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Search results for: protein folding
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The effect of topical treatment and psoriasis severity on serum retinol-binding protein-4 levels
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Expression profiles and genomic organisation of group A protein phosphatase 2C genes inBrassica oleracea
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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
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Patients with obstructive sleep apnea present with chronic upregulation of serum HIF-1α protein
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The plasma concentration of advanced oxidation protein products and arterial stiffness in apparently healthy adults
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Blood plasma protein and lipid profile changes in calves during the first week of life
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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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MIC1-MAG1-SAG1 chimeric protein, a most effective antigen for detection of human toxoplasmosis
PublicationThis study describes a Toxoplasma gondii IgG ELISA test based on a new chimeric antigen containing three immunodominant regions from MIC1, MAG1 and SAG1 proteins of a parasite and shows that this test is useful for diagnostic purposes and may replace the lysed and whole-cell antigens.
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Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis
PublicationW celu zbadania właściwości biochemicznych białka wiążącego się do jednoniciowego DNA (SSB) pochodzącego z Deinococcus geothermalis (DgeSSB), sklonowano gen ssb otrzymany w reakcji PCR, a następnie uzyskano wydajną biosyntezę białka DgeSSB. Gen składa się z 900 par zasad, kodujących białko złożone z 300 reszt aminokwasowych, o wyliczonej masie molekularnej równej 32.45 kDa. Sekwencja aminokwasowa wykazuje 43, 44% i 75% identyczności...
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Statistical Method for Analysis of Interactions Between Chosen Protein and Chondroitin Sulfate in an Aqueous Environment
PublicationWe present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of univariate time series of chosen features of the dynamics of mucin, which interact with chondroitin sulfate (4 and 6) in four different saline solutions. Our statistical approach is based on recurrence...
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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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Expression of goose parvovirus whole VP3 protein and its epitopes in Escherichia coli cells
PublicationThe aim of this study was the expression of goose parvovirus capsid protein (VP3) and its epitopes in Escherichia coli cells. Expression of the whole VP3 protein provided an insufficient amount of protein. In contrast, the expression of two VP3 epitopes (VP3ep4, VP3ep6) in E. coli, resulted in very high expression levels. This may suggest that smaller parts of the GPV antigenic determinants are more efficiently expressed than the...
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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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A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublicationWe report the identification and characterization of the single-stranded DNA-binding protein (SSB) from the mesophile and highly radiation-resistant Deinococcus radiopugnans (DrpSSB). PCR-derived DNA fragment containing the complete structural gene for DrpSSB protein was cloned and expressed in Escherichia coli. The gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated...
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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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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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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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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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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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Aravind Ayyolath
PeopleI am interested in the biology of bacterial stress response and its growth under stress conditions. Our lab focuses on two aspects; protein folding and lipopolysaccharide biosynthesis and we address them with Escherichia coli models. Our recent studies have provided more evidence regarding several genes involved in the survival of bacteria under stress. I am also interested in disease biology and also in identifying proper therapeutic...
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Artificial neural network based fatigue life assessment of friction stir welding AA2024-T351 aluminum alloy and multi-objective optimization of welding parameters
PublicationIn this paper, the fracture behavior and fatigue crack growth rate of the 2024-T351 aluminum alloy has been investigated. At first, the 2024-T351 aluminum alloys have been welded using friction stir welding procedure and the fracture toughness and fatigue crack growth rate of the CT specimens have been studied experimentally based on ASTM standards. After that, in order to predict fatigue crack growth rate and fracture toughness,...
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Moderately Reactive Molecules Forming Stable Ionic Compounds with Superhalogens
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Filling of Carbon Nanotubes: Containers for Magnetic Probes and Drug Delivery
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Reproducibility of Finding Enriched Gene Sets in Biological Data Analysis
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Study of the process of tool forming made of high-strength materials
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A polynomial algorithm for solving a general max‐min fairness problem
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Vibration Diagnostics of Rolling Mills Based on Nonlinear Effects in Dynamics
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NMR and MD Analysis of the Bonding Interaction of Vancomycin with Muramyl Pentapeptide
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Enzymatic Activity as New Moorsh-Forming Process Indicators of Peatlands
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Resistance of Polypropylene Membrane to Oil Fouling during Membrane Distillation
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Fouling of nanofiltration membranes used for separation of fermented glycerol solutions
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Long-Term Performance of Ultrafiltration Membranes: Corrosion Fouling Aspect
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Bonding of doxorubicin to nanosilica and human serum albumin in various media
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Modelling of the Heat Flux Density Distribution for Laser Beam Welding
PublicationGreat interest of the laser beam welding in industry is a new theoretical task, making planning the welding procedure specification and the quality control of welded joints easier. Estimating and calculating the dimensions of a weld pool and temperature distribution near weld mainly concern heat source modelling. In the presented work calculations of welding pool shape and thermal field for cylindrical-powered-normally model of...
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The Effect of Welding Conditions on Diffusible Hydrogen Content in Deposited Metal
PublicationThe article presents the results of a literature survey and preliminary tests which set out effects of welding conditions on the amount of diffusible hydrogen in deposited metal. Experiments were conducted by using rutile coated electrodes which generate high contents of diffusible hydrogen in deposited metal. The amount of diffusible hydrogen was determined by a glycerin test.Eleven factors were considered: the electrode angle,...
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Destructive Consequences of PWM Inverter Feeding for Traction AC Motors
PublicationThe electric traction drives with an AC motor fed by a frequency converter are used more and more often nowadays. The most significant side effects, of a converter's output voltage forming PWM method for AC motor windings, are steep voltage changes, which can initiate several destructive phenomena. The paper presents the adverse influence of a converter common mode voltage on the motor windings' increased voltage exposure and the...
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Variational Method of Finding Streamlines in Ring Cascades for Creeping Flows
PublicationThis paper presents a new, analytical method of finding streamlinesfor creeping flows inside a ring cascade which is composed of an infinite number of infinitely thin blades. An analytical solution has been obtained through minimisation of a dissipation functional by means of variational calculus method. The necessary condition for optimum of a functional gives the Stokes equation if some additional assumptions are introduced....
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The rolling contact fatigue of WC/C-coated spur gears
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AC motor feeding cable consequences on EMC performance of ASD
PublicationHigh level of conducted EMI emissions of adjustable speed drives (ASD) is one of the most difficult problems in contemporary applications. Many investigations are carried out in order to find more effective methods allowing to predict this emission at early stage of design, and therefore to predict adequate countermeasures. This paper deals with the method which allows to estimate by simulation the influence of motor feeding cable...
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Numerical Simulations of Laser and Hybrid S700MC T-Joint Welding
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Computational Techniques in Numerical Simulations of Arc and Laser Welding Processes
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APPLICATION OF NUMERICAL SIMULATIONS ON X10CRWMOVNB9-2 STEEL MULTILAYER WELDING
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Data Extraction, Transformation and Loading process in data warehouse development.
PublicationOmówiono podstawowe elementy procesu projektowania hurtowni danych.
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Solving nonlinear programming problems by using O&G software.
PublicationPraca opisuje pakiet optymalizacyjny oprogramowania O&G. Umożliwia on rozwiązywanie problemów programowania nieliniowego. Użytkownik może w wygodny sposób formułować rozwiązywane zadanie i dobierać metody obliczeniowe używając interaktywnego interfejsu.
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Loading pattern effects on fatigue resistance of slide bearing lining
PublicationPrzedstawiono relacje pomiędzy przebiegami obciążeń dynamicznych a stanem naprężeń w warstwie nośnej łożysk ślizgowych. Porównano przebiegi naprężeń dla maszyny badawczej MWO (z wirującym wektorem obciążenia) do naprężeń charakterystycznych dla maszyny SMOK (z jednokierunkowym zmiennym wektorem obciążenia).
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Diffusible Hydrogen Control in Flux Cored Arc Welding Process
PublicationOne of the types of hydrogen degradation of steel welded joints is cold cracking. The direct cause of the formation of cold cracks is simultaneous presence of hydrogen, residual stresses and brittle structure. The way of preventing the occurring of degradation is to eliminate at least one of these factors. Practice has shown that the best solution is to control the amount of hydrogen in deposited metal. In this paper an experimental...
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Reduction of Tire Rolling Resistance by Optimization of Road Surfaces and Tires
PublicationDuring interaction between tire and road surface three very important phenomena are always in effect. One of them (very desirable) is friction that is important for traction, braking and cornering. Two other phenomena are not desirable at all, that is rolling resistance and noise. This paper discusses relations between road surface and tire parameters versus tire rolling resistance. Road surface texture, porosity, impedance, strength...
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Comparison of Tire Rolling Resistance Measuring Methods for Different Surfaces
PublicationThe rolling resistance of car tires is one of the most important parameters characterizing tires today. This resistance has a very significant contribution to the energy consumption of wheeled vehicles. The climate crisis has forced tire and car manufacturers to place great emphasis on the environmental impact of their products. Paradoxically, the development of electric vehicles has led to an even greater importance of rolling...
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Excitonic stimulation of current flowing along thin tetracene layer
PublicationW pracy badane były prądy będące wynikiem oddziaływania ekscytonów tripletowych ze spułapkowanymi nośnikami ładunku w warstwach tetracenu. Badane próbki oświetlane były od strony podłoża oraz od strony przeciwległej podłożu.