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Search results for: PROTEIN DIMERISATION
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Function and Frustration of Multi-Drug ABC Exporter Protein and Design of Model Proteins for Drug Delivery Using Protein Hydration Thermodynamics
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Elastic-contractile model proteins: Physical chemistry, protein function and drug design and delivery
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Dissociative electron attachment and anion-induced dimerization in pyruvic acid
PublicationWe report partial cross sections for the dissociative electron attachment to pyruvic acid. A rich fragmentation dynamics is observed. Electronic structure calculations facilitate the identification of complex rearrangement reactions that occur during the dissociation. Furthermore, a number of fragment anions produced at electron energies close to 0 eV are observed, that cannot originate from single electron-molecule collisions....
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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The effects of confinement in pores built of folded graphene sheets on the equilibrium of nitrogen monoxide dimerisation reaction
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Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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The Protein Folding Problem
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Influence of Osmolytes on Protein and Water Structure: A Step To Understanding the Mechanism of Protein Stabilization
PublicationResults concerning the thermostability of hen egg white lysozyme in aqueous solutions with stabilizing osmolytes, trimethylamine-N-oxide (TMAO), glycine (Gly), and its N-methyl derivatives, N-methylglycine (NMG), N,N-dimethylglycine (DMG), and N,N,N-trimethylglycine (betaine, TMG), have been presented. The combination of spectroscopic (IR) and calorimetric (DSC) data allowed us to establish a link between osmolytes’ influence on...
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Proteins
PublicationStruktura białek wpływa na ich wartość odżywczą, właściwości funkcjonalne wżywności oraz reakcje w surowcach i produktach żywnościowych. Warunki prze-chowywania oraz obróbki w przemyśle i w czasie przygotowywania kulinarnegowywołują przemiany białek istotne dla jakości żywności. Przez celowe, enzy-matyczne i chemiczne modyfikowanie składu i struktury białek można wpływaćna ich właściwości funkcjonalne w żywności i wartość...
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5-Thiocyanato-2′-deoxyuridine as a possible radiosensitizer: electron-induced formation of uracil-C5-thiyl radical and its dimerization
PublicationIn this work, we have synthesized 5-thiocyanato-2′-deoxyuridine (SCNdU) along with the C6-deuterated nucleobase 5-thiocyanatouracil (6-D-SCNU) and studied their reactions with radiation-produced electrons. ESR spectra in γ-irradiated nitrogen-saturated frozen homogeneous solutions (7.5 M LiCl in H2O or D2O) of these compounds show that electron-induced S–CN bond cleavage occurs to form a thiyl radical (dU-5-S˙ or 6-D-U-5-S˙) and...
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Influence of Dimerization of Lipopeptide Laur-Orn-Orn-Cys–NH2 and an N-terminal Peptide of Human Lactoferricin on Biological Activity
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Alternative and New Protein Sources
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Stabilizing agents and protein stability
PublicationBiałka są kluczowymi elementami żywych organizmów, jak również efektywnymi katalizatorami w biotechnologii i medycynie. Szybki rozwój wielu gałęzi biotechnologii wiąże się z coraz większym zapotrzebowaniem na produkty białkowe charakteryzujące się wysoką stabilnością. Jednym ze sposobów osiągnięcia większej stabilności białek jest wykorzystanie małych związków organicznych, tzw. osmolitów. Do tej grupy związków należą aminokwasy,...
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Colloidal aspects of protein digestion
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On the Origin of Protein Superfamilies and Superfolds
PublicationDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublicationG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of 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 is not very different from bulk water. The local values of...
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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...
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Endocrine responses following exhaustive strength exercise with and without the use of protein and protein-carbohydrate supplements
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Occlusion phenomenon of redox probe by protein as a way of voltammetric detection of non-electroactive C-reactive protein
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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,...
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The Role of Proteins in Food
PublicationThis chapter describes the effect of proteins on the sensory attributes and the biological value and safety of foods. The role of proteins depends on their amino acid composition and structure, on changes due to storage and processing, as well as on interactions with other food components. The effect on the sensory quality of foods is brought about by hydrophobicity, solubility, water holding capacity, gelling, film formation,...
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The investigation of the effects of counterions in protein dynamics simulations
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Pea Protein for Hempseed Oil Nanoemulsion Stabilization
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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.
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Polysaccharide–Protein Complexes in a Coarse-Grained Model
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Apple pectin complexes with whey protein isolate
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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.
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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...
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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.
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Taurine as a water structure breaker and protein stabilizer
PublicationThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublicationBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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Construction and purification of his6-Thermus thermophilus MutS protein.
PublicationGen mutS z termofilnej bakterii Thermus thermophilus zamplifikowano przy użyciu PCR, sklonowano i przeprowadzono jego ekspresję w E. coli. Rekombinantowe białko MutS zawierające oligohistydynową domenę na N-końcu oczyszczono w jednoetapowej procedurze przy wykorzystaniu chromatografii powinowactwaNi(2+). Zdolność do rozpoznania niekomplementarności białka his(6)-MutS potwierdzono w eksperymentach ochrony DNA przed trawieniem...
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Novel primosomal protein B from Clostridium pasteurianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Construction and purification of his6-Thermus thermophilus MutS protein
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A bifunctional chimeric protein consisting of MutS and beta-galactosidase
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The protein folding problem: global optimization of force fields
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Lipid-protein interactions in membranes: a molecular modelling study
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A bifunctional chimeric protein consisting of MutS and beta-galactoside
PublicationPraca pokazuje konstrukcję DNA plazmidowego kodującego bifunkcjonalne białko chimeryczne złożone z MutS Thermus thermophilus i beta-galaktozydazy E.coli, optymalizację jego ekspresji i oczyszczania. Białko to testowano w metodzie wykrywania mutacji punktowych, wykorzystując kolorymetryczne mierzenie aktywności domeny reporterowej beta galaktozydazy.
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
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Role of Oligosaccharide Chain Polarity in Protein–Glycosaminoglycan Interactions
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Effect of increased protein intake on the risk of female infertility
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Novel primosomal protein B from Clostridium pastuerianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Copper containing protein sites - structure, properties and models
PublicationEnzymy organizmów żywych katalizują wiele reakcji stosowanych w przemyśle chemicznym. Przykładem potencjalnego zastosowania enzymu w produkcji jest synteza L-Dopy przy udziale tyrozynazy. Ze względu na możliwe praktyczne zastosowanie w katalizie, otrzymano i opisano wiele prostych modeli miejsc aktywnych enzymów. W artykule opisano niektóre modele białek zawierających miedź.
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Electrosynthesis of potato starch–whey protein isolate complexes
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Concentration of proteins in the whey stream
PublicationZastosowano metodę separacji pianowej do odzyskiwania białka z serwatki. Wykazano silny wpływ prędkości powietrza w kolumnie, początkowego stężenia białka w serwatce i pH roztworu na przebieg i skuteczność flotacji. Współczynnik wzbogacenia maleje ze wzrostem prędkości przepływu powietrza oraz ze wzrostem początkowego stężenia białka serwatkowego. Najwyższą wartość współczynnika wzbogacenia uzyskano dla pH naturalnej serwatki.
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Conservation and diversity of MutS proteins
PublicationThe homologues of MutS, mismatch repair protein, exist in all prokaryotes, with the exception of Actinobacteria, Mollicutes and part of the Archaea. Multiple alignments of 316 MutS amino acid sequences from 169 species revealed conserved residues and sequence motifs distinguishing MutS homologues. All MutS homologues show high conservation within the ATPase domain. MutS1, the homologue responsible for DNA mismatch recognition,...
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Conserved motifs of MutL proteins
PublicationtThe MutL protein is best known for its function in DNA mismatch repair (MMR). However, there isevidence to suggest that MutL is not only the linker connecting the functions of MutS and MutH in MMR,but that it also participates in other repair systems, such as Very Short Patch (VSP), Base Excision (BER)and Nucleotide Excision Repair (NER). This study set out to identify the most highly conserved aminoacid sequence motifs in MutL...