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Wyświetlanie 1-15 z 144
Tytuł:
Zinc ion adsorption on carbon nanotubes in an aqueous solution
Autorzy:
Ansari, A.
Mehrabian, M. A.
Hashemipour, H.
Powiązania:
https://bibliotekanauki.pl/articles/779155.pdf
Data publikacji:
2012
Wydawca:
Zachodniopomorski Uniwersytet Technologiczny w Szczecinie. Wydawnictwo Uczelniane ZUT w Szczecinie
Tematy:
adsorption
molecular dynamics simulation
heavy metals
electrostatic force
interaction energy
functional groups
Opis:
The literature devoted to numerical investigation of adsorption of heavy metal ions on carbon nanotubes is scarce. In this paper molecular dynamics is used to simulate the adsorption process and to investigate the effect of the infl uencing parameters on the rate of adsorption. The predictions of the molecular dynamics simulation show that the adsorption process is improved with increasing the temperature, pH of solution, the mass of nanotubes, and surface modifi cation of CNT using hydroxyl and carboxyl functional groups. The results predicted by the model are compared with the experimental results available in the literature; the close agreement validates the accuracy of the predictions. This study reveals that the water layers around the carbon nanotubes and the interaction energies play important roles in the adsorption process. The study also shows that electrostatic force controls the attraction of zinc ions on the nanotube sidewall.
Źródło:
Polish Journal of Chemical Technology; 2012, 14, 3; 29-37
1509-8117
1899-4741
Pojawia się w:
Polish Journal of Chemical Technology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Zastosowanie metod dynamiki molekularnej w badaniach nad układami z wiązaniami wodorowymi
An application of molecular dynamics methods in investigations of systems with hydrogen bonds
Autorzy:
Jezierska, A.
Panek, J. J.
Powiązania:
https://bibliotekanauki.pl/articles/172356.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
CPMD
dynamika molekularna Cara-Parrinello
klasyczna dynamika molekularna
wewnątrzcząsteczkowe wiązanie wodorowe
międzycząsteczkowe wiązanie wodorowe
zasada Schiffa
zasada Mannicha
N-tlenki
białka
Car-Parrinello molecular dynamics
classical MD
intramolecular HB
intermolecular HB
Schiff base
Mannich base
N-oxides
proteins
Opis:
Modern computational chemistry offers a wide variety of methods allowing us to investigate very complex systems. In the current study, we would like to focus on ab initio and classical molecular dynamics to show their applications in our research. Car-Parrinello molecular dynamics (CPMD) was carried out to study compounds possessing intra- and intermolecular hydrogen bonds. Our simulations were performed in vacuum, in solvent and in crystalline phase. It is well known that intramolecular hydrogen bonding stabilizes 3D structure of molecules. The strength of the bonding and its features are influenced by inductive and steric effects. Our short overview on CPMD application to systems with intramolecular HB we start from Schiff and Mannich bases -model compounds to investigate intramolecular hydrogen bonding. Other examples reported here derive from the class of N-oxide type compounds. Special attention was devoted to another representative structure in such investigations – picolinic acid N-oxide. In some examples listed above proton transfer phenomena occurred making these compounds interesting objects for future excited state studies. Aliphatic boronic acid was used as a model example to study intermolecular hydrogen bonds based on CPMD method. Further, classical molecular dynamics was applied to investigate proteins. Here, we would like to report our results for two biomolecules. The first one is proteinase K for which the impact of mercury(II) on its catalytic center was studied. The second one is streptavidin. For the latter one its complexes with biotinylated ligands were investigated. We close our review with a paragraph describing further development and perspectives related to CPMD method.
Źródło:
Wiadomości Chemiczne; 2017, 71, 7-8; 473-495
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Wykorzystanie dynamiki molekularnej w badaniach szkieł
Application of molecular dynamics in examination of glasses
Autorzy:
Goj, P.
Powiązania:
https://bibliotekanauki.pl/articles/169158.pdf
Data publikacji:
2018
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Ceramiki i Materiałów Budowlanych
Tematy:
dynamika molekularna
badania więźby szkieł
symulacje komputerowe
szkła krzemowo-sodowe
molecular dynamics
glass network examination
computer simulations
sodium silicate glasses
Opis:
Klasyczna dynamika molekularna MD jest jedną z technik symulacji komputerowych wieloatomowych lub wielocząsteczkowych układów. Pozwala na badanie struktury oraz właściwości zarówno materiałów krystalicznych, jak i amorficznych. Opiera się na rozwiązywaniu numerycznym klasycznych równań ruchu. Nie tylko uzupełnia badania eksperymentalne, ale jest również narzędziem pozwalającym na badanie budowy materiałów na poziomie nieosiągalnym konwencjonalnymi technikami. W celu przedstawienia klasycznej dynamiki molekularnej wykonano symulacje dwóch szkieł 80SiO2-20Na2O i 85SiO2-15Na2O [%mol]. Otrzymane wyniki dobrze zgadzały się z obecnym stanem wiedzy. Wykonane symulacje świadczą o tym, że technika ta jest niezwykle użyteczna przy poznawaniu struktury szkieł. Wykorzystując tę technikę, można przewidywać wpływ modyfikatorów na więźbę szkła, a przez to możliwe jest wskazywanie kierunku dalszych badań oraz optymalizacja składów chemicznych.
Molecular dynamics MD is one of computer simulation methods of multiatomic or multimolecular systems. It allows to examination of structure and properties both crystalline and amorphous materials. This technique consists of the numerical solution of the classical equation of motion. It complements not only experimental methods but also it is tool make possible examination of material structure on the unavailable level for conventional methods. In order to introduce to molecular dynamics, the simulations of two glasses 80SiO2‑20Na2O and 85SiO2-15Na2O [%mol] were performed. Obtained results corresponds well to the actual state of knowledge. Performed simulation testify that this technique is a very useful to examine glass structure. Using this method, it is possible to predict influence of modifiers on glass network, it’s make possible indication research direction and optimization of chemical composition.
Źródło:
Szkło i Ceramika; 2018, R. 69, nr 1, 1; 12-15
0039-8144
Pojawia się w:
Szkło i Ceramika
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Wpływ benzo[a]pirenu na własności fosfolipidów surfaktantu płucnego: modelowa analiza toksyczności spalin silników Diesla
Influence of benzo[a]pyrene on properties of the lung surfactant phospholipids: model analysis of diesel exhaust gases toxicity
Autorzy:
Sosnowski, T.
Koliński, M.
Gradoń, L.
Powiązania:
https://bibliotekanauki.pl/articles/2070891.pdf
Data publikacji:
2010
Wydawca:
Stowarzyszenie Inżynierów i Techników Mechaników Polskich
Tematy:
spaliny Diesla
toksyczność
surfaktant płucny
dynamika molekularna
diesel exhaust gases
toxicity
lung surfactant
molecular dynamics
Opis:
Doświadczalnie (waga Langmuird) i teoretycznie (dynamika molekularna) badano oddziaływania fizykochemiczne między benzo[a]pirenem (BAP) i głównym składnikiem surfaktantu płucnego, DPPC. Odnotowano zmiany dynamicznego napięcia powierzchniowego i ściśliwości filmu DPPC na powierzchni woda - powietrze, które wyjaśniono w oparciu o mechanizm wbudowywania się molekuł BAP w monowarstwę DPPC. Przyjmując, że podobne zjawiska przebiegają w naturalnym układzie surfaktantu płucnego, wyniki sugerują jedną z możliwych przyczyn toksyczności spalin silników Diesla.
Physicochemical interactions between benzo[a]pyrene (BAP) and a basic constituent of lung surfactant, DPPC, were studied experimentally (Lang-muir balance) and theoretically (molecular dynamic approach). Changes in dynamic surface tension and compressibility of DPPC film at air - water interface were observed and explained by the incorporation of BAP molecules into DPPC monolayer. Similar phenomena can be of importance during oscillations of lung surface during breathing, so the results suggest a potential mechanism of health effects from diesel exhaust gases inhalation.
Źródło:
Inżynieria i Aparatura Chemiczna; 2010, 2; 115-116
0368-0827
Pojawia się w:
Inżynieria i Aparatura Chemiczna
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Właściwości wewnątrzcząsteczkowych wiązań wodorowych w wybranych N-tlenkach pochodnych chinoliny
Intramolecular hydrogen bonds properties in selected N-oxides of quinoline derivatives
Autorzy:
Jezierska, Aneta
Panek, Jarosław J.
Błaziak, Kacper
Powiązania:
https://bibliotekanauki.pl/articles/171511.pdf
Data publikacji:
2019
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
DFT
teoria funkcjonału gęstości
MP2
metoda rachunku zaburzeń drugiego rzędu Møllera-Plesseta
CPMD
dynamika molekularna Cara-Parrinello
wewnątrzcząsteczkowe wiązanie wodorowe
N-tlenki pochodnych chinoliny
density functional theory
Møller-Plesset second order perturbation method
Car-Parrinello molecular dynamics
intramolecular HB
N-oxides of quinoline derivatives
Opis:
In the current article we would like to summarize our research shedding light onto properties of intramolecular hydrogen bonds present in N-oxide quinoline derivatives. The compounds for the current study were chosen to contain diverse types of hydrogen bonds. Therefore, in the current study we analyze three kinds of hydrogen bonding and their properties. It is well known, that the presence of intramolecular hydrogen bonds stabilizes conformations of molecules. Substituent effects (inductive and steric) influence the strength of the H-bonding as well as its features. Moreover, the intramolecular hydrogen bond in the studied N-oxides belongs to the family of resonance assisted hydrogen bonds (RAHB). Our short overview presents the summary of results obtained for twelve N-oxides of quinoline derivatives. Quantum-chemical simulations were performed on the basis of static models (classical DFT and MP2 approaches) as well as ab initio molecular dynamics (Car-Parrinello MD). The metadynamics method was applied to reproduce the maps of free energy for the motion of the bridged proton. The computations were performed in the gas and in the crystalline phases. Electronic ground state is a natural framework in which chemical compounds exist most of the time. However, in many chemical species we observe a spontaneous internal reorganization of their chemical bonds and atoms e.g. proton transfer phenomenon and the appearance of tautomeric forms already in the ground state. Therefore, it was interesting to investigate some N-oxides in the excited electron state knowing that they exhibit excited- state-induced proton transfer (ESIPT effect). At the end of the article we draw some conclusions related to the intramolecular H-bond properties present in the discussed N-oxides of quinoline derivatives.
Źródło:
Wiadomości Chemiczne; 2019, 73, 1-2; 75-95
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Właściwości czasowo-rozdzielcze słabych międzycząsteczkowych wiązań wodorowych C-H···F
Time-resolved properties of intermolecular C-H···F hydrogen bonds
Autorzy:
Polańska, Marta
Rodziewicz, Paweł
Powiązania:
https://bibliotekanauki.pl/articles/27310029.pdf
Data publikacji:
2023
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
wiązanie wodorowe
teoria funkcjonału gęstości
dynamika molekularna Cara i Parrinello
hydrogen bond
density functional theory
Car-Parrinello molecular dynamics
Opis:
The hydrogen bond is one of the most important and interesting phenomena in nature. In this publication we will shed light on the discovery of hydrogen bond and a time evolution of its definition in the last 100 years. Both structural and spectroscopic parameters of the hydrogen bond will be discussed. A special focus will be given to the latest IUPAC definition of the hydrogen bond and its consequences to scientific research. The main aim of this study is to highlight theoretical studies based on first principles calculations and molecular dynamics simulations which not only support experimental results but also provide parameters which are crucial to understand the nature of hydrogen bonds. Particular attention will be given to methods and theoretical ideas used in the computational studies of hydrogen bonds. Utilizing static DFT/ab initio calculations and molecular dynamics simulations enables comparison of different binding energies and studying time evolution of the hydrogen-bonded molecular system on the atomistic level. We will discuss time-resolved properties of weak intermolecular hydrogen bonds, using as an example C-H···F containing model systems, namely F3CH*(HF)n molecular complexes and (F3CH)2-4 aggregates.
Źródło:
Wiadomości Chemiczne; 2023, 77, 9-10; 899--919
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Water film structure during rupture as revealed by MDS image analysis
Autorzy:
Truong, N. T.
Dang, L. X.
Lin, C.-L.
Wang, X.
Miller, J. D.
Powiązania:
https://bibliotekanauki.pl/articles/110251.pdf
Data publikacji:
2018
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
image processing
molecular dynamics simulation
film stability
molecular porosity
Opis:
The structure of thin water films during the rupture process was investigated by a new approach, which combines molecular dynamics simulation (MDS) with image processing analysis. The analysis procedure was developed to convert MDS trajectories to readable 3D images. The water films were studied at different thicknesses by MDS to determine the critical thickness at which the film ruptures. The potential energy of each specific film thickness during the simulation time was analyzed, and the results showed that the potential energy of stable films remained unchanged while the potential energy kept decreasing for films which ruptured during the simulation time. By applying the new procedure, the molecular porosity, which is defined as the void fraction between the volume of molecular pores in the water film and the total volume of the water film, was calculated. The results of molecular porosity for different film thicknesses during the simulation time suggested a critical molecular porosity as 49%. In other words, stable films have a molecular porosity of less than 49%. If a water film has a molecular porosity greater than 49%, rupture occurs during the simulation.
Źródło:
Physicochemical Problems of Mineral Processing; 2018, 54, 4; 1060-1069
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
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:
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
Tytuł:
Thermodynamic Properties of Potassium Oxide (K₂O) Nanoparticles by Molecular Dynamics Simulations
Autorzy:
Guder, V.
Senturk Dalgic, S.
Powiązania:
https://bibliotekanauki.pl/articles/1032027.pdf
Data publikacji:
2017-03
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
65.80.-g
Opis:
Potassium oxide (K₂O) is a reagent for testing the presence of other compounds in chemical reactions. It is also used in compounding cement and in glass making. However properties of K₂O in nanoscale are still unclear. In this work, thermodynamic properties of spherical K₂O nanoparticles have been investigated. Size dependent cohesive energy, melting point and glass transition temperature have been computed for different sizes of K₂O nanoparticles by molecular dynamics simulations. Thermal expansion coefficients of nanoparticles at zero pressure and various temperatures have been also calculated. Melting point depression for K₂O nanoparticles was determined. The significant change in cohesive energy was obtained for particles smaller than 5.4 nm. The presented model is successful in understanding the size-dependent thermodynamics of spherical K₂O nanoparticles. Theoretical investigations of the thermal properties of K₂O nanoparticles have not been presented previously.
Źródło:
Acta Physica Polonica A; 2017, 131, 3; 490-494
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Thermal Expansion of Explosive Molecular Crystals: Anisotropy and Molecular Stacking
Autorzy:
Qian, W.
Zhang, C.
Xiong, Y.
Zong, H.
Zhang, W.
Shu, Y.
Powiązania:
https://bibliotekanauki.pl/articles/358262.pdf
Data publikacji:
2014
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Przemysłu Organicznego
Tematy:
energetic material
anisotropic thermal expansion
molecular stacking
molecular dynamics simulation
density functional theory method
Opis:
Molecular dynamics simulations of three typical explosive crystals, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), 1,1-diamino-2,2- dinitroethene (FOX-7) and 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), were carried out under NPT ensemble and selected force field. The equilibrium structures at elevated temperatures were obtained, which show that the stacking behaviour of the molecules does not change with temperature. The coefficient of thermal expansion (CTE) values were calculated by linear fitting methods, and the results show that the CTE values are close to the experimental results and are anisotropic. The total energies of the cells expanding along each single crystallographic axis were calculated by the periodic density functional theory method, indicating that the energy change rates are anisotropic, and correlation equations of the energy change vs. CTE values were established. The essence of the anisotropy of the explosive crystal’s thermal expansion was compared and elucidated.
Źródło:
Central European Journal of Energetic Materials; 2014, 11, 1; 59-81
1733-7178
Pojawia się w:
Central European Journal of Energetic Materials
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Theoretical studies of binding modes of two covalent inhibitors of cysteine proteases.
Autorzy:
Drabik, Piotr
Politowska, Ewa
Czaplewski, Cezary
Kasprzykowski, Franciszek
Łankiewicz, Leszek
Ciarkowski, Jerzy
Powiązania:
https://bibliotekanauki.pl/articles/1044228.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
cysteine proteases
covalent protease inhibitors
constrained simulated annealing
papain
molecular dynamics
Opis:
Physiological and pathological roles of cysteine proteases make them important targets for inhibitor development. Although highly potent inhibitors of this group of enzymes are known, their major drawback is a lack of sufficient specificity. Two cysteine protease covalent inhibitors, viz. (i) Z-RL-deoxo-V-peptide-epoxysuccinyl hybrid, and (ii) Z-RLVG-methyl-, have been developed and modeled in the catalytic pocket of papain, an archetypal thiol protease. A number of configurations have been generated and relaxed for each system using the AMBER force field. The catalytic pockets S3 and S4 appear rather elusive in view of the observed inhibitors' flexibility. This suggest rather limited chances for the development of selective structure-based inhibitors of thiol proteases, designed to exploit differences in the structure of catalytic pockets of various members of this family.
Źródło:
Acta Biochimica Polonica; 2000, 47, 4; 1061-1066
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Theoretical Predictions of Lattice Parameters and Mechanical Properties of Pentaerythritol Tetranitrate under the Temperature and Pressure by Molecular Dynamics Simulations
Autorzy:
Tan, J.J.
Hu, C.
Li, Y.
Ge, N.
Chen, T.
Ji, G.
Powiązania:
https://bibliotekanauki.pl/articles/1033453.pdf
Data publikacji:
2017-02
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
molecular dynamics
lattice parameter
equation of state
elasticity
mechanical properties
Opis:
Molecular dynamics simulations with condensed-phase optimized molecular potentials for atomistic simulation studies force field are performed to investigate the structure, equation of state, and mechanical properties of high energetic material pentaerythritol tetranitrate. The equilibrium structural parameters, pressure-volume relationship and elastic constants at ambient conditions agree excellently with experiments. In addition, fitting the pressure-volume data to the Birch-Murnaghan or Murnaghan equation of state, the bulk modulus B₀ and its first pressure derivative B'₀ are obtained. Moreover, the elastic constants are calculated in the pressure range of 0-10 GPa at room temperature and in the temperature range of 200-400 K at the standard pressure, respectively. By the Voigt-Reuss-Hill approximation, the mechanical properties such as bulk modulus B, shear modulus G, and the Young modulus E are also obtained successfully. The predicted physical properties under temperature and pressure can provide powerful guidelines for the engineering application and further experimental investigations.
Źródło:
Acta Physica Polonica A; 2017, 131, 2; 318-323
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers.
Autorzy:
Woźniak-Celmer, Edyta
Ołdziej, Stanisław
Ciarkowski, Jerzy
Powiązania:
https://bibliotekanauki.pl/articles/1044161.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein phosphatase inhibitors
constrained simulated annealing
protein phosphatase 1A and 2B
molecular dynamics
homology modeling
Opis:
The oligomeric metalloenzymes protein phosphatases dephosphorylate OH groups of Ser/Thr or Tyr residues of proteins whose actions depend on the phosphorus signal. The catalytic units of Ser/Thr protein phosphatases 1, 2A and 2B (PP1c, PP2Ac and PP2Bc, respectively), which exhibit about 45% sequence similarity, have their active centers practically identical. This feature strongly suggests that the unknown structure of PP2Ac could be successfully homology-modeled from the known structures of PP1c and/or PP2Bc. Initially, a theoretical model of PP1c was built, including a phosphate and a metal dication in its catalytic site. The latter was modeled, together with a structural hydroxyl anion, as a triangular pseudo-molecule (Zno or Mno), composed of two metal cations (double Zn2+ or Mn2+, respectively) and the OH- group. To the free PP1c two inhibitor sequences R29RRRPpTPAMLFR40 of DARPP-32 and R30RRRPpTPATLVLT42 of Inhibitor-1, and two putative substrate sequences LRRApSVA and QRRQRKpRRTI were subsequently docked. In the next step, a free PP2Ac model was built via homology re-modeling of the PP1c template and the same four sequences were docked to it. Thus, together, 20 starting model complexes were built, allowing for combination of the Zno and Mno pseudo-molecules, free enzymes and the peptide ligands docked in the catalytic sites of PP1c and PP2Ac. All models were subsequently subjected to 250-300 ps molecular dynamics using the AMBER 5.0 program. The equilibrated trajectories of the final 50 ps were taken for further analyses. The theoretical models of PP1c complexes, irrespective of the dication type, exhibited increased mobilities in the following residue ranges: 195-200, 273-278, 287-209 for the inhibitor sequences and 21-25, 194-200, 222-227, 261, 299-302 for the substrate sequences. Paradoxically, the analogous PP2Ac models appeared much more stable in similar simulations, since only their "prosegment" residues 6-10 and 14-18 exhibited an increased mobility in the inhibitor complexes while no areas of increased mobility were found in the substrate complexes. Another general observation was that the complexes with Mn dications were more stable than those with Zn dications for both PP1c and PP2Ac units.
Źródło:
Acta Biochimica Polonica; 2001, 48, 1; 35-52
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The structure of rarefied and densified PbSiO3 glass: a molecular dynamics study
Autorzy:
Bergmański, G.
Białoskórski, M.
Rychcik-Leyk, M.
Witkowska, A.
Rybicki, J.
Mancini, G.
Frigio, S.
Feliziani, S.
Powiązania:
https://bibliotekanauki.pl/articles/1954073.pdf
Data publikacji:
2004
Wydawca:
Politechnika Gdańska
Tematy:
oxide glasses
structure of glasses
ring analysis
MD simulations
Opis:
The paper is a molecular dynamics (MD) study of the structure of rarefied and densified lead-silicate glass of the PbSiO3 composition. Simulations have been performed in the constant volume regime for systems with densities of 3000, 4000, 5000, 5970 (normal density), 7000 and 8000kg/m3, using a two-body potential (Born-Mayer repulsive forces and Coulomb forces due to full ionic charges). All the systems were initially prepared as well equilibrated hot melts, and then slowly cooled down to 300K. The information on short-range correlations was obtained in a conventional way (from radial and angular distribution functions), while the middle-range order was studied via cation-anion ring analysis, using our new programme for basal ring determination. The structure of rarefied and densified glasses is compared with the structure of the same glasses under normal conditions. Moreover, the present results on PbSiO3 glass are compared with the corresponding data previously obtained for rarefied and densified PbGeO3 glass (Rybicki et al. 2001 Comput. Met. Sci. Technol. 7 91-112).
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2004, 8, 3; 393-412
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-15 z 144

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