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    Wyświetlanie 1-10 z 10
    Tytuł:
    Structural similarity of CheY-like proteins
    Autorzy:
    Banach, M.
    Konieczny, L.
    Roterman, I.
    Tematy:
    hydrophobicity
    tertiary structure
    hydrophobic core
    Pokaż więcej
    Wydawca:
    Politechnika Gdańska
    Powiązania:
    https://bibliotekanauki.pl/articles/1938624.pdf  Link otwiera się w nowym oknie
    Opis:
    The problem of structural similarity of polypeptide chains of low sequence similarity representing a similar 3D structural form has been the object of analysis of researchers engaged in the protein folding problem. Three homologous proteins of similar biological function with low sequence similarity are the objects of analysis presented in this paper. The structure of a hydrophobic core is used as the criterion for structural similarity assessment of these three proteins. The applied method allows recognition of differentiati on in topologically similar structures.
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    RNA dactyloscopy
    Autorzy:
    Gabryelska, Marta
    Wyszko, Eliza
    Barciszewski, Jan
    Tematy:
    hammerhead ribozyme
    RNA tertiary structure
    fingerprint
    Pokaż więcej
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Powiązania:
    https://bibliotekanauki.pl/articles/1038740.pdf  Link otwiera się w nowym oknie
    Opis:
    Despite the wealth of data on RNA secondary structure, conformational dynamics and tertiary structure in vitro and in vivo, predicting RNA biological activity in cellular environments remains difficult. Here, we present a comparison between in silico RNA fingerprinting and published experimental data that sheds light on efficient design of the hammerhead ribozyme molecules with a high intracellular efficiency. Our method, which we call RNA dactyloscopy, is a reliable tool for assessing the catalytic properties, modeling and design of RNA.
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Hydrophobic core in domains of immunoglobulin-like fold
    Autorzy:
    Chomilier, J.
    Prudhomme, N.
    Banach, Mateusz
    Roterman-Konieczna, Irena
    Opis:
    This work analyzes proteins which contain an immunoglobulin fold, focusing on their hydrophobic core structure. The "fuzzy oil drop" model was used to measure the regularity of hydrophobicity distribution in globular domains belonging to proteins which exhibit the above-mentioned fold. Light-chain IgG domains are found to frequently contain regular hydrophobic cores, unlike the corresponding heavy-chain domains. Enzymes and DNA binding proteins present in the data-set are found to exhibit poor accordance with the hydrophobic core model.
    Dostawca treści:
    Repozytorium Uniwersytetu Jagiellońskiego
    Artykuł
    Tytuł:
    Role of disulfide bonds in stabilizing the conformation of selected enzymes : an approach based on divergence entropy applied to the structure of hydrophobic core in proteins
    Autorzy:
    Kalinowska, Barbara
    Banach, Mateusz
    Roterman-Konieczna, Irena
    Konieczny, Leszek
    Opis:
    One of the factors responsible for tertiary structural stabilization in proteins is the presence of the hydrophobic core—a result of hydrophobic interactions within the protein body. In some proteins (especially extracellular ones) additional stabilization is provided by covalent bonds between selected Cys residues, commonly referred to as disulfide bonds. The mutual interplay of both factors and their respective contributions to stabilization are the focus of this work. The assessment of the effects of disulfide bonds isinterpreted by Fuzzy Oil Drop (FOD) model in which individual polypeptide chain fragments (including fragments which participate in SS bonds) can be evaluated in the context of their influence upon tertiary structural stabilization by comparing their corresponding theoretical and idealized hydrophobicity density distributions. The proteins were identified with both factors reinforcing each other, as well as proteins where they seem to counteract each other. The analysis presents a number of enzymes, including ribonuclease, lysozyme, disulfide isomerase and phospholipase.
    Dostawca treści:
    Repozytorium Uniwersytetu Jagiellońskiego
    Artykuł
    Tytuł:
    Correlated mutations in selected protein families
    Autorzy:
    Leluk, J.
    Sobczyk, M.
    Becella, Ł.
    Tematy:
    protein sequence
    multiple alignment
    tertiary structure
    mutational correlation
    genetic semihomology algorithm
    Pokaż więcej
    Wydawca:
    Politechnika Gdańska
    Powiązania:
    https://bibliotekanauki.pl/articles/1986920.pdf  Link otwiera się w nowym oknie
    Opis:
    Four different protein families (two proteinase inhibitor families, myoglobins and lysozymes) were surveyed for correlated mutations with respect to the position distance and their significance in structure stabilization and biological activity. They were chosen for this study in order to verify the currently admitted model of mutational correlation relationship with respect to spatial contact of the residues and contribution in protein biological activity. There was observed high contribution of spatially dispersed residues (which are also not involved in the protein active center) in mutational correlation. Because of the significantly large distance between correlated positions these cases do not correspond explicitly to any mechanism included in current hypotheses. It is suggested that the role of residue spatial contact in structure preservation, intermolecular interaction and active site rescue mechanisms only partially explains the correlation phenomenon.
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Structure of small G proteins and their regulators.
    Autorzy:
    Paduch, Marcin
    Jeleń, Filip
    Otlewski, Jacek
    Tematy:
    small G protein
    GAP
    protein-protein interaction
    GTPase
    GDI
    Rho
    Ras
    protein tertiary structure
    GEF
    Pokaż więcej
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Powiązania:
    https://bibliotekanauki.pl/articles/1043851.pdf  Link otwiera się w nowym oknie
    Opis:
    In recent years small G proteins have become an intensively studied group of regulatory GTP hydrolases involved in cell signaling. More than 100 small G proteins have been identified in eucaryotes from protozoan to human. The small G protein superfamily includes Ras, Rho Rab, Rac, Sar1/Arf and Ran homologs, which take part in numerous and diverse cellular processes, such as gene expression, cytoskeleton reorganization, microtubule organization, and vesicular and nuclear transport. These proteins share a common structural core, described as the G domain, and significant sequence similarity. In this paper we review the available data on G domain structure, together with a detailed analysis of the mechanism of action. We also present small G protein regulators: GTPase activating proteins that bind to a catalytic G domain and increase its low intrinsic hydrolase activity, GTPase dissociation inhibitors that stabilize the GDP-bound, inactive state of G proteins, and guanine nucleotide exchange factors that accelerate nucleotide exchange in response to cellular signals. Additionally, in this paper we describe some aspects of small G protein interactions with downstream effectors.
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Design and implementation of an algorithm for automatic RNA tertiary structures prediction using homology-based methods
    Projekt i implementacja algorytmu do automatycznego przewidywania struktur trzeciorzędowych RNA przy zastosowaniu metod homologicznych
    Autorzy:
    Kopciuch, Konrad
    Opis:
    This paper describes the desing and implementation of an algorithm for automatic RNA tertiarty structure prediction. This algorithm has three main parts: template recognition, query sequence to template sequence alignment and building a model using homology-based program. In desing of this algorithm we used SVM machine learning method, and a few similarity measures between template and query sequence. Among other things we used a Needleman-Wunsch algorithm, and stochastic context-free grammar.
    W ramach pracy zaprojektowany i zaimplementowany został algorytm do automatycznego przewidywania struktury trzeciorzędowej RNA. Algorytm ten można podzielić na trzy główne części: rozpoznanie szablonu, dopasowanie sekwencji celu do sekwencji szablonu oraz utworzenie modelu za pomocą programu do modelowania homologicznego. Przy projekcie wykorzystana została metoda SVM uczenia maszynowego, a także różne miary podobieństwa pomiędzy szablonem a sekwencją celu. Przy implementacji tych miar wykorzystany został m.in. algorytm Needlemana-Wunscha oraz stochastyczne gramatyki bezkontekstowe.
    Dostawca treści:
    Repozytorium Uniwersytetu Jagiellońskiego
    Inne
    Tytuł:
    Charakterystyka geomorfologiczna obszaru położonego wzdłuż Doliny Środkowej Noteci
    Autorzy:
    Ratajczak-Szczerba, M.
    Tematy:
    geological structure
    geomorphology
    relief
    Tertiary deposits
    Quaternary deposits
    end moraine
    Wyrzysk oscillation
    Pokaż więcej
    Wydawca:
    Stowarzyszenie Geomorfologów Polskich
    Powiązania:
    https://bibliotekanauki.pl/articles/294966.pdf  Link otwiera się w nowym oknie
    Opis:
    The investigated area is located along the Noteć Middle Valley and is situated on the border of several physical-geographical and geomorphologic units. There are according to Krygowski (2000): the Noteć Middle Valley, the Gwda Valley, the Wałcz Lake District, the Kraina Lake District, the Chodzież Lake District. Varied geological structure and the relief of the area. The expression of dynamic activity of the last Scandinavian ice sheet are impressive ladforms like end moraine hills of the Chodzież subphase, the Wyrzysk oscillation, glacial gully, outwash levels.
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-10 z 10

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