates slightly with encapsulation. The imine protonation of the intermediate...
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Tunable Dielectric Switching of (Quinuclidinium)[MnCl4] Hybrid Compounds
PublikacjaInorganic−organic hybrid QMnCl (Q = quinuclidinium) crystals were synthesized and characterized. The X-ray and variable-temperature IR/Raman analysis demonstrate that the crystals undergo a reversible structural phase transition, which originates from an order−disorder process and is related to the dynamics of the organic Q cation. Dielectric function measurements disclose a switchability between low (“OFF”) and high (“ON”) dielectric...
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Fungal L-Methionine Biosynthesis Pathway Enzymes and Their Applications in Various Scientific and Commercial Fields
PublikacjaL-methionine (L-Met) is one of the nine proteinogenic amino acids essential for humans since, in human cells, there are no complete pathways for its biosynthesis from simple precursors. L-Met plays a crucial role in cellular function as it is required for proper protein synthesis, acting as an initiator. Additionally, this amino acid participates in various metabolic processes and serves as a precursor for the synthesis of S-adenosylmethionine...
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Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans—Expression and characterization
PublikacjaDNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the...
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Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges
PublikacjaStaphylococci are increasingly recognized as etiological agents of many opportunistic human and animal infections, emphasizing the need for a rapid and accurate identification, even to a genotypical level of these bacteria. In the recent years, there has been a significant progress in typing and phylogenetic study of Staphylococcus species. Here, we describe molecular methods used in taxonomy as well as staphylococci characterization....
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Dissociative ionization dynamics of dielectric gas C3F7CN
PublikacjaFluoronitrile C3F7CN is a promising candidate for the replacement of SF6 dielectric gas in high-voltage insulation. We present a combined experimental and theoretical study on its ionization dynamics probed in the 0-100 eV energy range. We exploited the total ion collection technique to determine the absolute ionization cross section, mass spectrometry to determine the fragment branching ratios and ab initio nonadiabatic molecular...
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Localization and Orientation of Xanthophylls in a Lipid Bilayer
PublikacjaXanthophylls (polar carotenoids) play diverse biological roles, among which are modulation of the physical properties of lipid membranes and protection of biomembranes against oxidative damage. Molecular mechanisms underlying these functions are intimately related to the localization and orientation of xanthophyll molecules in lipid membranes. In the present work, we address the problem of localization and orientation of two xanthophylls...
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublikacjaG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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Efficient synthesis and antifungal investigation of nucleosides’ quaternary ammonium salt derivatives
PublikacjaQuaternary ammonium salts are a group of compounds with diverse biological properties, the most important of which are their antiviral, antibacterial, and antifungal activities. The quaternization reactions of 5'-O-tosyl derivatives of uridine and thymidine with triethylamine, trimethylamine, 4-(N ,N -dimethylamino)pyridine, 2-methylpyridine, and pyridine are described in this article. Two of the synthesized compounds are exceptional...
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Short-range order structure and free volume distribution in liquid bismuth: X-ray diffraction and computer simulations studies
PublikacjaThe structure of liquid bismuth was studied by X-ray diffraction and computer simulation methods. The contraction of the atomic structure within the first coordination sphere in the temperature interval of 575- 1225 K is reported. The temperature dependencies of the coordination numbers and of the free volume are analysed. On the basis of the temperature dependencies of the free volume, the temperature dependencies of viscosity...
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublikacjaWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
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The role of bile salts in digestion
PublikacjaBile salts (BS) are bio-surfactants present in the gastrointestinal tract (GIT) that play a crucial role in the digestion and absorption of nutrients. The importance of BS for controlled release and transport of lipid soluble nutrients and drugs has recently stimulated scientific interest in these physiological compounds. BS are so-called facial amphiphiles showing a molecular structure that is very distinct from classical surfactants....
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Regulated assembly of lipopolysaccharide and sensing of its alterations in Escherichia coli
PublikacjaThis thesis describes mechanism of the regulation of the transcription of the rpoE gene encoding an essential RNA polymerase subunit in Escherichia coli. The RpoE regulates extracytoplasmic stress response regulon and is required to initiate transcription of genes, whose products are involvedin the folding of periplasmic proteins and synthesis and transport of outer membrane components. The transcriptional regulation of the rpoE...
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In-depth characterization of icosahedral ordering in liquid copper
PublikacjaThe presence of icosahedral ordering in liquid copper at temperatures close to the melting point is now well-established both experimentally and through computer simulation. However, a more elaborate analysis of local icosahedral and icosahedron-like structures, together with a system for classifying such structures based on some measure of "icosahedrity", has so far been conspicuously absent in the literature. Similarly, the dynamics...
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Unraveling Energy Transfer and Fluorescence Quenching Dynamics in Biomolecular Complexes: A Comprehensive Study of Imiquimod-Rifampicin Interaction.
PublikacjaIn nature, numerous biomolecules are implicated in charge transfer (CT) and energy transfer (ET) mechanisms crucial for fundamental processes such as photosynthesis. Unveiling these mechanisms is pertinent to multiple disciplines including chemistry, engineering and biochemistry. This letter presents a study involving two molecules forming a model system with efficient ET properties. Specifically, their complex exhibits dark quenching...
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Nonlinear Influence of Sound on the Vibrational Energy of Molecules in a Relaxing Gas
PublikacjaDynamics of a weakly nonlinear and weakly dispersive flow of a gas where molecular vibrational relaxation takes place is studied. Variations in the vibrational energy in the field of intense sound is considered. These variations are caused by a nonlinear transfer of the acoustic energy into energy of vibrational degrees of freedom in a relaxing gas. The final dynamic equation which describes this is instantaneous, it includes a...
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Waldenstrom macroglobulinemia - Female, 50 - Tissue image [11290630017291461]
Dane BadawczeThis is the histopathological image of HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMS tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Waldenstrom macroglobulinemia - Female, 50 - Tissue image [11290630017282841]
Dane BadawczeThis is the histopathological image of HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMS tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2
PublikacjaWe combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while...
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A new B-D-galactosidase with a low temperature optimum isolated from the Antarctic Arthrobacter sp. 20B: gene cloning, purification and characterization.
PublikacjaA psychrotrophic bacterium producing a coldadaptedB-galactosidase upon growth at low temperatureswas classiWed as Arthrobacter sp. 20B. A genomic DNAlibrary of strain 20B introduced into Escherichia coliTOP10F' and screening on X-Gal (5-bromo-4-chloro-3-indolyl-B-D-galactopyranoside)-containing agar plates ledto the isolation of B-galactosidase gene. The B-galactosidasegene (bgaS) encoding a protein of 1,053 amino acids,with a...
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Expression of a GDSL esterase from Pseudomonas sp. S9 in Pichiapastoris
PublikacjaCold active lipolytic enzymes are promising to replace the conventional enzymes processes of biotechnological industries. One of the most important feature of the cold-active lipases and esterases is that they offer economic benefits through energy saving. In general, they exhibit high activity at low temperatures and low thermostability at moderate temperatures. Lipolytic enzyme EstS9 was isolated from Pseudomonas sp. S9. A multiple...
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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublikacjaF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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Visualizing spatially decomposed intermolecular correlations in the infrared spectra of aprotic liquids
PublikacjaInfrared (IR) spectroscopy is commonly used to study intermolecular interactions in the liquid phase, including solvation phenomena. On the other hand, ab initio molecular dynamics (AIMD) simulations offer the possibility to obtain IR spectra from first principles. Surpassing the experiment, AIMD simulations can deliver additional information on the spatial intermolecular correlations underlying the IR spectrum of the liquid. Although...
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The complete stereochemistry of the antibiotic candicidin A3 (syn. ascosin A3, levorin A3)
PublikacjaHerein, the stereostructure of the aromatic heptaene macrolide (AHM) antifungal antibiotic candicidin A3 (syn. ascosin A3, levorin A3) has been established upon the 2D NMR studies, consisting of DQF-COSY, TOCSY, ROESY, HSQC and HMBC experiments, as well as upon extensive molecular dynamics simulations. The geometry of the heptaenic chromophore was defined as: (22E, 24E, 26Z, 28Z, 30E, 32E, 34E). The previously unreported absolute...
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Structure of partially reduced xPbO (1-x)SiO2 glasses: combined EXAFS and MD study
PublikacjaWykorzystując połączenie metody EXAFS (extended X-ray absorption finestructure) i symulacji MD (molecular dynamics) zbadano strukturęczęściowo zredukowanych szkieł ołowiowo-krzemianowych o różnejstechiometrii wyjściowej. W wyniku analizy uzyskano szczegółowyopis struktury lokalnej wokół atomów ołowiu i jej zmiany w funkcjiskładu szkła i poziomu redukcji. Określono również jaką tendencjędo aglomeracji w metaliczne klastry wykazują...
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Water Behavior Near the Lipid Bilayer
PublikacjaIn this chapter, we focus on the dynamics of water molecules situated in the vicinity of a phospholipid bilayer. Using a molecular dynamics simulation method, we studied interactions between water and the bilayer and tracked trajectories of the water molecules. Based on the hypothesis that molecules trapped inside the bilayer make different motions than the ones which are either attached to the surface or move freely in the water...
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Structural, functional, and stability change predictions in human telomerase upon specific point mutations,
PublikacjaOverexpression of telomerase is one of the hallmarks of human cancer. Telomerase is important for maintaining the integrity of the ends of chromosomes, which are called telomeres. A growing number of human disease syndromes are associated with organ failure caused by mutations in telomerase (hTERT or hTR). Mutations in telomerase lead to telomere shortening by decreasing the stability of the telomerase complex, reducing its accumulation,...
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Ipertrofan Revisited—The Proposal of the Complete Stereochemistry of Mepartricin A and B
PublikacjaBeing a methyl ester of partricin, the mepartricin complex is the active substance of a drug called Ipertrofan (Tricandil), which was proven to be useful in treatment of benign prostatic hyperplasia and chronic nonbacterial prostatitis/chronic pelvic pain syndrome. Nevertheless, no direct structural evidence on the stereochemistry of its components has been presented to date. In this contribution, we have conducted detailed, NMR-driven...
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Central-force decomposition of spline-based modified embedded atom method potential
PublikacjaCentral-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamics simulations, enabling the calculation of the spatial distribution of stress in...
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Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublikacjaTelomerase plays a pivotal role in cell proliferation, homeostasis, and neoplastic transformation, making it a promising molecular target for cancer chemotherapy. Of note, although hTERT has been explored thoroughly as a target, none of the promising molecules has been approved as a drug until now. The subject of research conducted as part of my doctoral dissertation is explaining the cellular and molecular mechanism of action...
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Novel application of terminal restriction fragments length polymorphism method (t-RFLP) for identification of six clinically important Candida sp.
PublikacjaTerminal restriction fragments length polymorphism method (t-RFLP) is a modified classical RFLP method. The main difference is based on carrying out PCR using a fluorescently labeled primer or primers. The result of such modification is that after digestion of amplicons only terminal fragments of PCR product (containing fluorescent dye) are visualized. T-RFLP method has found application in environmental microbiology and epidemiology....
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Tailoring Diffusional Fields in Zwitterion/Dopamine Copolymer Electropolymerized at Carbon Nanowalls for Sensitive Recognition of Neurotransmitters
PublikacjaThe importance of neurotransmitter sensing in the diagnosis and treatment of many psychological illnesses and neurodegenerative diseases is non-negotiable. For electrochemical sensors to become widespread and accurate, a long journey must be undertaken for each device, from understanding the materials at the molecular level to real applications in biological fluids. We report a modification of diamondized boron-doped carbon nanowalls...
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Hyaluronan-Chondroitin Sulfate Anomalous Crosslinking Due to Temperature Changes
PublikacjaGlycosaminoglycans are a wide class of biopolymers showing great lubricating properties due to their structure and high affinity to water. Two of them, hyaluronic acid and chondroitin sulfate, play an important role in articular cartilage lubrication. In this work, we present results of the all-atom molecular dynamics simulations of both molecules placed in water-based solution. To mimic changes of the physiological conditions,...
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Development of chromatographic and mass spectrometry conditions for untargeted lipidomic analysis of human breast milk
PublikacjaHuman breast milk (HBM) is a complex biofluid containing components which are essential for the proper growth of the newborn (for example nutrients such as carbohydrates, proteins, lipids) and also bioactive substances. According to the literature, most of studies involving HBM nutrients investigations focused essentially on the determination of proteins. The molecular composition of lipids in HBM is not well known as the protein...
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Entropy of water calculated from harmonic approximation: estimation of the accuracy of method
PublikacjaSome molecular dynamics simulations were performed for liquid TIP4P and SPC water at a constant density (1.00 g/cm(3)) and within the temperature range of 5-90 degrees C. By using harmonic approximation, both the entropy of water S-H and the specific heat c(v) were calculated, and the results were compared to literature data. It was found that harmonic approximation overestimates absolute entropy of TIP4P water by 5.6 J/mol K (similar...
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Comparative molecular modelling of biologically active sterols
PublikacjaMembrane sterols are targets for a clinically important antifungal agent – amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction...
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Karaś P., Kochanowicz K., Pitek M., Domański P., Obuchowski I., Tomiczek B., Liberek K.: Evolution towards simplicity in bacterial small heat shock protein system// eLife -, (2023), s.1-21
PublikacjaEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either...
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Evolution towards simplicity in bacterial small heat shock protein system
PublikacjaEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either two...
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublikacjaIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Modelling charge transfer processes in C2+ -tetrahydrofuran collision for ion-induced radiation damage in DNA building blocks
PublikacjaInvestigations of collision-induced processes involving carbon ions and molecules of biological interest in particular DNA building blocks, are crucial to model the effect of radiation on cells in order to improve medical treatments for cancer therapy. Using carbon ions appears to be one of the most efficient ways to increase biological effectiveness to damage cancerous cells by irradiating deep-seated tumors. Therefore, interest...
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Antifungal Effect of Penicillamine Due to the Selective Targeting of L-Homoserine O-Acetyltransferase
PublikacjaDue to the apparent similarity of fungal and mammalian metabolic pathways, the number of established antifungal targets is low, and the identification of novel ones is highly desirable. The results of our studies, presented in this work, indicate that the fungal biosynthetic pathway of L-methionine, an amino acid essential for humans, seems to be an attractive perspective. The MET2 gene from Candida albicans encoding L-homoserine...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublikacjaBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations
PublikacjaCysteine–water cluster cations Cys(H2O)3,6 + and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collisioninduced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies...
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublikacjaHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
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c-Myc inhibition and p21 modulation contribute to unsymmetrical bisacridines-induced apoptosis and senescence in pancreatic cancer cells
PublikacjaBackground Pancreatic cancer (PC) is one of the most aggressive cancers and is the seventh leading cause of cancer-related death worldwide. PC is characterized by rapid progression and resistance to conventional treatments. Mutations in KRAS, CDKN2A, TP53, SMAD4/DPC4, and MYC are major genetic alterations associated with poor treatment outcomes in patients with PC. Therefore, optimizing PC therapy is a tremendous challenge. Unsymmetrical...
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Interaction of human serum albumin with volatiles and polyphenols from some berries
PublikacjaHeadspace solid-phase microextraction coupled with comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (HS-SPME/GC GCeTOFMS) identified 19 and quantified 6 monoterpenes in gooseberries, blueberries and cranberries. As a protein model human serum albumin (HSA) was used in interaction with terpenes. Specific binding of terpenes to HSA under the physiological conditions was a result of the formation...
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In silico assessment and sonochemical synthesis of 2-alkynyl 3-chloropyrazines as prospective ligands for SARS-CoV-2
PublikacjaThe recent global pandemic caused by COVID-19 has triggered an intense effort worldwide towards the development of an effective cure for this disease. In our effort we have explored the 2-alkynyl substituted 3-chloropyrazine framework as a potential template for the design of molecules for this purpose. Our strategy was supported by the in silico studies of representative compounds to assess their binding affinities via docking...
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THE GENE CLONING, OVEREXPRESSION, PURIFICATION AND BIOCHEMICAL CHARACTERISATION OF A NEW COLD-ADAPTED β–GALACTOSIDASE FROM ARTHROBACTER SP. VII-4
PublikacjaINTRODUCTION. β-Galactosidase [EC 3.2.1.23] is an enzyme that catalyzes the hydrolysis of O-glycosidic linkages in galactosides. It is commercially used in dairy industry for the production of milk with reduced lactose content. Potentially, the best method for lactose removal under cooling conditions should be carried out with a cold-adapted enzyme. AIM. The aim of this study was to determine the taxonomic affiliation of the isolate...
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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....