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1

The XLVII Winter School of the Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland; “Molecules, Pathways, and Games”

100%
Murzyn K.
Acta Biochimica Polonica
|
2020
|
tom 67
|
nr 3
2

Woda w symulacjach dynamiki molekularnej.

88%
Murzyn K.
Postępy Biologii Komórki
|
2002
|
tom 29
|
nr 1
87-101
3

Construction and optimisation of a computer model for a bacterial membrane

63%
Murzyn K., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
|
1999
|
tom 46
|
nr 3
The main steps in the construction of a computer model for a bacterial membrane are described. The membrane has been built of 72 lipid molecules, 54 of which being 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidylethanolamine (POPE) and 18 - 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidyl-rac-glycerol (POPG) molecules (thus in the proportion of 3:1). The membrane was hydrated with 1955 water molecules (approximately 27 water molecules per lipid). To neutralise the electronic charge (-e) on each POPG molecule, 18 sodium ions (Na+) were added to the membrane close to the POPG phosphate groups. The atomic charges on the POPE and POPG headgroups were obtained from ab initio quantum mechanical restrained electrostatic potential fitting (RESP) (Bayly et al., 1993, J. Phys. Chem. 97, 10269) using the GAMESS program at the 6-31G* level (Schmidt et al., 1993, J. Comput. Chem. 14, 1347). The model constructed in this way provided an initial structure for subsequent molecular dynamics simulation studies intended to elucidate the atomic level interactions responsible for the structure and dynamics of the bacterial membrane.
4

Orientation of lutein in a lipid bilayer - revisited

51%
Pasenkiewicz-Gierula M., Baczynski K., Murzyn K., Markiewicz M.
Acta Biochimica Polonica
|
2012
|
tom 59
|
nr 1
Lutein is present in the human retina and lens, where it plays a protective role. As lutein is associated with the lipid matrix of biomembranes, the role depends on its membrane location. Experimental studies predicted two orientations of lutein in a phosphatidylcholine (PC) bilayer: vertical and horizontal. Using a molecular dynamics simulation, we observed, in two different PC bilayers, both orientations of lutein, and in each bilayer, a single change from vertical to horizontal orientation or vice versa. Both orientations were stabilized by hydrogen bonding of lutein OH groups with mainly carbonyl but also phosphate oxygen atoms of PC.
5

Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions

51%
Rog T., Murzyn K., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
|
2003
|
tom 50
|
nr 3
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.
6

Peptide-lipid interactions in a bilayer: molecular modelling studies

51%
Pasenkiewicz-Gierula M., Rog T., Murzyn K.
Cellular and Molecular Biology Letters
|
2005
|
tom 10
|
nr Suppl.
7

Molecular dynamics simulation studies of lipid bilayer systems

51%
Pasenkiewicz-Gierula M., Murzyn K., Rog T., Czaplewski C.
Acta Biochimica Polonica
|
2000
|
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.
8

Molecular simulation studies of the interfacial region in lipid bilayers

51%
Pasenkiewicz-Gierula M., Rog T., Murzyn K.
Postępy Biologii Komórki. Suplement
|
2001
|
tom 16
9

Condensed phase properties of n-pentadecane emerging from application of biomolecular force fields

45%
Bratek M., Wojcik-Augustyn A., Kania A., Majta J., Murzyn K.
Acta Biochimica Polonica
|
2020
|
tom 67
|
nr 3
10

Biofizyczne badania blon i bialek metoda symulacji dynamiki molekularnej

39%
Pasenkiewicz-Gierula M., Jezierski G., Murzyn K., Rog T., Czaplewski C., Ciarkowski J.
Biotechnologia
|
2000
|
nr 2
83-97
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