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Search results for: DNA/PROTEIN INTERACTIONS
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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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Międzyłańcuchowe sieciowanie DNA jako mechanizm biologicznego działania an- tracenodionów.**2003, 100 s. 30 rys. 20 tab. bibliogr. 110 poz. maszyn. Rozprawa doktorska /23.06.2003/ P. Gdań. Wydz. Chem. Promotor: prof. dr hab. inż. J. Konopa.
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Changes in gene methylation patterns in neonatal murine hearts: Implications for the regenerative potential
PublicationBackground The neonatal murine heart is able to regenerate after severe injury; this capacity however, quickly diminishes and it is lost within the first week of life. DNA methylation is an epigenetic mechanism which plays a crucial role in development and gene expression regulation. Under investigation here are the changes in DNA methylation and gene expression patterns which accompany the loss of regenerative potential. Results The...
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Seabed characterisation using spectral moments of the echo signal
PublicationZbadano użyteczność zastosowania momentów spektralnych obwiedni echa w rozpoznawaniu i klasyfikacji dna morskiego. Przeprowadzono obliczenia momentów spektralnych dla około 15000 ech od dna zarejestrowanych w rejonie Bałtyku Południowego i potwierdzono tezę, że wartości tych momentów skorelowane są silnie z typem dna i rodzajem osadów.
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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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Metylotransferazy ssaków – inhibitory i aktywatory
PublicationWśród metylotransferaz ssaków możemy wyróżnić metylotransferazy histonowe oraz metylotransferazy DNA. Metylacja DNA w obrębie wysp CpG oraz metylacja histonów wpływają na poziom ekspresji genów w komórkach ssaczych. Dodatkowo dzięki metylacji zapewniana jest stabilność i integralność genomu ludzkiego. Metylotransferazy DNA, będące głównym tematem tego artykułu, są często przedmiotem badań, gdyż nieprawidłowa metylacja DNA jest...
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DDLMS PCR double digestion Ligation Mediated Suppression PCR - a new technique for bacterial specific differentiation
PublicationA new diagnostic kit for K. oxytoca specific differentiation based on ddLMS PCR (ang. double digest ligation Mediated PCR) technique is shown. As a species-specific DNA fragment pehX gene, encoding the enzyme polygalactouronase, was chosen. The genome sequence of K. oxytoca is digested with two endonucleases: AclI and BclI which cut DNA before and after pehX gene. The polymorphic DNA fragments are ligated with AclI-end-specific...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Loop-mediated isothermal amplification (LAMP) as a diagnostic tool in detection of infectious diseases
PublicationLoop-mediated isothermal amplification (LAMP) is a gene amplification method which amplifies DNA with high specificity and efficiency under isothermal conditions. Because of its rapidity and simplicity, it is a valuable diagnostic tool in the early detection and identification of infectious diseases. LAMP method is based on the use of a set of four to six specially designed primers spanning six to eight distinct sequences on the...
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Bodybuilders and high-level meat consumers’ behavior towards rabbit, beef, chicken, turkey, and lamb meat: A comparative review
PublicationIn bodybuilders’ diets, protein plays a crucial role in supporting muscle growth and repairing damaged muscle tissue. These individuals meet their protein needs by combining dietary sources with supplements. Animal-based proteins are often preferred over plant-based proteins because they are believed to better support muscle protein synthesis. This review explores the meat consumption patterns of bodybuilders and high-level meat...
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The development of an indirect ELISA for the detection of goose parvovirus antibodies using specific VP3 subunits as the coating antigen
PublicationIn Poland, the leader in goose production in Europe, goose parovirus infection, or Derzsy’s disease (DD), must be reported to the veterinary administration due to the serious economic and epizootic threat to waterfowl production. Prophylactic treatment for DD includes attenuated live or inactivated vaccines. Moreover, the control of DD includes the monitoring of maternal derived antibody (MDA) levels in the offspring and antibody...
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Sensitivity of echo parameters to seafloor properties and depth variability.
PublicationPrzeprowadzono badanie użyteczności wybranych parametrów echa akustycznego, w szczególności wymiaru fraktalnego oraz momentów spektralnych obwiedni, w klasyfikacji dna morskiego, ze szczególnym uwzględnieniem wpływu zmieniającej się głębokości. Wykorzystano numeryczną symulację rozpraszania echa na dnie oraz innych elementów procesu akustycznego sondowania dna, w tym także procedurę kompensacji wpływu zmian głębokości dna na echo.
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The antioxidative properties of white cabbage (Brassica oleracea var. capitata f. alba) fresh and submitted to culinary processing
PublicationKapusta biała stanowi jeden z podstawowych składników diety w Europie centralnej. W publikacji autorzy skupili się na określeniu właściwościach przeciwutleniających kapusty świeżej, kiszonej i poddanej obróbce termicznej. Te właściwości zostały oszacowane dla soków przy wykorzystaniu systemów pozakomórkowych, w komórkach HT29 pod kątem ochrony przed utlenieniem DNA oraz poprzez symulację GSTs i naprawę DNA. Wszystkie badane soki...
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The construction of bifunctional fusion proteins consisting of MutS and GFP
PublicationSkonstruowano białka chimeryczne zawierające białko MutS z Thermus thermophilus i białko zielonej fluoresceiny GFP z Aequorea victoria, posiadające dla łatwiejszego oczyszczania domeny oligo-histydynowe na N- lub C-końcu. Fuzyjne białka rozpoznawały niekomplementarności w DNA podobnie do MutS T. thermophilus. Fluorescencyjne białka rozpoznające niekomplementarne DNA mogą być użyteczne w wykrywaniu jednonukleotydowych polimorfizmów...
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PCR-ELISA: inexpensive alternative to quantitative PCR
PublicationPCR-ELISA (polymerase chain reaction-enzyme linked immunosorbent assay), a combination of PCR and ELISA methods, has been used since late 1980s. The technique is based on specially labelled DNA fragments which are captured by specific DNA sequences and detected by antibodies. The whole procedure of PCR-ELISA is divided into three steps: DNA extraction, PCR reaction and detection by ELISA. The method has been found as very specific...
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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublicationF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface
PublicationAlbumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions...
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Bile salts in digestion and transport of lipids
PublicationBecause of their unusual chemical structure, bile salts (BS) play a fundamental role in intestinal lipid digestion and transport. BS have a planar arrangement of hydrophobic and hydrophilic moieties, which enables the BS molecules to form peculiar self-assembled structures in aqueous solutions. This molecular arrangement also has an influence on specific interactions of BS with lipid molecules and other compounds of ingested food...
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Mechanism of Osmolyte Stabilization–Destabilization of Proteins: Experimental Evidence
PublicationIn this work, we investigated the influence of stabilizing (N,N,N-trimethylglycine) and destabilizing (urea) osmolytes on the hydration spheres of biomacromolecules in folded forms (trpzip-1 peptide and hen egg white lysozyme─hewl) and unfolded protein models (glycine─GLY and N-methylglycine─NMG) by means of infrared spectroscopy. GLY and NMG were clearly limited as minimal models for unfolded proteins and should be treated with...
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Triazoloacridone C-1305 impairs XBP1 splicing by acting as a potential IRE1α endoribonuclease inhibitor
PublicationInositol requiring enzyme 1 alpha (IRE1α) is one of three signaling sensors in the unfolding protein response (UPR) that alleviates endoplasmic reticulum (ER) stress in cells and functions to promote cell survival. During conditions of irrevocable stress, proapoptotic gene expression is induced to promote cell death. One of the three signaling stressors, IRE1α is an serine/threonine-protein kinase/endoribonuclease (RNase) that...
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Molecular Modeling of the Neurohypophyseal Receptor/Atosiban Complexes
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Molecular Dynamics Study of the Internal Water Molecules in Vasopressin and Oxytocin Receptors
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Synthesis and SAR Studies of Antibacterial Peptidyl Derivatives Based upon the Binding Site of Human Cystatin C
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Construction, purification, and functional characterization of His-tagged Candida albicans glucosamine-6-phosphate synthase expressed in Escherichia coli
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Purification to Homogeneity of Candida albicans Glucosamine-6-phosphate Synthase Overexpressed in Escherichia coli
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Analogues of Trypsin Inhibitor SFTI-1 with Disulfide Bridge Substituted by Various Length of Carbonyl Bridges
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Molecular Simulations of Rhodopsin Tetrameter
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A two-plasmid Escherichia coli system for expression of Dr adhesins
PublicationPraca opisuje konstrukcję wydajnego systemu produkcji fimbrii Dr. System składa się z dwóch plazmidów. Plazmid pACYCpBAD-DraC-C-His zawiera pod kontrolą promotora arabinozowego gen draC kodujący białko kanałotwórcze DraC. Plazmid pET-30b-sygDraBE zawiera pod kontrolą promotora T7lac geny draB i draE kodujące odpowiednio białko opiekuńcze DraB oraz adhezynę DraE. Oba plzamidy posiadają różne ori replikacji co pozwala na ich jednoczesne...
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Extracellular secretion of Pseudoalteromonas sp. cold-adapted esterase in Escherichia coli in the presence of Pseudoalteromonas sp. components of ABC transport system
PublicationEnzymy lipolityczne, głównie lipazy i esterazy, stanowią cenną grupę biokatalizatorów wykorzystywanych w przemyśle. Coraz większe zainteresowanie tą klasą enzymów sprawiło, że poszukuje się alternatywnych źródeł ich pozyskiwania. W celu zbadania wpływu białek transportu ABC Pseudoalteromonas sp. 643A na ekspresję genu, sekrecję i aktywność esterazy EstA z tego mikroorganizmu w systemie ekspresyjnym E. coli skonstruowano układ do...
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Novel method of expression and purification of hirudin based on pBAD TOPO, pTYB12 vectors and gene synthesis
PublicationW pracy przedstawiono nową, szybką i tanią metodę otrzymywania, ekspresji i oczyszczania białka hirudyny naturalnie izolowanego z ślinianek pijawki lekarskiej. Hirudyna pełni funkcje bezpośredniego inhibitora trombiny, głównego białka biorącego udział w tworzeniu skrzepów krwi. Właściwości te wykorzystywane są od wielu lat w klinice. Opracowana metoda pozwoliła uzyskać 17 mg/l hodowli E. coli białka o wysokiej czystości i aktywności...
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Therapy-Related Changes in the Serum Proteome Patterns of Early Stage Breast Cancer Patients with Different Outcomes
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Low-Molecular-Weight Aldehyde Inhibitors of Cathepsin G
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Pegylated Fluorescent Peptides as Substrates of Proteolytic Enzymes
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Designing of Substrates and Inhibitors of Bovine α-Chymotrypsin with Synthetic Phenylalanine Analogues in Position P1
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New conjugates of tuftsin and muramyl dipeptide as stimulators of human monocytes-derived dendritic cells
PublicationMuramyl dipeptide (MDP) and tuftsin are known biologically active compound displaying a significant influence on various cell populations of innate immune response. MDP, as a fragment of bacterial cell wall, stimulates not only macrophages and monocytes, but also dendritic cells. In contrast, little is known about tuftsin influence on these cells. Therefore it seemed vital to access whether tuftsin or its derivatives conjugated...
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Characterization of recombinant homocitrate synthase from Candida albicans
PublicationLYS21 and LYS22 genes from Candida albicans encoding isoforms of homocitrate synthase (HCS), an enzyme catalyzing the first committed step in the L-lysine biosynthetic pathway, were cloned and expressed as NoligoHistagged fusion proteins in Escherichia coli. The purified gene products revealed HCS activity, i.e. catalyzed the condensation of α-ketoglutarate with acetyl-coenzyme A to yield homocitrate. The recombinant enzymes were purified...
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Introduction of Pro and Its Analogues in the Conserved P1 Position of Trypsin Inhibitor SFTI-1 Retains Its Inhibitory Activity
PublicationA number of monocyclic SFTI-1 analogues modified in the conserved inhibitor P1 position by Pro, its L-hydroxyproline (Hyp) derivative as well as mimetics with different ring size were synthesized by the solid-phase method. Replacement of Ser6 by Pro, Hyp, and a four-member ring, L-azetidine-2-carboxylic acid (Aze), retained trypsin or chymotrypsin inhibitory activity. The determined association equilibrium constants of these analogues...
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Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus-expression and purification
PublicationSklonowano w system ekspresyjny pET-30LIC Escherichia coli gen kodujący białka SSB-podobne Thermus thermophilus i T. aquaticus. Oczyszczono do homogenności białka SSB-podobne, a uzyskane preparaty umożliwiają wykonanie badań strukturalnych w/w białek.
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High yield expression and single step purification of Toxoplasma gondii SAG1, GRA1, GRA7 antigens in Escherichia coli.
PublicationPraca przedstawia metodę uzyskiwania antygenów rekombinowanych Toxoplasmagondii o wysokiej czystości, które można zastosować w immunodiagnostyce. Antygeny T. gondii eksprymowane w komórkach E. coli zawierały polihistydynowedomeny fuzyjne na końcu N i C białka. Pozwalało to na jednoetapowe oczyszczanie białek metodą chromatografii metalopowinowactwa na złożu Ni2+ -IDA-Sepharose. Immunoreaktywność antygenów rekombinowanych...
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High level expression, secretion and purification of the termostable aqualysin I from Thermus aquaticus YT-1 in Pichia pastoris.
PublicationOtrzymano aktywną proteazę serynową Thermus aquaticus z systemu nadprodukcji Escherichia coli. Oczyszczono enzym przy zastosowaniu chromatografii metalo-powinowactwa.
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Classification methods and criteria
PublicationKlasyfikacja akustyczna dna morskiego jest najnowszą metodologią zaprojektowaną w celu zdalnego wykrywania rozmaitych charakterystyk dna morskiego z informacji zawartych w echch od dna akustycznych impulsów transmitowanych z różnego typu sonarów. Poza szególnymi chrakterystykami sprzętowymi każdego systemu ASC, istotą każdej metody jest klasyfikacja modułu, który wyciąga serie cech z echa sygnału i przetwarza je aby posortować...
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Experience-Oriented Knowledge Management for Internet of Things
PublicationIn this paper, we propose a novel approach for knowledge management in Internet of Things. By utilizing Decisional DNA and deep learning technologies, our approach enables Internet of Things of experiential knowledge discovery, representation, reuse, and sharing among each other. Rather than using traditional machine learning and knowledge discovery methods, this approach focuses on capturing domain’s decisional events via Decisional...
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Scarabaeidae as human food – A comprehensive review
PublicationRising global population and sustainable protein demand have sparked interest in unique food sources. Entomophagy, or insect consumption, presents a solution and Scarab beetles, part of the Scarabaeidae family, offer a novel food option. The comprehensive review underscores their potential as human food, with strong nutrition, low environmental impact, and the ability to ease strain on conventional agriculture. Nutritional analysis...
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Możliwości zastosowań, potencjalne źródła oraz ewolucja technologiczna sposobu otrzymywania trehalozy ze szczególnym uwzględnieniem enzymu syntazy trehalozy [EC 5.4.99.16]
PublicationJedna z wiodących gałęzi współczesnej biotechnologii opiera się na produkcji białek – przede wszystkim enzymów. Są one powszechnie wykorzystywane: od przemysłu chemicznego poprzez przemysł spożywczy aż po medycynę i życie codzienne (czy ktoś wyobraża sobie w dzisiejszych czasach proszek do prania „bez enzymu”). Przed rozwojem nowoczesnych metod biologii molekularnej i inżynierii genetycznej pozyskiwano interesujące substancje z...
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Genotyping Techniques for Determining the Diversity of Microorganisms
PublicationTyping of microbial pathogens, or identifying bacteria at the strain level, is particularly important for diagnosis, treatment, and epidemiological surveillance of bacterial infections. This is especially the case for bacteria exhibiting high levels of antibiotic resistance or virulence, and those involved in nosocomial or pandemic infections. Strain typing also has applications in studying bacterial population dynamics. The part...
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions
PublicationThe biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide)...
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Preparation and characterization of porous scaffolds from chitosan-collagen-gelatin composite
PublicationNovel porous scaffolds composed of chitosan, collagen and gelatin were prepared and characterized. For preparing scaffolds gelatin and collagen isolated from fish skins with various physicochemical properties were used. In order to reduce preparation solubility glutaraldehyde in the amount of 1%, w/w relative to the total biopolymers weight in solution was used. All obtained biomaterials showed a homogeneous porosity. Protein polymer...
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Texture or Linker? Competitive Patterning of Receptor Assembly toward Ultra-Sensitive Impedimetric Detection of Viral Species at Gold-Nanotextured Titanium Surfaces
PublicationIn this work, we study the electrodes with a periodic matrix of gold particles pattered by titanium dimples and modified by 3-mercaptopropionic acid (MPA) followed by CD147 receptor grafting for specific impedimetric detection of SARS-CoV-2 viral spike proteins. The synergistic DFT and MM/MD modeling revealed that MPA adsorption geometries on the Au–Ti surface have preferential and stronger binding patterns through the carboxyl...
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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublicationPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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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...