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    Wyświetlanie 1-4 z 4
    Tytuł:
    A simple model for predicting the free energy of binding between anthracycline antibiotics and DNA.
    Autorzy:
    Rudnicki, Witold
    Kurzepa, Małgorzata
    Szczepanik, Teresa
    Priebe, Waldemar
    Lesyng, Bogdan
    Powiązania:
    https://bibliotekanauki.pl/articles/1044384.pdf
    Data publikacji:
    2000
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    anthracyclines
    free energy
    modelling
    DNA
    Opis:
    A theoretical model for predicting the free energy of binding between anthracycline antibiotics and DNA was developed using the electron density functional (DFT) and molecular mechanics (MM) methods. Partial DFT-ESP charges were used in calculating the MM binding energies for complexes formed between anthracycline antibiotics and oligodeoxynucleotides. These energies were then compared with experimental binding free energies. The good correlation between the experimental and theoretical energies allowed us to propose a model for predicting the binding free energy for derivatives of anthracycline antibiotics and for quickly screening new anthracycline derivatives.
    Źródło:
    Acta Biochimica Polonica; 2000, 47, 1; 1-9
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Analysis of oxygen binding by hemoglobin on the basis of mean intrinsic thermodynamic quantities
    Autorzy:
    Bordbar, Abdol-Khalegh
    Mousavi, Sayed
    Dazhampanah, Hamid
    Powiązania:
    https://bibliotekanauki.pl/articles/1041216.pdf
    Data publikacji:
    2006
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    cooperativity
    mean intrinsic Gibbs free energy
    linkage phenomena
    hemoglobin
    Opis:
    The binding data for oxygenation of human hemoglobin, Hb, at various temperatures and in the absence and presence of 2,3-diphosphoglycerate, DPG, and inositol hexakis phosphate, IHP, were analyzed for extraction of mean intrinsic Gibbs free energy, ΔGo, enthalpy, ΔHo, and entropy, ΔSo, of binding at various partial oxygen pressures. This method of analysis considers all the protein species present such as dimer and tetramer forms which were not considered by Imai et al. (Imai K et al., 1970, Biochim Biophys Acta 200: 189 - 196) , in their analysis which was based on Adair equation. In this regard, the values of Hill equation parameters were estimated with high precision at all points of the binding curve and used for calculation of ΔGo, ΔHo and ΔSo were also calculated by analysis of ΔGo values at various temperatures using van't Hoff equation. The results represent the enthalpic nature of the cooperativity in Hb oxygenation and the compensation effect of intrinsic entropy. The interpretation of results also to be, into account the decrease of the binding affinity of sites for oxygen in the presence of DPG and IHP without any considerable changes in the site - site interaction (extent of cooperativity). In other words, the interactions between bound ligands, organic phosphates and oxygen, are more due to a decreasing binding affinity and not to the reduction of the cooperative interaction between sites. The results also document the more heterotropic effect of IHP compared to DPG.
    Źródło:
    Acta Biochimica Polonica; 2006, 53, 3; 563-568
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The function of complexes between the outer mitochondrial membrane pore (VDAC) and the adenine nucleotide translocase in regulation of energy metabolism and apoptosis.
    Autorzy:
    Vyssokikh, Mikhail
    Brdiczka, Dieter
    Powiązania:
    https://bibliotekanauki.pl/articles/1043614.pdf
    Data publikacji:
    2003
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    cytochrome c
    hexokinase
    free energy
    creatine kinase
    permeability transition pore
    Bax
    Opis:
    The outer mitochondrial membrane pore (VDAC) changes its structure either voltage-dependently in artificial membranes or physiologically by interaction with the adenine nucleotide translocase (ANT) in the c-conformation. This interaction creates contact sites and leads in addition to a specific organisation of cytochrome c in the VDAC-ANT complexes. The VDAC structure that is specific for contact sites generates a signal at the surface for several proteins in the cytosol to bind with high capacity, such as hexokinase, glycerol kinase and Bax. If the VDAC binding site is not occupied by hexokinase, the VDAC-ANT complex has two critical qualities: firstly, Bax gets access to cytochrome c and secondly the ANT is set in its c-conformation that easily changes conformation into an unspecific channel (uniporter) causing permeability transition. Activity of bound hexokinase protects against both, it hinders Bax binding and employs the ANT as anti-porter. The octamer of mitochondrial creatine kinase binds to VDAC from the inner surface of the outer membrane. This firstly restrains interaction between VDAC and ANT and secondly changes the VDAC structure into low affinity for hexokinase and Bax. Cytochrome c in the creatine kinase complex will be differently organised, not accessible to Bax and the ANT is run as anti-porter by the active creatine kinase octamer. However, when, for example, free radicals cause dissociation of the octamer, VDAC interacts with the ANT with the same results as described above: Bax-dependent cytochrome c release and risk of permeability transition pore opening.
    Źródło:
    Acta Biochimica Polonica; 2003, 50, 2; 389-404
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Molecular simulation of adsorption from dilute solutions
    Autorzy:
    Billes, Werner
    Tscheliessnig, Rupert
    Fischer, Johann
    Powiązania:
    https://bibliotekanauki.pl/articles/1041376.pdf
    Data publikacji:
    2005
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    dilute solutions
    potential of mean force
    adsorption
    change of free energy
    molecular simulation
    Opis:
    Adsorption of biomolecules on surfaces is a perennial and general challenge relevant to many fields in biotechnology. A change of the Helmholtz free energy ΔA takes place when a molecule becomes adsorbed out of a bulk solution. The purpose of our investigations is to explore routes for the calculation of ΔA by molecular simulations. ΔA can be obtained both by integration over the mean force on a molecule and via the local density. It turns out that the route via the potential of mean force prevails over the latter due to better consistency. In this work we present results for systems of 1-centre and 2-centre Lennard-Jones mixtures at a 9/3 Lennard-Jones wall.
    Źródło:
    Acta Biochimica Polonica; 2005, 52, 3; 685-689
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-4 z 4

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