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1
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Molecular dynamics simulation studies of lipid bilayer systems.

100%
Pasenkiewicz-Gierula M., Murzyn K., Róg T., Czaplewski C.
Acta Biochimica Polonica
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2000
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vol. 47
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issue 3
601-611
EN
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.
2
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Elucidation of neurophysin/bioligand interactions horn rnolecular rnodeling

100%
Kaźmierkiewicz R., Czaplewski C., Ciarkowski J.
Acta Biochimica Polonica
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1997
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vol. 44
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issue 3
453-466
3
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Molecular modelling of the vasopressin V2 receptor/antagonist interactions

100%
Czaplewski C., Kaźmierkiewicz R., Ciarkowski J.
Acta Biochimica Polonica
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1998
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vol. 45
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issue 1
19-26
4
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Fluorescence decay time distribution analysis of cyclic enkephalin analogues. Influence of the solvents and configuration of amino acids in position 2 and 3 on changes in conformation

88%
Malicka J., Groth M., Czaplewski C., Liwo A., Wiczk W.
Acta Biochimica Polonica
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1999
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vol. 46
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issue 3
615-629
5
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Design of a knowledge-based force field for off-lattice simulations of protein structure

88%
Liwo A., Ołdziej S., Kaźmierkiewicz R., Groth M., Czaplewski C.
Acta Biochimica Polonica
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1997
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vol. 44
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issue 3
527-547
6
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Theoretical studies of binding modes of two covalent inhibitors of cysteine proteases.

76%
Drabik P., Politowska E., Czaplewski C., Kasprzykowski F., Łankiewicz L., Ciarkowski J.
Acta Biochimica Polonica
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2000
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vol. 47
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issue 4
1061-1066
EN
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.
7
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Fluorescence decay time distribution analysis of cyclic enkephalin analogues; Influence of solvent and Leu configuration in position 5 on conformation

76%
Malicka J., Ganzynkowicz R., Groth M., Czaplewski C., Karolczak J., Liwo A., Wiczk W.
Acta Biochimica Polonica
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2001
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vol. 48
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issue 1
95-102
EN
Lifetime distribution analysis were performed to study the influence of Leu configuration in position 5 on changes of the peptide chain of cyclic analogues of enkephalins containing a fluorescence donor and acceptor in different solvents. The configuration change of Leu5 in all the analogues of enkephalins studied which contain donor-acceptor pairs has no apparent influence on Trp lifetime distributions. In contrast, there is a significant solvent effect on the shape of lifetime distribution.
8
Content available remote

Molecular modeling of the oxytocin receptor/bioligand interactions

75%
Politowska E., Czaplewski C., Ciarkowski J.
Acta Biochimica Polonica
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1999
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vol. 46
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issue 3
581-590
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