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Search results for: protein dynamics
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Expression of a GDSL esterase from Pseudomonas sp. S9 in Pichiapastoris
PublicationCold 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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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublicationMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Enzyme Conjugation - A Promising Tool for Bio-catalytic and Biotransformation Applications – A Review
PublicationEnzymes have revolutionized conventional industrial catalysts as more efficient, eco-friendly, and sustainable substitutes that can be used in different biotechnological processes, food, and pharmaceutical industries. Yet, the enzymes from nature are engineered to make them adapt and enhance their durability in the industrial environment. One promising approach involves the combined use of multiple enzymes that catalyze highly...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublicationF1-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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Chicken feather keratin as a source of bioactive peptides useful in prevention of metabolic disorders – in silico and in vitro hydrolysis
PublicationProtein derived bioactive peptides not only serve as nutrients but can also exert drug-like activity, e.g. antidiabetic, antihypertensive, or antimicrobial, to name a few. Most biopeptides have beneficial effects on health that make them attractive for nutraceutical applications. The majority of bioactive peptides have been obtained from food proteins, but protein-rich by-products generated by agriculture...
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Simplified AutoDock force field for hydrated binding sites
Publicationhas 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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Dehydration converts DsbG crystal diffraction from low to high resolution
PublicationDiffraction quality crystals are essential for crystallographic studies of protein structure, and the production of poorly diffracting crystals is often regarded as a dead end in the process. Here we show a dramatic improvement of poorly diffracting DsbG crystals allowing high-resolution diffraction data measurement. Before dehydration, the crystals are fragile and the diffraction pattern is streaky, extending to 10 Å resolution....
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New PCR test for detection of Candida glabrata based on the molecular target chosen by the RAPD technique
PublicationRapid, reliable diagnosis is a necessary condition for the successful treatment of infections. Such diagnostic assays are continually being developed. #e paper presents a method for selecting the molecular target for PCR-based diagnostics based on the comparison of RAPD patterns. A sequence encoding Candida glabrata CBS138 hypothetical protein was selected. The limit of detection for PCR and real-time PCR reactions with DNA extracted...
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Sequence variants of p21 gene of the MRL/MpJ mouse: a possible association with the deficit of p21 protein and regenerative phenotype.
PublicationThe MRL/MpJ mouse is known for its enhanced regeneration abilities that manifested themselves by scarless ear-hole wound closure. The deficit of p21 found in the MRL is associated with the regenerative capacity as the p21 gene knockout in a mouse strain unrelated to the MRL mouse results in an ear-hole closure effect, similar to that observed in the MRL mouse. Cdkn1a gene encodes p21 protein, a cyclin-dependent kinase inhibitor,...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublicationWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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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
PublicationEvolution 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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CYP3A4 overexpression enhances apoptosis induced by anticancer agent imidazoacridinone C-1311, but does not change the metabolism of C-1311 in CHO cells
PublicationWe examine whether CYP3A4 overexpression influences the rate and pattern of antitumor imidazoacridinone C-1311 metabolism, in relation to the impact of this overexpression on cell cycle progression and final cellular response of CHO cells following C-1311 treatment. Methods: Three CHO cell lines: CHO-WT, wild type, CHO-HR, overexpressing cytochrome P450 reductase (CPR) and CHO-HR-3A4, coexpressing CPR and CYP3A4 were applied....
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn 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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Alphitobius diaperinus larvae (lesser mealworm) as human food – An approval of the European Commission – A critical review
PublicationDue to the increasing threat of climate change and the need for sustainable food sources, human consumption of edible insects or entomophagy has gained considerable attention globally. The larvae of Alphitobius diaperinus Panzer (Coleoptera: Tenebrionidae), also known as the lesser mealworm, have been identified as a promising candidate for mass-rearing as a food source based the on evaluation on several aspects such as the production...
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Identification of antigen Ag43 in uropathogenic Escherichia coli Dr+ strains and defining its role in the pathogenesis of urinary tract infections
PublicationUrinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are among the most common bacterial infectious diseases in the developed world. The urovirulence of UPEC is mainly associated with the surface-exposed fimbrial adhesins and adhesins of the autotransporter (AT) family. The best studied of theses proteins is antigen 43 (Ag43) mediating cell aggregation, adhesion and biofilm development as the causes of...
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublicationWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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Edible Lepidoptera as human foods – a comprehensive review
PublicationAs the global population continues to grow, traditional protein sources like meat and fish are becoming increasingly unsustainable due to their environmental impact. Edible insects, on the other hand, are highly nutritious, require minimal resources to produce, and emit significantly fewer greenhouse gases than traditional livestock. Lepidoptera, one of the most diverse insect orders, contains some popular edible species that have...
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Evolution towards simplicity in bacterial small heat shock protein system
PublicationEvolution 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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In vitro studies of polyphenols, antioxidants and other dietary indices in kiwifruit (Actinidia deliciosa)
PublicationOpisano wyniki badań poziomu protein oraz potencjału przeciwutleniającego w próbkach owoców kiwi, przechowywanych i dojrzewających w atmosferze etylenu ( w ciągu pierwszych 10 dni). Próbki owoców kiwi podzielono (w sposób przypadkowy) na dwie grupy:-próbki nie poddawane obróbce,-próbki poddawane obróbce (dojrzewanie w atmosferze etylenu).W próbkach oznaczano między innymi: wolne cukry, proteiny, polifenole oraz zdolność przeciwutleniającą....
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In silico design of telomerase inhibitors.
PublicationTelomerase is a reverse transcriptase enzyme involved in DNA synthesis at the end of linear chromosomes. Unlike in most other cells, telomerase is reactivated most cancerous cells and, therefore, has become a promising new anticancer target. Despite extensive research, direct telomerase inhibitors have yet not been introduced to the clinics because of the complexity of this enzyme. Structures of this protein from simple organisms...
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Amino Acid Based Antimicrobial Agents – Synthesis and Properties
PublicationStructures of several dozen of known antibacterial, antifungal or antiprotozoal agents are based on the amino acid scaffold. In most of them, the amino acid skeleton is of a crucial importance for their antimicrobial activity, since very often they are structural analogs of amino acid intermediates of different microbial biosynthetic pathways. Particularly, some aminophosphonate or aminoboronate analogs of protein amino acids are...
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Extremophile Deinococcus geothermalis as potential source of proteolytic enzymes
PublicationAmong many extremozymes, thermophilic enzymes have attracted most attention during the past four decades. Such enzymes are of considerable industrial and biotechnological interest due to the fact that the enzymes are better suited for harsh industrial processes. There are many advantages of conducting industrial processes at high temperature, such as the increased solubility of many polymeric substrates, resulting in decreased...
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Saccharides
PublicationSaccharides are widely distributed in nature as the major component of fruits and vegetables (primarily monosaccharides), milk and malt (mainly disaccharides), and grains (mostly polysaccharides). They are an important source of energy, structural material, as well as flavor and taste factors. Molecules of this class of compounds contain mainly carbon, hydrogen, and oxygen atoms; however, most natural saccha- rides do not have...
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Natural fish oil improves the differentiation and maturation of oligodendrocyte precursor cells to oligodendrocytes in vitro after interaction with the blood–brain barrier
PublicationThe blood–brain barrier (BBB) tightly controls the microenvironment of the central nervous system (CNS) to allow neurons to function properly. Additionally, emerging studies point to the beneficial effect of natural oils affecting a wide variety of physiological and pathological processes in the human body. In this study, using an in vitro model of the BBB, we tested the influence of natural fish oil mixture (FOM) vs. borage oil...
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Assembly of Lipopolysaccharide in Escherichia coli Requires the Essential LapB Heat Shock Protein
PublicationHere, we describe two new heat shock proteins involved in the assembly of LPS in Escherichia coli, LapA and LapB (lipopolysaccharide assembly protein A and B). lapB mutants were identified based on an increased envelope stress response. Envelope stress responsive pathways control key steps in LPS biogenesis and respond to defects in the LPS assembly. Accordingly, the LPS content in ΔlapB or Δ(lapA lapB) mutants was elevated, with...
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Enzymatic cross-linking of β-lactoglobulin in solution and at air–water interface: Structural constraints
PublicationEffective and controlled use of cross-linking enzymes in structure engineering of food systems depends on characterization of the favorable conditions for enzyme-substrate complex and the limiting factors for the desired modification. In this respect, we analyzed the susceptibility of bovine β-lactoglobulin (BLG) to enzymatic cross-linking by Trichoderma reesei tyrosinase (TrTyr) and transglutaminase (TG). Changes in BLG molecular...
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c-Myc inhibition and p21 modulation contribute to unsymmetrical bisacridines-induced apoptosis and senescence in pancreatic cancer cells
PublicationBackground 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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Edible black ant Smith (Carebara vidua) as human food – A systematic review
PublicationMeeting food security is one of the major global challenges to ensure sufficient supply of food for current and future generations, considering increasing population growth and climate change issues. Consequently, the consumption of edible insects as an alternative food source has recently gained global attention for combating global food insecurity. The present review aims to provide information on the recent progress in consumption...
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublicationHsp70 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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Effect of microwave and convection heating on selected nutrients of human milk
PublicationThe aim of this study was to determine the influence of the microwave heating method (MWH) on selected determinants of the nutritional value of human milk (HM) and compare to the effect exerted by the standard convection heating (CH) method, including holder pasteurization (HoP). It was showed that using MWH under conditions assumed to ensure microbiological safety, changes in the level of the nutrients were not observed. In these...
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Efficient three-dimensional fluorescence measurements for characterization of binding properties in some plants
PublicationThe main aim of this research was to characterize some plants and to determine their similarities and differences, using spectroscopic methods. The interactions of soluble polyphenols of different plants with human serum albumin (HSA) were investigated by 3D-fluorescence. The obtained fluorescence results allow to classify the investigated plants according to their binding properties. The HSA-binding capacities of these plants...
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A new division of bacterial UvrA homologues
PublicationThe UvrA protein is a DNA-binding and damage-recognition enzyme which participates in the prokaryotic type nucleotide excision repair (NER) pathway. It has recently been noted that some bacterial genomes comprise additional uvrA genes which encode five distinct types of UvrA homologue. We investigated the sequences of over 2400 bacterial genomes and found 130 examples of bacteria containing uvrA 2 genes. The sequence analyses conducted...
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Nonprotein nitrogenous compounds
PublicationThe non-protein nitrogen (NPN) fraction is an important group of food components for both technological and nutritional reasons. Free amino acids (FAAs), oligopeptides, amines, nucleic acids, and nucleotides, as well as other low-molecular nitrogen-containing components (cyanogenic glycosides, alkaloids, thiazoles, oxazoles, pyrroles, and pyrazines), are found in most foods. Their content depends on many factors, starting from...
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Reactions on the surface of the implant under the influence of biofilm
PublicationThe contact of a biomaterial with the biological environment in in vitro and in vivo tests leads to the production of a particular ecosystem in which the active roles perform both, the material surface and the extracellular matrix protein forming a biofilm. Proteins affect cell and bacteria adhesion processes, biological activity of cells and activation of inflammatory response.The knowledge of the reaction mechanisms active on...
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Structure of EstA esterase from psychrotrophic Pseudoalteromonas sp. 643A covalently inhibited by monoethylphosphonate.
PublicationThe crystal structure of the esterase EstA from the cold-adapted bacteriumPseudoalteromonas sp. 643A was determined in a covalently inhibited form at aresolution of 1.35 A˚. The enzyme has a typical SGNH hydrolase structureconsisting of a single domain containing a five-stranded beta-sheet, with threehelices at the convex side and two helices at the concave side of the sheet, and isornamented with a couple of very short helices...
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Fungal L-Methionine Biosynthesis Pathway Enzymes and Their Applications in Various Scientific and Commercial Fields
PublicationL-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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Diamond Nanofilm Normalizes Proliferation and Metabolism in Liver Cancer Cells
PublicationPurpose: Surgical resection of hepatocellular carcinoma can be associated with recurrence resulting from the degeneration of residual volume of the liver. The objective was to assess the possibility of using a biocompatible nanofilm, made of a colloid of diamond nanoparticles (nfND), to fill the side after tumour resection and optimize its contact with proliferating liver cells, minimizing their cancerous transformation. Methods:...
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Voltammetric and biological studies of folate-targeted non-lamellar lipid mesophases
PublicationFolate-targeted lipid nanostructures are promising strategies for the development of biocompatible drug delivery systems. The objective of this study was to evaluate the efficacy of drug delivery to cancer cells by folate-targeted lipid mesophases, cubosomes (CUB) and hexosomes (HEX), loaded with doxorubicin (DOX). Three cancer-derived cell lines (KB, HeLa, T98G) exhibiting different expressional levels of folate receptor protein...
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Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges
PublicationStaphylococci 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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Role of Human UDP-Glucuronosyltransferases in the Biotransformation of the Triazoloacridinone and Imidazoacridinone Antitumor Agents C-1305 and C-1311 : Highly Selective Substrates for UGT1A10
Publication5-Diethylaminoethylamino-8-hydroxyimidazoacridinone, C-1311 (NSC-645809), is an antitumor agent shown to be effective against breast cancer in phase II clinical trials. A similar compound, 5-dimethylaminopropylamino-8-hydroxytriazoloacridinone, C-1305, shows high activity against experimental tumors and is expected to have even more beneficial pharmacological properties than C-1311. Previously published studies showed that these...
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THE GENE CLONING, OVEREXPRESSION, PURIFICATION AND BIOCHEMICAL CHARACTERISATION OF A NEW COLD-ADAPTED β–GALACTOSIDASE FROM ARTHROBACTER SP. VII-4
PublicationINTRODUCTION. 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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Biofilm Production and Presence of ica and bap Genes in Staphylococcus aureus Strains Isolated from Cows with Mastitis in the Eastern Poland
PublicationThe aim of the study was phenotypic and genotypic analysis of 132 S. aureus strains isolated from mastitis in eastern Poland in respect to their biofilm formation ability. The analysis of the size polymorphism of fragment X in the gene encoding protein A (spa) revealed high genetic differentiation of the analyzed group of isolates. The ability of biofilm formation by the isolates was tested using two phenotypic methods. The Congo...
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Aminy w środowisku - niebezpieczeństwo czy jego naturalny element?
PublicationA lot of amines and their compounds are used in the industry. First of all they are used for the preparation of medicines, plant protection agents, fertilizers and plastics. Amines are also released into the environment as a result of natural biological processes such as the release of certain species of flowers to lure insects, and also biochemical breakdown of amino acids in the protein during decomposition of organic matter. Unfortunately,...
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Targeting shelterin proteins for cancer therapy.
PublicationAs a global health challenge, cancer prompts continuous exploration for innovative therapies that are also based on new targets. One promising avenue is targeting the shelterin protein complex, a safeguard for telomeres crucial in preventing DNA damage. The role of shelterin in modulating ataxia- telangiectasia mutated (ATM) and ataxia-telangiectasia and Rad3-related (ATR) kinases, key players in the DNA damage response (DDR),...
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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
PublicationThe 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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Chiral Pyrazolo[4,3-e][1,2,4]triazine Sulfonamides—Their Biological Activity, Lipophilicity, Protein Affinity, and Metabolic Transformations
PublicationReferring to our previous laboratory results related to the tyrosinase and urease inhibition by pyrazolo[4,3-e][1,2,4]triazine sulfonamides, we examined here in silico the mechanism of action at the molecular level of the investigated pyrazolotriazine sulfonamides by the molecular docking method. The studied compounds being evaluated for their cytotoxic effect against cancer cell lines (MCF-7, K-562) and for recombinant Abl and...
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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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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...