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Search results for: protein hydrolyzate solutions
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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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Periodic solutions of Lagrangian systems under small perturbations
PublicationIn this paper we prove the existence of mountain pass periodic solutions of a certain class of generalized Lagrangian systems under small perturbations. We show that the found periodic solutions converge to a periodic solution of the unperturbed system if the perturbation tends to 0. The proof requires to work in a rather unusual (mixed) Orlicz–Sobolev space setting, which bears several challenges.
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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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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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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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Investigation of environmental influences to the precise GNNS solutions
PublicationThe results presented in this paper concern investigation of environmental influences to GNNS coordinates on the example of ASG-EUPOS network. The problem of the impact of environmental effects is crucial for observing gravity. Satellite systems are not as susceptible to changes in local hydrology or atmospheric effects, although significant influences are clearly visible in the change of coordinates. The authors analyzed daily...
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Understanding the interactions between protein stabilizers and the peptide bond through the analysis of the volumetric and compressibility properties for the model systems
PublicationThis work confirms our earlier supposition, that volumetric and acoustic parameters for simple model proposed by us are directly related to stabilizing/destabilizing effect of osmolytes on proteins structure. The apparent molar volumes, V and the apparent molar isentropic compressions, KS,, of glycine and N,N,N –trimethylglycine (betaine) were determined from densities and speed of sound measurements in aqueous solution of N-methylacetamide...
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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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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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The interaction parameters for solutions of n-butylurea in aqueous solutions of N-methylacetamide – The volumetric and compressibility studies between 288.15 K and 308.15 K
PublicationDensities and speed of sound were measured for solutions of n-butylurea in aqueous solution of Nmethylacetamide 2, 4, 6 and 8 (mol/kg) at T = (288.15, 298.15 and 308.15) K. From these data the apparent molar volumes, Vf, the apparent molar isentropic compressions, KSf, of the solute were determined. The concentration dependencies of the calculated quantities have been used to obtain the standard partial molar parameters. The latter...
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The Protein Folding Problem
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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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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Kinetics of the crosslinking reaction between genipin and chitosan solutions
PublicationThe kinetics of the chitosan crosslinking reaction with genipin was examined. The strong relationship was found between crosslinking agent concentration, chitosan concentration, temperature and gelling time. Data obtained will be used in the proper selection of optimal genipin concentration for crosslinking chitosan solutions.
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Fundamental properties of solutions to fractional-order Maxwell's equations
PublicationIn this paper, fundamental properties of solutions to fractional-order (FO) Maxwell's equations are analysed. As a starting point, FO Maxwell's equations are introduced in both time and frequency domains. Then, we introduce and prove the fundamental properties of electromagnetic field in FO electromagnetics, i.e. energy conservation, uniqueness of solutions, and reciprocity. Furthermore, the algorithm of the plane wave simulation...
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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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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Periodic Solutions of Generalized Lagrangian Systems with Small Perturbations
PublicationIn this paper we study the generalized Lagrangian system with a small perturbation. We assume the main term in the system to have a maximum, but do not suppose any condition for perturbation term. Then we prove the existence of a periodic solution via Ekeland’s principle. Moreover, we prove a convergence theorem for periodic solutions of perturbed systems.
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Quasi-solutions for generalized second order differential equations with deviating arguments
PublicationThis paper deal with boundary value problems for generalized second order differential equations with deviating arguments. Existence of quasi-solutions and solutions are proved by monotone iterative method. Examples with numerical results are added.
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Existence of unbounded solutions to parabolic equations with functional dependence
PublicationThe Cauchy problem for nonlinear parabolic differential-functional equations is considered. Under natural generalized Lipschitz-type conditions with weights, the existence and uniqueness of unbounded solutions is obtained in three main cases: (i) the functional dependence u(·); (ii) the functional dependence u(·) and ∂xu(·); (iii) the functional dependence u(·)and the pointwise dependence ∂xu(t,x).
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Existence of solutions with an exponential growth for nonlinear differential-functional parabolic equations
PublicationWe consider the Cauchy problem for nonlinear parabolic equations with functional dependence.We prove Schauder-type existence results for unbounded solutions. We also prove existence of maximal solutions for a wide class of differential functional equations.
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Evolution towards simplicity in bacterial small heat shock protein system
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 two...
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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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A study of concentration depolarization and quenching of photoluminescence of solutions
PublicationThe concentration-dependence of emission anisotropy r/r0 and quantum yield eta/eta0 of the photoluminescence of glycerol-water solutions of rhodamine B in two systems of viscosities 7.4 P and 0.72 P is investigated. The experimental data are compared with the new theory of concentraticn depolarization (J. Lumin., 5, 413 (1972)) and concentration quenching of photoluminescence (Acta Phys. Hungar., 30, 145 (1972)), which takes...
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Weak Solutions within the Gradient-Incomplete Strain-Gradient Elasticity
PublicationIn this paper we consider existence and uniqueness of the three-dimensional static boundary-value problems in the framework of so-called gradient-incomplete strain-gradient elasticity. We call the strain-gradient elasticity model gradient-incomplete such model where the considered strain energy density depends on displacements and only on some specific partial derivatives of displacements of first- and second-order. Such models...
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Topological Behaviour of Solutions of Vibro-Impact Systems in the Neighborhood of Grazing
PublicationThe grazing bifurcation is considered for the Newtonian model of vibro-impact systems. A brief review on the conditions, sufficient for the existence of a grazing family of periodic solutions, is given. The properties of these periodic solutions are discussed. A plenty of results on the topological structure of attractors of vibro-impact systems is known. However, since the considered system is strongly nonlinear, these attractors...
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Interactions in aqueous solutions of K-peptide and DMSO – spectroscopic and calorimetric studies
PublicationIntroduction K-peptide (GILQINSRW) – short 9 amino acid fragment of the hen egg white lysozyme has the ability to form amyloid structures. Dimethyl sulfoxide (DMSO) is an osmolyte which can alter this ability. Our goal was to get an insight into the mechanism of Kpeptide-DMSO interactions in aqueous solutions. Such a knowledge can be helpful to understand processes leading to various neurodegenerative diseases. Methods ATR-FTIR...
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Modern Material Solutions Applied in Pediatric Facilities
PublicationNew tendencies in forming of the health services functional buildings’ systems shaped along with the emergence of caring for patient’s mental condition in medical sciences. The interior design harmonized with the medical function became an incredibly important feature. This opened up new opportunities for the architecture of health care facilities. A positive architecture’s impact on the user’s well-being is remarkably important...
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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Positive solutions to advanced fractional differential equations with nonlocal boundary conditions
PublicationWe study the existence of positive solutions for a class of higher order fractional differential equations with advanced arguments and boundary value problems involving Stieltjes integral conditions. The fixed point theorem due to Avery-Peterson is used to obtain sufficient conditions for the existence of multiple positive solutions. Certain of our results improve on recent work in the literature.
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Comparison of selected off-the-shelf solutions for emotion recognition based on facial expressions
PublicationThe paper concerns accuracy of emotion recognition from facial expressions. As there are a couple of ready off-the-shelf solutions available in the market today, this study aims at practical evaluation of selected solutions in order to provide some insight into what potential buyers might expect. Two solutions were compared: FaceReader by Noldus and Xpress Engine by QuantumLab. The performed evaluation revealed that the recognition...
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Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublicationWe have reported that the hsp70 chaperone DnaK from Escherichia coli might assist protein folding by catalyzing the cis/trans isomerization of secondary amide peptide bonds in unfolded or partially folded proteins. In this study a series of fatty acylated benzamido inhibitors of the cis/trans isomerase activity of DnaK was developed and tested for antibacterial effects in E. coli MC4100 cells. Nα-[Tetradecanoyl-(4-aminomethylbenzoyl)]-l-asparagine...
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Positive solutions to Sturm–Liouville problems with non-local boundary conditions
PublicationIn this paper, the existence of at least three non-negative solutions to non-local boundary-value problems for second-order differential equations with deviating arguments α and ζ is investigated. Sufficient conditions, which guarantee the existence of positive solutions, are obtained using the Avery–Peterson theorem. We discuss our problem for both advanced and delayed arguments. An example is added to illustrate the results.
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Toxoplasma gondii Recombinant antigen AMA1: Diagnostic Utility of Protein Fragments for the Detection of IgG and IgM Antibodies
PublicationToxoplasma gondii is an important zoonotic protozoan that infects a wide variety of vertebrates as intermediate hosts. For this reason, the diagnosis of this disease is very important and requires continuous improvement. One possibility is to use recombinant antigens in serological tests. Apical membrane antigen 1 (AMA1), a protein located in specific secretory organelles (micronemes) of T. gondii, is very interesting in regard...
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Certain family of analytical solutions of nonlinear von Neumann equations
PublicationIn this paper we present a slight generalization of certain type of Darboux transformation, that may be used sub-sequently in a convenient way. This method allows to obtain families of solutions of nonlinear von Neumann equations, that are used in particular in DNA modeling.
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Technological innovation and cost-benefit analysis of safety-related solutions
PublicationW rozdziale przedstawia się aktualne zagadnienia dotyczące innowacji technologicznych oraz analizę kosztów i efektów rozwiązań związanych z bezpieczeństwem na przykładzie systemów elektrycznych, elektronicznych i programowalnych elektronicznych (E/E/PE), pełniących funkcje monitorowania, sterowania i zabezpieczeń w instalacjach podwyższonego ryzyka. Podkreśla się znaczenie kryteriów związanych z bezpieczeństwem, takich jak tolerowalność...
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How water mediates the long-range interactions between remote protein molecules
PublicationThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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A convergence result for mountain pass periodic solutions of perturbed Hamiltonian systems
PublicationIn this work, we study second-order Hamiltonian systems under small perturbations. We assume that the main term of the system has a mountain pass structure, but do not suppose any condition on the perturbation. We prove the existence of a periodic solution. Moreover, we show that periodic solutions of perturbed systems converge to periodic solutions of the unperturbed systems if the perturbation tends to zero. The assumption on...
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Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublicationWater molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...
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On weak solutions of boundary value problems within the surface elasticity of Nth order
PublicationA study of existence and uniqueness of weak solutions to boundary value problems describing an elastic body with weakly nonlocal surface elasticity is presented. The chosen model incorporates the surface strain energy as a quadratic function of the surface strain tensor and the surface deformation gradients up to Nth order. The virtual work principle, extended for higher‐order strain gradient media, serves as a basis for defining...
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Environmental impact of construction. Methods of conscious shaping architecture in terms of ecological solutions
PublicationShaping an ecologically conscious society is a process that also affects architecture. Currently, designers are eagerly looking for solutions that are beneficial in terms of carbon footprint. For the proper multi-criteria assessment and selection of adequate solutions, it is necessary to use appropriate tools such as, for example, the Life Cycle Assessment (LCA) method or the rules of ecological certification (BREEAM and LEED)....
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Problems in designing and operating the functional safety solutions of higher integriity levels
PublicationThe aim of this article is to identify and discuss some problems that have been encountered in designing and operating the functional safety solutions of higher safety integrity levels (SIL 3 and SIL 4) in the light of analyses outlined in a new version of the international standard IEC 61508:2010. Examples of such solutions are the electric / electronic / programmable electronic systems (E/E/PESs) and the safety instrumented systems...
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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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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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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublicationEfficient brain function requires as much as 20% of the total oxygen intake to support normal neuronal cell function. This level of oxygen usage, however, leads to the generation of free radicals, and thus can lead to oxidative stress and potentially to age-related cognitive decay and even neurodegenerative diseases. The regulation of this system requires a complex monitoring network to maintain proper oxygen homeostasis. Furthermore,...
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Antimicrobial properties of chitosan solutions, chitosan films and gelatin-chitosan films
PublicationThe antimicrobial properties of chitosan solutions and films against selected bacteria and the effect of chitosan incorporation into gelatin films were studied. The bactericidal effect of chitosan solutions increased with time and temperature of sample incubation. Two psychrotrophic strains Pseudomonas fluorescens and Listeria innocua were more sensitive to chitosan than mesophilic strains Escherichia coli and Staphylococcus aureus....
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Potential for ITS/ICT Solutions in Urban Freight Management
PublicationThe article presents a study on applying ITS solutions in planning and management of urban freight transport in Gdynia. The traffic management system Tristar which is under implementation and its related systems show a potential to assist in development of freight transport measures. Recommendations for urban freight policy development supplementing Gdynia's Sustainable Urban Mobility Plan were used as a basis for identification...
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...