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    Wyświetlanie 1-4 z 4
    Tytuł:
    Prediction of binding affinities for DNA intercalators by molecular dynamics simulations
    Autorzy:
    Mazerski, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/1965824.pdf
    Data publikacji:
    2001
    Wydawca:
    Politechnika Gdańska
    Tematy:
    molecular modelling
    free energy of binding
    intercalation into DNA
    linear responce method
    free energy perturbation method
    Opis:
    The computer modelling and simulation methods are widely used in rational drug design to obtain information necessary for understanding interactions between a ligand (drug molecule) and its cellular macromolecular target on molecular level. The determination of free energies of binding for ligand-target complexes is one of the crucial points in those studies. In recent years several methods have been proposed to solve this problem. The majority of them use molecular dynamics (MD) simulations. Two, most popular methods: (i) a free energy perturbation method (FEP), and (ii) a linear response (LR) method, are shortly presented in this paper together with their limitations and advantages. In this work I presented the first attempt to use LR approach to 10 anti-tumour agents able to intercalate into DNA. The LR relationship obtained in the present study indicated that in the system studied the electrostatic term has no influence on the free energy of binding. The relationship is now successfully used in our research group in further molecular modelling studies concerning DNA intercalators with similar structure.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 3; 301-310
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Properties of water hydrating the galactolipid and phospholipid bilayers: a molecular dynamics simulation study
    Autorzy:
    Markiewicz, Michał
    Baczyński, Krzysztof
    Pasenkiewicz-Gierula, Marta
    Powiązania:
    https://bibliotekanauki.pl/articles/1038986.pdf
    Data publikacji:
    2015
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    molecular modelling
    hydrogen bonds
    water diffusion
    water dipole orientation
    inter-lamellar water
    Opis:
    Molecular dynamics simulations of 1,2-di-O-acyl-3-O-β-D-galactopyranosyl-sn-glycerol (MGDG) and 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) bilayers were carried out to compare the effect of the lipid head group's chemical structure on the dynamics and orientational order of the water molecules hydrating the bilayer. The effect of the bilayers on the diffusion of water is strong for the neighbouring water molecules i.e., those located not further than 4 Å from any bilayer atom. This is because the neighbouring water molecules are predominantly hydrogen bonded to the lipid oxygen atoms and their mobility is limited to a confined spatial volume. The choline group of DOPC and the galactose group of MGDG affect water diffusion less than the polar groups located deeper in the bilayer interface, and similarly. The latter is an unexpected result since interactions of water with these groups have a vastly different origin. The least affected by the bilayer lipids is the lateral diffusion of unbound water in the bilayer plane (x,y-plane) - it is because the diffusion is not confined by the periodic boundary conditions, whereas that perpendicular to the plane is. Interactions of water molecules with lipid groups also enforce certain orientations of water dipole moments. The profile of an average water orientation along the bilayer normal for the MGDG bilayer differs from that for the DOPC bilayer. In the DOPC bilayer, the ordering effect of the lipid head groups extends further into the water phase than in the MGDG bilayer, whereas inside the bilayer/water interface, ordering of the water dipoles in the MGDG bilayer is higher. It is possible that differences in the profiles of an average water orientation across the bilayer in the DOPC and MGDG bilayers are responsible for differences in the lateral pressure profiles of these bilayers.
    Źródło:
    Acta Biochimica Polonica; 2015, 62, 3; 475-481
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Targets for majority of drugs: G protein-coupled receptors - their structure and interaction with bioligands
    Autorzy:
    Ciarkowski, J.
    Czaplewski, C.
    Pasenkiewicz-Gierula, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/1953953.pdf
    Data publikacji:
    1998
    Wydawca:
    Politechnika Gdańska
    Tematy:
    G protein-coupled receptor
    molecular modelling
    GPCR/bioligand interaction
    molecular dynamics
    membrane
    Opis:
    G protein-coupled receptors (GPCRs) are the most frequent targets for many drugs. They form the largest superfamily of integral membrane proteins, of which more than 1000 members have the following common features: (i) All GPCRs form 7 hydrophobic a-helices of length ~38A (25 amino acids, 7 turns) along a single chain. The consecutive helices alternatively cross the membrane, starting from the extracellular side, so that they form a heptahelical transmembrane domain interwoven with 6 loops, of which the even ones plus the N-terminus create the receptor's extracellular domain while the odd ones plus the C-terminus form its intracellular domain. (ii) All GPCRs are stimulated by diverse extracellular (primary) signals. (iii) Stimulated GPCRs convey the primary signals via their transmembrane and intracellular domains to the cytosolic peripheral heterotrimeric GTP-binding proteins (G proteins), mediating the signal's further transduction to various cellular second messenger systems. A current status of structural studies on GPCRs, consisting of low ~7.5A resolution experimental structures and supplementary molecular modeling, is outlined. Subsequently, some results of authors' own work on studying essential interactions of the V2 vasopressin renal receptor (V2R) with its agonist [Arg8]Vasopressin (AVP) and selected antagonists are presented, as well as their possible impact on the biological signal transduction is discussed. Finally, perspectives for future developments are sketched.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 583-599
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Molecular modelling in the rational design of some anti-tumor and antifungal agents
    Autorzy:
    Mazerski, J.
    Borowski, E.
    Powiązania:
    https://bibliotekanauki.pl/articles/1953949.pdf
    Data publikacji:
    1998
    Wydawca:
    Politechnika Gdańska
    Tematy:
    molecular modelling
    molecular mechanics
    molecular dynamics
    semiempirical methods
    antifungal agents
    anti-tumor agents
    rational design
    Opis:
    In this paper we present our approaches and results concerning application of molecular modelling techniques in the design of new chemotherapeutic agents for the control of eukariotic systems, comprising compounds for the treatment of systemic fungal infections and tumor deseases. In the case of anti-tumor agents we focused our attention on molecular properties of natural and synthetic anthraquinones. In the area of antifungal compounds we adopted two approaches. In one of them we examine molecular nature of undesirable properties of polyene macrolide antifungal antibiotic - amphotericin B using molecular modelling techniques. Another approach was aimed at the development of selective inactivator of glucosamine synthase, a novel target for antifungal compounds. In this problem we have used computational chemistry methods to identify structural features responsible for the selective inactivation of the target enzyme.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 511-550
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-4 z 4

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