Filtry
wszystkich: 1359
wybranych: 1191
wyświetlamy 1000 najlepszych wyników Pomoc
Wyniki wyszukiwania dla: PROTEIN VOLUME PARADOX
-
X-ray and UV Radiation Damage of dsDNA/Protein Complexes
PublikacjaRadiation and photodynamic therapies are used for cancer treatment by targeting DNA. However, efficiency is limited due to physico-chemical processes and the insensitivity of native nucleobases to damage. Thus, incorporation of radio- and photosensitizers into these therapies should increase both efficacy and the yield of DNA damage. To date, studies of sensitization processes have been performed on simple model systems, e.g.,...
-
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublikacjaWe 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...
-
Evolution towards simplicity in bacterial small heat shock protein system
PublikacjaEvolution 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...
-
The Impact of Thermal Stresses on Volume Resistivity: Performance Comparison between TR-XLPE and XLPE Cables
PublikacjaMost failures in electric power cables are attributed to the development of water trees inside the insulating materials. Thus, the development and utilization of Tree Retardant Cross-Linked Polyethylene (TR-XLPE) based cables have recently been given great attention to overcome the treeing issues. TR-XLPE cables use low-density polyethylene compounds suppressing the formation of water trees while retaining excellent electrical,...
-
Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublikacjaTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
-
Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublikacjaPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
-
Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublikacjaPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
-
Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublikacjaWe have reported that the hsp70 chaperone DnaK from Escherichia coli might assist protein folding by catalyzing the cis/trans isomerization of secondary amide peptide bonds in unfolded or partially folded proteins. In this study a series of fatty acylated benzamido inhibitors of the cis/trans isomerase activity of DnaK was developed and tested for antibacterial effects in E. coli MC4100 cells. Nα-[Tetradecanoyl-(4-aminomethylbenzoyl)]-l-asparagine...
-
Toxoplasma gondii Recombinant antigen AMA1: Diagnostic Utility of Protein Fragments for the Detection of IgG and IgM Antibodies
PublikacjaToxoplasma gondii is an important zoonotic protozoan that infects a wide variety of vertebrates as intermediate hosts. For this reason, the diagnosis of this disease is very important and requires continuous improvement. One possibility is to use recombinant antigens in serological tests. Apical membrane antigen 1 (AMA1), a protein located in specific secretory organelles (micronemes) of T. gondii, is very interesting in regard...
-
How water mediates the long-range interactions between remote protein molecules
PublikacjaThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
-
Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublikacjaWater molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...
-
Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublikacjaSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
-
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublikacjaPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
-
The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublikacjaEfficient brain function requires as much as 20% of the total oxygen intake to support normal neuronal cell function. This level of oxygen usage, however, leads to the generation of free radicals, and thus can lead to oxidative stress and potentially to age-related cognitive decay and even neurodegenerative diseases. The regulation of this system requires a complex monitoring network to maintain proper oxygen homeostasis. Furthermore,...
-
Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublikacjaEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
-
Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublikacjaThe 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...
-
Stabilizing agents and protein stability
PublikacjaBiałka są kluczowymi elementami żywych organizmów, jak również efektywnymi katalizatorami w biotechnologii i medycynie. Szybki rozwój wielu gałęzi biotechnologii wiąże się z coraz większym zapotrzebowaniem na produkty białkowe charakteryzujące się wysoką stabilnością. Jednym ze sposobów osiągnięcia większej stabilności białek jest wykorzystanie małych związków organicznych, tzw. osmolitów. Do tej grupy związków należą aminokwasy,...
-
Alternative and New Protein Sources
Publikacja -
Colloidal aspects of protein digestion
Publikacja.
-
Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublikacjaRadiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions,...
-
Apparent molar volume and compressinility of tetrabutylphosphonium bromide in various solvents
PublikacjaW oparciu o pomiary gęstości wyznaczono pozorne objętości molowe bromku czero-n-butylofosfoniowego w etanolu, 1-propanolu, 1-butanolu, acetonie i acetonitrylu w przedziale temperatur od 288,15 K do 323,15 K. Ponadto zmierzone w 298,15 K szybkości rozchodzenia się dźwięku w badanych cieczach pozwoliły obliczyć pozorne ściśliwości adiabatyczne bromku. Wielkości pozorne ekstrapolowano do nieskończenie rozcieńczonego stężenia w celu...
-
Investigation method of large-volume tire with mobile test rig
PublikacjaThe goal of this research is to develop the tire test method and mobile tire test rig. The test rig enables measurement of tire properties as stiffness and viscous damping in vertical direction, and tire–ground characteristics on the asphalt rigid surface. The tire-ground characteristics are measured by force and a torque measurement hub. The design, calibration and the algorithm for calculating the forces in the wheel center are...
-
On the importance of initial volume of eroded material for cavitation erosion curve
PublikacjaW pracy przedstawiono rozważania na temat wpływu początkowej objętości erodowanego materiału na przebieg krzywych erozyjnego niszczenia
-
Determination of representative volume element in concrete under tensile deformation
PublikacjaW artykule podano sposoby określenia elementu reprezentatywnej objętości w betonie podczas rozciągania. Obliczenia wykonano przy zastosowaniu izotropowego modelu degradacji sztywności rozszerzonego o długość charakterystyczną mikrostruktury w ramach teorii nielokalnej. Zaproponowano 2 różne metody wyznaczania elementu reprezentatywnej objętości niezależnego od warunków brzegowych.
-
Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublikacjaNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
-
Assembly of Lipopolysaccharide in Escherichia coli Requires the Essential LapB Heat Shock Protein
PublikacjaHere, 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...
-
A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.
PublikacjaThe presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified...
-
How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublikacjaTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
-
Identification of evolutionary conserved DNA sequence and corresponding S21 ribosomal protein region for diagnostic purposes of all Borrelia spirochetes
PublikacjaIt is still under investigation, whether all Borrelia sp. causing Lyme borreliosis and other diseases are already identified and properly classified as human pathogens. For this reason, it is of great importance to develop a diagnostic ELISA test that detects all Borrelia sp. The aim of this study was to identify conserved DNA and protein regions present in all currently known Borrelia sp. In experimental studies 31 available Borrelia...
-
Quality Control of Bacterial Extracellular Vesicles with Total Protein Content Assay, Nanoparticles Tracking Analysis, and Capillary Electrophoresis
PublikacjaExtracellular vesicles (EVs) were isolated from Pectobacterium zantedeschiae culturing media using direct ultracentrifugation (UC), iodixanol cushion ultracentrifugation (ICUC), and iodixanol density gradient ultracentrifugation (IDGUC) techniques. The isolates were characterized with total protein content assay (bicinchoninic acid assay, BCA), nanoparticles tracking analysis (NTA), and capillary electrophoresis (CE). A satisfactory...
-
Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublikacjaLow 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...
-
Endocrine responses following exhaustive strength exercise with and without the use of protein and protein-carbohydrate supplements
Publikacja -
"Creating a numerical model of noise conditions based on the analysis of traffic volume changes in cities with low and medium structure.
PublikacjaThe subject of this research study is to analyze noise conditions of the selected area in the city of Gdańsk using data related to traffic volume changes during a day. This is because daily distribution of noise levels is much more helpful for noise control and reduction than traditional maps with Lden levels indicated. Calculations are made with the use of a numerical model developed at the Gdansk Univ. of Technology and implemented...
-
"Creating a numerical model of noise conditions based on the analysis of traffic volume changes in cities with low and medium structure.
PublikacjaThe subject of this research study is to analyze noise conditions of the selected area in the city of Gdańsk using data related to traffic volume changes during a day. This is because daily distribution of noise levels is much more helpful for noise control and reduction than traditional maps with Lden levels indicated. Calculations are made with the use of a numerical model developed at the Gdansk Univ. of Technology and implemented...
-
Identification, cloning, expression, and characterizationof a highly thermostable single-stranded-DNA-binding protein (SSB) from Deinococcus murrayi
PublikacjaZidentyfikowano i scharakteryzowano białko SSB-podobne, pochodzące z Deinococcus murrayi (DmuSSB). Otrzymany w reakcji PCR fragment zawierający kompletny gen ssb sklonowano w systemie ekspresyjnym Escherichia coli. Gen składa się z 826 nt, kodujących 276 reszt aminokwasowych z wyliczoną teoretycznie masą cząsteczkową monomeru równą 30,14 kDa. DmuSSB zawiera dwie domeny wiążące jednoniciowe DNA OBna monomer I funkcjonuje jako homodimer....
-
A cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublikacjaThe expression of reporter gene may be induced by activation of cryptic signalling sequences, as we found while constructing the mutS-lacZ fusion gene. We cloned the Escherichia coli lacZ gene encoding beta-galactosidase into a plasmid vector carrying the Thermus thermophilus mutS gene. The clones expected to produce beta-galactosidase as the C-terminal fusion were selected for the complementation of beta-galactosidase activity...
-
Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis
PublikacjaSingle-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNAreplication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-likegene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoal-teromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism.PhaSSB possesses...
-
US not bright but right method of thyroid volume estimation even in large and substernal extended goitres. Comparison of US and three methods of CT thyroid evaluation - prospective study.ON LINE
PublikacjaBackground Ultrasound is nowadays a method of choice for thyroid volume assessment. However, its disadvantage is some inaccuracy, which is said to be higher in huge, especially substernally extended goitres. Aims The aim of the study was to compare the US and CT thyroid volumetric measurements: multi-observers (CT MO) and one-observer (CT OO) to CT planimetry results (CT Pl) in patients with large goitres. Materials & Methods The...
-
Occlusion phenomenon of redox probe by protein as a way of voltammetric detection of non-electroactive C-reactive protein
Publikacja -
Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans—Expression and characterization
PublikacjaDNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the...
-
t-SNE Highlights Phylogenetic and Temporal Patterns of SARS-CoV-2 Spike and Nucleocapsid Protein Evolution
PublikacjaWe propose applying t-distributed stochastic neighbor embedding to protein sequences of SARS-CoV-2 to construct, visualize and study the evolutionary space of the coronavirus. The basic idea is to explore the COVID-19 evolution space by using modern manifold learning techniques applied to evolutionary distances between variants. Evolutionary distances have been calculated based on the structures of the nucleocapsid and spike proteins.
-
CMS Physics Technical Design Report, Volume II: Physics Performance
Publikacja -
Volume efficiency loss in axial pumps caused by working fluid compressibility.
PublikacjaPrzedstawiono teoretyczną analizę wpływu ściśliwości cieczy roboczej konstrukcji mechanizmu rozrządu pompy wielotłoczkowej osiowej na straty energetyczne w przestrzeni martwej. Podano wyniki uzyskane dla typowych konstrukcji.
-
One year performance evaluation of low volume road with cold recycled base course on the basis of FWD and Dynamic Modulus tests
PublikacjaArticle presents results of assessment of performance of trial section of flexible pavement with cold recycled base constructed on low volume road within typical contract conditions. Performance evaluation was made based on Falling Weight Deflectometer (FWD) test performed during construction stage – 2 times on the top of cold recycled base course – 28 and 180 days after compaction of base course and 2 times on the top of the wearing...
-
Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublikacjaFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
-
Highly selective impedimetric determination of Haemophilus influenzae protein D using maze-like boron-doped carbon nanowall electrodes
PublikacjaThis study reports a novel impedimetric immunosensor for protein D detection in purified and bacterial (Haemophilus influenzae, Hi) samples. The detection was based on antigen recognition by anti-protein D antibodies (apD) immobilised at the maze-like boron-doped carbon nanowall electrodes (B:CNW). The B:CNW electrodes were synthesised, and their surface was characterised by scanning electron microscopy (SEM) and X-ray photoelectron...
-
Effective mode volume of a natural mode of an open dielectric resonator with an active region
Publikacja -
Nonradiative long range energy transfer in donor-acceptor systems with excluded volume
PublikacjaW pracy analizowano bezpromienisty długozasięgowy transfer energii w układach donor-akceptor z uwzględnieniem objętości wyłączonej. Stwierdzono, że zanik fluorescencji pierwotnie wzbudzonych donorów jest wolniejszy, jeżeli uwzględnia się objętość wyłączoną. Ten efekt jest znacznie wzmocniony, gdy akceptory znajdują się w pewnej objętości niedostępnej dla donorów. Analizę numeryczną przeprowadzono stosując metodę symulacji Monte...
-
Impact of Boundary Conditions on Acoustic Excitation of EntropyPerturbations in a Bounded Volume of Newtonian Gas
PublikacjaExcitation of the entropy mode in the field of intense sound, that is, acoustic heating, is theoreticallyconsidered in this work. The dynamic equation for an excess density which specifies the entropy mode,has been obtained by means of the method of projections. It takes the form of the diffusion equation withan acoustic driving force which is quadratically nonlinear in the leading order. The diffusion coefficient isproportional...
-
ANALYSIS OF POSSIBILITIES FOR THE USE OF VOLUME-DELAY FUNCTIONS IN THE PLANNING MODULE OF THE TRISTAR SYSTEM
Publikacja.