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    Tytuł:
    Treatment of disulfide bonds in coarse-grained UNRES force field
    Autorzy:
    Krupa, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/1938623.pdf
    Data publikacji:
    2016
    Wydawca:
    Politechnika Gdańska
    Tematy:
    molecular dynamics
    protein folding
    disulfide bonds
    coarse-grained force field
    Opis:
    Disulfide bonds, despite the advances of the computational methods, are underrepresented in theoretical chemistry and the role of disulfide bonds is of ten diminished in bioinformatical studies. Most of the molecular modeling tools do not allow studying the process of disulfide bond formation and breaking, which is equally important as the sole presence of disulfide bonds in proteins and peptides. The UNRES (UNited RESidue) coarse-grained force field allows treating disulfide bonds in two ways: as static (formed or broken in the simulation) or dynamic (all specified cysteine residues can form and break disulfide bonds during simulation). The comparison between those two approaches of disulfide-bond treatment is presented for protein folding on the example of four small β - and α + β proteins with one, two, three and four disulfide bonds. The results clearly show that proper disulfide bond treatment is important in simulations and significantly enhances the quality of folded structures.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 393-398
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    A new approach to homology modeling
    Autorzy:
    He, Y.
    Scheraga, H. A.
    Rackovsky, S.
    Powiązania:
    https://bibliotekanauki.pl/articles/1954429.pdf
    Data publikacji:
    2022-02-01
    Wydawca:
    Politechnika Gdańska
    Tematy:
    protein structure prediction
    physical properties
    Kidera factors
    Fourier transformation
    coarse-grained force field
    Opis:
    The need to interpret experimental results led to, first, an all-atom force field, followed by a coarse-grained one. As an aid to these force fields, a new approach is introduced here to predict protein structure based on the physical properties of th e amino acids. This approach includes three key components: Kidera factors describing the physical properties, Fourier transformation and UNRES coarse-grained force field simulations. Different from traditional homology modeling methods which are based on evolution, this approach is physics-based, and does not have the same weaknesses as the traditional homology modeling methods. Our results show that this approach can produce above average prediction results, and can be used as a useful tool for protein structure prediction.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 211--218
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Influence of substitutions of Isu1 residues on binding to Jac1 protein
    Autorzy:
    Mozolewska, M. A.
    Powiązania:
    https://bibliotekanauki.pl/articles/1938619.pdf
    Data publikacji:
    2016
    Wydawca:
    Politechnika Gdańska
    Tematy:
    Saccharomyces cerevisiae
    Isu1-Jac1 protein complex
    alanine scan
    molecular dynamics
    coarse-grained UNRES force field
    Opis:
    The iron-sulfur (Fe/S) clusters are the most ancient co-factors of proteins involved in the most essential processes in bacterial systems and yeast, such as Saccharomyces cerevisiae. The main protein involved in the Fe/S cluster transfer is the Iron sulfur cluster assembly protein 1 (Isu1), which interacts with Jac1 during one of the stages of the Fe/S cluster biogenesis cycle forming a binary complex. In this work, the interaction interface of Isu1 was investigated by selective substitutions of amino-acid residues to understand their role in binding to the Jac1 protein. An initial alanine scan was done to limit the number of possible residues subjected to the replacement and to confirm the previously obtained results. Then, MD simulations using the coarse-grained UNRES force field were run for two selected mutants: L63 V72 F94 and L63 V64 G65 D71. The analysis of the dynamics and interaction patterns of the Isu1-Jac1 complexes confirmed that the investigated residues played an important role in their binding.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 417-423
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-3 z 3

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