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    Wyświetlanie 1-13 z 13
    Tytuł:
    Molecular dynamics simulation studies of lipid bilayer systems.
    Autorzy:
    Pasenkiewicz-Gierula, Marta
    Murzyn, Krzysztof
    Róg, Tomasz
    Czaplewski, Cezary
    Powiązania:
    https://bibliotekanauki.pl/articles/1044295.pdf
    Data publikacji:
    2000
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    phosphatidylethanolamine
    cholesterol
    vasopressin receptor,molecular dynamics simulations
    magainin-2
    phosphatidylcholine
    phosphatidylglycerol
    Opis:
    The main structural element of biological membranes is a liquid-crystalline lipid bilayer. Other constituents, i.e. proteins, sterols and peptides, either intercalate into or loosely attach to the bilayer. We applied a molecular dynamics simulation method to study membrane systems at various levels of compositional complexity. The studies were started from simple lipid bilayers containing a single type phosphatidylcholine (PC) and water molecules (PC bilayers). As a next step, cholesterol (Chol) molecules were introduced to the PC bilayers (PC-Chol bilayers). These studies provided detailed information about the structure and dynamics of the membrane/water interface and the hydrocarbon chain region in bilayers built of various types of PCs and Chol. This enabled studies of membrane systems of higher complexity. They included the investigation of an integral membrane protein in its natural environment of a PC bilayer, and the antibacterial activity of magainin-2. The latter study required the construction of a model bacterial membrane which consisted of two types of phospholipids and counter ions. Whenever published experimental data were available, the results of the simulations were compared with them.
    Źródło:
    Acta Biochimica Polonica; 2000, 47, 3; 601-611
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions.
    Autorzy:
    Róg, Tomasz
    Murzyn, Krzysztof
    Pasenkiewicz-Gierula, Marta
    Powiązania:
    https://bibliotekanauki.pl/articles/1043453.pdf
    Data publikacji:
    2003
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    membrane hydration
    cut-off distance
    chain order
    phospholipid
    lateral diffusion
    particle-mesh Ewald
    Opis:
    Molecular dynamics (MD) simulations complement experimental methods in studies of the structure and dynamics of lipid bilayers. The choice of algorithms employed in this computational method represents a trade-off between the accuracy and real calculation time. The largest portion of the simulation time is devoted to calculation of long-range electrostatic interactions. To speed-up evaluation of these interactions, various approximations have been used. The most common ones are the truncation of long-range interactions with the use of cut-offs, and the particle-mesh Ewald (PME) method. In this study, several multi-nanosecond cut-off and PME simulations were performed to establish the influence of the simulation protocol on the bilayer properties. Two bilayers were used. One consisted of neutral phosphatidylcholine molecules. The other was a mixed lipid bilayer consisting of neutral phosphatidylethanolamine and negatively charged phosphatidylglycerol molecules. The study shows that the cut-off simulation of a bilayer containing charge molecules generates artefacts; in particular the mobility and order of the charged molecules are vastly different from those determined experimentally. In the PME simulation, the bilayer properties are in general agreement with experimental data. The cut-off simulation of bilayers containing only uncharged molecules does not generate artefacts, nevertheless, the PME simulation gives generally better agreement with experimental data.
    Źródło:
    Acta Biochimica Polonica; 2003, 50, 3; 789-798
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    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:
    The geometry of intercalation complex of antitumor mitoxantrone and ametantrone with DNA: Molecular dynamics simulations
    Autorzy:
    Mazerski, Jan
    Martelli, Sante
    Borowski, Edward
    Powiązania:
    https://bibliotekanauki.pl/articles/1044846.pdf
    Data publikacji:
    1998
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Źródło:
    Acta Biochimica Polonica; 1998, 45, 1; 1-11
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The role of side chains in the interaction of new antitumor pyrimidoacridinetriones with DNA: Molecular dynamics simulations.
    Autorzy:
    Mazerski, Jan
    Antonini, Ippolito
    Martelli, Sante
    Powiązania:
    https://bibliotekanauki.pl/articles/1044390.pdf
    Data publikacji:
    2000
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    molecular dynamics simulations
    structure of intercalation complex
    pyrimidoacridinetrione antitumor agents
    role of side chain(s)
    Opis:
    Pyrimidoacridinetriones (PATs) are a new group of highly active antitumor compounds. It seems reasonable to assume that, like for some other acridine derivatives, intercalation into DNA is a necessary, however not a sufficient condition for antitumor activity of these compounds. Rational design of new compounds of this chemotype requires knowledge about the structure of the intercalation complex, as well as about interactions responsible for its stability. Computer simulation techniques such as molecular dynamics (MD) may provide valuable information about these problems. The results of MD simulations performed for three rationally selected PATs are presented in this paper. The compounds differ in the number and position of side chains. Each of the compounds was simulated in two systems: i) in water, and ii) in the intercalation complex with the dodecamer duplex d(GCGCGCGCGCGC)2. The orientation of the side chain in relation to the ring system is determined by the position of its attachment. Orientation of the ring system inside the intercalation cavity depends on the number and position of side chain(s). The conformations of the side chain(s) of all PATs studied in the intercalation complex were found to be very similar to those observed in water.
    Źródło:
    Acta Biochimica Polonica; 2000, 47, 1; 47-57
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Effect of antisense peptide binding on the dimerization of human cystatin C - gel electrophoresis and molecular modeling studies.
    Autorzy:
    Stachowiak, Krystyna
    Rodziewicz-Motowidło, Sylwia
    Sosnowska, Renata
    Kasprzykowski, Franciszek
    Łankiewicz, Leszek
    Grubb, Anders
    Grzonka, Zbigniew
    Powiązania:
    https://bibliotekanauki.pl/articles/1043334.pdf
    Data publikacji:
    2004
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    dimerization
    antisense peptides
    human cystatin C
    molecular dynamics
    Opis:
    Human cystatin C (HCC) shows a tendency to dimerize. This process is particularly easy in the case of the L68Q HCC mutant and might lead to formation of amyloid deposits in brain arteries of young adults. Our purpose was to find ligands of monomeric HCC that can prevent its dimerization. Eleven antisense peptide ligands of monomeric HCC were designed and synthesized. The influence of these ligands on HCC dimerization was studied using gel electrophoresis and molecular modeling methods. The results suggest that all the designed peptides interact with monomeric HCC facilitating its dimerization rather than preventing it.
    Źródło:
    Acta Biochimica Polonica; 2004, 51, 1; 153-160
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The effect of the Glu342Lys mutation in α1-antitrypsin on its structure, studied by molecular modelling methods.
    Autorzy:
    Jezierski, Grzegorz
    Pasenkiewicz-Gierula, Marta
    Powiązania:
    https://bibliotekanauki.pl/articles/1044164.pdf
    Data publikacji:
    2001
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    serpins
    protein structure
    energy minimisation
    molecular dynamics simulation
    Opis:
    The structure of native α1-antitrypsin, the most abundant protease inhibitor in human plasma, is characterised primarily by a reactive loop containing the centre of proteinase inhibition, and a β-sheet composed of five strands. Mobility of the reactive loop is confined as a result of electrostatic interactions between side chains of Glu342 and Lys290, both located at the junction of the reactive loop and the β structure. The most common mutation in the protein, resulting in its inactivation, is Glu342→Lys, named the Z mutation. The main goal of this work was to investigate the influence of the Z mutation on the structure of α1-antitrypsin. Commonly used molecular modelling methods have been applied in a comparative study of two protein models: the wild type and the Z mutant. The results indicate that the Z mutation introduces local instabilities in the region of the reactive loop. Moreover, even parts of the protein located far apart from the mutation region are affected. The Z mutation causes a relative change in the total energy of about 3%. Relatively small root mean square differences between the optimised structures of the wild type and the Z mutant, together with detailed analysis of 'conformational searching' process, lead to the hypothesis that the Z mutation principally induces a change in the dynamics of α1-antitrypsin.
    Źródło:
    Acta Biochimica Polonica; 2001, 48, 1; 65-75
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Free energy of helix propagation in short polyalanine chains determined from peptide growth simulations of La3+-binding model peptides. Comparison with experimental data
    Autorzy:
    Maciejczyk, Maciej
    Hermans, Jan
    Bierzyński, Andrzej
    Powiązania:
    https://bibliotekanauki.pl/articles/1041277.pdf
    Data publikacji:
    2006
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    thermodynamics
    peptide
    helix-coil equilibrium
    thermodynamic integration
    molecular dynamics
    Opis:
    Molecular dynamics (MD) is, at present, a unique tool making it possible to study, at the atomic level, conformational transitions in peptides and proteins. Nevertheless, because MD calculations are always based on a more or less approximate physical model, using a set of approximate parameters, their reliability must be tested by comparison with experimental data. Unfortunately, it is very difficult to find a peptide system in which conformational transitions can be studied both experimentally and using MD simulations so that a direct comparison of the results obtained in both ways could be made. Such a system, containing a rigid α-helix nucleus stabilized by La3+ coordination to a 12-residue sequence taken from an EF-hand protein has recently been used to determine experimentally the helix propagation parameters in very short polyalanine segments (Goch et al. (2003) Biochemistry 42: 6840-6847). The same parameters were calculated here for the same peptide system using the peptide growth simulation method with, alternatively, charmm 22 and cedar potential energy functions. The calculated free energies of the helix-coil transition are about two times too large for cedar and even three times too large for charmm 22, as compared with the experimental values. We suggest that these discrepancies have their origin in the incorrect representation of unfolded peptide backbone in solution by the molecular mechanics force fields.
    Źródło:
    Acta Biochimica Polonica; 2006, 53, 1; 121-130
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Molecular docking-based test for affinities of two ligands toward vasopressin and oxytocin receptors.
    Autorzy:
    Ślusarz, Rafał
    Kaźmierkiewicz, Rajmund
    Giełdoń, Artur
    Lammek, Bernard
    Ciarkowski, Jerzy
    Powiązania:
    https://bibliotekanauki.pl/articles/1044173.pdf
    Data publikacji:
    2001
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    simulated annealing
    bioligand docking
    GPCR receptor/bioligand interaction
    molecular dynamics
    Opis:
    Molecular docking simulations are now fast developing area of research. In this work we describe an effective procedure of preparation of the receptor-ligand complexes. The amino-acid residues involved in ligand binding were identified and described.
    Źródło:
    Acta Biochimica Polonica; 2001, 48, 1; 131-135
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    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:
    The intercalation of imidazoacridinones into DNA induces conformational changes in their side chain.
    Autorzy:
    Mazerski, Jan
    Muchewicz, Karolina
    Powiązania:
    https://bibliotekanauki.pl/articles/1044393.pdf
    Data publikacji:
    2000
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    molecular dynamics simulations
    conformational changes
    structure of intercalation complex
    C-1311
    antitumor drugs
    imidazoacridinones
    Opis:
    Imidazoacridinones (IAs) are a new group of highly active antitumor compounds. The intercalation of the IA molecule into DNA is the preliminary step in the mode of action of these compounds. There are no experimental data about the structure of an intercalation complex formed by imidazoacridinones. Therefore the design of new potentially better compounds of this group should employ the molecular modelling techniques. The results of molecular dynamics simulations performed for four IA analogues are presented. Each of the compounds was studied in two systems: i) in water, and ii) in the intercalation complex with dodecamer duplex d(GCGCGCGCGCGC)2. Significant differences in the conformation of the side chain in the two environments were observed for all studied IAs. These changes were induced by electrostatic as well as van der Waals interactions between the intercalator and DNA. Moreover, the results showed that the geometry of the intercalation complex depends on: i) the chemical constitution of the side chain, and ii) the substituent in position 8 of the ring system.
    Źródło:
    Acta Biochimica Polonica; 2000, 47, 1; 65-78
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    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:
    15N magnetic relaxation study of backbone dynamics of the ribosome-associated cold shock response protein Yfia of Escherichia coli
    Autorzy:
    Zhukov, Igor
    Bayer, Peter
    Schölermann, Beate
    Ejchart, Andrzej
    Powiązania:
    https://bibliotekanauki.pl/articles/1040866.pdf
    Data publikacji:
    2007
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    anisotropic overall molecular diffusion
    model-free approach
    15N NMR spectroscopy
    stress adaptation
    disordered polypetide chain motion
    protein Y
    Opis:
    In the solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli in the free state two structural segments can be distinguished: a well structured, rigid N-terminal part displaying a βαβββα topology and a flexible C-terminal tail comprising last 20 amino-acid residues. The backbone dynamics of Yfia protein was studied by 15N nuclear magnetic relaxation at three magnetic fields and analyzed using model-free approach. The overall diffusional tumbling of the N-terminal part is strongly anisotropic with a number of short stretches showing increased mobility either on a subnanosecond time scale, or a micro- to millisecond time scale, or both. In contrast, the unstructured polypeptide chain of the C-terminal part, which cannot be regarded as a rigid structure, shows the predominance of fast local motions over slower ones, both becoming faster closer to the C-terminus.
    Źródło:
    Acta Biochimica Polonica; 2007, 54, 4; 769-775
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-13 z 13

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