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1

Badania ukladow blonowych metodami modelowania molekularnego

100%
Pasenkiewicz-Gierula M.
Kosmos
|
2009
|
tom 58
|
nr 1-2
49-56
2

Metoda symulacyjnego wyzarzania - zastosowanie do badania struktury i dynamiki bialek.

63%
Jezierski G., Pasenkiewicz-Gierula M.
Postępy Biologii Komórki. Suplement
|
2001
|
tom 16
305-317
3

Orientation of lutein in a lipid bilayer – revisited

63%
Pasenkiewicz-Gierula M., Markiewicz M.
Acta Biologica Cracoviensia. Series Botanica. Supplement
|
2011
|
tom 53
|
nr 1
4

Oddzialywanie cholesterolu z fosfolipidami w blonie - badania metoda symulacji dynamiki molekularnej.

63%
Rog T., Pasenkiewicz-Gierula M.
Postępy Biologii Komórki. Suplement
|
2001
|
tom 16
277-283
5

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.
6

Conformations, orientations and time scales characterising dimyristoylphosphatidylcholine bilayer membrane. Molecular dynamics simulation studies

63%
Pasenkiewicz-Gierula M., Rog T.
Acta Biochimica Polonica
|
1997
|
tom 44
|
nr 3
The results of molecular dynamics simulation of fully hydrated dimyristoyl­phosphatidylcholine (DMPC) bilayer membrane in the liquid-crystalline phase are presented. They show that the probability of a gauche conformation varies periodically along the chain with only a slight increase towards the end of the chain. However, the frequency of transition between conformations increases, due to a decrease in the lifetime of the trans conformation, along the chain. The average lifetimes for trans conformations are in the range of 1-2 x 10-10 s and for gauche conformations in the range of 4-7 x 10-11 s. The α-chain of the DMPC head group has mainly an extended conformation, due to predominantly trans conformation of α5 torsion. The rotational correlation time for the P-N vector is 3.7 ns. The C2-C1-011-P fragment of the DMPC head group (θ1, α1, α2 torsions) is rigid while the P-012-C11-C12 fragment ( α3, α4, α5 torsions) is flexible. The lateral diffusion coefficient for DMPC self-diffusion in the mem­brane is 2 x 10-7 cm2/s; the rate of transverse diffusion is the same. Large differences in the calculated rotational correlation times for the a-, β-, γ-chains and for the 021-Cl-vector indicate that in the liquid-crystalline bilayer each segment of the DMPC molecule exhibits its own rotational freedom, in addition to its internal flexibility resulting from rotational isomerism. The results obtained in these calculations, although in general agreement with some ex­perimental data, shed new light on the dynamical behaviour of phosphatidyl­choline molecules in the bilayer membrane in the liquid-crystalline phase.
7

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

63%
Jezierski G., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
|
2001
|
tom 48
|
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.
8

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.
9

Properties of water hydrating the galactolipid and phospholipid bilayers: a molecular dynamics simulation study

51%
Markiewicz M., Baczynski K., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
|
2015
|
tom 62
|
nr 3
10

Crystal or membrane domain? Characterisation of order cholesterol aggregates in bilayers oversaturated with cholesterol – Results of computer simulations

51%
Pasenkiewicz-Gierula M., Plesnar E., Subczynski W.
Current Topics in Biophysics. Supplement
|
2013
|
tom 36
|
nr 2A: Plenary lectures
11

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

51%
Koloczek H., Jezierski G., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
|
1996
|
tom 43
|
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.
12

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.
13

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.
14

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.
15

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
16

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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