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Search results for: primosomal protein b
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Influence of B/N co-doping on electrical and photoluminescence properties of CVD grown homoepitaxial diamond films
PublicationBoron doped diamond (BDD) has great potential in electrical, and electrochemical sensing applications. The growth parameters, substrates, and synthesis method play a vital role in the preparation of semiconducting BDD to metallic BDD. Doping of other elements along with boron (B) into diamond demonstrated improved efficacy of B doping and exceptional properties. In the present study, B and nitrogen (N) co-doped diamond has been...
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Synthesis of 3-Carbamoyl b-Lactams via Manganese(III)-Promoted Cyclization of N-Alkenylmalonamides
PublicationManganese(III)-promoted cyclization of N-alkenylmalonamides (¼N-alkenylpropanediamides) gave 3-(aryl/(alkylamino)carbonyl) b-lactams as well as 3-(aryl/(alkylamino)thiocarbonyl) b-lactams. The relative configuration of the obtained products was unambiguously determined by X-ray crystallography. The proposed method is very useful for the one-pot synthesis of a number of 3-(aryl/ (alkylamino)carbonyl) b-lactams, especially those...
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An MTA-phosphorylase gene discovered in the metagenomic library derived from Antarctic top soil during screening for lipolytic active clones confers strong pink fluorescence in the presence of rhodamine B.
PublicationIn this work, we present the construction of a metagenomic library in Escherichiacoli using the pUC19 vector and environmental DNA directly isolated fromAntarctic topsoil and screened for lipolytic enzymes. Unexpectedly, the screeningon agar supplemented with olive oil and rhodamine B revealed one unusual pinkfluorescent clone (PINKuv) out of 85 000 clones. This clone harbored a plasmid,pPINKuv, which has an insert of 8317 bp that...
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Charge-based deep level transient spectroscopy of B-doped and undoped polycrystalline diamond films
PublicationThe undoped and B-doped polycrystalline diamond thin film was synthesized by hot filament chemical vapor deposition and microwave plasma, respectively. The structural characterization was performed by scanning electron microscopy, X-ray diffraction and Raman spectroscopy. The electrical properties of synthesized diamond layer were characterized by dc-conductivity method and charge deep level transient spectroscopy. The B-doped...
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Spotkanie TEST B
e-Learning Courses -
Geomatyka B 2021
e-Learning CoursesZapoznanie studentów z zagadnieniami pozyskiwania, analizowania, interpretowania i praktycznego stosowania geoinformacji poprzez wzajemne powiązanie aspektów geometrycznych i fizycznych przechodzących od zagadnień globalnych do regionalnych.
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Geomatyka B Ćwiczenia_2023
e-Learning CoursesPodstawy teorii potencjału; Wyrażenie na potencjał elipsoidy ekwipotencjalnej; Powierzchniowe harmoniki sferyczne; System wysokości; Altymetria; Grawimetria; Przyrządy do pomiarów grawimetrycznych; Redukcja szumu sygnału grawimetrycznego; Anomalie grawimetryczne. Redukcje i poprawki; Odchylenie pionu; Pływy skorupy ziemskiej.
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Geomatyka B Ćwiczenia_2023
e-Learning Courses -
Ultrasensitive electrochemical determination of the cancer biomarker protein sPD-L1 based on a BMS-8-modified gold electrode
PublicationThis work describes the modification of a gold electrode with the BMS-8 compound that interacts with the Programmed Death-Ligand 1 (PD-L1), an immune checkpoint protein. The results show that we can confirm the presence of the sPD-L1 in the concentration range of 10−18 to 10−8 M using electrochemical impedance spectroscopy (EIS) with a limit of detection (LOD) of 1.87 × 10−14 M for PD-L1 (S/N = 3.3) and at a concentration of 10−14...
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The Protein Folding Problem
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Justification of quasi-stationary approximation in models of gene expression of a self-regulating protein
PublicationWe analyse a model of Hes1 gene transcription and protein synthesis with a negative feedback loop. The effect of multiple binding sites in the Hes1 promoter as well as the dimer formation process are taken into account. We consider three, possibly different, time scales connected with: (i) the process of binding to/dissolving from a binding site, (ii) formation and dissociation of dimers, (iii) production and degradation of Hes1...
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PROTEIN AND PEPTIDE LETTERS
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Interaction of amphotericin B with phospholipids in the model membrane - molecular dynamics study.
PublicationAmfoterycyna B jest antybiotykiem używanym w leczeniu układowych infekcji grzybowych. Jej mechanizm działania polega na tworzeniu kanałów wewnątrz błon lipidowych. W przedstawianej pracy publikowane są wyniki symulacji przeprowadzonej dynamiką molekularną monomerycznej i dimerycznej formy antybiotyku wewnątrz błony lipidowej zbudowanej z cząsteczek DMPC. Wyniki te wskazują, że powinowactwo cząsteczek amfoterycyny wewnątrz dimeru...
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Wpływ domieszkowania w podsieci B wysokotemperaturowego przewodnika protonowego LaNbO4
PublicationW artykule przeprowadzono analizę wpływu domieszkowania w podsieci B niobanu lantanu korzystając z opublikowanych wyników zespołów badawczych z całego świata. Przeanalizowano wpływ domieszkowania pod kątem domieszek akceptorowych i izowalentnych. Przeanalizowano wpływ zastosowania wielu różnych domieszek tj. Ga, Ge, Si, Ti i Mn na strukturę fazową i przewodność elektryczną materiału. Domieszkowanie akceptorowe w podsieci B pozwala...
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Molecular modelling of membrane activity of amphotericin B, a polyene macrolide antifungal antibiotic
PublicationPraca dotyczy różnego typu modelowań molekularnych cząsteczki przeciwgrzybowego antybiotyku (amfoterycyny B). Praca przeglądowa obejmuje opis badań nad właściwościami molekularnymi samej cząsteczki antybiotyku, jej oddziaływań z powierzchnią błony oraz struktur kanałowych jakie tworzą cząsteczki amfoterycyny wewnątrz błony lipidowej.
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
PublicationRNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA....
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X-ray and UV Radiation Damage of dsDNA/Protein Complexes
PublicationRadiation 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.,...
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JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS
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CURRENT PROTEIN & PEPTIDE SCIENCE
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Current Protocols in Protein Science
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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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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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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo 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....
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The Escherichia coli RNA polymerase alpha subunit and transcriptional activation by bacteriophage lambda CII protein.
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Synthesis of disubstituted 1,3,4,9-tetrahydropyrano-[3,4-b]indole-1-acetic acids derivatives
Publication1,3,4,9-tetrahydropyrano[3,4-b ]indole-1-acetic acid derivatives are of interest for pharmaceutical research as a core structure for synthesis of biological active substance - Etodolac (selective Cyclooxygenase-2 inhibitor, which belongs to the Non-steroidal Anti-inflammatory Drug, NSAID, that shows a clin-ically effective analgesic and anti-inflammatory activity). Here the way of synthesis of two 1,3,4,9-tetrahydropyrano[3,4-b...
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Thermal properties of terpoly(ester-b-ether-b-amide)s with aliphatic ester blocks
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Interactions of amphotericin B derivative of low toxicity with biological membrane components - the Langmuir monolayer approach
PublicationMetodą monowarstw Langmuira zbadano naturę oddziaływań nowej pochodnej antybiotyku przeciwgrzybowego amfoterycyny B o niskiej toksyczności, tj. estru metylowego N-metylo-N-D-fruktopiranozyloamfoterycyny B (MF-AME)z komponentami błon biologicznych: ergosterolem, występującym w komórkach grzybowych i cholesterolem występującym w komórkach zwierzęcych oraz z modelowym fosfolipidem DPPC i na tej podstawie stwierdzono, że zróżnicowanie...
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB 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...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate 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...
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublicationAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublicationWe 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...
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Krytyczny stosunek ciśnień b w rozumieniu norm ISO 6358 i ISO 6953
PublicationJednym z parametrów służących do opisu właściwości przepływowych elementu pneumatycznego jest krytyczny stosunek ciśnień b, zdefiniowany i wykorzystywany w ISO 6358 oraz ISO 6953. Jednak w myśl metod jego wyznaczania opisanych w ISO 6358 i ISO/DIS 6358 definicja ta wydaje się być inna. W pracy omówiono warunki jakie musi spełniać element pneumatyczny, aby wartość b wyznaczona tymi metodami była zbliżona do wartości definicyjnej....
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Internacjonalizacja działalności badawczo-rozwojowej (B+R) przedsiębiorstw high-tech. Wyniki badań empirycznych
PublicationGłownym celem artykułu jest przedstawienie roli badań i rozwoaju (B+R) w procesie internacjonalizacji przedsiębiorstw high-tech. Artykuł obejmuje przegląd literatury oraz wyniki badań 263 przedsiębiorstw high-tech przeprowadzonych na terytorium Polski. Artykuł powstał w ramach projektu badawczego OPUS 6 pt. Wzorce internacjonalizacji małych i średnich przedsiębiorstw działających w branżach high-tech finansowanego przez Narodowe...
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Toxoplasma gondii Recombinant antigen AMA1: Diagnostic Utility of Protein Fragments for the Detection of IgG and IgM Antibodies
PublicationToxoplasma 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...
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Interaction of amphotericin B and its low toxic derivative, N-methyl-N-D-fructosyl amphotericin B methyl ester, with fungal, mammalian and bacterial cells measured by the energy transfer method.
PublicationPochodna amfoterycyny B ( AMB) ester metylowy N-metylo-N-D-fruktozylo amfoterycyny B (MFAME) wykazuje szerokie spektrum i wysoką aktywność przeciwgrzybową wyjściowego amtybiotyku i równocześnie toksyczność mniejszą o dwa rzędy wielkości. Celem tej pracy było ustalenie czy obserwowane różnice między toksycznością pochodnej i wyjściowego antybiotyku wynikają z różnic w powinowactwie do błon komórkowych grzybów i komórek ssakowych....
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How water mediates the long-range interactions between remote protein molecules
PublicationThe 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...
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Agregacja amfoterycyny B i wybranych pochodnych - chemometryczna analiza widm UV-Vis
PublicationPrezentowane badania miały na celu poznanie procesu agregacji nowej generacji pochodnych polienowego antybiotyku przeciwgrzybowego - amfoterycyny B. Przebieg procesu agregacji w roztworach wodnych o różnym składzie monitorowano przy pomocy absorpcyjnej spektroskopii UV-Vis. Otrzymane zestawy widm analizowano z zastosowaniem zaawansowanych technik chemometrycznych (PCA, NSD), co pozwoliło na określenie liczby, typu i ilości form...
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Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublicationWater 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...
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Molecular modeling of amphotericin B - ergosterol primary complex in water II
PublicationPrezentowane badania dotyczą oddziaływania antybiotyku polienowego anfoterycyny B (AmB) i ergosterolu (ERG) (typowego sterolu błonowego komórek grzybowych) na poziomie molekularnym. W odróżnieniu od badanego poprzednio kompleksu binarnego analizowany obecnie kompleks AnB/ERG/AmB charakteryzuje się zdecydowanie wiekszą stabilnością i wzglednie sztywną, sandwiczową geometrią. Za trwałość i geometrie kompleksu odpowiedzialne są oddziaływania...
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublicationSurface 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...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization 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...
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublicationEfficient 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,...
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE 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...
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Analiza redystrybucji środków finansowych przeznaczonych na działalność B+R (na przykładzie wybranej uczelni)
PublicationAutor zwraca uwagę na wyjątkowo niskie finansowanie działalności B+R w Polsce na tle innych krajów nowo przyjętych do UE. Przeprowadza analizę redystrybucji tych skromnych środków w skali Polski oraz na przykładzie konkretnej uczelni. Dostrzega dwa charakterystyczne zjawiska, określona jako asymetrie. Pierwsze-dotyczące podziału tych środków między szkoły wyższe, jednostki badawczo-rozwojowe i placówki PAN. Drugie - dotyczące struktury...
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The Polish adaptation of the Burnout Assessment Tool (BAT-PL) by W. Schaufeli et al.
PublicationAim. The study aimed to present the Polish version of the Burnout Assessment Tool (BAT-PL) by Schaufeli et al. and to assess its validity and reliability. The tool measures the core symptoms of burnout (BAT-C): exhaustion, mental distance, cognitive and emotional impairment, and its secondary symptoms (BAT-S): psychosomatic complaints and psychological distress. Method. The participants were 255 nursing staff members. The construct...
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Within- and between-person factor structure of the Oldenburg Burnout Inventory: Analysis of a diary study using multilevel confirmatory factor analysis
PublicationThe study examined the factor structure of burnout, as measured with the Oldenburg Burnout Inventory. The participants were 235 employees of a public administration agency who assessed their burnout online for 10 consecutive working days. Two models were tested with multilevel confirmatory factor analysis, assuming the same one or two-factor structure at the within- and between-person levels. Both models showed a reasonable fit...
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Linear viscoelastic transversely isotropic model based on the spectral decomposition of elasticity tensors
PublicationThe linear viscoelasticity is still a useful model in the engineering for studying the behavior of materials loaded with different loading rates (frequencies). Certain types of materials reveal also an anisotropic behavior: fiber reinforced composites, asphalt concrete mixtures, or wood, to name a few. In general, researchers try to identify experimentally the dependence of engineering constants like: directional Young’s moduli...