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Search results for: PROTEIN COEVOLUTION
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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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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublicationWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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Molecular targets for antifungals in amino acid and protein biosynthetic pathways
PublicationFungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems...
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublicationIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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MutL protein as a constituent of vsp, ner and mmr repair systems
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mis- match repair system (MMR). However, there is growing evidence that MMR system is not the only field of action for these pro- teins. Moreover, the participation in MMR does not even have to be their primary function. There are some reports indicat- ing involvement of MutL in BER, NER and VSP (very short patch repair)....
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Antioxidants and proteins in ethylene-treated kiwifruits
PublicationW pracy porównano właściwości przeciwutleniające i profil białek owoców kiwi poddanych działaniu etylenu i powietrza. Wysokie współczynniki korelacji między całkowitą zawartością fenoli i właściwościami przeciwutleniającymi uzyskano dla trzech metod określania właściwości przeciwutleniających: ABTS, TEAC i CUPRAC. W paśmie białek owoców kiwi rozdzielonych za pomocą elektroforezy stwierdzono różnice w paśmie siarczanu dodecylu sodu...
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The role of proteins in food. Chapter 6
PublicationStruktura i konformacja wpływają na biologiczne oraz funkcjonalne właściwości białek i na ich rolę w tworzeniu pożądanych cech produktów żywnościowych. Właściwości funkcjonalne to rozpuszczalność w środowisku wodnym o różnej sile jonowej, wodochłonność oraz zdolność żelowania, tworzenia błon, emulgowania lipidów i pienienia się. Białka mięsa, ryb, mleka, jaj, nasion roślin strączkowych, nasion zbóż oraz drobnoustrojów różnią się...
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Targeting shelterin proteins for cancer therapy.
PublicationAs a global health challenge, cancer prompts continuous exploration for innovative therapies that are also based on new targets. One promising avenue is targeting the shelterin protein complex, a safeguard for telomeres crucial in preventing DNA damage. The role of shelterin in modulating ataxia- telangiectasia mutated (ATM) and ataxia-telangiectasia and Rad3-related (ATR) kinases, key players in the DNA damage response (DDR),...
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Impact mobility rEVolution'18
EventsPatronat nad wydarzeniem objął rektor Politechniki Gdańskiej. WEiA został zakwalifikowany do grona wystawców kongresu. Koordynatorem udziału PG w kongresie jest Centrum Transferu Wiedzy i Technologii.
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EFFICIENT LINE DETECTION METHOD BASED ON 2D CONVOLUTION FILTER
PublicationThe article proposes an efficient line detection method using a 2D convolution filter. The proposed method was compared with the Hough transform, the most popular method of straight lines detection. The developed method is suitable for local detection of straight lines with a slope from -45˚ to 45˚. Also, it can be used for curve detection which shape is approximated with the short straight sections. The new method is characterized...
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Comparing some convolution-based methods for creation of surround sound
PublicationW referacie przedstawiono eksperymenty związane z symulacją dźwięku dookólnego w sali koncertowej. W tym celu wykorzystano splot odpowiedzi impulsowej z danego wnętrza (wielokanałowe nagrania odpowiedzi impulsowej) z nagraniami z komory bezechowej. Uzyskany w ten sposób sygnał został następnie przypisany do odpowiednich kanałów w systemie dookólnym. Uzyskane w ten sposób nagrania były następnie porównywane w testach subiektywnych...
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Karaś P., Kochanowicz K., Pitek M., Domański P., Obuchowski I., Tomiczek B., Liberek K.: Evolution towards simplicity in bacterial small heat shock protein system// eLife -, (2023), s.1-21
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...
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Pressure evolution of LiBaF3:Eu2+luminescence
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Time evolution of luminescence of Sr2SiO4:Eu2+
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Introductory Chapter: Evolution of Sample Preparation
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Neural Networks and the Evolution of Environmental Change
PublicationZmiany środowiskowe na Ziemii są odwieczne i liczą około 4 miliardy lat. Homo sapiens wpłynął na każdy aspekt środowiska ziemskiego w wyniku rozwoju ludzkości na przestrzeni ostatnich milionów lat. Ale nic tak nie wpłynęło na wzrost i szybkość zmian na Ziemi jak ludzka aktywność w ciągu ostatnich dwóch stuleci. Po raz pierwszy zmiany ekosystemów były tak intensywne i zachodziły na tka wielką skalę i z taką szybkością jak nigdy...
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Concept of Generic IT Organization Evolution Model
PublicationThe purpose of this publication is to present a generic model of the IT organization evaluation process as an attempt to systematize and describe the continuous actions and changes in the organization.
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Evolution of End-User Participation in IT Projects.
PublicationThis chapter is aimed at presenting a review of evolutionary design paradigms which determine the end-user’s role in IT (Information Technology) projects across recent decades. This review covers different perspectives starting from technology-oriented sequential software development lifecycles, through user-centred approaches, ending finally in contemporary service design approaches supported by e-business and social media. Finally,...
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Developing Prognostic Models of Organization Evolution
PublicationThe work focuses on the problem of measuring evolution of IT organizations. Changes in business influence functioning of the IT organization. IT departments or companies must ensure that the needs of their parent company/customers will be met. Therefore they must constantly evolve. Following question can be raised: is it possible to support process of changes the IT organization to run it smoother, faster, easier but with reduced...
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Introductory Chapter: Evolution of Sample Preparation
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Selected aspects of the evolution of the industry analysis
PublicationPorter's five forces is a significant tool of analysis of industries. It helps evaluating variables of industry profitability and assessing firm performance. Using the framework, managers can take a decision as to which industries they can effectively compete in and position their companies to reduce the adverse effects of the mentioned forces. According to the critics, the five forces model is limited to its static nature. The...
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Relationship between Milk Protein Polymorphism and Selected Cows’ Reproductive Indices
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DSC and electrophoretic studies on protein denaturation of Anodonta woodiana (Lea, 1834)
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TOLLIP Protein Expression Predicts Unfavorable Outcome in Renal Cell Carcinoma
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Functional Protein Composition in Femoral Glands of Sand Lizards (Lacerta agilis)
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Zeta potential and droplet size of n-tetradecane/ethanol (protein) emulsions
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Two-dimensional gel-based serum protein profile of growing piglets
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Effect of Functionalization of Carbon Nanotubes with Psychosine on Complement Activation and Protein Adsorption
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Trial Proteomic Qualitative and Quantitative Analysis of the Protein Matrix of Submandibular Sialoliths
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Riboflavin binding protein—Chiral stationary phase: Investigation of retention mechanism
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The Nutritional Value and Biological Activity of Concentrated Protein Fraction of Potato Juice
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Serum Fatty Acid-Binding Protein 4 is Increased in Patients with Psoriasis
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Survivin DEx3 as a biomarker of thyroid cancers: A study at the mRNA and protein level
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CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
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BALCONY: an R package for MSA and functional compartments of protein variability analysis
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Myotilin, a New Topotecan Resistant Protein in Ovarian Cancer Cell Lines
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C-reactive protein as a diagnostic and prognostic factor in inflammatory bowel diseases
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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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Inhibition of protein glycosylation reverses the MDR phenotype of cancer cell lines
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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
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Stability of delay induced oscillations in gene expression of Hes1 protein model
PublicationW pracy prezentowana jest matematyczna analiza modelu ekspresji genu białka Hes1. Rozważamy układ równań z dwoma opóźnieniami - w produkcji białka Hes1 oraz jego mRNA. Dowodzimy istnienia i jednoznaczności oraz nieujemności rozwiązań. Pokazujemy istnienie dokładnie jednego dodatniego stanu stacjonarnego. Wykazujemy, że stabilność stanu stacjonarnego zależy od sumy opóźnień. Podajemy warunek dostateczny na wystąpienie bifurkacji...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublicationWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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Mathematical analysis of a generalised p53-Mdm2 protein gene expression model
PublicationWe propose the generalisation of the p53-Mdm2 protein gene expression model introduced by Monk (2003). We investigate the stability of a unique positive steady state and formulate conditions which guarantee the occurrence of the Hopf bifurcation. We show that oscillatory behaviour can be caused not only by time lag in protein transcription process, but also can be present in the model without time delay. Moreover, we investigate...
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Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1
PublicationIn this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules....
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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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Protein overproduction alters exosome secretion in Chinese hamster ovary cells
PublicationDespite the abundance of available cell lines, nearly 70% of all recombinant therapeutic proteins today are produced in Chi-nese hamster ovary (CHO) cells. The impact of protein overproduction on the secretion of exosomes by CHO cells has been investigated here. Increased secretion of extracellular vesicles (EVs) by protein overexpressing CHO cells was demonstrated with protein content assay, nanoparticle tracking analysis, and...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....