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1
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Badania układów błonowych metodami modelowania molekularnego

100%
Pasenkiewicz-Gierula M.
Kosmos
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2009
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vol. 58
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issue 1-2
49-56
EN
Biological membranes enclose every cell (plasma membrane) and some intracellular organelles (internal membranes). The main structural element of a biological membrane is a liquid-crystalline lipid bilayer. Experimental studies of lipid bilayers are difficult to carry out and to interpret because of their structural disorder and superposition of motions occurring in different time scales. Besides, due to limited spatial and time resolutions, they provide only an averaged behaviour of the molecules in the bilayer. Detailed information about the dynamical structure and time scales of events in the membrane can be obtained using molecular dynamics (MD) simulation methods. Although MD simulation is, in principle, characterized by an atomic resolution and time resolution in the femtosecond time scale in principle, the total simulation time is limited at present to several hundred nanoseconds. So, the method allows observation of the processes up to the 10-7 s time scale. MD simulation studies of hydrated lipid bilayers have shown that at the membrane/water interface there are numerous but short-lived hydrogen (H-) bonds between lipid headgroups and water molecules as well as an extended network of interlipid links via water molecules that are simultaneously H-bonded to two lipid molecules, i.e., so called water bridges. Exchange of H2O by D2O affects the time-averaged properties of the PC bilayer to some extent. When the bilayer is hydrated by D2O it becomes more compact than in the case of H2O. This can be assigned to the more stable H-bonds between PC and D2O than H2O and, particularly, to the more stable network of D2O water bridges compared with the H2O ones. In effect, the self-diffusion coefficient of D2O averaged over all water molecules in the bilayer is almost twice smaller than that of H2O and ∼2.5 times smaller than in pure D2O (∼1.7 in the case of H2O).
2
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The effect of the Glu342Lys mutation in α1-antitrypsin on its structure, studied by molecular modelling methods.

64%
Jezierski G., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
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2001
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vol. 48
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issue 1
65-75
EN
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.
3
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Conformations, orientations and time scales characterising dimyristoylphosphatidylcholine bilayer membrane. Molecular dynamicssimulation studies

64%
Pasenkiewicz-Gierula M., Róg T.
Acta Biochimica Polonica
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1997
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vol. 44
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issue 3
607-624
4
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Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions.

51%
Róg T., Murzyn K., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
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2003
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vol. 50
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issue 3
789-798
EN
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.
5
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Molecular dynamics simulation studies of lipid bilayer systems.

51%
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.
6
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Computer modelling of human α^1-antitrypsin reactive site loop behaviour under mild conditions

51%
Kołoczek H., Jezierski G., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
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1996
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vol. 43
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issue 3
467-474
7
Publication available in full text mode
Content available

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

51%
Markiewicz M., Baczyński K., Pasenkiewicz-Gierula M.
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EN
Molecular dynamics simulations of 1,2-di-O-acyl-3-O-β-D-galactopyranosyl-sn-glycerol (MGDG) and 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) bilayers were carried out to compare the effect of the lipid head group's chemical structure on the dynamics and orientational order of the water molecules hydrating the bilayer. The effect of the bilayers on the diffusion of water is strong for the neighbouring water molecules i.e., those located not further than 4 Å from any bilayer atom. This is because the neighbouring water molecules are predominantly hydrogen bonded to the lipid oxygen atoms and their mobility is limited to a confined spatial volume. The choline group of DOPC and the galactose group of MGDG affect water diffusion less than the polar groups located deeper in the bilayer interface, and similarly. The latter is an unexpected result since interactions of water with these groups have a vastly different origin. The least affected by the bilayer lipids is the lateral diffusion of unbound water in the bilayer plane (x,y-plane) - it is because the diffusion is not confined by the periodic boundary conditions, whereas that perpendicular to the plane is. Interactions of water molecules with lipid groups also enforce certain orientations of water dipole moments. The profile of an average water orientation along the bilayer normal for the MGDG bilayer differs from that for the DOPC bilayer. In the DOPC bilayer, the ordering effect of the lipid head groups extends further into the water phase than in the MGDG bilayer, whereas inside the bilayer/water interface, ordering of the water dipoles in the MGDG bilayer is higher. It is possible that differences in the profiles of an average water orientation across the bilayer in the DOPC and MGDG bilayers are responsible for differences in the lateral pressure profiles of these bilayers.
8
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Orientation of lutein in a lipid bilayer - revisited

51%
Pasenkiewicz-Gierula M., Baczyński K., Murzyn K., Markiewicz M.
Acta Biochimica Polonica
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2012
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vol. 59
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issue 1
115-118
EN
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
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Construction and optimisation of a computer model for a bacterial membrane

51%
Murzyn K., Pasenkiewicz-Gierula M.
Acta Biochimica Polonica
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1999
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vol. 46
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issue 3
631-639
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