Search results for: conformation of protein - albumin
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Anticancer Study on IrIII and RhIII Half-Sandwich Complexes with the Bipyridylsulfonamide Ligand
PublicationTwo 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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Comparison of the main bioactive compounds and antioxidants in garlic and white and red onion after treatment protocols
PublicationPolski czosnek, biała i czerwona cebula była blanszowana, gotowana, smażona i poddawana działaniom promieniowania mikrofalowego. Następnie były w nich oznaczane m.in. takie związki jak polifenole, flawonoidy, kwas ascorbinowy i aktywne antyoksydanty. Udowodniono, że blanszowanie, smażenie i poddawanie działaniu promieniowania mikrofalowego nie wpływa znacząco na zmiejszenie zawartości badanych związków w czosnku i cebuli. Wyznaczono...
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Influence of the ionic strength on the amyloid fibrillogenesis of hen egg white lysozyme
PublicationThe study investigates the role of the electrostatic interactions in the fibrillation of the hen egg white lysozyme (HEWL). In order to achieve this aim the influence of the cations Na+, Mg2+ and Al3+ on the amyloid fibril formation and amorphous aggregation was tested. The amyloids are formed in the solution without added salt but the Thioflavin T fluorescence gives the false-negative result. In these conditions, the HEWL fibrils...
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Ligand-Modified Boron-Doped Diamond Surface: DFT Insights into the Electronic Properties of Biofunctionalization
PublicationWith 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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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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The biological role of prolyl oligopeptidase and the procognitive potential of its peptidic inhibitors from food proteins
PublicationProlyl oligopeptidase (POP) is a conserved serine protease belonging to proline-specific peptidases. It has both enzymatic and non-enzymatic activity and is involved in numerous biological processes in the human body, playing a role in e.g., cellular growth and differentiation, inflammation, as well as the development of some neurodegenerative and neuropsychiatric disorders. This article describes the physiological and pathological...
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The Boltzmann sequence-structure channel
PublicationWe rigorously study a channel that maps binary sequences to self-avoiding walks in the two-dimensional grid, inspired by a model of protein statistics. This channel, which we also call the Boltzmann sequence-structure channel, is characterized by a Boltzmann/Gibbs distribution with a free parameter corresponding to temperature. In our previous work, we verified experimentally that the channel capacity has a phase transition for...
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An Investigation of Polyamides Based on Isoidide-2,5-dimethyleneamine as a Green Rigid Building Block with Enhanced Reactivity
PublicationNovel, semicrystalline polyamides and copolyamides were synthesized from a new carbohydrate-based diamine, namely isoidide-2,5-dimethyleneamine (IIDMA). In combination with 1,6-hexamethylene diamine (1,6-HDA) as well as the biobased sebacic acid (SA) or brassylic acid (BrA), the desired copolyamides were obtained via melt polymerization of the nylon salts followed by a solid-state polycondensation (SSPC) process. Depending on the...
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The electrochemical response to BDD electrode functionalization with CD147 receptor
Open Research DataThis dataset contains the results of the electrochemical impedance spectroscopy (EIS) measurements of the boron-doped diamond (BDD) electrode functionalization with CD147 receptor. The functionalized electrode was then used for the electrochemical detection of the SARS-CoV-2 virus S1 protein.
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The electrochemical response to BDD electrode functionalization with ACE2 receptor
Open Research DataThis dataset contains the results of the electrochemical impedance spectroscopy (EIS) measurements of the boron-doped diamond (BDD) electrode functionalization with ACE2 receptor. The functionalized electrode was then used for the electrochemical detection of the SARS-CoV-2 virus S1 protein.
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The electrochemical response to BDD electrode functionalization with IgG2B receptor
Open Research DataThis dataset contains the results of the electrochemical impedance spectroscopy (EIS) measurements of the boron-doped diamond (BDD) electrode functionalization with IgG2B receptor. The functionalized electrode was then used for the electrochemical detection of the SARS-CoV-2 virus S1 protein.
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Structural features responsible for control of the eukaryotic GlcN-6-P synthase activity
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. As UDP-GlcNAc, the final product of the hexosamine path, constitutes one of the essential substrates for assembly of bacterial and fungal cell walls, the enzyme is an interesting target for antimicrobial therapy.The structure of E. coli enzyme, known since 2001, forms a dimer of two identical...
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Does the chemical modification of Nystatin A1 affect the drug's ability to overcome the multidrug resistance of fungi?
PublicationAlthough the contemporary medicine keeps moving forward, disseminated infections caused by fungal pathogens are an emerging challenge. The dramatic rise of fungal diseases, especially the most life-threatening systemic mycoses is associated with a permanently growing number of immunodeficient patients. Undoubted difficulties in the treatment of fungal infections are caused by lack of highly effective and selective antifungal drugs,...
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Regulated assembly of lipopolysaccharide and sensing of its alterations in Escherichia coli
PublicationThis 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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Regulation of LPS assembly via controlled proteolysis and sensing of LPS stress in Escherichia coli
PublicationLipopolysaccharide (LPS) is a complex glycolipid, essential for the bacterial viability and along with phospholipids, it constitutes the major amphiphilic component of outer membrane (OM) in most of the Gram-negative bacteria, including Escherichia coli. LPS molecules confer an effective permeability barrier to the OM and play a crucial role in bacteria-environment and -host interactions. The synthesis and accumulation of this...
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Sodium alginate decreases the permeability of intestinal mucus
PublicationIn the small intestine the nature of the environment leads to a highly heterogeneous mucus layer primarily composed of the MUC2 mucin. We set out to investigate whether the soluble dietary fibre sodium alginate could alter the permeability of the mucus layer. The alginate was shown to freely diffuse into the mucus and to have minimal effect on the bulk rheology when added at concentrations below 0.1%. Despite this lack of interaction...
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Białka prokariotycznego systemu MMR: rola oraz interakcje
PublicationUszkodzenia komórkowego DNA w postaci błędnie sparowanych lub niesparowanych zasad azotowych są wynikiem niewłaściwie zachodzących procesów metabolizmu DNA, takich jak replikacja, rekombinacja oraz naprawa DNA. Utrwalenie tego rodzaju zmian prowadzi do powstania mutacji. System MMR (ang. DNA mismatch repair) usuwa te uszkodzenia przyczyniając się do zwiększenia wierności replikacji DNA oraz utrzymania stabilności genomu komórki....
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Influence of mussels (Mytilus galloprovincials) from polluted and non-polluted areas on some atherosclerosis indices in rats fed cholesterol
PublicationBadano wpływ diety z dodatkiem małży z obszarów zanieczyszczonych i obszarów czystych ekologicznie na niektóre objawy arteriosklerozy u szczurów.Na podstawie wyników badań in vitro, małże pochodzące z obszarów zanieczyszczonych charakteryzują sie większą zawartością protein, metali ciężkich oraz przeciwutleniaczy.Badania przeprowadzono na 28 szczurach podzielonych na 4 grupy. Szczury z grupy kontrolnej otrzymywały podstawową diete...
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Electronic noses: Powerful tools in meat quality assessment
PublicationMain factors that are considered by consumers when choosing meat products are colour and aroma, of which the latter is a more reliable indicator of quality. However, a simple sensory evaluation of hedonistic qualities is often not sufficient to determine whether protein is past its shelf life, and consumption of spoiled meat can lead to serious health hazards. Some volatile compounds can be used as spoilage indicators, and so a...
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Analytical Strategies and Applications in Lipidomics
PublicationLipidomics is a field of study aiming at a comprehensive analysis of a set of lipids in biological systems. This includes both quantitative and qualitative characterization of lipid profiles, comparative studies of lipidomes, and analysis of lipid-protein interactions. Lipids are structurally diversified that make their analysis a challenging task. The constant advances in analytical technologies, especially in the field of high-performance...
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Amino Acid and Peptide‐Based Antiviral Agents
PublicationA significant number of antiviral agents used in clinical practice are amino acids, short peptides, or peptidomimetics. Among them, several HIV protease inhibitors (e. g. lopinavir, atazanavir), HCV protease inhibitors (e. g. grazoprevir, glecaprevir), and HCV NS5A protein inhibitors have contributed to a significant decrease in mortality from AIDS and hepatitis. However, there is an ongoing need for the discovery of new antiviral...
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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MRM–MS of marker peptides and their abundance as a tool for authentication of meat species and meat cuts in single-cut meat products
PublicationThe abundance of protein markers in different types of meat cuts was explored in the context of authentication of raw meat (pork, beef and chicken) and processed meat products. Peptides originating from myoglobin (Mb) and myosin (My) were analyzed using multiple reaction monitoring mass spectrometry (MRM–MS). Analytical protocol was optimized for good repeatability (CV < 10%) and high sensitivity. The MS signal intensity of Mb...
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Development of chromatographic and mass spectrometry conditions for untargeted lipidomic analysis of human breast milk
PublicationHuman 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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In silico epitope prediction of Borrelia burgdorferi sensu lato antigens for the detection of specific antibodies
PublicationDespite many years of research, serodiagnosis of Lyme disease still faces many obstacles. Difficulties arise mainly due to the low degree of amino acid sequence conservation of the most immunogenic antigens among B. burgdorferi s.l. genospecies, as well as differences in protein production depending on the environment in which the spirochete is located. Mapping B-cell epitopes located on antigens allows for a better understanding...
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Isolation of Citrus lemon extracellular vesicles: Development and process control using capillary electrophoresis
PublicationA new and scalable method for the isolation of extracellular vesicles (EV) from Citrus lemon juice samples was developed. The methodology included preliminary preconcentration of the sample using ultrafiltration (UF) followed by size-exclusion chromatography (SEC) purification and final preconcentration of the eluates. Transmission electron microscopy and proteomic analysis showed that isolates contained exosome-like vesicles, exocyst-positive...
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Keratinocyte-derived small extracellular vesicles supply antigens for CD1a-resticted T cells and promote their type 2 bias in the context of filaggrin insufficiency
PublicationIntroduction: Exosome-enriched small extracellular vesicles (sEVs) are nanosized organelles known to participate in long distance communication between cells, including in the skin. Atopic dermatitis (AD) is a chronic inflammatory skin disease for which filaggrin (FLG) gene mutations are the strongest genetic risk factor. Filaggrin insufficiency affects multiple cellular function, but it is unclear if sEV-mediated cellular communication...
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Engineering Candida albicans glucosamine-6-phosphate synthase for efficient enzyme purification
PublicationRationally designed muteins of Candida albicans glucosamine-6-phosphate synthase, an enzyme known as a promising target for antifungal chemotherapy, were constructed, overexpressed in Escherichia coli and purified to near homogeneity. To facilitate and to optimize the purification of the enzyme, three recombinant versionscontaining internal oligoHis fragments were constructed: (i) by substituting residues 343 - 348...
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Przydatność białka rybiego w postaci kolagenu lub żelatyny oraz polisacharydu - kapa-karagenu do wytwarzania aktywnych opakowań biodegradowalnych = Usefulness of fish collagen, gelatin and carrageenan for preparation of active biodegradable packages
PublicationSummary - The possibility of use of protein films made of fish collagen or gelatin as well as polysaccharide carrageenan films as carriers of enzymes (lysozyme or lysostaphyne), for preparation of microbiologically active packages, was investigated. It was found that crosslinking of such systems with N-[3(dimethylamino)propyl]-N'-ethylcarboimide (EDC) does not influence the activity of lysozyme immobilized in the films (Table 1)....
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Cyanogenic Compounds and Estrogen Disruptors
PublicationBalanced diet consists largely of plants containing cyanogenic compounds in the form of the more common cyanogenic glycosides and sometimes lipids. Maize, wheat, rye, apples, barley, oats, sugar cane and yet many other plants consumed by humans contain cyanogenic compounds. However the risk of poisoning is negligible as it is very easy to remove the toxic HCN by grinding and drying in air or soaking in water and an additional...
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Drop-coating deposition surface-enhanced Raman spectroscopy on silver substrates for biofluid analysis
PublicationUtilization of surface-enhanced Raman spectroscopy as a measurement technique is of particular interest in biodetection due to its superb chemical specificity and high sensitivity. The use of SERS substrates further improve this method by massive enhancement of the molecule Raman spectrum, permitting very low levels of detection. Therefore it is important to seek for new ways to develop reliable substrates, which are quickly and...
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Photonic sensor to detect rapid changes in CRP levels
PublicationOne of the most important biomarkers used to determine inflammation is C-reactive protein (CRP). Its level, when it is within the range that does not define inflammation, informs about the risk of cardiovascular events. If the norm is exceeded and inflammation is detected in the body, CRP level can increase 1000 times within a few hours. The type of infection can also be determined based on the level of elevated CRP. All this makes...
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Low-power microwave-induced fabrication of functionalised few-layer black phosphorus electrodes: A novel route towards Haemophilus Influenzae pathogen biosensing devices
PublicationIn this paper, various passivation schemes were applied at few-layer black phosphorus (FLBP) to achieve covalent functionalisation with 4-azidobenzoic acid, improving its electrochemical response intended for analytical and biosensing applications. The thermal and microwave assisted modification procedures in toluene and dime-thylformamide resulted in high reversibility of reactions on functionalised FLBP using a ferricyanide/ferrocya-nide...
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DMSO and TMAO—Differences in Interactions in Aqueous Solutions of the K-Peptide
PublicationInteractions 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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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen AMA1-MIC1-MIC3
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen MIC3-MAG1-ROP1
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen MIC1-MIC3-ROP1
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen MIC3-MAG1-AMA1
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen AMA1-MIC1-ROP1
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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Niebiałkowe związki azotowe
PublicationNiebiałkowe związki azotowe (NPN - non protein nitrogen) są grupą składników wchodzących w skład produktów żywnościowych ważną nie tylko z punktu widzenia producentów żywności, ale także dla specjalistów do spraw żywienia. Do grupy tej należą przede wszystkim wolne aminokwasy i krótkie peptydy, aminy, kwasy nukleinowe i nukleotydy oraz inne mało cząsteczkowe składniki zawierające azot (glikozydy cyjanogenne, alkaloidy, tiazole,...
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Niebiałkowe związki azotowe
PublicationNiebiałkowe związki azotowe (ang. non protein nitrogen, NPN) są grupą składników wchodzących w skład produktów żywnościowych ważną nie tylko z punktu widzenia producentów żywności, lecz także dla specjalistów do spraw żywienia. Do tej grupy należą przede wszystkim wolne aminokwasy i oligopeptydy, aminy, kwasy nukleinowe i nukleotydy oraz inne mało cząsteczkowe składniki zawierające azot (glikozydy cyjanogenne, alkaloidy, tiazole,...
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Heterogeneity of quaternary structure of glucosamine-6-phosphate deaminase from Giardia lamblia
PublicationThe oligoHis-tagged versions of glucosamine-6- phosphate deaminase from Giardia lamblia (GlmNagB-HisN, GlmNagB-HisC) were constructed and purified to hear homogeneity, and their kinetic and structural properties were compared to those of the wild-type enzyme (GlmNagB). Introduction of the oligoHis tag at the GlmNagB C-terminus resulted in almost complete loss of the catalytic activity, while the catalytic properties of GlmNagB-HisN...
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublicationWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor
PublicationGranulocyte macrophage colony stimulating factor (GMCSF) is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with biologically active compounds is critical...
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In silico assessment and sonochemical synthesis of 2-alkynyl 3-chloropyrazines as prospective ligands for SARS-CoV-2
PublicationThe 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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Role of cholesterol in substrate recognition by -secretase
Publication-Secretase is an enzyme known to cleave multiple substrates within their transmembrane domains, with the amyloid precursor protein of Alzheimer’s Disease among the most prominent examples. The activity of -secretase strictly depends on the membrane cholesterol content, yet the mechanistic role of cholesterol in the substrate binding and cleavage remains unclear. In this work, we used all-atom molecular dynamics simulations to examine...
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Fragmentomic analysis of biopeptides in silico released from milk proteins
PublicationThe fragmentomic-assisted method was employed to predict the biological potential of peptides derived from milk proteins hydrolyzed by papain and bromelain. Firstly, protein sequences were acquired from the BIOPEP-UWM database and then hydrolyzed by the above enzymes using a BIOPEP-UWM tool called “Enzyme(s) action”. The released peptides were defined as parent peptides and further analyzed for the presence of shorter peptidic...
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Phage-Directed Synthesis of Photoluminescent Zinc Oxide Nanoparticles under Benign Conditions
PublicationBiological systems, especially bacteriophages and peptides, are an attractive green alternative to other known methods of nanoparticle synthesis. In this work, for the first time, bacteriophages were employed to synthesize a specific peptide, capable of producing nanoparticles (NPs). Derivatives of M13 bacteriophage exposing a ZnO-binding peptide (TMGA-LGLKWPV) on either pIII or pVIII phage coat protein were constructed and used...
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Nanoparticle Tracking Analysis of Urinary Extracellular Vesicle Proteins as a New Challenge in Laboratory Medicine
PublicationUrinary extracellular vesicle (uEV) proteins may be used as specific markers of kidney damage in various pathophysiological conditions. The nanoparticle-tracking analysis (NTA) appears to be the most useful method for the analysis of uEVs due to its ability to analyze particles below 300 nm. The NTA method has been used to measure the size and concentration of uEVs and also allows for a deeper analysis of uEVs based on their protein...
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen MIC1-MAG1-MIC3
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...