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    Wyświetlanie 1-11 z 11
    Tytuł:
    Beyond sequence similarity – the curious case of GW/WG protein domain
    Autorzy:
    Karlowski, W.M.
    Powiązania:
    https://bibliotekanauki.pl/articles/79861.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    RNA silencing
    gene expression
    protein domain
    amino acid sequence
    Arabidopsis thaliana
    Vitis vinifera
    cysteine
    phenylalanine
    histidine
    methionine
    tyrosine
    sequence similarity
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 4
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Protein modeling with reduced representation: statistical potentials and protein folding mechanism
    Autorzy:
    Ekonomiuk, Dariusz
    Kielbasinski, Marcin
    Kolinski, Andrzej
    Powiązania:
    https://bibliotekanauki.pl/articles/1041306.pdf
    Data publikacji:
    2005
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    B1 domain of protein G
    statistical potentials
    folding mechanism
    Monte Carlo simulations
    high resolution lattice proteins
    protein folding
    Opis:
    A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational propensities and protein-like chain stiffness, a model of directional and cooperative hydrogen bonds, and properly designed knowledge-based potentials of the long-range interactions between the side groups. The folding of the model protein is cooperative and very fast. In a single trajectory, a number of folding/unfolding cycles were observed. Typically, the folding process is initiated by assembly of a native-like structure of the C-terminal hairpin. In the next stage the rest of the four-ribbon β-sheet folds. The slowest step of this pathway is the assembly of the central helix on the scaffold of the β-sheet.
    Źródło:
    Acta Biochimica Polonica; 2005, 52, 4; 741-748
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    PDZ domains - common players in the cell signaling.
    Autorzy:
    Jeleń, Filip
    Oleksy, Arkadiusz
    Śmietana, Katarzyna
    Otlewski, Jacek
    Powiązania:
    https://bibliotekanauki.pl/articles/1043370.pdf
    Data publikacji:
    2003
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    PDZ domain
    module
    protein-protein interaction
    signaling
    Opis:
    PDZ domains are ubiquitous protein interaction modules that play a key role in cellular signaling. Their binding specificity involves recognition of the carboxyl-terminus of various proteins, often belonging to receptor and ion channel families. PDZ domains also mediate more complicated molecular networks through PDZ-PDZ interactions, recognition of internal protein sequences or phosphatidylinositol moieties. The domains often form a tandem of multiple copies, but equally often such tandems or single PDZ domain occur in combination with other signaling domains (for example SH3, DH/PH, GUK, LIM, CaMK). Common occurrence of PDZ domains in Metazoans strongly suggests that their evolutionary appearance results from the complication of signaling mechanisms in multicellular organisms. Here, we focus on their structure, specificity and role in signaling pathways.
    Źródło:
    Acta Biochimica Polonica; 2003, 50, 4; 985-1017
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Role of genetic modification of the PNPLA3 gene in predicting metabolically unhealthy obesity and metabolic associated fatty liver disease in children
    Autorzy:
    Abaturov, Aleksandr
    Nikulina, Anna
    Powiązania:
    https://bibliotekanauki.pl/articles/2207159.pdf
    Data publikacji:
    2023-03-25
    Wydawca:
    Uniwersytet Rzeszowski. Wydawnictwo Uniwersytetu Rzeszowskiego
    Tematy:
    children
    metabolic associated fatty liver disease
    obesity
    patatin‐like phospholipase domain‐containing protein 3
    single nucleotide variants
    Opis:
    Introduction and aim. Single nucleotide variants (SNV) of the patatin‐like phospholipase domain‐containing protein 3 (PNP-LA3) gene play an important role in hepatic lipid remodeling and lipogenesis de novo, which is associated with the development of metabolically unhealthy obesity (MUO) and metabolic associated fatty liver disease (MAFLD). The aim of the study was to define the contribution of SNV PNPLA3 gene to the development of MUO, complicated by MAFLD in children. Material and methods. 200 obese children aged 6-18 years were examined. The main group (n=118) was represented by children with MUO. The control group (n=82) consolidated of children with metabolically healthy obesity (MHO). Whole genome sequencing (CeGat) was performed in 31 children of the main and 21 children of the control group. Results. Among obese children, 14 variants of SNV PNPLA3 (rs139051, rs34179073, rs2294918, rs139047, rs779127153, rs2076212, rs738409, rs738408, rs4823173, rs2072906, rs2076213, rs141106484, rs138736228) were identified, including SNV PNPLA3 g.44322818, not described in the dbSNP core database. The role of the following SNV PNPLA3 genotypes in the development of MUO complicated by MAFLD was revealed: rs738409 C/G (Relative risk (RR)=1.71); rs738408 C/T (RR=1.71); rs4823173 G/A (RR=1.57); rs2072906 A/G (RR=1.57) with Sensitivity (Se)=0.63 and Specificity (Sp)=0.72. Conclusion. The contribution to the development of MUO complicated by MAFLD in children is made by the linked association of genotypes: rs738409 C/G, rs738408 C/T, rs4823173 G/A and rs2072906 A/G out of 14 PNPLA3 SNVs diagnosed by us.
    Źródło:
    European Journal of Clinical and Experimental Medicine; 2023, 1; 5-13
    2544-2406
    2544-1361
    Pojawia się w:
    European Journal of Clinical and Experimental Medicine
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Structure, function, and regulation of myosin 1C.
    Autorzy:
    Barylko, Barbara
    Jung, Gwanghyun
    Albanesi, Joseph
    Powiązania:
    https://bibliotekanauki.pl/articles/1041416.pdf
    Data publikacji:
    2005
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    myosin 1
    membrane protein translocation
    domain structure
    Opis:
    Myosin 1C, the first mammalian single-headed myosin to be purified, cloned, and sequenced, has been implicated in the translocation of plasma membrane channels and transporters. Like other forms of myosin I (of which eight exist in humans) myosin 1C consists of motor, neck, and tail domains. The neck domain binds calmodulins more tightly in the absence than in the presence of Ca^(2+). Release of calmodulins exposes binding sites for anionic lipids, particularly phosphoinositides. The tail domain, which has an isoelectic point of 10.5, interacts with anionic lipid headgroups. When both neck and tail lipid binding sites are engaged, the myosin associates essentially irreversibly with membranes. Despite this tight membrane binding, it is widely believed that myosin 1C docking proteins are necessary for targeting the enzyme to specific subcellular location. The search for these putative myosin 1C receptors is an active area of research.
    Źródło:
    Acta Biochimica Polonica; 2005, 52, 2; 373-380
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Unexpected domain composition of MACC1 links MET signaling and apoptosis
    Autorzy:
    Kokoszyńska, Katarzyna
    Kryński, Jacek
    Rychlewski, Leszek
    Wyrwicz, Lucjan
    Powiązania:
    https://bibliotekanauki.pl/articles/1040592.pdf
    Data publikacji:
    2009
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    protein structure modeling
    colorectal cancer
    bioinformatics
    death domain
    Opis:
    Colorectal cancer, one of the most challenging malignancies, still has a limited number of recognized prognostic and predictive markers indicating appropriate treatment. MACC1 (metastasis-associated in colon cancer-1), a novel regulator of tumor growth and metastasis has recently been identified as an important prognostic factor of metastatic disease in colorectal cancer. The mechanism of MACC1 activity remains undetermined. Here we apply a combination of fold recognition and homology modeling algorithms to draft MACC1 function. The applied methods revealed that the MACC1 protein consists of four domains: ZU5, SH3, and two C-terminal death domains (DD). Previously a similar domain architecture (ZU5-DD) was observed in other proteins, involved mainly in signal transduction and apoptosis regulation. Based on the specific aspects of the closest homologues' biology functional hypotheses on MACC1 are proposed. A broad range of bioinformatic analyzes indicates that MACC1, besides its involvement in signal transduction from the MET receptor, links MET signaling and apoptosis.
    Źródło:
    Acta Biochimica Polonica; 2009, 56, 2; 317-324
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    AtDeg2 - a chloroplast protein with dual protease/chaperone activity
    Autorzy:
    Jagodzik, P.
    Adamiec, M.
    Jackowski, G.
    Powiązania:
    https://bibliotekanauki.pl/articles/57301.pdf
    Data publikacji:
    2014
    Wydawca:
    Polskie Towarzystwo Botaniczne
    Tematy:
    chloroplast protein
    protease
    proteolytic enzyme
    chaperone
    enzyme activity
    chloroplast
    PDZ domain
    Opis:
    Chloroplast protease AtDeg2 (an ATP-independent serine endopeptidase) is cytosolically synthesized as a precursor, which is imported into the chloroplast stroma and deprived of its transit peptide. Then the mature protein undergoes routing to its functional location at the stromal side of thylakoid membrane. In its linear structure AtDeg2 molecule contains the protease domain with catalytic triad (HDS) and two PDZ domains (PDZ1 and PDZ2). In vivo AtDeg2 most probably exists as a supposedly inactive haxamer, which may change its oligomeric stage to form active 12-mer, or 24-mer. AtDeg2 has recently been demonstrated to exhibit dual protease/chaperone function. This review is focused on the current awareness with regard to AtDeg2 structure and functional significance.
    Źródło:
    Acta Societatis Botanicorum Poloniae; 2014, 83, 3
    0001-6977
    2083-9480
    Pojawia się w:
    Acta Societatis Botanicorum Poloniae
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Protective antigen domain 4 of Bacillus anthracis as a candidate for use as vaccine for anthrax
    Autorzy:
    Żakowska, D.
    Graniak, G.
    Rutyna, P.
    Naylor, K.
    Glowacka, P.
    Niemcewicz, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/2085049.pdf
    Data publikacji:
    2019
    Wydawca:
    Instytut Medycyny Wsi
    Tematy:
    Bacillus anthracis
    cloning pag gene
    domain 4
    protective antigen
    protein
    recombinant
    vaccine
    Opis:
    Existing research for using the protective antigen (PA) of Bacillus anthracis as a vaccine component shows that protection against anthrax may be obtained using fragments of this protein. The aim of the research is to check whether the selected protein fragment of the protective antigen (domain 4) encoded by an appropriate nucleotide sequence of gene pag of B. anthracis, was expressed in the bacterial system of E. coli. In order to examine the selected sequence of the pag gene, a PCR reaction and a highly effective TOPO cloning strategy were used, followed by purification of the recombinant proteins and their detection by a western-blot method. In the planning of the PA4 antigen expression a higher level of effectiveness in production of small protein – domain 4 – was anticipated. As a result, the 139 amino acids protein fragment of B. anthracis PA (domain 4) was isolated. The research may have found the basis for in vivo research aimed at finding potential anthrax vaccine components.
    Źródło:
    Annals of Agricultural and Environmental Medicine; 2019, 26, 3; 392-395
    1232-1966
    Pojawia się w:
    Annals of Agricultural and Environmental Medicine
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    3D Domain swapping, protein oligomerization, and amyloid formation.
    Autorzy:
    Jaskólski, Mariusz
    Powiązania:
    https://bibliotekanauki.pl/articles/1043850.pdf
    Data publikacji:
    2001
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    protein aggregation
    amyloid
    amyloid fibrils
    3D domain swapping
    conformational diseases
    amyloidosis
    Opis:
    In 3D domain swapping, first described by Eisenberg, a structural element of a monomeric protein is replaced by the same element from another subunit. This process requires partial unfolding of the closed monomers that is then followed by adhesion and reconstruction of the original fold but from elements contributed by different subunits. If the interactions are reciprocal, a closed-ended dimer will be formed, but the same phenomenon has been suggested as a mechanism for the formation of open-ended polymers as well, such as those believed to exist in amyloid fibrils. There has been a rapid progress in the study of 3D domain swapping. Oligomers higher than dimers have been found, the monomer-dimer equilibrium could be controlled by mutations in the hinge element of the chain, a single protein has been shown to form more than one domain-swapped structure, and recently, the possibility of simultaneous exchange of two structural domains by a single molecule has been demonstrated. This last discovery has an important bearing on the possibility that 3D domain swapping might be indeed an amyloidogenic mechanism. Along the same lines is the discovery that a protein of proven amyloidogenic properties, human cystatin C, is capable of 3D domain swapping that leads to oligomerization. The structure of do-main-swapped human cystatin C dimers explains why a naturally occurring mutant of this protein has a much higher propensity for aggregation, and also suggests how this same mechanism of 3D domain swapping could lead to an open-ended polymer that would be consistent with the cross-β structure, which is believed to be at the heart of the molecular architecture of amyloid fibrils.
    Źródło:
    Acta Biochimica Polonica; 2001, 48, 4; 807-827
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    3D domain swapping – implications for conformational disorders and ways of control
    Autorzy:
    Jaskolski, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/80151.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    3D domain swapping
    amyloid
    crystalline
    cystatin
    fibril
    human cystatin C
    mutagenesis
    oligomerization
    polypeptide chain
    prion protein
    protein aggregation
    protein engineering
    ribonuclease A
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 1
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Cloning and expression of a new recombinant thrombolytic and anthithrombotic agent - a staphylokinase variant
    Autorzy:
    Kowalski, Michał
    Brown, George
    Bieniasz, Magdalena
    Oszajca, Katarzyna
    Chabielska, Ewa
    Pietras, Tadeusz
    Szemraj, Zofia
    Makandjou-Ola, Eusebio
    Bartkowiak, Jacek
    Szemraj, Janusz
    Powiązania:
    https://bibliotekanauki.pl/articles/1040615.pdf
    Data publikacji:
    2009
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    K2 domain of t-PA
    thrombolytic and antithrombotic agents
    thrombolysis
    staphylokinase
    recombinant protein
    hirulog
    antiplatelet activity
    Opis:
    To develop a more potent antithrombin agent with thrombolytic and antiplatelet properties, a new staphylokinase (SAK) variant was constructed. The kringle 2 domain (K2) of tissue type-plasminogen activator (t-PA) containing a fibrin-specific binding site (i), the RGD sequence (Arg-Gly-Asp) for the prevention of platelet aggregation (ii) and the antithrombotic agent - hirulog (iii) was assembled to the C-terminal part of recombinant staphylokinase (r-SAK). cDNA for the hybrid protein SAK-RGD-K2-Hirul was cloned into Pichia pastoris pPIC9K yeast expression vector. The introduction of K2 t-PA, the RGD sequence and hirulog into the C-terminus of r-SAK did not alter the staphylokinase activity. We observed a higher clot lysis potency of SAK-RGD-K2-Hirul as evidenced by a faster and more profound lysis of 125I-labeled human fibrin clots. The potency of thrombin inhibition by the hirulog C-terminal part of the recombinant fusion protein was almost identical to that of r-Hir alone. These results suggest that the SAK-RGD-K2-Hirul construct can be a more potent and faster-acting thrombolytic agent with better antithrombin and antiplatelet properties compared to r-SAK and SAK-RGD-K2-Hir.
    Źródło:
    Acta Biochimica Polonica; 2009, 56, 1; 41-53
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-11 z 11

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