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Search results for: ANTIFREEZE PROTEIN
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Effect of Functionalization of Carbon Nanotubes with Psychosine on Complement Activation and Protein Adsorption
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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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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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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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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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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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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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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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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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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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The measurement of conformational stability of proteins adsorbed on siloxanes
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1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins
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Coarse-Grained Models of Proteins: Theory and Applications
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Computational techniques for efficient conformational sampling of proteins
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Molecular basis of TRF proteins and their interactions with peptides
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Patterned protein microarrays for bacterial detection. Langmuir**2003 vol.19 s. 436-439, 5 rys. bibliogr. 25 poz. Specyficzne mikroukłady protein do wykrywania bakterii.
PublicationSkonstruowano i przetestowano specyficzne mikroukłady przeciwciał selektyw-nie wiążących bakterie. Otrzymane układy umożliwiają wykrywanie bakterii E.coli0157:H7 oraz Renibacterium salmoninarum (RS). Matryce wytworzono techni-ką nadruku mikrokontaktów (ćCP). Charakterystykę układów uzyskano stosującmikroskopię skaningową (SPM). Ustalono, że selektywność otrzymanych układówobniża się podczas ekspozycji na bakterie niespecyficzne.
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Proprotein Convertase Subtilisin/Kexin Type 9, Angiopoietin-Like Protein 8, Sortilin, and Cholesteryl Ester Transfer Protein—Friends of Foes for Psoriatic Patients at the Risk of Developing Cardiometabolic Syndrome?
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Chitosan-protein scaffolds loaded with lysostaphin as potential antistaphylococcal wound dressing materials.
PublicationAIMS: The development of technology for preparing chitosan-protein scaffolds loaded with lysostaphin, which potentially could be used as dressing for wound treatment and soft tissue infections caused by Staphylococcus aureus. METHODS AND RESULTS: The unique technology of chitosan solubilization using gaseous CO(2) instead of organic or inorganic acids was used for the incorporation of lysostaphin, the enzyme that exhibits bactericidal...
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Depression as is Seen by Molecular Spectroscopy. Phospholipid- Protein Balance in Affective Disorders and Dementia
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MUTL PROTEIN AS A COMMON CONSTITUENT OF VSP, BER, NER AND MMR REPAIR SYSTEMS
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mismatch repair system (MMR). However, there is growing evidence that MMR system is not the only field of action of these proteins. Moreover, involvement in MMR does not even have to be their primary function. There are some reports indicating involvement of MutL in BER, NER and VSP (very short patch repair). MutL protein...
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Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field
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Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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Recent improvements in prediction of protein structure by global optimization of a potential energy function
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Assembly of Lipopolysaccharide in Escherichia coli Requires the Essential LapB Heat Shock Protein
PublicationHere, we describe two new heat shock proteins involved in the assembly of LPS in Escherichia coli, LapA and LapB (lipopolysaccharide assembly protein A and B). lapB mutants were identified based on an increased envelope stress response. Envelope stress responsive pathways control key steps in LPS biogenesis and respond to defects in the LPS assembly. Accordingly, the LPS content in ΔlapB or Δ(lapA lapB) mutants was elevated, with...
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublicationInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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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 Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublicationA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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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...
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Hot spot identification by ligand-protein surface interactions mapping – in silico study
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A comparative study of water distribution and dehydrin protein localization in maturing pea seeds
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Mapping Mechanostable Pulling Geometries of a Therapeutic Anticalin/CTLA-4 Protein Complex
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Molecular dynamics insights into protein‐glycosaminoglycan systems from microsecond‐scale simulations
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Local and long range potentials for heparin‐protein systems for coarse‐grained simulations
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Chromatin-associated microprocessor assembly is regulated by the U1 snRNP auxiliary protein PRP40
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Justification of quasi-stationary approximation in models of gene expression of a self-regulating protein
PublicationWe analyse a model of Hes1 gene transcription and protein synthesis with a negative feedback loop. The effect of multiple binding sites in the Hes1 promoter as well as the dimer formation process are taken into account. We consider three, possibly different, time scales connected with: (i) the process of binding to/dissolving from a binding site, (ii) formation and dissociation of dimers, (iii) production and degradation of Hes1...
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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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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...