Search
Filters
total: 3364
filtered: 2815
-
Catalog
Chosen catalog filters
displaying 1000 best results Help
Search results for: folded proteins
-
The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
-
Zastosowanie addytywów w separacji pianowej białek serwatkowych i białek mlecznych
PublicationZaproponowano proces separacji pianowej do wydzielania białek ze strumieni poprodukcyjnych przemysłu mleczarskiego Ponadto zaproponowano zastosowanie w separacji pianowej białek serwatkowych i mlecznych addytywów dopuszczonych ustawą do stosowania w żywności. Jako cel pracy przyjęto uzyskanie wyników uzasadniających wybór takich addytywów, które intensyfikują przebieg i polepszają wynik procesu separacji pianowej białek. W części...
-
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...
-
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...
-
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...
-
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...
-
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...
-
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...
-
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...
-
Carotenoid binding to proteins: Modeling pigment transport to lipid membranes
Publication -
Oxidative Modification of Proteins in Pediatric Cystic Fibrosis with Bacterial Infections
Publication -
Contribution of small heat shock proteins to muscle development and function
Publication -
Structure and function of natural proteins for water transport: general discussion
Publication -
Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants
Publication -
Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants
Publication -
Occlusion phenomenon of redox probe by protein as a way of voltammetric detection of non-electroactive C-reactive protein
Publication -
Application of Barkhausen method to determine internal stresses in cold-rolled and hot-rolled sheets
PublicationThe paper presents investigations on internal stress distribution in plane hot—or cold-rolled sheets dedicated for the cold-formed profiles. The motivation of the research is a new profile design whose bending technology, incorporating a longitudinal welded joint and hot-dip galvanization after bending and welding introduces additional internal stresses. In order to identify the entirety of stresses in the process of sheet production...
-
Thermoplastic Elastomers Filled With GTR
PublicationIn recent years, searching for new and cost-effective methods of recycling waste tires has been a subject of research in many laboratories worldwide. This is due to regulations in the law and environmental factors, which have both stimulated industry to re-use high quality rubber found in ground tire rubber (GTR). One of the most promising solutions in this area seems to be thermoplastic elastomers (TPEs) filled with GTR, which...
-
Fracture in Asymmetric Bonded Joints
PublicationAdhesion was studied in asymmetric bonded joints using fracture mechanics tests. The asymmetric bonded joints consist of two different type and/or thickness materials bonded by an adhesive. Mentions of asymmetric bonded joint tests employed so far are rare in the literature. They are imperfect and therefore are not standardized. Accordingly three new tests were introduced in this work to study bonded joints. The new metrological...
-
Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublicationBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
-
Generalization of the Elastic Network Model for the Study of Large Conformational Changes in Proteins
Publication -
The Extracellular Bacterial HtrA Proteins as Potential Therapeutic Targets and Vaccine Candidates
Publication -
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
Publication -
Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne 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...
-
Porcine myofibrillar proteins as potential precursors of bioactive peptides – an in silico study
Publication -
Analysis of differences in the stability of proteins encoded in mitochondrial DNA of model organisms
Publication -
Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-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...
-
Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-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...
-
Partial characterization of proteins from mussel Mytilus galloprovincialis as a biomarker of contamination
PublicationPrzedmiotem 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,...
-
General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublicationThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
-
Pea Protein for Hempseed Oil Nanoemulsion Stabilization
Publication -
Polysaccharide–Protein Complexes in a Coarse-Grained Model
Publication -
Some applications of thermophiles and their enzymes for protein processing
PublicationPrzedstawiono charakterystykę, właściwości oraz możliwości zastosowań enzymów proteolitycznych wytwarzanych przez termofile. Zaletą tych biokatalizatorów jest między innymi duża odporność na działanie rozpuszczalników organicznych, detergentów i innych czynników denaturujących białka oraz mała wrażliwość na zmiany pH. Dokonano też przeglądu czynników powodujących dużą stabilność proteaz z termofili.
-
Apple pectin complexes with whey protein isolate
Publication -
The investigation of the effects of counterions in protein dynamics simulations
Publication -
Protein thermal stabilization in aqueous solutions of osmolytes
PublicationProteins’ thermal stabilization is a significant problem in various biomedical, biotechnological, and technological applications. We investigated thermal stability of hen egg white lysozyme in aqueous solutions of the following stabilizing osmolytes: Glycine (GLY), N-methylglycine (NMG), N,N-dimethylglycine (DMG), N,N,N-trimethylglycine (TMG), and trimethyl-N-oxide (TMAO). Results of CD-UV spectroscopic investigation were compared...
-
Modelling gene expression of a self-regulating protein
PublicationWe analyze a model of gene transcription and protein synthesis. We take into account the number of sites on the protein’s promoter at which the protein’s dimers can bind blocking transcription of protein mRNA.
-
ANALYSIS OF THE p53 PROTEIN GENE EXPRESSION MODEL
PublicationWe study the asymptotic behaviour of the solutions of the p53-Mdm2 model proposed by Monk (2003). The p53 gene is crucial for cellular inhibition of the angiogenesis process, while Mdm2 is a negative regulator of the p53 tumor-suppressor. We investigate the stability of the positive steady state and perform some numerical experiments.
-
Modelling of vibrations of a liquid filled tank
PublicationPrzeprowadzono analizę teoretyczną i numeryczną zbiorników długich i krótkich wypełnionych całkowicie lub częściowo cieczą. Wyznaczenie obciążeń hydrodynamicznych dotyczy bezpośrednio wytrzymałości konstrukcji samego zbiornika, a przez to pozwala określić wytrzymałość konstrukcyjną całego kadłuba. Szczególne wymagania stawiane są zbiornikom do przewozu cieczy radioaktywnych, gdyż należy zapewnić bardzo wysoki stopień bezpieczeństwa...
-
Hazard prevention by forced time constraints
PublicationMinimalne Zbiory Przyczyn powstałe podczas analizy Drzew Błędów wskazują zdarzenia, które jeśli nastąpią razem, mogą doprowadzić do Hazardu. W niektórych zastosowaniach opis zdarzeń może zostać poszerzony o informację czasową, wtedy zdarzenia z MZP mogą doprowadzić do Hazardu tylko jeśli wystąpi pomiędzy nimi określona zależność czasowa. W tym artykule przedstawione zostało jak informacja czasowa może zostać wprowadzona do Drzew...
-
On the crack front curvature in bonded joints
PublicationStandard tests of adhesively bonded specimens are likely to produce heterogeneous stress distribution along the crack front and its vicinity. High separation rate mode I dominated fracture test is performed.Observation of post mortem fractured surfaces with an optical microscope reveals characteristic features of mixed mode I/III fracture near the sides of the specimen but not in the middle. At first, finite elements calculations...
-
Underwater welded joint properties investigation
PublicationPrzeprowadzono badania mikro- i makroskopowe złączy spawanych typu implant wykonanych pod wodą metodą lokalnej komory suchej. Wyniki badań świadczą o tym, że w SWC badanych złączy tworzą się kruche struktury hartownicze, które są odpowiedzialne za zwiększoną skłonność stali o podwyższonej wytrzymałości do tworzenia pęknieć zimnych. Analiza rozkładów twardości złączy implant również potwierdza istnienie szkodliwego wpływu środowiska...
-
Stability of an imperfect truss loaded by wind
PublicationThe present paper is devoted to the numerical research of stability of a truss loaded by wind and stiffened by elastic supports located at the top chord. The lateral braces or lateral and torsional braces were taken into account. In this paper, the linear buckling analysis re- sults for the beam and shell model were presented. Two different shapes of initial geometric imperfections were considered in the non-linear static analysis...
-
Hydrodynamics of tank partially filled with liquid.
PublicationW artykule podano podstawowe równania dynamiki zbiornika wypełnionego częściowo cieczą. Na modelu tego zbiornika przeprowadzono badania eksperymentalne i wyniki tych badań przedstawiono jako efekt końcowy.
-
Forming of explosively welded metal plates.
PublicationW pracy przedstawiono możliwości kształtowania plastycznego poprzez walcowanie, tłoczenie, gięcie, skręcanie blach wielowarstwowych zgrzewanych wybuchowo.
-
The Characteristics of New SSB Proteins from Metagenomic Libraries and Their Use in Biotech Applications
Publication -
Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS
Publication -
Proteins Structure Models in the Evaluation of Novel Variant (C.472_477del) in the MOCS2 Gene
Publication -
Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
Publication -
Why the solvation water around proteins is more dense than bulk water
PublicationThe main aim of this work is to propose a rational explanation of commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that geometry of the water-water hydrogen bond network within solvation layer differs from the one in bulk water and it is the effect of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the structure...