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    Wyświetlanie 1-3 z 3
    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:
    Preliminary studies of interaction between nanotubes and toll-like receptors
    Autorzy:
    Mozolewska, M. A.
    Krupa, P.
    Rasulev, B.
    Liwo, A.
    Leszczyński, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/1935817.pdf
    Data publikacji:
    2014
    Wydawca:
    Politechnika Gdańska
    Tematy:
    CNTs
    toll-like receptors
    molecular dynamics
    receptory toll-like
    dynamika molekularna
    Opis:
    Toll-like receptors ( TLR s) are a group of proteins which play a crucial role in the innate immune system. The main function of TLR s is to recognize structurally conserved molecules, which are inserted to the organism of the host by microbes, and then to activate the immune response. Current development of drugs is often connected not only with the drug itself, but also with the way it is delivered into the human body to interact direc tly with the source of the problem. Carbon nanostructures, particularly nanotubes, are one of the car rier molecules of the future. However, there is still no knowledge about the exact mechani sms of toxicity and possible interactions with macromolecules, such as proteins. In our study we tr ied to determine, if the nanotubes could interfere with the innate immune system by interac ting with TLR s. For this purpose, we used the following TLR structures downloaded from the RCSB Protein Data Bank: TLR 2 (3 A 7 C ), TLR 4/ MD (3 FXI ), TLR 5 (3 V 47), TLR 3 (2 A 0 Z ), and the complexes of TLR 1/ TLR 2 (2 Z 7 X ) and TLR 2/ TLR 6 (3 A 79). The preliminary results of our Steered Molecular Dynamics ( SMD ) simulations have shown that nanotubes interact very strongly with the binding pockets of some receptors ( e.g. TLR 2), which results in their binding to these sites without subst antial use of the external force.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 4; 351--355
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Towards mechanisms of nanotoxicity - interaction of gold nanoparticles with proteins and DNA
    Autorzy:
    Krupa, P.
    Mozolewska, M. A.
    Rasulev, B.
    Czaplewski, C.
    Leszczyński, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/1935819.pdf
    Data publikacji:
    2014
    Wydawca:
    Politechnika Gdańska
    Tematy:
    gold nanoparticles
    proteins
    DNA
    molecular dynamics
    nanocząstki złota
    białka
    dynamika molekularna
    Opis:
    Even though most of the existing studies of gold nanoparticles indicate that they are safe to use, some researchers show that specific forms of nanoparticles (e.g. nanorods) are able to destroy the cell membrane and very small nanoparticles (below 37nm in diameter) in high concentration have been deadly for mice. We used the Amber12 package to perform a series of molecular dynamics (MD) simulations of gold nanoparticles with various small proteins important for the human body and a DNA molecule to determine the interactions and consequently the possible toxicity of gold clusters. Lennard-Jones interactions were used to simulate the behavior of gold nanoparticles with biomacromolecules in water with an optimal set of parameters (selected based on a comparison of MD structures and structures computed by DFT). Gold nanoparticle structures were obtained as a result of MD simulations from an initial structure, where gold atoms were at a distance of 10 ̊ A from one another. A predicted BDNA structure of a palindromic sequence‘ CGCATGAGTACGC ’ and a 2 JYK molecule were used as representatives of the DNA molecule. The preliminary results show that, in particular small gold nanoparticles, interact strongly with proteins and DNA by creating stable complexes, which can then cause harmful reactions to the human body when present in high concentration.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 4; 337--341
    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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