Wyniki wyszukiwania

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

100%

Rog T., Murzyn K., Pasenkiewicz-Gierula M.

Acta Biochimica Polonica

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2003

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tom 50

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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.

2

Planar, cylindrical and spherical electrical double layers in biological systems. The effect of counterion size

100%

Bohinc K., Iglic A., Slivnik T., Kralj-Iglic V.

Cellular and Molecular Biology Letters

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2002

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tom 07

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nr 3

The effect of counterion size on the electrical properties of an electrolyte solution in contact with charged planar, cylindrical and spherical surfaces is considered. Electrostatic interaction is considered by means of the mean electrostatic field, while the finite size of particles constituting the electrolyte solution is considered via the excluded volume effect within the lattice statistics. Different sizes of counterion are described by different values of the lattice constant. It is shown that the excluded volume effect considerably decreases the calculated number density of counterions near the charged surface. This effect is more pronounced in cylindrical geometry than in spherical geometry, and less pronounced than in planar geometry.

3

Interaction of an anticancer ruthenium complex HInd[RuInd2CI4] with cytochrome C

80%

Trynda-Lemiesz L.

Acta Biochimica Polonica

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2004

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tom 51

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nr 1

Cytochrome c is an important electron transfer protein in the respiratory chain, shuttling electrons from cytochrome c reductase to cytochrome c oxidase. Extensive chemical modification studies indicate significant electrostatic interactions between these proteins and show that all structural and conformational changes of cytochrome c can influence the electron transport. In the present work we examine the effect of an anticancer ruthenium complex, trans-Indazolium (bisindazole) tetra- chlororuthenate(III) (HInd[RuInd2Cl4]), on the conformation of cytochrome c, the state of the heme moiety, formation of the protein dimer and on the folding state of apocytochrome c. For this purpose, gel-filtration chromatography, absorption second derivative spectroscopy, circular dichroism (CD) and inductively coupled plasma atomic emission spectroscopy (ICP(AES)) were used. The present data have revealed that binding of the potential anticancer drug HInd[RuInd2Cl4] complex to cytochrome c induces a conformation of the protein with less organized secondary and tertiary structure.

Ograniczanie wyników

2 Acta Biochimica Polonica

1 Cellular and Molecular Biology Letters

1 Bohinc K.

1 Iglic A.

1 Kralj-Iglic V.

1 Murzyn K.

1 Pasenkiewicz-Gierula M.

1 Rog T.

1 Slivnik T.

1 Trynda-Lemiesz L.

1 2004

1 2003

1 2002

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

Planar, cylindrical and spherical electrical double layers in biological systems. The effect of counterion size

Interaction of an anticancer ruthenium complex HInd[RuInd2CI4] with cytochrome C