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Search results for: dna protein interactions
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IFI16 Impacts Metabolic Reprogramming during Human Cytomegalovirus Infection
PublicationCellular lipid metabolism plays a pivotal role in human cytomegalovirus (HCMV) infection, as increased lipogenesis in HCMV-infected cells favors the envelopment of newly synthesized viral particles. As all cells are equipped with restriction factors (RFs) able to exert a protective effect against invading pathogens, we asked whether a similar defense mechanism would also be in place to preserve the metabolic compartment from HCMV...
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MutS3: a MutS homologue of unknown biological function
PublicationThe homologues of MutS proteins are widespread among both Prokaryotes and Eukaryotes. MutS designated as MutS1 is a part of MMR (mismatch repair) system which is responsible for removal of mispaired bases and small insertion/deletion loops in DNA. Initially, the only MutS homologues known were those engaged in mismatch repair and these were later designated as MutS1. Subsequently, the MutS2 homologue was distinguished. MutS2 does...
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Abstract DNA-type systems
PublicationAbstrakcyjny system typu DNA jest definiowany przez zestaw nieliniowych kinetycznych równań z wielomianowymi nieliniowościami, które przyjmują rozwiązania solitonowe związane z geometrią helis. Zestaw równań pozwala na dwie różne reprezentacje Laxa: forma von Neumanna i Darboux-kowariantna para Laxa. Wyjaśniamy dlaczego nie-Kolmogorowskie modele prawdopodobieństwa pojawiające się w kinetyce solitonowej są naturalnie związane z...
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Anticancer imidazoacridinone C-1311 inhibits hypoxia-inducible factor-1α (HIF-1α), vascular endothelial growth factor (VEGF) and angiogenesis
PublicationAntitumor imidazoacridinone C-1311 is a DNA-reactive topoisomerase II and FLT3 receptor tyrosine kinase inhibitor. Here, we demonstrate the mechanism of C-1311 inhibitory action on novel targets: hypoxia-inducible factor-1α (HIF-1α), vascular-endothelial growth factor (VEGF), and angiogenesis. In a cell-free system, C-1311 prevented HIF-1α binding to an oligonucleotide encompassing a canonical hypoxia-responsive element (HRE),...
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CYP3A4 overexpression enhances apoptosis induced by anticancer agent imidazoacridinone C-1311, but does not change the metabolism of C-1311 in CHO cells
PublicationWe examine whether CYP3A4 overexpression influences the rate and pattern of antitumor imidazoacridinone C-1311 metabolism, in relation to the impact of this overexpression on cell cycle progression and final cellular response of CHO cells following C-1311 treatment. Methods: Three CHO cell lines: CHO-WT, wild type, CHO-HR, overexpressing cytochrome P450 reductase (CPR) and CHO-HR-3A4, coexpressing CPR and CYP3A4 were applied....
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Processing of 1-nitroacridine-induced DNA-DNA cross-links by topoisomerase I is associated with enhanced cellular survival: a possible role of topoisomerase I in the removal of DNA cross-links
PublicationW tej pracy wykazujemy, że modyfikacje plazmidu indukowane przez wzrastające dawki 1-nitroakrydyn (nitracrine i związek C-857) prowadzą do zahamowania aktywności katalitycznej topoizomerazy I. Hamowanie to związane jest z pojawieniem się pojedynczoniciowych uszkodzeń DNA i tworzeniem kowalencyjnych kompleksów topoizomeraza I-DNA. Nie obserwowano takich efektów dla topoizomerazy typu II.Dalsze badania wykazały, że jedna z 1-nitroakrydyn...
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THE GENE CLONING, OVEREXPRESSION, PURIFICATION AND BIOCHEMICAL CHARACTERISATION OF A NEW COLD-ADAPTED β–GALACTOSIDASE FROM ARTHROBACTER SP. VII-4
PublicationINTRODUCTION. β-Galactosidase [EC 3.2.1.23] is an enzyme that catalyzes the hydrolysis of O-glycosidic linkages in galactosides. It is commercially used in dairy industry for the production of milk with reduced lactose content. Potentially, the best method for lactose removal under cooling conditions should be carried out with a cold-adapted enzyme. AIM. The aim of this study was to determine the taxonomic affiliation of the isolate...
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Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges
PublicationStaphylococci are increasingly recognized as etiological agents of many opportunistic human and animal infections, emphasizing the need for a rapid and accurate identification, even to a genotypical level of these bacteria. In the recent years, there has been a significant progress in typing and phylogenetic study of Staphylococcus species. Here, we describe molecular methods used in taxonomy as well as staphylococci characterization....
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Applying fuzzy logic to decisional DNA digital TV
PublicationWprowadzono wspomaganie oparte na logice rozmytej do modelu telewizji wykorzystujacej decyzyjny DNA.
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Identification and molecular modeling of a novel lipase from an Antarctic soil metagenomic library.
PublicationIn this work, we present the construction of a metagenomic library in Escherichia coli using pUC19 vector and environmental DNA directly isolated from Antarctic topsoil and screened for lipolytic enzymes. The screening on agar supplemented with olive oil and rhodamine B revealed one clone with lipolytic activity (Lip1) out of 11,000 E. coli clones. This clone harbored a plasmid, pLip1, which has an insert of 4722 bp that has been...
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Naturally occurring mitochondrial DNA heteroplasmy in the MRL mouse
PublicationThe MRL/MpJ mouse is an inbred laboratory strain of Mus musculus, known to exhibit enhanced autoimmunity, increased wound healing, and increased regeneration properties. We report the full-length mitochondrial DNA (mtDNA) sequence of the MRL mouse (Accession # EU450583), and characterize the discovery of two naturally occurring heteroplasmic sites. The first is a T3900C substitution in the TpsiCloop of the tRNA methionine gene...
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Conservation and diversity of MutS proteins
PublicationThe homologues of MutS, mismatch repair protein, exist in all prokaryotes, with the exception of Actinobacteria, Mollicutes and part of the Archaea. Multiple alignments of 316 MutS amino acid sequences from 169 species revealed conserved residues and sequence motifs distinguishing MutS homologues. All MutS homologues show high conservation within the ATPase domain. MutS1, the homologue responsible for DNA mismatch recognition,...
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PROTEIN EXPRESSION AND PURIFICATION
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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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DNA modification by 1-nitroacridine derivatives. Comparison of 32P-Postlabeling and restriction enzyme analysis method for the detection of DNA adducts formed by 1-nitroacridines C-1748 and C-857
Publication4-podstawione 1-nitroakrydyny reprezentują nową grupę pochodnych akrydyny, zsyntetyzowanych na Politechnice Gdańskiej. Metoda 32P-postlabellingu wykazała, że pochodne C-1748 i C-857 tworzą od 4-6 adduktów DNA w systemie komórkowym i bezkomórkowym o innym rozkładzie plam chromatograficznych, jednakże niezależnym od zastosowanego systemu aktywacyjnego. Metoda enzymatycznej analizy restrykcyjnej pozwoliła natomiast śledzić kinetykę...
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Interstrand crosslinking of DNA by C-1311 (Symadex) and other imidazoacridinones
PublicationImidazoakrydony, w tym pochodna C-1311 (Symadex) znajdująca się w pierwszej fazie badań klinicznych prowadzonych w USA, należą do grupy bardzo aktywnych związków przeciwnowotworowych zsyntetyzowanych w Katedrze Technologii Leków i Biochemii PG. Za pomocą zmodyfikowanej metody Parsons'a wykazaliśmy, że C-1311 indukuje, w sposób zależny od stężenia, międzyłańcuchowe wiązania sieciujące w komórkach różnych nowotworów ludzkiego pochodzenia...
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On the Origin of Protein Superfamilies and Superfolds
PublicationDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis
PublicationThe thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular...
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Interaction of antitumor triazoloacridone C-1305 and its analogs with telomeric DNA
PublicationBadaliśmy oddziaływanie pochodnej triazoloakrydonu C-1305 i jego bliskich analogów strukturalnych z oligonukleotydami zawierającycmi sekwencje telomerowe TTAGGG oraz oligonukleotydami sfałdowanymi w strukturę G-kwadrupleksu. Wykazaliśmy, że spośród badanych związków pochodna C-1305 wykazała największą specyficzność w stosunku do telomerowego DNA. Związek ten stabilizował także strukturę G-kwadrupleksu, podczas gdy jego analogi...
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Cellular senescence induced by DNA damage and its role in carcinogenesis and chemotherapy
PublicationUszkodzenia DNA indukują w komórce różne procesy, w tym starzenie komórkowe, co może uruchamiać proces karcinogenezy jak i być związane z odpowiedzią na leki przecinowotworowe. Biologiczna rola starzenia komórkowego nie jest jednak jasna. Zasugerowano, że proces starzenia komórkowego może hamować proces karcinogenezy poprzez indukcję nieodwracalnego zahamowania wzrostu przez czynniki genotoksyczne. Indukcja starzenia komórkowego...
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Folding‐upon‐repair DNA nanoswitches for monitoring DNA repair enzymes activity
PublicationWe demonstrate here a new class of DNA‐based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding‐upon‐repair DNA nanoswitches are synthetic DNA sequences containing O6‐methyl‐guanine (O6‐MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation...
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Comet assay-based methods for measuring DNA repair in vitro; estimates of inter- and intra-individual variation.
PublicationZdolność do naprawy uszkodzeń DNA jest jednym z najważniejszych wyznaczników podatności na choroby nowotworowe. Dlatego też użytecznym staje się możliwość pomiaru stopnia naprawy DNA w próbkach materiału badawczego pobranego od ochotników. Celem pracy było, po pierwsze, opracowanie w warunkach in vitro prostej metody (z wykorzystaniem techniki testu kometowego), w której naprawa DNA odbywa się poprzez wycinanie nukleotydów (NER)....
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Epigenetic Basis of Regeneration: Analysis of Genomic DNA Methylation Profiles in the MRL/MpJ Mouse
PublicationEpigenetic regulation plays essential role in cell differentiation and dedifferentiation, which are the intrinsic processes involved in regeneration. To investigate the epigenetic basis of regeneration capacity, we choose DNA methylation as one of the most important epigenetic mechanisms and the MRL/MpJ mouse as a model of mammalian regeneration known to exhibit enhanced regeneration response in different organs. We report the...
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Construction and purification of his6-Thermus thermophilus MutS protein.
PublicationGen mutS z termofilnej bakterii Thermus thermophilus zamplifikowano przy użyciu PCR, sklonowano i przeprowadzono jego ekspresję w E. coli. Rekombinantowe białko MutS zawierające oligohistydynową domenę na N-końcu oczyszczono w jednoetapowej procedurze przy wykorzystaniu chromatografii powinowactwaNi(2+). Zdolność do rozpoznania niekomplementarności białka his(6)-MutS potwierdzono w eksperymentach ochrony DNA przed trawieniem...
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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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Geologia dna morskiego 2021/2022
e-Learning CoursesKurs przeznaczony jest dla studentów I semestru studiów II stopnia kierunku Inżynieria Morska i Brzegowa na WOiO i WILIŚ. Tematyka kursu obejmuje zagadnienia geologii morza, procesów formujących dno morskie i oceaniczne a także strefę brzegową oraz skał powstających w środowisku morskim.
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Taurine as a water structure breaker and protein stabilizer
PublicationThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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Hydration of molecules and intermolecular interactions 2023
e-Learning Courses -
Problem of aggregation in dye-DNA interaction, calorimetry studies
PublicationNucleic acids are the biological target for many antimicrobial, antitumor and antiviral drugs. Ligand-DNA interactions can be classified into two major categories: 1. covalent binding, which can provide to intermolecular adducts, 2. physico-chemical interactions, which can be divided into intercalation (e.g. adriamycin) or groove binding (e.g. dystamycin). There are several methods to investigate interactions between drug and DNA....
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Interactions with recognized objects
PublicationImplicit interaction combined with object recognition techniques opens a new possibility for gathering data and analyzing user behavior for activity and context recognition. The electronic eyewear platform, eGlasses, is being developed, as an integrated and autonomous system to provide interactions with smart environment. In this paper we present a method for the interactions with the recognized objects that can be used for electronic...
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Interstrand crosslinking of DNA in tumor and fibroblast cells by C-1311 (Symadex) and other imidazoacridinones
PublicationImidazoakrydony, w tym pochodna C-1311 znajdująca się w pierwszej fazie badań klinicznych prowadzonych przez firmę Xanthus Life Sciences, należą do grupy bardzo aktywnych związków przeciwnowotworowych zsyntetyzowanych w Katedrze Technologii Leków i Biochemii PG. Za pomocą zmodyfikowanej metody Parsons'a wykazaliśmy, że C-1311 indukuje w sposób zależny od stężenia międzyłańcuchowe wiązania sieciujące w komórkach różnych nowotworów...
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DNA REPAIR
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Mobile DNA
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DNA SEQUENCE
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DNA Reporter
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Environmental DNA
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Mitochondrial DNA
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Influence of Osmolytes on Protein and Water Structure: A Step To Understanding the Mechanism of Protein Stabilization
PublicationResults concerning the thermostability of hen egg white lysozyme in aqueous solutions with stabilizing osmolytes, trimethylamine-N-oxide (TMAO), glycine (Gly), and its N-methyl derivatives, N-methylglycine (NMG), N,N-dimethylglycine (DMG), and N,N,N-trimethylglycine (betaine, TMG), have been presented. The combination of spectroscopic (IR) and calorimetric (DSC) data allowed us to establish a link between osmolytes’ influence on...
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Measuring the density of DNA films using ultraviolet-visible interferometry
PublicationIn order to determine a proper value for the density of dry DNA films we have used a method based upon the measurement of interference effects in transmission spectra of thin DNA layers. Our results show that the methodology is effective and the density of DNA in this state, 1.407 g/cm3, is much lower than the commonly used 1.7 g/cm3. Obtaining accurate values for the DNA film density will allow the optical constants for DNA to...
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Intercultural interactions in multinational subsidiaries
PublicationPurpose - Our aim is to show how individuals perceive the quality of intercultural interactions at work in multinational subsidiaries, and to address the question of what actually prevails in their accounts, i.e. ‘the dark side’ or ‘the bright side’. Design/methodology/approach - We report the findings from five subsidiaries located in Poland and interviews with 68 employees of these companies. Findings - The ‘bright side’ dominated...
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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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Targeting of FLT3-ITD kinase contributes to high selectivity of imidazoacridinone C-1311 against FLT3-activated leukemia cells
PublicationDrugs targeting receptor tyrosine kinase FLT3 are of particular interest since activating FLT3-internal tandem duplication (ITD) mutations abundantly occur in fatal acute myeloid leukemias (AMLs). Imidazoacridinone C-1311, a DNA-reactive inhibitor of topoisomerase II, has been previously shown to be a potent and selective inhibitor of recombinant FLT3. Here, we expand those findings by studying its effect on leukemia cells with...
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5-Thiocyanato-2′-deoxyuridine as a possible radiosensitizer: electron-induced formation of uracil-C5-thiyl radical and its dimerization
PublicationIn this work, we have synthesized 5-thiocyanato-2′-deoxyuridine (SCNdU) along with the C6-deuterated nucleobase 5-thiocyanatouracil (6-D-SCNU) and studied their reactions with radiation-produced electrons. ESR spectra in γ-irradiated nitrogen-saturated frozen homogeneous solutions (7.5 M LiCl in H2O or D2O) of these compounds show that electron-induced S–CN bond cleavage occurs to form a thiyl radical (dU-5-S˙ or 6-D-U-5-S˙) and...
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Determination of viscosity changes of protein hydrolyzate solutions depending on shear rate
Open Research DataRheological characteristics of connective tissue protein solutions were made on the basis of viscosity measurement using a Brookfield viscometer using LV SC4 - 27 spindles and shear rate of 85 s-1 (Fig. 1). Solutions of protein hydrolysates with a concentration of 2% in 0.5M acetic acid were prepared.
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Interactions of positrons with atoms and molecules
PublicationThe positron is the antiparticle of the electron. It has the same mass as the electron, but opposite charge. The understanding of the interactions of positrons with normal matter, like atoms and molecules, is of interest in various scientific fields, like nuclear medicine, plasma physics and astronomy. In this talk we will give a short introduction to some theoretical methods to describe the interactions of positrons with atoms...
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VUV irradiation studies of plasmid DNA in aqueous solution
PublicationInteractions of VUV light and DNA samples in aqueous solutions are reported. The damage induced by such radiation is quantified by monitoring both loss of supercoiled DNA and formation of single and double strand breaks using agarose gel electrophoresis. Irradiations were performed using synchrotron VUV photons of 130, 150, 170 and 190 nm. VUV irradiation experiments revealed enhanced damage upon irradiation with 170 nm photons...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Identification and properties of the Deinococcus grandis andDeinococcus proteolyticus single-stranded DNA binding proteins (SSB)
PublicationW celu poznania właściwości biochemicznych białek SSB pochodzących z Deinococcus grandis (DgrSSB) i Deinococcus proteolyticus (DprSSB) sklonowano zaamplifikowane w reakcji PCR geny ssb w systemie ekspresyjnym Escherichia coli. Geny składają się z 891(DgrSSB) i 876 (DprSSB) nukleotydów kodujących odpowiednio 296 i 291 reszt aminokwasowych o teoretycznie wyznaczonej masie cząsteczkowej dla białek, równej 32,29 i 31,33 kDa. Sekwencja...