Search results for: antifreeze%20proteins
-
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...
-
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...
-
Cadmium tri-tert-butoxysilanethiolates. Structural and spectroscopic models of metal sites in proteins.
PublicationW publikacji opisano syntezy i struktury dla dwóch heteroleptycznych kompleksów kadmu z rdzeniem CdS2NO2 i CdS2N2. Bis(tri-tert-butoksysilanotiolato)(1-metyloimidazol)kadmu(II) oraz bis(tri-tert-butoksysilanotiolato)bis(1-metyloimidazol)kadmu(II) współistnieją w roztworze chloroformu przy różnych stężeniach Bis(tri-tert-butoksysilanotiolanu) kadmu(II) i 1 metyloimidazolu. Rotzwór ten został scharakteryzowany za pomocą analizy spektralnej...
-
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 -
The Characteristics of New SSB Proteins from Metagenomic Libraries and Their Use in Biotech Applications
Publication -
FT-Raman Spectroscopy as a Tool to Study the Secondary Structures of Wheat Gliadin Proteins
Publication -
Does Nitrogen Fertilization Affect the Secondary Structures of Gliadin Proteins in Hypoallergenic Wheat?
Publication -
Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
Publication -
Differentially expressed proteins in the blood serum of piglets in response to a diet supplemented with inulin
Publication -
Single-stranded DNA-binding proteins (SSBs) - sources and applicationsin molecular biology
PublicationBiałka wiążące się do jednoniciowego DNA (SSB) odgrywają ważną rolę w replikacji, rekombinacji i naprawie DNA u bakterii, archea i eukariota. Ostatnio wzrosło zainteresowanie białkami SSB jako przydatnymi narzędziami w metodach badawczych biologii molekularnej, analitycznych i diagnostycznych. Większość znanych prokariotycznych białek SSB zbudowanych jest z czterech podjednostek (homotetramer) z jedną domeną wiążąca (OB) jednoniciowe...
-
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 the commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that the geometry of the water–water hydrogen bond network within solvation layer differs from the one in bulk water, and it is the result of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the...
-
Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
-
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...
-
Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublicationWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
-
Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublicationTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
-
Two bacterial small heat shock proteins, IbpA and IbpB, form a functional heterodimer
PublicationSmall heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones which in stress conditions bind to unfolded protein substrates and prevent their irreversible aggregation. Substrates trapped in sHsps-containing aggregates are efficiently refolded into native structures by ATP-dependent Hsp70 and Hsp100 chaperones. Most γ-proteobacteria possess a single sHsp (IbpA), while in a subset of Enterobacterales, as...
-
Effect of urea and glycine betaine on the hydration sphere of model molecules for the surface features of proteins
PublicationWater properties may significantly affect protein stability. Osmolytes are compounds that intrinsically affect water in many different ways and thus can influence proteins with this type of indirect mechanism. In this study, we characterize water properties in ternary solutions: model–water–osmolyte, with two model molecules: N-methylacetamide (NMA) and dimethyl sulfoxide (DMSO) and two osmolytes: glycine betaine (TMG)and urea....
-
Optimized procedure of extraction, purification and proteomic analysis of nuclear proteins from mouse brain
Publication -
Electrodes Based on a Titanium Dioxide Nanotube–Spherical Silver Nanoparticle Composite for Sensing of Proteins
Publication -
Expression of INHβA and INHβB proteins in porcine oocytes cultured in vitro is dependent on the follicle size
Publication -
Elastic-contractile model proteins: Physical chemistry, protein function and drug design and delivery
Publication -
Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals
Publication -
Nanoparticle Tracking Analysis of Urinary Extracellular Vesicle Proteins as a New Challenge in Laboratory Medicine
PublicationUrinary extracellular vesicle (uEV) proteins may be used as specific markers of kidney damage in various pathophysiological conditions. The nanoparticle-tracking analysis (NTA) appears to be the most useful method for the analysis of uEVs due to its ability to analyze particles below 300 nm. The NTA method has been used to measure the size and concentration of uEVs and also allows for a deeper analysis of uEVs based on their protein...
-
The Impact of the Antigenic Composition of Chimeric Proteins on Their Immunoprotective Activity against Chronic Toxoplasmosis in Mice
PublicationToxoplasmosis may pose a serious threat for individuals with weakened or undeveloped immune systems. However, to date, there is no specific immunoprophylaxis for humans. Thus, the aim of this study was to evaluate the immunogenicity of three trivalent—SAG2-GRA1-ROP1L (SGR), SAG1L-MIC1-MAG1 (SMM), and GRA1-GRA2-GRA6 (GGG)—and two tetravalent—SAG2-GRA1-ROP1-GRA2 (SGRG) and SAG1-MIC1-MAG1-GRA2 (SMMG)—chimeric T. gondii proteins, as...
-
Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublicationTo study the biochemical properties of SSB from Desulfolatea psychrophila (DpsSSB), 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 426 nucleotides encoding SSB protein of 142 amino acids with a calculated molecular mass of 15.6 kDa and it is the smallest known bacterial SSB protein indentified to date. The amino-acid sequence...
-
RecA Proteins from Deinococcus geothermalis and Deinococcus murrayi - Cloning, Purification and Biochemical Characterisation
PublicationEscherichia coli RecA plays a crucial role in recombinational processes, the induction of SOS response and mutagenic lesion bypasses. It has also been demonstrated that RecA protein is indispensable when it comes to the reassembly of shattered chromosomes in gamma-irradiated Deinococcus radiodurans, one of the most radiation-resistant organisms known. Moreover, some functional differences between E. coli and D. radiodurans RecA...
-
Determination of denaturation temperature of connective tissue proteins by viscometric measurements.
Open Research DataViscometric denaturation temperature of connective tissue proteins was determined by measuring viscosity with a Brookfield viscometer, using a LV SC4 - 18, 25 or LV3 spindle and shear rates from 50 to 110 s-1 (Fig.1). Freeze-dried protein samples were dissolved in 0.5 M acetic acid at 4 °C and concentration of 20 mg/mL. The solution was stirred with...
-
The Immunogenic and Immunoprotective Activities of Recombinant Chimeric T. gondii Proteins Containing AMA1 Antigen Fragments
PublicationToxoplasmosis, one of the most common parasitoses worldwide, is potentially dangerous for individuals with a weakened immune system, but specific immunoprophylaxis intended for humans is still lacking. Thus, efforts have been made to create an efficient universal vaccine for both animals and humans to overcome the shortcomings of currently used treatment methods and protect all hosts against toxoplasmosis. The current work represents...
-
Protective Effect of Black Tea Against Ethanol-Induced Oxidative Modifications of Liver Proteins and Lipids
Publication -
Efficient removal of dyes and proteins by nitrogen-doped porous graphene blended polyethersulfone nanocomposite membranes
Publication -
Investigations of changes in the arabinogalactan proteins (AGPs) structure, size and composition during the fruit ripening process
Publication -
Ovocystatin Induced Changes in Expression of Alzheimer’s Disease Relevant Proteins in APP/PS1 Transgenic Mice
Publication -
Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis
PublicationThe thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular...
-
Bacterial SSB-like proteins of family Deinococcaceae - indentification, isolation, obtaining, purification and molecular characteristic
PublicationWiększość poznanych białek SSB jest aktywna w formie homotetramerycznej. Od 2002 roku znane są białka organizmów ekstremofilnych. Scharakteryzowano białka mikroorganizmów rodziny Deinococaceae. Uzyskane termostabilne białka stanowią atrakcyjną alternatywę w stosunku do znanych białek SSB w metodach diagnostyki molekularnej, technikach biologii molekularnej i analityce.
-
Identification and properties of the Deinococcus grandis andDeinococcus proteolyticus single-stranded DNA binding proteins (SSB)
PublicationW celu poznania właściwości biochemicznych białek SSB pochodzących z Deinococcus grandis (DgrSSB) i Deinococcus proteolyticus (DprSSB) sklonowano zaamplifikowane w reakcji PCR geny ssb w systemie ekspresyjnym Escherichia coli. Geny składają się z 891(DgrSSB) i 876 (DprSSB) nukleotydów kodujących odpowiednio 296 i 291 reszt aminokwasowych o teoretycznie wyznaczonej masie cząsteczkowej dla białek, równej 32,29 i 31,33 kDa. Sekwencja...
-
Discrimination of normal oral mucosa from oral cancer by mass spectrometry imaging of proteins and lipids
Publication -
Extracellular Matrix Proteins Expression Profiling in Chemoresistant Variants of the A2780 Ovarian Cancer Cell Line
Publication -
Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds
Publication -
Human sperm proteins identified by 2-dimensional electrophoresis and mass spectrometry and their relevance to a transcriptomic analysis
Publication -
Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus - expression and purification
PublicationBiałka SSB są niezbędne do życia każdemu organizmowi. W tej pracy prezentujemy wyniki otrzymania i oczyszczania białek SSB Thermus thermophilus i T. aquaticus. Dotąd były znane białka SSB jedynie o budowie homotetrameru lub heterotrimeru. Białka SSB Thermus thermophilus i T. aquaticus stanowią nową klasę białek SSB - białek homodimerycznych. Ponadto dowiedziono, iż białka te są użyteczne w reakcji PCR.
-
Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus-expression and purification
PublicationSklonowano w system ekspresyjny pET-30LIC Escherichia coli gen kodujący białka SSB-podobne Thermus thermophilus i T. aquaticus. Oczyszczono do homogenności białka SSB-podobne, a uzyskane preparaty umożliwiają wykonanie badań strukturalnych w/w białek.
-
The biological role of prolyl oligopeptidase and the procognitive potential of its peptidic inhibitors from food proteins
PublicationProlyl oligopeptidase (POP) is a conserved serine protease belonging to proline-specific peptidases. It has both enzymatic and non-enzymatic activity and is involved in numerous biological processes in the human body, playing a role in e.g., cellular growth and differentiation, inflammation, as well as the development of some neurodegenerative and neuropsychiatric disorders. This article describes the physiological and pathological...
-
Relationship between seawater pollution and qualitative changes in the extracted proteins from mussels Mytilus galloprovincialis
PublicationCelem badań było znalezienie wiarygodnego bioznacznika dla oceny poziomu zanieczyszczenia wody morskiej. W tym celu porównano:-zawartość żelaza (Fe) oraz miedzi (Cu)-białek-poziomu aktywności przeciwutleniającejmałży (Mytilus galloprovincialis)zebranych z rejonów zanieczyszczonych i niezanieczyszczonych bułgarskiej strefy ekonomicznej Morza Czarnego.W badanich wykorzystano takie techniki analityczne jak: -spektroskopia w podczerwieni...
-
Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures
PublicationInteractions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions. In this paper, the influence of NMA and N,N-dimethylacetamide...
-
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...
-
Borrelia burgdorferi BmpA-BBK32 and BmpA-BBA64: New Recombinant Chimeric Proteins with Potential Diagnostic Value
PublicationCurrently, the diagnosis of Lyme disease is based mostly on two-tiered serologic testing. In the new generation of immunoenzymatic assays, antigens comprise whole-cell lysates of members of the Borrelia burgdorferi sensu lato (s.l.) species complex, with the addition of selected recombinant proteins. Due to the high diversity of members of the B. burgdorferi s.l. genospecies and the low degree of conservation among the amino acid...
-
Influence of milk, milk fractions and milk proteins on the growth and viability of mastitis-causing Staphylococcus aureus strain
Publication -
Molecular Characterisation of Uterine Endometrial Proteins during Early Stages of Pregnancy in Pigs by MALDI TOF/TOF
Publication -
Fibronectin-, vitronectin- and laminin-binding proteins at the cell walls of Candida parapsilosis and Candida tropicalis pathogenic yeasts
Publication