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Substrate profiling of Zika virus NS2B‐NS3 protease
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The construction of bifunctional fusion proteins consisting of MutS and GFP
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublikacjaTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Dynamics of Chains as a Tool to Study Thermomechanical Properties of Proteins.
PublikacjaPolymer dynamics can be formulated on different levels of detail. One approach eliminates microscopic degrees of freedom and a polymer molecule is represented by a simplified structure—a chain. In the simplest case monomers of ideal chain have fixed length, and their orientation is independent of the orientations and positions of neighbouring monomers. This is reason that two monomers can co-exist at the same place. Ideal chain...
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Mechanism of Osmolyte Stabilization–Destabilization of Proteins: Experimental Evidence
PublikacjaIn 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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The construction of bifunctional fusion proteins consisting of MutS and GFP
PublikacjaSkonstruowano 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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Recent Developments in Data-Assisted Modeling of Flexible Proteins
PublikacjaMany proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this...
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Structural and Functional Analysis of Human HtrA3 Protease and Its Subdomains
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Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants
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Biochemical and Structural Characterization of SplD Protease from Staphylococcus aureus
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Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants
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Temperature-induced changes of HtrA2(Omi) protease activity and structure
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Oxidative Modification of Proteins in Pediatric Cystic Fibrosis with Bacterial Infections
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Contribution of small heat shock proteins to muscle development and function
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Carotenoid binding to proteins: Modeling pigment transport to lipid membranes
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Structure and function of natural proteins for water transport: general discussion
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Characteristic and specificity of protease activity of thermophilic bacteria Meiothermus ruber
PublikacjaThe primary purpose of research was to establish the possibility of using thermophilic bacteria Meiothermus ruber as a source of proteolytic enzymes. The main reason of searching new proteases is their commercial value especially in production of detergents, food, pharmaceuticals, leather, diagnostics or waste management. The development of this type processes will be possible by utilization of enzymes which have unique characteristics...
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Immunogenic and protective activity of recombinant chimeric Toxoplasma gondii proteins
PublikacjaToxoplasmosis, one of the most common parasitic invasions worldwide, may pose a great threat for individuals with weakened immune system. The parasite also causes considerable economic losses due to infection of livestock. To date there is no efficient immunoprophylaxis for humans and animals, which would provide long-lasting protection against T. gondii invasion. Chimeric proteins, containing several selected fragments of parasite...
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Analysis of the Factors Affecting Static In Vitro Pepsinolysis of Food Proteins
PublikacjaIn this meta-analysis, we collected 58 publications spanning the last seven decades that reported static in vitro protein gastric digestion results. A number of descriptors of the pepsinolysis process were extracted, including protein type; pepsin activity and concentration; protein concentration; pH; additives; protein form (e.g., ‘native’, ‘emulsion’, ‘gel’, etc.); molecular weight of the protein; treatment; temperature; and...
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Fragmentomic analysis of biopeptides in silico released from milk proteins
PublikacjaThe fragmentomic-assisted method was employed to predict the biological potential of peptides derived from milk proteins hydrolyzed by papain and bromelain. Firstly, protein sequences were acquired from the BIOPEP-UWM database and then hydrolyzed by the above enzymes using a BIOPEP-UWM tool called “Enzyme(s) action”. The released peptides were defined as parent peptides and further analyzed for the presence of shorter peptidic...
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublikacjaCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublikacjaThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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GIS for remote sensing, analysis and visualisation of marine pollution and other marine ecosystem components
PublikacjaW artykule przedstawiono koncepcję oraz prototyp morskiego systemu GIS do zdalnego monitorowania w czasie rzeczywistym zanieczyszczeń środowiska morskiego. System pozwala na gromadzenie i integrowanie danych z różnego rodzaju sensorów, takich jak echosondy jednowiązkowe, sonary boczne i echosondy wielowiązkowe.
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Organotin compounds in marine sediments
PublikacjaZwiązki cynoorganiczne są szeroko wykorzystywane w różnych sektorach gospodarki. Farby zawierające czynniki przeciwporostowe (biocydy), były wykorzystywane w ochronie przeciwkorozyjnej kadłubów statków i okrętów, są głównym źródłem emisji trójbutylo- i trójfenylocyny do środowiska morskiego.Międzynarodowa Organizacja Morska (IMO) wprowadziła w roku 2001 powszechny zakaz stosowania tych związków jako biocydów w powłokach malarskich....
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Serial control of CNC machines
PublikacjaIn this paper a new method of the serial control of CNC machines is proposed. Actuators are controlled locally and the role of the central computer is limited to sending commands to the controller instead of sending it directly to actuators. It has been achieved with the use of the serial protocol with the use of the USB port. The taken approach leads to more reliable operation because commands are buffered and no synchronization...
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Determination of tributyltin in marine sediment.
PublikacjaPrzedstawiono wyniki badań międzynarodowego porównawczego, międzylaboratoryjnego oznaczania zawartości tributylocyny w osadzie morskim. Badania były organizowane przez Comite Consultatif pour la Quantite de Matiere (CCQM) pilot study P-18 international intercomparison i była to ich pierwsza część - badania pilotażowe. W badaniach uczestniczyło 11 laboratoriów. Uzyskano zadowalająco zgodne wyniki oznaczeń tributylocyny.
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On organic coatings in marine applications
PublikacjaZnaczna liczba konstrukcji eksploatowanych w warunkach morskich ulega zniszczeniu wskutek zmęczeniowego oddziaływania cyklicznych naprężeń mechanicznych. Również w przypadku powłok organicznych chroniących wspomniane konstrukcje obserwuje się przedwczesną degradację zmęczeniową. W poniższym artykule autorzy przedstawiają metodologię oceny wpływu cyklicznych naprężeń mechanicznych na trwałość ochronnych układów powłokowych. Badaniu...
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Modulation of polyene antibiotics self-association by ions from the hofmeister series
PublikacjaZbadano wpływ soli z serii hofmeistera na zjawisko samoasocjacji antybiotyku polienowego amfoterycyny B i jego pochodnych. Wykazano, że sole te zmieniając właściwości wody, wpływają istotnie na strukturę roztworów tych antybiotyków. Sole kosmotropowe zmniejszają rozpuszczalność związków, chaotropowe dają efekt przeciwny. Informacja ta jest istotna dla zrozumienia natury toksyczności amfoterycyny B i jej pochodnych.
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Generalization of the Elastic Network Model for the Study of Large Conformational Changes in Proteins
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Structural Determinants of Substrate Specificity of SplF Protease from Staphylococcus aureus
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Substrate specificity and inhibitory study of human airway trypsin-like protease
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Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2
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Porcine myofibrillar proteins as potential precursors of bioactive peptides – an in silico study
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Analysis of differences in the stability of proteins encoded in mitochondrial DNA of model organisms
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The Extracellular Bacterial HtrA Proteins as Potential Therapeutic Targets and Vaccine Candidates
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Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNA insequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination. Although there are differences in amino...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNAinsequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination.Although there are differences in amino acid...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublikacjaOne 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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Partial characterization of proteins from mussel Mytilus galloprovincialis as a biomarker of contamination
PublikacjaPrzedmiotem zainteresowania były:- funkcjonalne i przeciwutleniające właściwości białek małża Mytilus galloprovincialis,- poziom zawartości metali ciężkich (ołów i kadm) w tkankach.Badania przeprowadzono dla małży zebranych zarówno w zanieczyszczonych, jak i w czystych obszarach strefy brzegowej Morza Czarnego w regionie Warny (Bułgaria). W badaniach wykorzystano takie techniki analityczne jak: spektroskopia FTIR, fluorescencja,...
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New plasma preparation approach to enrich metabolome coverage in untargeted metabolomics: plasma protein bound hydrophobic metabolite release with proteinase K
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Coordination in serial-parallel image processing
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Dynamically configurable platform for service integration
PublikacjaW artykule opisano architekturę konfigurowalnego dynamicznie środowiska dla aplikacji zorientowanych na usługi, w szczególnosci na usługi webowe. Środowisko szkieletowe bazujace na specyfikacji OSGi dostarcza interfejsu, dzięki któremu zarzadzanie logika aplikacji nie wymaga jej ponownego uruchomienia. Opisano kluczowe problemy, które muszą być rozwiązane podczas wytwarzania tego typu rozwiązań. zaprezentowano sposób współpracy...
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Interoperability Constraints in Service Selection Algorithms
PublikacjaIn Service Oriented Architecture, composite applications are developed by integration of existing, atomic services that may be available in alternative versions realizing the same functionality but having different Quality of Service (QoS) attributes. The development process requires effective service selection algorithms that balance profits and constraints of QoS attributes. Additionally, services operate in a heterogeneous environment,...
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THE IPV4 TO IPV6 MIGRATION OF APPLICATIONS AND SERVICE
PublikacjaThis article presents the problems related to IPv4 to IPv6 migration of applications supporting network services. It summarizes the needs of executing such migration. It shows the basic problems of automating the migration process, having defined the basic terms, i.e.: a network service, a network application. It shows a sample implementation of the automation of the migration process between IP technologies for selected network...
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Comparison and Analysis of Service Selection Algorithms
PublikacjaIn Service Oriented Architecture, applications are developed by integration of existing services in order to reduce development cost and time. The approach, however, requires algorithms that select appropriate services out of available, alternative ones. The selection process may consider both optimalization requirements, such as maximalization of performance, and constraint requirements, such minimal security or maximum development...
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KOALA Graph Theory Internet Service
PublikacjaKOALA has been created with the idea of C++ library templates, implementing a broad set of procedures in the fields of algorithmic graph theory and network problems in discreate optimization. During the C2NIWA project, a library has been greatly ectended, the code refactored and enclosed with the internet service available in the public repository of thr project. Today it contains interconnected educational materials in the form...
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Service Recommendation on WIKI-WS Platform
PublikacjaThe article presents the issues of recaommendation services for users. The commonly used solutions include known classes of recommendation systems and information about their area of use and the most frequently used algorithms. the issue of choosing the services has been described based on the Wiki-WS platform including a model of cooperation with the recommendation system. The conclusion from the analysis of the proposed model...
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Estimation of a smoothness parameter by spline wavelets
PublikacjaWe consider the smoothness parameter s*(f) of a function f∈L2(R) in terms of Besov spaces. The existing results on estimation of smoothness [K. Dziedziul, M. Kucharska and B. Wolnik, J. Nonparametric Statist. 23 (2011)] employ the Haar basis and are limited to the case 0
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Communication Networks in the Service of the Environmental Monitoring
PublikacjaIn the paper selected issues relating to communication networks in the services of the environmental monitoring (EM) have been described. It is divided into three main parts: introduction, wire and wireless networks. At the beginning of the basic definitions were explained. The wire part focuses on a plain old telephone service (POTS), an integrated services digital network (ISDN), a digital subscriber line (DSL) and a fiber-optic...