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    Wyświetlanie 1-8 z 8
    Tytuł:
    Monte Carlo simulations of protein-like heteropolymers.
    Autorzy:
    Sikorski, Andrzej
    Romiszowski, Piotr
    Powiązania:
    https://bibliotekanauki.pl/articles/1044166.pdf
    Data publikacji:
    2001
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    lattice models
    protein structure
    Monte Carlo method
    protein dynamics
    protein folding
    Opis:
    Properties of a simple model of polypeptide chains were studied by the means of the Monte Carlo method. The chains were built on the (310) hybrid lattice. The residues interacted with long-range potential. There were two kinds of residues: hydrophobic and hydrophilic forming a typical helical pattern -HHPPHPP-. Short range potential was used to prefer helical conformations of the chain. It was found that at low temperatures the model chain formes dense and partially ordered structures (non-unique). The presence of the local potential led to an increase of helicity. The effect of the interplay between the two potentials was studied. After the collapse of the chain further annealing caused rearrangement of helical structures. Dynamic properties of the chain at low temperature depended strongly on the local chain ordering.
    Źródło:
    Acta Biochimica Polonica; 2001, 48, 1; 77-81
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Coarse-grained modeling of protein structure, dynamics and protein-protein interactions
    Autorzy:
    Koliński, A.
    Kmiecik, S.
    Jamróz, M.
    Błaszczyk, M.
    Kouza, M.
    Kurciński, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/1954428.pdf
    Data publikacji:
    2014
    Wydawca:
    Politechnika Gdańska
    Tematy:
    coarse-grained modeling
    protein folding
    protein dynamics
    molecular docking
    protein docking
    Opis:
    Theoretical prediction of protein structures and dynamics is essential for understanding the molecular basis of drug action, metabolic and signaling pathways in living cells, designing new technologies in the life science and material sciences . We developed and validated a novel multiscale methodology for the study of protein folding processes including flexible docking of proteins and peptides. The new modeling technique starts from coarse-grained large-scale simulations, followed by selection of the most plausible final structures and intermediates and, finally, by an all-atom rectification of the obtained structures. Except for the most basic bioinformatics tools, the entire computational methodology is based on the models and algorithms developed in our lab. The coarse-grained simulations are based on a high-resolution lattice representation of protein structures, a knowledge based statistical force field and efficient Monte Carlo dynamics schemes, including Replica Exchange algorithms. This paper focuses on the description of the coarse-grained CABS model and its selected applications.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 219--229
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    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:
    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:
    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:
    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:
    In silico prediction and characterization of three-dimensional structure of actin-1 of Arabidopsis thaliana
    Autorzy:
    Sahu, M.
    Dehury, B.
    Sarmah, R.
    Sahoo, S.
    Sahu, J.
    Sarma, K.
    Sen, P.
    Modi, M.K.
    Barooah, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/80321.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    actin-1
    protein sequence
    Arabidopsis thaliana
    comparative modelling
    three-dimensional structure
    molecular dynamics simulation
    Opis:
    Actin-1 is a ubiquitous protein belonging to the reproductive class of Actin family in Arabidopsis thaliana . This protein is involved in the formation of filaments that are major components of the cytoskeleton. Despite the importance of this protein, very little information is available regarding its structure and function in plants. In this study, analysis of the protein sequence was done and comparative model of Actin-1 was constructed (UNIPROT ID: P0CJ46) from Arabidopsis thaliana using the crystal structure of Dictyostelium discoideum actin (PDB ID: 1NLV-A) as template employing Modeller version 9.9. The stable structure was generated by 5 nanosecond molecular dynamics simulation steps using GROMOS43A1 96 force field that characterized its structural and dynamic feature. The biochemical function of the final simulated structure was also investigated using PROFUNC. The molecular simulation study suggested that the modeled Actin-1 protein retain its stable conformation in aqueous solution. The predicted binding sites in the modeled Actin-1 protein are very informative for further protein-ligand interaction study.
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 4
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Influence of substitutions of Isu1 residues on binding to Jac1 protein
    Autorzy:
    Mozolewska, M. A.
    Powiązania:
    https://bibliotekanauki.pl/articles/1938619.pdf
    Data publikacji:
    2016
    Wydawca:
    Politechnika Gdańska
    Tematy:
    Saccharomyces cerevisiae
    Isu1-Jac1 protein complex
    alanine scan
    molecular dynamics
    coarse-grained UNRES force field
    Opis:
    The iron-sulfur (Fe/S) clusters are the most ancient co-factors of proteins involved in the most essential processes in bacterial systems and yeast, such as Saccharomyces cerevisiae. The main protein involved in the Fe/S cluster transfer is the Iron sulfur cluster assembly protein 1 (Isu1), which interacts with Jac1 during one of the stages of the Fe/S cluster biogenesis cycle forming a binary complex. In this work, the interaction interface of Isu1 was investigated by selective substitutions of amino-acid residues to understand their role in binding to the Jac1 protein. An initial alanine scan was done to limit the number of possible residues subjected to the replacement and to confirm the previously obtained results. Then, MD simulations using the coarse-grained UNRES force field were run for two selected mutants: L63 V72 F94 and L63 V64 G65 D71. The analysis of the dynamics and interaction patterns of the Isu1-Jac1 complexes confirmed that the investigated residues played an important role in their binding.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 417-423
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-8 z 8

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