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1

The intercalation of imidazoacridinones into DNA induces conformational changes in their side chain

100%
Mazerski J., Muchewicz K.
Acta Biochimica Polonica
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2000
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tom 47
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nr 1
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 position8 of the ring system.
2

Computer modelling of human alpha 1-antitrypsin reactive site loop behaviour under mild conditions

100%
Koloczek H., Jezierski G., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
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1996
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tom 43
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nr 3
Human ai-antitrypsin (cti-PI) is a member of the serpin superfamily of proteins. The reactive site loop (RSL) of the serpin binds to the active site of its target proteinase. Deficiency of ai-antitrypsin is associated with a spontaneous conformational transition in the molecule which leads to a polymer formation. Mild conditions (1 M guanidinium-HCl), temperature and point mutations within the RSL are the factors that induce polymerisation. Initiation of this process has been associated with the disruption of a salt bridge Glu342-»Lys290. In this paper the interaction of guani- dinium ion with Glu342 and Lys290 as well as the effect of this interaction on the mobility of RSL is studied by molecular modelling.
3
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In silico prediction and characterization of three-dimensional structure of actin-1 of Arabidopsis thaliana

86%
Sahu M., Dehury B., Sarmah R., Sahoo S., Sahu J., Sarma K., Sen P., Modi M. K., Barooah M.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
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2013
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tom 94
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nr 4
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.
4

Characterisation and molecular dynamic simulations of J15 asparaginase from Photobacterium sp. strain J15

72%
Yaacob M. A., Wan Hasan W. A. N., Ali M. S. M., Abdul Rahman R. N. Z. R., Salleh A. B., Basri M., Leow T. C.
Acta Biochimica Polonica
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2014
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tom 61
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nr 4
5

The effect of the Glu342Lys mutation in alpha1-antitrypsin on its structure, studied by molecular modelling medhods

72%
Jezierski G., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
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2001
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tom 48
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nr 1
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 aβ-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.
6

Molecular dynamics simulation studies of lipid bilayer systems

58%
Pasenkiewicz-Gierula M., Murzyn K., Rog T., Czaplewski C.
Acta Biochimica Polonica
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2000
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tom 47
|
nr 3
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.
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