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Wyniki wyszukiwania dla: PROTEIN-LIGAND INTERACTIONS
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Hot spot identification by ligand-protein surface interactions mapping – in silico study
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
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Lipid-protein interactions in membranes: a molecular modelling study
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Role of Oligosaccharide Chain Polarity in Protein–Glycosaminoglycan Interactions
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Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito
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How water mediates the long-range interactions between remote protein molecules
PublikacjaThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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Influence of temperature and interactions with ligands on dissociation of dsDNA and ligand-dsDNA complexes of various types of binding : an electrochemical study.
PublikacjaSeveral medicinally important compounds that bind to dsDNA strands via intercalation (C-1311, C-1305, EtBr), major groove binding (Hoechst 33258) and covalent binding (cis-Pt) were examined. The obtained results suggest that both the transfer of conformation B to C and the denaturation process, for the ligand-dsDNA complexes, except for covalently bound cis-Pt, took place at higher temperatures compared to the unbound helix. Furthermore,...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublikacjaShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
PublikacjaRNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA....
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Statistical Method for Analysis of Interactions Between Chosen Protein and Chondroitin Sulfate in an Aqueous Environment
PublikacjaWe present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of univariate time series of chosen features of the dynamics of mucin, which interact with chondroitin sulfate (4 and 6) in four different saline solutions. Our statistical approach is based on recurrence...
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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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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The effect of sunscreen 4‐methylbenzylidene camphor in different and reproductive models, its bioaccumulation and molecular effects on ligand‐receptor interaction, and protein expression
Publikacja4-Methylbenzylidene camphor (4-MBC) is a photo-absorbing UV filter prevalently used in cosmetics, which can be absorbed into circulation and cause systemic effects. 4-MBC is continued to be released in the environment despite the growing knowledge about its bioaccumulation and endocrine disrupting effects. Previous reviews have mentioned UV-filter together but this review considers 4-MBC alone, due to its prevalence and concerning...
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Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublikacjaRadiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions,...
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Understanding the interactions between protein stabilizers and the peptide bond through the analysis of the volumetric and compressibility properties for the model systems
PublikacjaThis work confirms our earlier supposition, that volumetric and acoustic parameters for simple model proposed by us are directly related to stabilizing/destabilizing effect of osmolytes on proteins structure. The apparent molar volumes, V and the apparent molar isentropic compressions, KS,, of glycine and N,N,N –trimethylglycine (betaine) were determined from densities and speed of sound measurements in aqueous solution of N-methylacetamide...
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublikacjaEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublikacjaEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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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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Simplified AutoDock force field for hydrated binding sites
Publikacjahas been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on...
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublikacjaReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: AAEC191A/pACYCpBAD to polystyrene in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: AAEC191A/pACYCpBAD to glass in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pCC90 to polystyrene in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pACYCpBAD to glass in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pCC90 to glass in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pACYCpBAD to polystyrene in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: AAEC191A/pCC90 to glass in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: AAEC191A/pCC90 to polystyrene in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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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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Adolfo Poma
OsobyDr. Adolfo Poma (see my biosketch) is the group leader of the Multiscale Modelling of Complex Systems divison. In 2008, he got a MSc. degree in computational physics from the State University of Campinas (Brazil). Then he moved to Germany and under the supervision of Prof. Kurt Kremer (head of the polymer theory group, Max Planck Institute for Polymer Research) and Prof. Luigi Delle Site (Frei University of Berlin) got a PhD degree...
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Ligand-Modified Boron-Doped Diamond Surface: DFT Insights into the Electronic Properties of Biofunctionalization
PublikacjaWith the increasing power of computation systems, theoretical calculations provide a means for quick determination of material properties, laying out a research plan, and lowering material development costs. One of the most common is Density Functional Theory (DFT), which allows us to simulate the structure of chemical molecules or crystals and their interaction. In developing a new generation of biosensors, understanding the nature...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublikacjaOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state
PublikacjaHuman 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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The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein
PublikacjaThe environment has rapidly looked at proven specialist task forces in the aftermath of the COVID-19 pandemic to build public health policies and measures to mitigate the effects of emerging coronaviruses. According to the researchers, taking 10 μg of 25-hydroxy vitamin D daily is recommended to keep us safe. There have been several studies recently indicating that there is a reduced risk of contracting Coronavirus by 25-hydroxy...
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A Highly Selective Biosensor Based on Peptide Directly Derived from the HarmOBP7 Aldehyde Binding Site
PublikacjaThis paper presents the results of research on determining the optimal length of a peptide chain to eectively bind octanal molecules. Peptides that map the aldehyde binding site in HarmOBP7 were immobilized on piezoelectric transducers. Based on computational studies, four Odorant Binding Protein-derived Peptides (OBPPs) with dierent sequences were selected. Molecular modelling results of ligand docking with selected peptides were...
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Ultrasensitive electrochemical determination of the cancer biomarker protein sPD-L1 based on a BMS-8-modified gold electrode
PublikacjaThis work describes the modification of a gold electrode with the BMS-8 compound that interacts with the Programmed Death-Ligand 1 (PD-L1), an immune checkpoint protein. The results show that we can confirm the presence of the sPD-L1 in the concentration range of 10−18 to 10−8 M using electrochemical impedance spectroscopy (EIS) with a limit of detection (LOD) of 1.87 × 10−14 M for PD-L1 (S/N = 3.3) and at a concentration of 10−14...
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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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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublikacjaIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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Optimization of vortex-assisted supramolecular solvent-based liquid liquid microextraction for the determination of mercury in real water and food samples
PublikacjaA novel method was developed for sample preparation for spectrophotometric determination of Hg(II) in water and food samples. The method was based on vortex-assisted supramolecular solvent-assisted liquid-liquid microextraction (VA-SUPRASs-LLME). Analytical parameters such as pH, chelating agent, solvent type and volume, vortex time and salting out effect were optimized. Surface and normal probability plots were drawn for the variables...
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Determination of long-chain aldehydes using a novel quartz crystal microbalance sensor based on a biomimetic peptide
PublikacjaThere is an increasingly popular trend aimed at improvement of fundamental metrological parameters of sensors via implementation of materials mimicking biological olfactory systems. This study presents investigation on usefulness of the peptide mimicking HarmOBP7 region as a receptor element of the piezoelectric sensor for selective analysis of long-chain aldehydes. Identification of odorant binding proteins creates new possibilities...
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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublikacjaThe solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential -- a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublikacjaF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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PROTEIN EXPRESSION AND PURIFICATION
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On the Origin of Protein Superfamilies and Superfolds
PublikacjaDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Anticancer Study on IrIII and RhIII Half-Sandwich Complexes with the Bipyridylsulfonamide Ligand
PublikacjaTwo non-platinum compounds, organometallic half-sandwich complexes [(η 5 -Cp)IrCl(L)]PF 6 (1) and [(η 5 -Cp)RhCl(L)]PF 6 (2) were prepared by treating pentamethylcyclopentadienyl chloride dimers of iridium(III) or rhodium(III) with the obtained 4-amino-N-(2,2'-bipyridin-5- yl)benzenesulfonamide ligand (L) and ammonium hexafluorophosphate. The crystal structures of ligand (L) and complexes 1 and 2 were obtained and then analyzed. Coordination...
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Jacek Namieśnik prof. dr hab. inż.
OsobyUrodził się 10 grudnia 1949 r. w Mogilnie, zmarł 14 kwietnia 2019 r. w Gdańsku – polski chemik, profesor nauk chemicznych, specjalizujący się w chemii analitycznej i środowiskowej. Rektor Politechniki Gdańskiej w latach 2016–2019. Studia wyższe ukończył w 1972 r. na Wydziale Chemicznym Politechniki Gdańskiej, uzyskując tytuł magistra inżyniera chemika. W 1972 r. rozpoczął pracę na Politechnice Gdańskiej, gdzie w 1978 r. obronił...
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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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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublikacjaThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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Interactions with recognized objects
PublikacjaImplicit interaction combined with object recognition techniques opens a new possibility for gathering data and analyzing user behavior for activity and context recognition. The electronic eyewear platform, eGlasses, is being developed, as an integrated and autonomous system to provide interactions with smart environment. In this paper we present a method for the interactions with the recognized objects that can be used for electronic...
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Hydration of molecules and intermolecular interactions 2023
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Computational methods for calculation of binding free energy for ligand-receptor complexes
PublikacjaAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
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Hydrothermal reactions: From the synthesis of ligand to new lanthanide 3D-coordination polymers
PublikacjaThe organic ligand 2,5-piperazinedione-1,4-diaceticacid (H2PDA) was synthesized under hydrothermal conditions starting from the iminodiacetic acid and catalyzed by oxalic acid. The X-ray powder diffraction data indicates that the compound crystallizes in the P21/c space group as reported in the literature. The ligand was also characterized by elemental analysis, magnetic nuclear resonance, infrared spectroscopy and thermogravimetric...
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublikacjaA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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Influence of Osmolytes on Protein and Water Structure: A Step To Understanding the Mechanism of Protein Stabilization
PublikacjaResults concerning the thermostability of hen egg white lysozyme in aqueous solutions with stabilizing osmolytes, trimethylamine-N-oxide (TMAO), glycine (Gly), and its N-methyl derivatives, N-methylglycine (NMG), N,N-dimethylglycine (DMG), and N,N,N-trimethylglycine (betaine, TMG), have been presented. The combination of spectroscopic (IR) and calorimetric (DSC) data allowed us to establish a link between osmolytes’ influence on...
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Intercultural interactions in multinational subsidiaries
PublikacjaPurpose - Our aim is to show how individuals perceive the quality of intercultural interactions at work in multinational subsidiaries, and to address the question of what actually prevails in their accounts, i.e. ‘the dark side’ or ‘the bright side’. Design/methodology/approach - We report the findings from five subsidiaries located in Poland and interviews with 68 employees of these companies. Findings - The ‘bright side’ dominated...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublikacjaPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublikacjaIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Determination of viscosity changes of protein hydrolyzate solutions depending on shear rate
Dane BadawczeRheological characteristics of connective tissue protein solutions were made on the basis of viscosity measurement using a Brookfield viscometer using LV SC4 - 27 spindles and shear rate of 85 s-1 (Fig. 1). Solutions of protein hydrolysates with a concentration of 2% in 0.5M acetic acid were prepared.
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Interactions of positrons with atoms and molecules
PublikacjaThe positron is the antiparticle of the electron. It has the same mass as the electron, but opposite charge. The understanding of the interactions of positrons with normal matter, like atoms and molecules, is of interest in various scientific fields, like nuclear medicine, plasma physics and astronomy. In this talk we will give a short introduction to some theoretical methods to describe the interactions of positrons with atoms...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Electroabsorption study of metal-to-ligand charge transfer in an organic complex of iridium (III).
PublikacjaW pracy zmierzono i zinterpretowano widmo elektroabsorpcji (EA) próżniowo naparowanych warstw organicznego kompleksu Ir(ppy)3, powszechnie stosowanego jako emiter fosforescencyjny w organicznych diodach elektroluminescencyjnych. Analiza widma EA potwierdziła fakt,że niskoenergetyczne stany elektronowe tego kompleksu związane są z przeniesieniem ładunku metal-ligand.
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Kompleksy metali przejściowych zawierające ligand R2P-P
PublikacjaBadania obejmują kompleksy metali przejściowych zawierające ligandy fosfanylofosfinidenowe oraz fosfanylofosfidowe. Kompleksy te są pochodnymi kompleksów fosfinidenowych oraz fosfidowych, gdzie grupa alkilowa została zastąpiona grupą fosfanylową (R’2P). W pracy można wydzielić trzy główne obszary badań. Pierwszym było zbadanie reaktywności R2PP(SiMe3)Li względem diamidowych bądź β-diketiminowych kompleksów cyrkonu zawierających...
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Protein & Cell
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Earth Interactions
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HYPERFINE INTERACTIONS
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INTERNATIONAL INTERACTIONS
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PROTEIN JOURNAL
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DMSO and TMAO—Differences in Interactions in Aqueous Solutions of the K-Peptide
PublikacjaInteractions between a solvent and their co-solute molecules in solutions of peptides are crucial for their stability and structure. The K-peptide is a synthetic fragment of a larger hen egg white lysozyme protein that is believed to be able to aggregate into amyloid structures. In this study, a complex experimental and theoretical approach is applied to study systems comprising the peptide, water, and two co-solutes: trimethylamide...
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Modelling gene expression of a self-regulating protein
PublikacjaWe analyze a model of gene transcription and protein synthesis. We take into account the number of sites on the protein’s promoter at which the protein’s dimers can bind blocking transcription of protein mRNA.
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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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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublikacjaInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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Methods for Elucidation of DNA-Anticancer Drug Interactions and Their Applications in the Development of New Drugs
PublikacjaDNA damaging agents including anthracyclines, camptothecins and platinum drugs are among most frequently used drugs in the chemotherapeutic routine. Due to their relatively low selectivity for cancer cells, administration is associated with adverse side effects, whereas the inherent genotoxicity of these drugs is associated with risk of developing secondary cancers. Development of new drugs, which could be spared of these drawbacks...
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Novel primosomal protein B from Clostridium pasteurianum
PublikacjaPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Novel primosomal protein B from Clostridium pastuerianum
PublikacjaPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublikacjaBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublikacjaBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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[NCh-bio] Advances in Biotechnology: Protein Folding and Assembly
Kursy Online{mlang pl} Dyscyplina: nauki chemiczne Zajęcia obowiązkowe dla doktorantów I i II roku z obszaru biotechnologii Prowadzący: dr hab. Gracjana Klein-Raina, prof. PG Liczba godzin: 15 Forma zajęć: wykład {mlang} {mlang en} Discipline: chemical sciences Obligatory course for 1st and 2nd-year PhD students from biotechnology area Academic teachers: dr hab. Gracjana Klein-Raina, prof. PG Total hours of training: 15 teaching...
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Individual Resources and Intercultural Interactions
PublikacjaThe work environment in multinational corporations (MNCs) is specific and demanding including intercultural interactions with co-workers and clients and using a foreign language. Some individual resources can help in dealing with these circumstances. Individual resources refer to personal dispositions, competencies and prior experiences. With regard to previous studies, a caravan of personal resources, namely Psychological Capital...
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Intercultural interactions at multinational corporations' workplace: Grounded theory.
Publikacjaenvironments is a new challenge for employees and managers. The aim of the paper is to analyze the social interactions in multicultural environments of multinational corporations (MNCs) as well as to propose a model of intercultural social interactions in MNCs’ specifi c context. Design/methodology/approach: The grounded theory approach was applied to create a model of intercultural interactions in MNCs. The data was obtained during...
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Journal of Receptor Ligand and Channel Research
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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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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublikacjaThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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Protein thermal stabilization in aqueous solutions of osmolytes
PublikacjaProteins’ thermal stabilization is a significant problem in various biomedical, biotechnological, and technological applications. We investigated thermal stability of hen egg white lysozyme in aqueous solutions of the following stabilizing osmolytes: Glycine (GLY), N-methylglycine (NMG), N,N-dimethylglycine (DMG), N,N,N-trimethylglycine (TMG), and trimethyl-N-oxide (TMAO). Results of CD-UV spectroscopic investigation were compared...
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Discovering interactions between applications with log analysis
PublikacjaApplication logs record the behavior of a system during its runtime and their analysis can provide useful information. In this article, we propose a method of automated log analysis to discover interactions taking place between applications in an enterprise. We believe that such an automated approach can greatly support enterprise architects in building an up-to-date view of a governed system in a modern, fast-paced development...
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The investigation of the effects of counterions in protein dynamics simulations
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Synthesis, crystal structure and cytotoxic activity of ruthenium(II) piano-stool complex with N,N-chelating ligand
PublikacjaA mononuclear compound of the general formula [(η6-p-cymene)RuIICl(2,2′-PyBIm)]PF6 has been synthesized from a bidentate N,N-donor ligand, viz. 2,-(2′-pyridyl)benzimidazole (2,2′-PyBIm) and the corresponding chloro-complex [(η6-p-cymene)Ru(μ-Cl)Cl]2 (precursor). The isolated coordination compound was characterized by IR, UV–vis and 1H, 13C NMR spectroscopies. The single crystal X-ray analysis of the complex reveals that the asymmetric...
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Construction and purification of his6-Thermus thermophilus MutS protein
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Construction and purification of his6-Thermus thermophilus MutS protein.
PublikacjaGen mutS z termofilnej bakterii Thermus thermophilus zamplifikowano przy użyciu PCR, sklonowano i przeprowadzono jego ekspresję w E. coli. Rekombinantowe białko MutS zawierające oligohistydynową domenę na N-końcu oczyszczono w jednoetapowej procedurze przy wykorzystaniu chromatografii powinowactwaNi(2+). Zdolność do rozpoznania niekomplementarności białka his(6)-MutS potwierdzono w eksperymentach ochrony DNA przed trawieniem...
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Role of the Synergistic Interactions of Environmental Pollutants in the Development of Cancer
PublikacjaThere is a growing awareness that the large number of environmental pollutants we are exposed to on a daily basis are causing major health problems. Compared to traditional studies that focus on individual pollutants, there are relatively few studies on how pollutants mixtures interact. Several studies have reported a relationship between environmental pollutants and the development of cancer, even when pollutant levels are below...
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PROTEIN SCIENCE
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MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publikacja—Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence...
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Interactions in aqueous solutions of K-peptide and DMSO – spectroscopic and calorimetric studies
PublikacjaIntroduction K-peptide (GILQINSRW) – short 9 amino acid fragment of the hen egg white lysozyme has the ability to form amyloid structures. Dimethyl sulfoxide (DMSO) is an osmolyte which can alter this ability. Our goal was to get an insight into the mechanism of Kpeptide-DMSO interactions in aqueous solutions. Such a knowledge can be helpful to understand processes leading to various neurodegenerative diseases. Methods ATR-FTIR...
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Low-energy interactions related to atmospheric and extreme conditions
PublikacjaThis Topical Issue, entitled “Low-Energy Interactions Related to Atmospheric and Extreme Conditions”, showcases a collection of eighteen articles that reported recent theoretical and experimental findings pertaining to the following topics: – low-energy interactions of charged particles (electrons [1–7], protons [8], positrons [9]), and photons [10] with atoms and molecules of biological [1–4,7,8], astrochemical [10], industrial,...
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Syntheses, Structures and Reactivity of Terminal Phosphido Complexes of Iron(II) Supported by a β-Diketiminato Ligand
PublikacjaWe report the synthesis of the first series of terminal phosphido iron complexes supported by a β‐diketiminato ligand (Dippnacnac) and their catalytic activity in dehydrocoupling of secondary phosphines. Anionic and neutral mono‐ or diphosphido complexes were obtained from the reaction of [(Dippnacnac)FeCl2Li(dme)2] with the R2PLi (R = iPr, tBu, Cy, Ph) phosphides by tuning the stoichiometric ratio, polarity of the solvent, and...
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublikacjaGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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MutL protein as a constituent of vsp, ner and mmr repair systems
PublikacjaMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mis- match repair system (MMR). However, there is growing evidence that MMR system is not the only field of action for these pro- teins. Moreover, the participation in MMR does not even have to be their primary function. There are some reports indicat- ing involvement of MutL in BER, NER and VSP (very short patch repair)....
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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...