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Search results for: PROTEIN COEVOLUTION
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublicationOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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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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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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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow 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...
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Proteolysis of whey protein isolates in nanoemulsion systems: impact of nanoemulsification and additional synthetic emulsifiers
PublicationNanoemulsions are currently of interest in the functional food sector because their small droplet size (100–500 nm) provides a number of potential advantages over conventional emulsions. This study concerned the behavior of nanoemulsions stabilized with whey proteins and two synthetic emulsifiers (Tween 80 and Croduret), and exposed to conditions simulating the human upper gastrointestinal tract. In particular, the effect of synthetic...
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublicationA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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Clonal Evolution of Multiple Myeloma—Clinical and Diagnostic Implications
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Cobalt/Carbon Nanocomposite as Oxygen Evolution Reaction Electrocatalyst
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Impedance Investigations of the Mechanism of Oxygen Evolution on Composite Electrodes
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The Evolution of China’s Economic Engagement in Central and Eastern Europe
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Intelligent Knowledge-Based Model for IT Support Organization Evolution
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Plastic ductile damage evolution and collapse of plates and shells.
PublicationPraca jest poswięcona problemowi numerycznej symulacji zniszczenia w płytach i powłokach z uwzględnieniem efektów nieliniowości geometrycznej i materialowej. Uwzględniono skończone przemieszczenia i obroty; przyjęty model materiałowy obejmuje zachowanie sprężysto-plastyczne, wzmocnienie izotropowe i kinematyczne, oraz zniszczenie ciągliwe. Specjalną uwagę poświecono problemom lokalizacji zniszczenia, rozwoju zniszczenia oraz całkowitej...
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Evolution of concept of agent system for information technology evaluation
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Adaptive selection of control parameters in differential evolution algorithms
PublicationW pracy przedstawiono metodę adaptacyjnej selekcji parametrów kontrolnych w różnicowych algorytmach ewolucyjnych. Wartości parametrów takich jak: stopień krzyżowania i współczynnik różnicowej mutacji są odpowiednio zmieniane. Funkcje testowe użyte do testowania proponowanej metody były zaczerpnięte z literatury. Rezultaty uzyskane przy użyciu opisanej metody zostały porównane z innymi metodami selekcji różnicowej. Wyniki te, uzyskane...
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Intelligent Knowledge-Base Model for IT Support Organization Evolution
PublicationThe goal of the paper is building the knowledge-based model for predicting the state of the IT support organization. These organizations, critical for development of various business sectors, are facing the problem of their transformation. It is the result of the fundamental change in the role of the IT organizations in the current economy. The complexity of the processes, the difficulty adjusting the operations and limited ability...
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Final state of thermal evolution of Jupiter-type planet
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The evolution of China's economic engagement in Central and Eastern Europe
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Hybrid model of the evolution of information technology support organisation
PublicationPrzedstawiono etapy budowy, weryfikacji i implementacji hybrydowego rozmytego modelu ewolucji organizacji wspomagania IT (information technology).
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Evolution of Animats Following a Moving Target in an Artificial Ecosystem
PublicationMany biological animals, even microscopically small, are able to track moving sources of food. In this paper, we investigate the emergence of such behavior in artificial animals (animats) in a 2-dimensional simulated liquid environment. These "predators" are controlled by evolving artificial gene regulatory networks encoded in linear genomes. The fate of the predators is determined only by their ability to gather food and reproduce—no...
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Protect our right to light
Publication“The struggle for light” is how the Swiss architect Le Corbusier described the history of architecture in 1935. Today, with the skies crowded out by buildings in modern cities, those words should ring in the ears of policymakers and planners. Skyscraper construction is booming. China is the leader, last year completing 88 of the 143 buildings around the world that are taller than 200 metres (see ‘Vertical growth’). As the nation’s...
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Single-Slope ADC With Embedded Convolution Filter for Global-Shutter CMOS Image Sensors
PublicationThis brief presents an analog-to-digital converter (ADC) suitable for acquisition and processing of images in the global-shutter mode at the pixel level. The ADC consists of an analog comparator, a multi-directional shift register for the comparator states, and a 16-bit reversible binary counter with programmable step size. It works in the traditional single-slope mode. The novelty is that during each step of the reference ramp,...
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Fourth industrial revolution and new challenges in post-pandemic world
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Data on solutions of Hes1 system
Open Research DataHes1 protein (hairy and enhancer of split 1) belongs to the helix-loop-helix (bHLH) family of transcription proteins, i.e. DNA-binding proteins in the promoter region or in another region where regulation of transcription processes occurs. The database collects data on solutions of the Hes1 systems with multiple binding sites and the dimer formation...
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Carotenoid binding to proteins: Modeling pigment transport to lipid membranes
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Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants
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Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants
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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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Structure and function of natural proteins for water transport: general discussion
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Immunogenic and protective activity of recombinant chimeric Toxoplasma gondii proteins
PublicationToxoplasmosis, 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
PublicationIn 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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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe 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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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical 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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Fragmentomic analysis of biopeptides in silico released from milk proteins
PublicationThe 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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Human Evolution: international journal
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Evolution Equations and Control Theory
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GENETIC RESOURCES AND CROP EVOLUTION
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Evolution Medicine and Public Health
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Israel Journal of Ecology & Evolution
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ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES
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Comparison of Antioxidant Activity of Protein Isolates Derived from Selected Dry-Cured Meat Products
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E2/E3‐independent ubiquitin‐like protein conjugation by Urm1 is directly coupled to cysteine persulfidation
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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublicationThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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Post mortem changes in M. iliotibialis lateralis muscle protein profile of emu (Dromaius novaehollandiae)
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Excessive amount of lactose in the diet of two-week-old calves induces urinary protein changes
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Sulforaphane, a cruciferous vegetable-derived isothiocyanate, inhibits protein synthesis in human prostate cancer cells
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CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
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