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T Róg

Publications and source records attributed to T Róg.

11 recordsLinked to original sources
PubMed2005

Cholesterol effects on a mixed-chain phosphatidylcholine bilayer: a molecular dynamics simulation study.

A molecular dynamics simulation of a mono-cis-unsaturated 1-palmitoyl-2-oleoyl-phosphatidylcholine bilayer containing approximately 22 mol% of cholesterol (POPC-Chol) was carried out for 15 ns. An 8-ns trajectory was analysed to determine the effects of Chol on the membrane properties and compare it with that on the fully saturated 1,2-dimyristoyl-phosphatidylcholine bilayer containing approximately 22 mol% of Chol (DMPC-Chol). The study suggests that the experimentally observed weaker effect of Chol on the POPC than DMPC bilayer might result from a different vertical localisation of the Chol hydroxyl group (OH-Chol) in both bilayers: in the POPC-Chol bilayer, OH-Chol is placed approximately 3 A higher in the bilayer interface than in the DMPC-Chol bilayer. Because of the rigid cis double bond in the beta-chain of POPC, Chol fits worse to the POPC-Chol membrane environment and is pushed up, in effect all Chol ring atoms are, on average, located above the double bond. Both in mono-cis-unsaturated and fully saturated PC bilayers, Chol induces stronger van der Waals interactions among the chains, whereas its interactions with the chains are weak. In contrast to DMPC, the smooth alpha-face of the Chol ring lowers the order of POPC chains, whereas the rough beta-face increases the order.

Cholesterol↗
PubMed2003

nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations.

We present a new implementation of the program nMoldyn, which has been developed for the computation and decomposition of neutron scattering intensities from Molecular Dynamics trajectories (Comp. Phys. Commun 1995, 91, 191-214). The new implementation extends the functionality of the original version, provides a much more convenient user interface (both graphical/interactive and batch), and can be used as a tool set for implementing new analysis modules. This was made possible by the use of a high-level language, Python, and of modern object-oriented programming techniques. The quantities that can be calculated by nMoldyn are the mean-square displacement, the velocity autocorrelation function as well as its Fourier transform (the density of states) and its memory function, the angular velocity autocorrelation function and its Fourier transform, the reorientational correlation function, and several functions specific to neutron scattering: the coherent and incoherent intermediate scattering functions with their Fourier transforms, the memory function of the coherent scattering function, and the elastic incoherent structure factor. The possibility to compute memory function is a new and powerful feature that allows to relate simulation results to theoretical studies.

Journal Article↗
PubMed2003

Effects of a carane derivative local anesthetic on a phospholipid bilayer studied by molecular dynamics simulation.

Molecular dynamics (MD) simulations of two hydrated palmitoyloleoylphosphatidylcholine (POPC) bilayers each containing eight carane derivative (KP-23) local anesthetic (LA) molecules in neutral (POPC-LA) or protonated (POPC-LAH) forms were carried out to investigate the effect of KP-23 and its protonation on the bilayer. 3-ns trajectories were used for analyses. A pure POPC bilayer was employed as a reference system. In both POPC-LA and POPC-LAH systems a few KP-23 molecules intercalated into the bilayer and moved near the bilayer/water interface. They were located on the hydrophobic core side of the interface in the POPC-LA bilayer, but on the water phase side in the POPC-LAH bilayer. The order of the POPC chains was higher in the POPC-LA bilayer than in the pure POPC bilayer and was lower in the POPC-LAH bilayer. Interactions between polar groups of KP-23 and POPC or water were responsible for a lower hydration of POPC headgroups in POPC bilayers containing KP-23 than in the pure POPC bilayer. KP-23 molecules were found to form aggregates both in POPC-LA and POPC-LAH bilayers. Due to higher amphiphilicity of LAH, the LAH aggregate was more micelle-like and larger than the LA one. The results demonstrate the rapid timescales of the initial processes that take place at and near the bilayer interface as well as details of the atomic level interactions between local anesthetic and the lipid matrix of a cell membrane.

Anesthetics, Local↗
PubMed2001

Cholesterol effects on the phospholipid condensation and packing in the bilayer: a molecular simulation study.

A 15-ns molecular dynamics simulation of the fully hydrated liquid-crystalline dimyristoylphosphatidylcholine-cholesterol (DMPC-Chol) bilayer containing approximately 22 mol% Chol was carried out. The generated trajectory was analysed to investigate the mechanism of the Chol condensing effect on DMPC hydrocarbon chains and the influence of Chol on the chain packing in the membrane. Chol was found to induce stronger van der Waals interactions among the chains, whereas its interactions with the chains were weak. In the DMPC-Chol bilayer, as in the DMPC bilayer, DMPC chains were regularly packed around a chosen chain but around a Chol molecule they were not. DMPC gamma chains made closer contacts with Chol than the beta chains.

Cholesterol↗
PubMed2001

Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study.

Molecular dynamics (MD) simulations of fully hydrated bilayers in the liquid-crystalline state made of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) or 1-palmitoyl-2-elaidoyl-phosphatidylcholine (PEPC) were carried out to investigate the effect of the incorporation of a double bond in the phosphatidylcholine (PC) beta-chain (cis or trans) on the membrane/water interface. The bilayers reached thermal equilibrium after 3 and 1 ns of MD simulations, respectively, and productive runs were carried out for 3 ns for each bilayer. As reference systems, the 1,2-dimyristoyl-phosphatidylcholine (DMPC) bilayer (M. Pasenkiewicz-Gierula, Y. Takaoka, H. Miyagawa, K. Kitamura, and A. Kusumi, 1999, Biophys. J. 76:1228-1240) and DMPC-cholesterol (Chol) bilayer containing 22 mol % Chol (M. Pasenkiewicz-Gierula, T. Róg, K. Kitamura, A. and Kusumi, 2000, Biophys. J. 78:1376-1389) were used. The study shows that at the interface of POPC, PEPC, and DMPC-Chol bilayers, average numbers of PC-water and PC-PC interactions are similar and, respectively, greater and smaller than in the DMPC bilayer. The average area/PC in mono-unsaturated bilayers is approximately 4 A(2) larger than in the DMPC bilayer; nevertheless, a strong correlation was found between a single molecular area (SMA) of a PC and the number of interactions this PC makes; i.e., PCs (either saturated or unsaturated) with the same SMA form similar numbers of intermolecular links. The numbers and corresponding SMAs are distributed about averages pertinent to each bilayer. No significant difference between cis and trans bonds was found.

Binding Sites↗
PubMed2001

Cholesterol effects on the phosphatidylcholine bilayer nonpolar region: a molecular simulation study.

A 15-ns molecular dynamics (MD) simulation of the fully hydrated dimyristoylphosphatidylcholine-cholesterol (DMPC-Chol) bilayer in the liquid-crystalline state was carried out to investigate the effect of Chol on the hydrocarbon chain region of the bilayer. The last 8-ns fragment of the generated trajectory was used for analyses. As a reference system, a pure DMPC bilayer (M. Pasenkiewicz-Gierula, Y. Takaoka, H. Miyagawa, K. Kitamura, and A. Kusumi, 1999, Biophys. J. 76:1228-1240) simulated for 14 ns was used. The study shows that a Chol-induced increase of the bulk molecular order parameter along both beta- and gamma-chain is mainly caused by a decrease of the average tilt of the chains, because the bulk average number of gauche rotamers/myristoyl chain is not significantly changed by Chol. Nevertheless, for DMPCs located near Chol molecules both the number of gauche rotamers/chain and the chain tilt are decreased. The magnitude of the Chol effect on the PC alkyl chains depends, in addition to the PC-Chol distance, on the side of the Chol molecule (alpha- or beta-face) that the chains are in contact with. This study provides some new insight into the properties of the coexistence region of the partial phase diagram for DMPC-Chol bilayers.

Cholesterol↗
PubMed2000

Cholesterol effects on the phosphatidylcholine bilayer polar region: a molecular simulation study.

A molecular dynamics (MD) simulation of a fully hydrated, liquid-crystalline dimyristoylphosphatidylcholine (DMPC)-Chol bilayer membrane containing approximately 22 mol% Chol was carried out for 4.3 ns. The bilayer reached thermal equilibrium after 2.3 ns of MD simulation. A 2.0-ns trajectory generated during 2.3-4.3 ns of MD simulation was used for analyses to determine the effects of Chol on the membrane/water interfacial region. In this region, 70% of Chol molecules are linked to DMPC molecules via short-distance interactions, where the Chol hydroxyl group (OH-Chol) is 1) charge paired to methyl groups of the DMPC choline moiety ( approximately 34%), via the hydroxyl oxygen atom (Och); 2) water bridged to carbonyl ( approximately 19%) and nonester phosphate ( approximately 14%) oxygen atoms, via both Och and the hydroxyl hydrogen atom (Hch); and 3) directly hydrogen (H) bonded to carbonyl ( approximately 11%) and nonester phosphate ( approximately 5%) oxygen atoms, via Hch ( approximately 17% of DMPC-Chol links are multiple). DMPC's gamma-chain carbonyl oxygen atom is involved in 44% of water bridges and 51% of direct H bonds formed between DMPC and Chol. On average, a Chol molecule forms 0.9 links with DMPC molecules, while a DMPC molecule forms 2.2 and 0.3 links with DMPC and Chol molecules, respectively. OH-Chol makes hydrogen bonds with 1.1 water molecules, preferentially via Hch. The average number of water molecules H bonded to the DMPC headgroup is increased by 7% in the presence of Chol. These results indicate that inclusion of Chol decreases interlipid links and increases hydration in the polar region of the membrane.

Cholesterol↗
PubMed2000

Molecular dynamics simulation studies of lipid bilayer systems.

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.

Animals↗
PubMed1997

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

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 alpha-chain of the DMPC head group has mainly an extended conformation, due to predominantly trans conformation of alpha5 torsion. The rotational correlation time for the P-N vector is 3.7 ns. The C2-C1-O11-P fragment of the DMPC head group (theta1, alpha1, alpha2 torsions) is rigid while the P-O12-C11-C12 fragment (alpha3, alpha4, alpha5 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 alpha-, beta-, gamma-chains and for the O21-C1 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.

Dimyristoylphosphatidylcholine↗
PubMedDate not supplied

[Epilepsy and tremor in the XXY syndrome].

Extrapyramidal tremor and epilepsy uncommon in Klinefelter syndrome were found in a 30 year old patient. CT scans revealed partially empty sella and subcortical cerebral atrophy. Chromosomal studies showed the karyotype 47, XXY.

Adult↗