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    Wyświetlanie 1-4 z 4
    Tytuł:
    Modelling drug-receptor interactions in an average binding site for NK2
    Autorzy:
    Alagona, G.
    Ghio, C.
    Monti, S.
    Powiązania:
    https://bibliotekanauki.pl/articles/1953954.pdf
    Data publikacji:
    1998
    Wydawca:
    Politechnika Gdańska
    Tematy:
    receptor modelling
    docking
    non covalent interactions
    molecular mechanics
    molecular dynamics
    substituent effects
    Opis:
    A tentative procedure applied to the search for a new antagonist of neurokinin A (NKA) is presented. In parallel a tentative 3-D model of the NK2 receptor was created, using bacteriorhodopsin (BRD) as a template. The residue substitutions were performed in BRD to obtain the sequence for NK2R_H and the seven a-helical segments were optimized forcing the a-helical backbone to match the corresponding aligned parts of BRD, while the arrangements of the side chains were model built based on available site-directed mutagenesis studies. Constrained MM and molecular dynamics simulations were carried out H-bonding a low energy conformer of the known drugs to residues in the receptor site, allowing both the receptor site and drugs to relax. The Connolly surface for each ligand allowed to determine an "average" binding site in which all the low energy conformers of known and prospective drugs were docked and classified according to a statistical index. The whole procedure was repeated exploiting the lately published structure of an actual G protein coupled receptor as a better template, thus producing a cavity in the binding site to directly dock the drugs. Corollary validations of the force fields used are also mentioned. In addition intra- and intermolecular interactions suitable to produce more active drugs were evaluated.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 563-581
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Polymer Reinforced DNAN/RDX Energetic Composites: Interfacial Interactions and Mechanical Properties
    Autorzy:
    Qian, W.
    Chen, X.
    Luo, G.
    Powiązania:
    https://bibliotekanauki.pl/articles/358170.pdf
    Data publikacji:
    2017
    Wydawca:
    Sieć Badawcza Łukasiewicz - Instytut Przemysłu Organicznego
    Tematy:
    energetic composites
    dinitroanisole
    molecular dynamics
    interfacial interactions
    mechanical properties
    Opis:
    2,4-Dinitroanisole (DNAN) has excellent properties as a replacement for 1,3,5-trinitrotoluene (TNT) in melt-cast explosives, and the polymeric modifier used is critical to the mechanical modification of the DNAN/RDX energetic composite. In our research, the typical polymeric modifier acrolein-pentaerythritol resin (APER) was successfully added experimentally to the DNAN/RDX system, and the effects of interfacial interactions on the mechanical properties of these polymers in reinforcing the DNAN/RDX energetic composites were investigated by molecular dynamics simulations, scanning electron microscopy (SEM) and mechanical testing. The results showed that strong attractive interactions exist between the polymer and the explosives, wherein van der Waals forces were found to play the main role. The morphological micro-images also showed tight binding between the polymer/explosive interfaces, which supported the calculated strong interfacial interactions. The mechanical tests confirmed that adding the polymers can obviously reinforce the mechanical strength and toughness of DNAN/RDX systems. The above observations revealed that the cooperative effects of the APER polymer can help to reinforce the interfacial interactions and mechanical properties of DNAN/RDX composites, which is of importance in the formulation and mechanical evaluation of advanced energetic composites.
    Źródło:
    Central European Journal of Energetic Materials; 2017, 14, 3; 726-741
    1733-7178
    Pojawia się w:
    Central European Journal of Energetic Materials
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Fluctuations of kinetic energy at molecular dynamics and the atomic interactions in crystals
    Autorzy:
    Andriyevsky, B.
    Piekarski, J.
    Andriyevska, L.
    Powiązania:
    https://bibliotekanauki.pl/articles/118444.pdf
    Data publikacji:
    2018
    Wydawca:
    Politechnika Koszalińska. Wydawnictwo Uczelniane
    Tematy:
    interatomic interactions
    molecular dynamics
    silicon
    phonon relaxation time
    oddziaływania międzyatomowe
    dynamika molekularna
    krzem
    czas relaksacji fononów
    Opis:
    The calculation method of the molecular dynamics has been applied to study the correlation of the kinetic energy fluctuations and the relaxation time of the velocity autocorrelation function and the phonon relaxation time in a crystal. On the basis of the molecular dynamics data for silicon crystal obtained at different temperatures in the range 200 K – 1000 K the correlation between the kinetic energy fluctuations and the relaxation time of the velocity autocorrelation function has been calculated with the relatively high coefficient of determination R2 = 0.9396. The correlation obtained and the corresponding approach substantiate a use of the kinetic energy fluctuations for the calculation of values related to the heat conductivity in the silicon based semiconductors (coefficients of thermal conductivity and diffusivity).
    Obliczeniowa metoda dynamiki molekularnej została zastosowana do badania korelacji fluktuacji energii kinetycznej i czasu relaksacji autokorelacyjnej funkcji prędkości i czasu relaksacji fononów w krysztale. Na bazie danych dynamiki molekularnej kryształu krzemu otrzymanych w różnych temperaturach w zakresie 200 K – 1000 K została obliczona korelacja fluktuacji energii kinetycznej i czasu relaksacji autokorelacyjnej funkcji prędkości, która cechuje się stosunkowo wysokim współczynnikiem determinacji R2 = 0.9396. Otrzymana korelacja uzasadnia zastosowanie fluktuacji energii kinetycznej do badań obliczeniowych wielkości powiązanych z przewodnością cieplną półprzewodników na bazie krzemu (współczynniki przewodności i dyfuzyjności cieplnej).
    Źródło:
    Zeszyty Naukowe Wydziału Elektroniki i Informatyki Politechniki Koszalińskiej; 2018, 12; 19-24
    1897-7421
    Pojawia się w:
    Zeszyty Naukowe Wydziału Elektroniki i Informatyki Politechniki Koszalińskiej
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Badanie struktury i dynamiki N-terminalnych sekwencji dermorfiny i ich analogów z wykorzystaniem spektroskopii NMR w ciele stałym i rentgenografii
    Studies on the structure and dynamics of N-terminal sequences of dermorphin and their analogs by means of solid state NMR spectroscopy and XRD
    Autorzy:
    Trzeciak-Karlikowska, K.
    Powiązania:
    https://bibliotekanauki.pl/articles/171648.pdf
    Data publikacji:
    2012
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    peptydy opioidowe
    oddziaływania CH-pi
    dynamika molekularna
    oddziaływanie peptyd–fosfolipid
    spektroskopia NMR
    1H Ultra Fast MAS NMR
    PISEMA MAS
    PILGRIM
    XRD
    opioid peptides
    CH-pi interactions
    molecular dynamics
    peptide–phospholipid interaction
    NMR spectroscopy
    Opis:
    Deltorphin I (Tyr-d-Ala-Phe-Asp-Val-Val-Gly-NH_2) and dermorphin (Tyr-d-Ala-Phe- -Gly-Tyr-Pro-Ser-NH_2) are natural opioid peptides that have been isolated from the skin of South American frogs [1]. The presence of d-amino acid is crucial for their biological activity. The synthetic analogs of given heptapeptides containing l-alanine are not analgesics [2]. Analysis of the influence of stereochemistry on molecular packing, dynamics and biological functions of neuropeptides is still important for receptor studies and practical applications (e.g. design of new selective pain killers). Presented research is focused on the structure and dynamics of two N-terminal sequences of dermorphin: tripeptide Tyr-d-Ala-Phe 1, tetrapeptide Tyr-D-Ala-Phe-Gly 2, and their analogs with l-alanine: Tyr-Ala-Phe 3 and Tyr-Ala-Phe-Gly 4, using solid state NMR and X-ray diffraction. This study clearly demonstrates that 1 and 2 crystallized under different conditions to form exclusively one structure [3, 4]. In contrast, tripeptide and tetrapeptide with l-Ala in the sequence very easily form different crystal modifications. Tyr-Ala-Phe 3 crystallizes into two forms: 3a and 3b [5], while Tyr-Ala-Phe-Gly 4 gives three modifications: 4a, 4b and 4c [4]. It seems that one of the factors, which can be important in the preorganization mechanism anticipating the formation of crystals, is the intramolecular CH-đ interaction between aromatic rings of tyrosine and/or phenylalanine and the methyl group of alanine. Such interaction is possible only for d-Ala residue. For l-Ala in the peptide sequence, the methyl group is aligned on the opposite side with respect at least to one of the aromatic groups. It can be further speculated that such internal CH-π contacts can also occur during the interaction of ligand–receptor, making the message sequence of opioid peptides more rigid and finally selective. By employing different NMR experiments (e.g. PISEMA MAS and PILGRIM) it was proven that the main skeleton of analyzed peptides is rigid, whereas significant differences in the molecular motion of the aromatic residues were observed [4, 6]. Solid state 2H NMR spectroscopy of samples with deuterium labeled aromatic rings: Tyrd4-d-Ala-Phe 5, Tyr-d-Ala-Phed5 6, Tyrd4-Ala-Phe 7, Tyr-Ala-Phe^d5 8 was used to analyze the geometry and time scale of the molecular motion. At ambient temperature, the tyrosine ring of sample 5 is rigid and in the sample 6 the phenylalanine ring undergoes a "π -flip". The tyrosine rings of form I of 7 and 8 are static, while the phenylalanine rings of form II of 7 and 8 undergo a fast regime exchange [6]. Variable temperature 2H measurements proved that the tyrosine and phenylalanine rings of two forms of compounds 7 and 8 became more mobile with increasing temperature. In contrast, the aromatic rings of samples 5 and 6 preserve their dynamics regime (static tyrosine and "π -flip" phenylalanine) in a large range of temperatures [6]. The analysis of 13C, 15N labeled tetrapeptide Tyr-D-Ala-Phe-Gly 2’-phospholipid membrane interactions suggests that peptide 2’ is aligned on the surface of the membrane (RFDR MAS) and the sandwich-like π -CH_3-π arrangement of the pharmacophore is preserved (DARR) [7].
    Źródło:
    Wiadomości Chemiczne; 2012, 66, 9-10; 867-891
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-4 z 4

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