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Search results for: protein stability
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Two-step mechanism of J-domain action in driving Hsp70 function
PublicationJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s...
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Identification of Substrates of Cytoplasmic Peptidyl-Prolyl Cis/Trans Isomerases and Their Collective Essentiality in Escherichia Coli
PublicationProtein folding often requires molecular chaperones and folding catalysts, such as peptidyl-prolyl cis/trans isomerases (PPIs). The Escherichia coli cytoplasm contains six well-known PPIs, although a requirement of their PPIase activity, the identity of their substrates and relative enzymatic contribution is unknown. Thus, strains lacking all periplasmic and one of the cytoplasmic PPIs were constructed. Measurement of their PPIase...
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The Anti-Staphylococcal Potential of Ethanolic Polish Propolis Extracts
PublicationAbstract: The principal objective of this study was to determine the anti-staphylococcal potential of ethanol extracts of propolis (EEPs). A total of 20 samples of propolis collected from apiaries located in different regions of Poland were used in the study. The two-fold broth microdilution method revealed some important differences in the antimicrobial activity of investigated EEPs. Up to the concentration of 4096 µg/mL no activity...
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Anticancer Imidazoacridinone C-1311 is Effective in Androgen-Dependent and Androgen-Independent Prostate Cancer Cells
PublicationAndrogen receptor (AR) plays a crutial role in prostate cancer (PCa) development and metastasis. Here, we reported potent anti-PCa activity of a small molecule imidazoacridinone C-1311. In AR-positive PCa cells, C-1311 was found to inhibit the transcriptional activity of AR uncovering a novel mechanism that may be relevant for its anticancer effect. Mechanistically, C-1311 decreased AR binding to prostate-specific antigen (PSA)...
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Differential expression profile between amygdala and blood during chronic lithium treatment in a rat model of depression – a pilot study
PublicationLithium is a mood stabilizer widely used in the pharmacotherapy of bipolar disorder and treatment‑resistant depression. Taking into account dysregulated inflammatory activity in depression and the immunomodulatory role of lithium, we hypothesized that genes associated with inflammatory responses may be potential biomarkers of lithium action. We aimed to compare gene expression changes between the brain and the periphery after...
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Expression of cyclin D1 after treatment with doxorubicin in the HL-60 cell line
PublicationIncreased levels of cyclin D1 and amplification of CCND1 gene occur in many types of cancers. We have followed the expression of cyclin D1 after treatment with doxorubicin with reference to cell death and other possible therapeutic implications. The effect of the treatment on the cell cycle, survival, intracellular level (flow cytometry), and intracellular localization of cyclin D1 (fluorescence microscopy) and expression of...
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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublicationUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
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Keratin-Butyrate Scaffolds Promote Skin Wound Healing in Diabetic Rats Through Down-Regulation of IL-1β and Up-Regulation of Keratins 16 and 17
PublicationImpaired wound healing particularly in diabetics creates a significant healthcare burden. The study aimed to evaluate the effect of keratin-butyrate fibers (FKDP +0.1%NaBu) in a full-thickness skin wound model in 30 diabetic rats. Physicochemical examination showed that the obtained dressing possesses a heterogeneous structure and butyrate was slowly released into the wound. Moreover, the obtained dressing is nontoxic and supports...
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Electrostatic interactions in finite systems treated with periodic boundary conditions: Application to linear-scaling density functional theory
PublicationWe present a comparison of methods for treating the electrostatic interactions of finite, isolated systems within periodic boundary conditions (PBCs), within density functional theory (DFT), with particular emphasis on linear-scaling (LS) DFT. Often, PBCs are not physically realistic but are an unavoidable consequence of the choice of basis set and the efficacy of using Fourier transforms to compute the Hartree potential. In such...
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Novel application of terminal restriction fragments length polymorphism method (t-RFLP) for identification of six clinically important Candida sp.
PublicationTerminal restriction fragments length polymorphism method (t-RFLP) is a modified classical RFLP method. The main difference is based on carrying out PCR using a fluorescently labeled primer or primers. The result of such modification is that after digestion of amplicons only terminal fragments of PCR product (containing fluorescent dye) are visualized. T-RFLP method has found application in environmental microbiology and epidemiology....
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublicationThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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An examination of an Antarctic soil metagenomic-derivate putative methylthioadenosine phosphorylase gene as a novel reporter gene for promoter trapping
PublicationThe rsfp gene was discovered during examination ofan Antarctic soil-derived metagenome library and encodesa bacterial methylthioadenosine phosphorylase (GenBank accession number GQ202582). In a previous study, we found that E. coli colonies expressing the rsfp gene reveal strong pink fluorescence after exposure to UV light when grown on culture medium supplemented with rhodamine B (Cieśliński et al., 2009). In contrast to that,...
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A new Toxoplasma gondii chimeric antigen containing fragments of SAG2, GRA1, and ROP1 proteins—impact of immunodominant sequences size on its diagnostic usefulness
PublicationThis study presents the first evaluation of new Toxoplasma gondii recombinant chimeric antigens containing three immunodominant regions of SAG2, GRA1, and one of two ROP1 fragments differing in length for the serodiagnosis of human toxoplasmosis. The recombinant chimeric antigens SAG2-GRA1-ROP1L (with large fragment of ROP1, 85-396 amino acid residues) and SAG2-GRA1-ROP1S (with a small fragment of ROP1, 85-250 amino acid residues)...
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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
Publication4-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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Optimization of vortex-assisted supramolecular solvent-based liquid liquid microextraction for the determination of mercury in real water and food samples
PublicationA 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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The Effect of Hyperbaric Storage on the Nutritional Value and Retention of Certain Bioactive Proteins in Human Milk
PublicationHuman milk (HM) contains the essential macronutrients and bioactive compounds necessary for the normal growth and development of newborns. The milk collected by human milk banks is stored frozen and pasteurized, reducing its nutritional and biological value. The purpose of this study was to determine the effect of hyperbaric storage at subzero temperatures (HS-ST) on the macronutrients and bioactive proteins in HM. As control samples,...
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Boron-doped diamond nanosheet volume-enriched screen-printed carbon electrodes: a platform for electroanalytical and impedimetric biosensor applications
PublicationThis paper focuses on the development of a novel electrode based on boron-doped diamond nanosheet full-volume-enriched screen-printed carbon electrodes (BDDPE) for use as an impedimetric biosensor. Impedimetric biosensors offer high sensitivity and selectivity for virus detection, but their use as point-of-care devices is limited by the complexity of nanomaterials’ architecture and the receptor immobilisation procedures. The study...
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Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublicationTelomerase plays a pivotal role in cell proliferation, homeostasis, and neoplastic transformation, making it a promising molecular target for cancer chemotherapy. Of note, although hTERT has been explored thoroughly as a target, none of the promising molecules has been approved as a drug until now. The subject of research conducted as part of my doctoral dissertation is explaining the cellular and molecular mechanism of action...
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A review on computer‐aided chemogenomics and drug repositioning for rational COVID ‐19 drug discovery
PublicationApplication of materials capable of energy harvesting to increase the efficiency and environmental adaptability is sometimes reflected in the ability of discovery of some traces in an environment―either experimentally or computationally―to enlarge practical application window. The emergence of computational methods, particularly computer-aided drug discovery (CADD), provides ample opportunities for the rapid discovery and development...
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A method for the analysis of methylmercury and total Hg in fungal matrices
PublicationThe aim of the study was to develop an efficient method for the determination of monomethyl-mercury (MeHg) and total mercury (THg) content in materials such as fungal sporocarps and sclerotia. Certified Reference Materials (CRMs) with the assigned values of MeHg and THg as well as the control materials (dried mushrooms) with known content of THg were evaluated for method validation. Recovery of MeHg from reference materials was...
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A new factor LapD is required for the regulation of LpxC amounts and lipopolysaccharide trafficking
PublicationLipopolysaccharide (LPS) constitutes the major component of the outer membrane and is essential for bacteria, such as Escherichia coli. Recent work has revealed the essential roles of LapB and LapC proteins in regulating LPS amounts; although, if any additional partners are involved is unknown. Examination of proteins co-purifying with LapB identified LapD as a new partner. The purification of LapD reveals that it forms a complex...
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Tailoring Diffusional Fields in Zwitterion/Dopamine Copolymer Electropolymerized at Carbon Nanowalls for Sensitive Recognition of Neurotransmitters
PublicationThe importance of neurotransmitter sensing in the diagnosis and treatment of many psychological illnesses and neurodegenerative diseases is non-negotiable. For electrochemical sensors to become widespread and accurate, a long journey must be undertaken for each device, from understanding the materials at the molecular level to real applications in biological fluids. We report a modification of diamondized boron-doped carbon nanowalls...
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Torsional elasticity and energetics of F1-ATPase
PublicationFoF1-ATPase is a rotary motor protein synthesizing ATP from ADP driven by a cross-membrane proton gradient. The proton flow through the membrane-embedded Fo generates the rotary torque that drives the rotation of the asymmetric shaft of F1. Mechanical energy of the rotating shaft is used by the F1 catalytic subunit to synthesize ATP. It was suggested that elastic power transmission with transient storage of energy in some compliant...
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Modulation of CYP19 expression by cabbage juices and their active components: indole-3-carbinol and 3,30-diindolylmethene in human breast epithelial cell lines
PublicationThe aim of this study was to evaluate the effect of white cabbage and sauerkraut juices of different origin and indole-3-carbinol (I3C) and diindolylmethane (DIM) on expression of CYP19 gene encoding aromatase, the key enzyme of estrogen synthesis.Remarkable differences in the effect on CYP19 transcript and protein level were found between the cab- bage juices (in 2.5-25 mL/L concentrations) and indoles (in 2.5-50 lM doses) in...
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Adipokine and cytokine levels in non-functioning adrenal incidentalomas (NFAI)
PublicationDue to the fact that overweight or obesity is accompanied by hormonally active adrenal tumors: Cushing Syndrome-(CS) and Subclinical Cushing Syndrome (SCS), it is of high interest the correlation between different adipokines and cytokines secreted by adipose tissue, with metabolic disorders and hormonal activity in this group. Even in non-functioning adrenal incidentalomas (NFAI) elevated risk for cardiovascular disease and metabolic...
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse 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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Molecular basis of essentiality of early critical steps in the lipopolysaccharide biogenesis in Escherichia coli K-12: requirement of MsbA, cardiolipin, LpxL, LpxM and GcvB
PublicationTo identify the physiological factors that limit the growth of Escherichia coli K-12 strains synthesizing minimal lipopolysaccharide (LPS), we describe the first construction of strains devoid of the entire waa locus and concomitantly lacking all three acyltransferases (LpxL/LpxM/LpxP), synthesizing minimal lipid IVA derivatives with a restricted ability to grow at around 21 °C. Suppressors restoring growth up to 37 °C of Δ(gmhD-waaA)...
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Determination of long-chain aldehydes using a novel quartz crystal microbalance sensor based on a biomimetic peptide
PublicationThere 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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Simultaneous optical and electrochemical label-free biosensing with ITO-coated lossy-mode resonance sensor
PublicationIn this work we discuss a new label-free biosensing device based on indium tin oxide (ITO) overlaid section of a multimode optical fiber fused silica core. The sensor has been used to optical measurements also simultaneously interrogated electrochemically (EC). Due to optimized thickness and optical properties of ITO film, a lossy-mode resonance (LMR) could be observed in the optical domain, where electrical properties of the film...
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublicationIn 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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Biochemical, Structural Analysis, and Docking Studies of Spiropyrazoline Derivatives
PublicationIn this study, we evaluated the antiproliferative potential, DNA damage, crystal struc‐ tures, and docking calculation of two spiropyrazoline derivatives. The main focus of the research was to evaluate the antiproliferative potential of synthesized compounds towards eight cancer cell lines. Compound I demonstrated promising antiproliferative properties, especially toward the HL60 cell line, for which IC50 was equal to 9.4 μM/L....
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Novel molecules containing structural features of NSAIDs and 1,2,3-triazole ring: Design, synthesis and evaluation as potential cytotoxic agents
PublicationFor the first time the template containing structural features of more than one NSAIDs and the 1,2,3-triazole ring was explored for the identification of potential cytotoxic agents. These new and complex molecules were predicted to be effective inhibitors of PDE4B by molecular modelling studies in silico. The multi-step synthesis of these compounds were carried out starting from the well-known drug nimesulide and involved the use...
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The Impact of the Antigenic Composition of Chimeric Proteins on Their Immunoprotective Activity against Chronic Toxoplasmosis in Mice
PublicationToxoplasmosis may pose a serious threat for individuals with weakened or undeveloped immune systems. However, to date, there is no specific immunoprophylaxis for humans. Thus, the aim of this study was to evaluate the immunogenicity of three trivalent—SAG2-GRA1-ROP1L (SGR), SAG1L-MIC1-MAG1 (SMM), and GRA1-GRA2-GRA6 (GGG)—and two tetravalent—SAG2-GRA1-ROP1-GRA2 (SGRG) and SAG1-MIC1-MAG1-GRA2 (SMMG)—chimeric T. gondii proteins, as...
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A New Expression System Based on Psychrotolerant Debaryomyces macquariensis Yeast and Its Application to the Production of Cold-Active β-D-Galactosidase from Paracoccus sp. 32d
PublicationYeasts provide attractive host/vector systems for heterologous gene expression. The currently used yeast-based expression platforms include mesophilic and thermotolerant species. A eukaryotic expression system working at low temperatures could be particularly useful for the production of thermolabile proteins and proteins that tend to form insoluble aggregates. For this purpose, an expression system based on an Antarctic psychrotolerant...
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Impact of high-pressure processing on the bioactive compounds of milk - A comprehensive review
PublicationHigh-pressure processing (HPP) is a promising alternative to thermal pasteurization. Recent studies highlighted the effectivity of HPP (400–600 MPa and exposure times of 1–5 min) in reducing pathogenic microflora for up to 5 logs. Analysis of modern scientific sources has shown that pressure affects the main components of milk including fat globules, lactose, casein micelles. The behavior of whey proteins under HPP is very important...
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Enhancing the bioconversion rate and end products of black soldier fly (BSF) treatment – A comprehensive review
PublicationFood security remains a pressing concern in the face of an increasing world population and environmental challenges. As climate change, biodiversity loss, and water scarcity continue to impact agricultural productivity, traditional livestock farming faces limitations in meeting the growing global demand for meat and dairy products. In this context, black soldier fly larvae (BSFL) have emerged as a promising alternative for sustainable...
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Electrochemical determination of neurotransmitter serotonin using boron/nitrogen co-doped diamond-graphene nanowall-structured particles
PublicationElectrode fouling is a major issue in biological detection due to the adhesion of the protein itself and polymerization of biomolecules on the electrode surface, impeding the electron transfer ability and decreasing the current response. To overcome this issue, the use of anti-fouling material, especially boron-doped diamond (BDD) electrode, is an alternative way. However, the electrocatalytic activity of BDD is inadequate compared...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-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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The role of microbial coagulants on the physicochemical, proteolysis, microstructure and sensory properties of low-fat Edam cheese manufactured from ultrafiltered buffalo milk
PublicationThis work investigates the influence of using microbial coagulants, including Rhizomucor miehei (MCR) protease and Cryphonectria parasitica (MCC) protease, on the quality characteristics of low-fat Edam cheese made from ultrafiltered buffalo milk (LFUE). Concurrently, a benchmark with calf rennet (CR) has been also performed. Throughout a 90-day ripening period, the cheeses were assessed for their physicochemical features, proteolysis,...
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Targeting Spike‐ACE2 Interface of SARS‐CoV‐2 and its Omicron Variant: A Comparative Screening of Potential Inhibitors for Existing and Anticipating Variants Using Molecular Modelling Approach
PublicationThe recent COVID pandemic has shown major impact on public health and economic crisis. Despite the development of many vaccines and drugs against the severe acute respiratory syndrome (SARS) coronavirus 2, the pandemic still persists. The continued spread of the virus is largely driven by the emergence of viral variants such as α, β, γ, delta, epsilon spike, omicron and its subvariants (BA.1,2,3) which can evade the current vaccines...
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Antifungal Effect of Penicillamine Due to the Selective Targeting of L-Homoserine O-Acetyltransferase
PublicationDue to the apparent similarity of fungal and mammalian metabolic pathways, the number of established antifungal targets is low, and the identification of novel ones is highly desirable. The results of our studies, presented in this work, indicate that the fungal biosynthetic pathway of L-methionine, an amino acid essential for humans, seems to be an attractive perspective. The MET2 gene from Candida albicans encoding L-homoserine...
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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublicationThe 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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The role of bile salts in digestion
PublicationBile salts (BS) are bio-surfactants present in the gastrointestinal tract (GIT) that play a crucial role in the digestion and absorption of nutrients. The importance of BS for controlled release and transport of lipid soluble nutrients and drugs has recently stimulated scientific interest in these physiological compounds. BS are so-called facial amphiphiles showing a molecular structure that is very distinct from classical surfactants....
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The first study on the usefulness of recombinant tetravalent chimeric proteins containing fragments of SAG2, GRA1, ROP1 and AMA1 antigens in the detection of specific anti-Toxoplasma gondii antibodies in mouse and human sera
PublicationThis study presents an evaluation of four tetravalent recombinant chimeric proteins containing fragments of the Toxoplasma gondii antigens, SAG2, GRA1, ROP1 and AMA1, as potential replacements of a the soluble, whole-cell tachyzoite lysate (TLA) used in serological assays. Recombinant chimeric proteins (SAG2-GRA1-ROP1-AMA1N, AMA1N-SAG2-GRA1-ROP1, AMA1C-SAG2-GRA1-ROP1, and AMA1-SAG2-GRA1-ROP1) obtained by genetic engineering were...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Establishing the allosteric mechanism in CRISPR‐Cas9
PublicationAllostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three...
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Antiproliferative, Antiangiogenic, and Antimetastatic Therapy Response by Mangiferin in a Syngeneic Immunocompetent Colorectal Cancer Mouse Model Involves Changes in Mitochondrial Energy Metabolism
PublicationIn spite of the current advances and achievements in cancer treatments, colorectal cancer (CRC) persists as one of the most prevalent and deadly tumor types in both men and women worldwide. Drug resistance, adverse side effects and high rate of angiogenesis, metastasis and tumor relapse remain one of the greatest challenges in long-term management of CRC and urges need for new leads of anticancer drugs. We demonstrate that CRC...
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Retained features of embryonic metabolism in the adult MRL mouse
PublicationThe MRL mouse is an inbred laboratory strain that was derived by selective breeding in 1960 from the rapidly growing LG/J (Large) strain. MRL mice grow to nearly twice the size of other commonly used mouse strains, display uncommonly robust healing and regeneration properties, and express later onset autoimmune traits similar to Systemic Lupus Erythematosis. The regeneration trait (heal) in the MRL mouse maps to 14-20 quantitative...
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More than just a beer – Brewers' spent grain, spent hops, and spent yeast as potential functional fillers for polymer composites
PublicationBeer is among the most popular beverages in the world, with the production distributed uniformly between the biggest continents, so the utilization of brewing by-products is essential on a global scale. Among their potential recipients, the plastics industry offers extensive range of potential products. Herein, the presented study investigated the application of currently underutilized solid brewing by-products (brewers' spent...
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Conserved motifs of MutL proteins
PublicationtThe MutL protein is best known for its function in DNA mismatch repair (MMR). However, there isevidence to suggest that MutL is not only the linker connecting the functions of MutS and MutH in MMR,but that it also participates in other repair systems, such as Very Short Patch (VSP), Base Excision (BER)and Nucleotide Excision Repair (NER). This study set out to identify the most highly conserved aminoacid sequence motifs in MutL...