Membrane: A program for simulation and analysis of x‐ray diffraction patterns of thin multilayer films

Kastowsky, Manfred; Sabisch, Andreas; Bradaczek, H.

doi:10.1002/masy.19910460123

Cited by 3 publications

(1 citation statement)

References 6 publications

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“…We used the formulas given by Tanford (1972) for the estimation of V and lc for saturated hydrocarbon chains with n atoms. Using parameters from MEMBRANE (Kastowsky et al, 1991a), the headgroup area was calculated every 0.1 ps for each simulation from the projection of the headgroup along the vector between sugar residues and the acyl chains, which also substitutes the membrane normal in the calculation of the order parameter.…”

Section: Methodsmentioning

confidence: 99%

Molecular dynamics simulations of six different fully hydrated monomeric conformers of Escherichia coli re-lipopolysaccharide in the presence and absence of Ca2+

Obst

Kastowsky

Bradaczek

1997

Biophysical Journal

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Six previously published conformational models of Escherichia coli Re lipopolysaccharide (ReLPS) were subjected to molecular dynamics simulations using the CHARMM force field. The monomers of ReLPS were completely immersed in a water box. The dynamic behavior of the solvated models in the presence and absence of calcium cations was compared. The structure of the solvent shell was analyzed in terms of radial distribution functions. Diffusion coefficients and mean residence times were analyzed to characterize the dynamic behavior of the solvent. Order parameters and number of gauche defects were used for the description of the dynamics of the acyl chains. The cations are preferentially located between the carboxylate and phosphate groups of the headgroup. Their presence leads to a rigidification of the headgroup structure and alters the conformation of the backbone, thus influencing the structure and flexibility of the hydrophobic region as well. The effect of calcium on the backbone flexibility was measured in terms of glycosidic torsion angles. The six fatty acid chains of each ReLPS monomer adopt a highly ordered micromembrane structure. The packing parameter indicates that aggregation of these ReLPS monomers will lead to lamellar structures. Evaluation of all data enables us to present one conformation, C, which is thought to best represent the average structure of the ReLPS conformers.

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Section: Methodsmentioning

confidence: 99%

Molecular dynamics simulations of six different fully hydrated monomeric conformers of Escherichia coli re-lipopolysaccharide in the presence and absence of Ca2+

Obst

Kastowsky

Bradaczek

1997

Biophysical Journal

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Structural analysis of mixed LB multilayers and superlattice films

et al. 1997

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Comparison of X‐ray powder‐diffraction data of various bacterial lipopolysaccharide structures with theoretical model conformations

Kastowsky

Gutberlet

Bradaczek

1993

European Journal of Biochemistry

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X-ray powder-diffraction experiments have been performed on dry samples of lipid A and various rough-mutant lipopolysaccharides (LPS) of Salmonella minnesota, Salmonella typhimurium and Escherichia coli. The diffraction patterns obtained indicated exclusively lamellar, bilayered arrangements in all samples. The periodicities were found to be in the range 4.5 nm for lipid A to 8.8 nm for Ra-LPS. Upon treatment with water-saturated air, swelling of the lamellar structures was achieved, as indicated by shifts of reflections. The increase in bilayer dimensions normally was about 0.3 nm.X-ray intensities were used for the determination of the inner bilayer structure, i.e. for calculation of the one-dimensional electron-density distribution across the bilayer. For lipid A and several Re-LPS, Rd2-LPS, Rd,-LPS and Rc-LPS samples, a striking coincidence of the electron-density distributions in the lipid-A domain was found, suggesting that in all these structures the lipid-A portion is similarly arranged. For Rb, and Ra-LPS, the lipid-A domain could not be resolved due to the limited number of observed reflections. For other Re-mutant lipopolysaccharide samples, quite different X-ray patterns were obtained. Some samples yielded diffraction patterns indicating a very high state of order in the lipid-A domain, whereas, in others, a significantly reduced order in the lipid-A domain was infered.Comparison of the X-ray data with features of a calculated three-dimensional molecular model of lipopolysaccharide revealed reasonable agreement in molecular dimensions and bilayer structure.Lipopolysaccharides (LPS) are constituents of the outer leaflet of the outer membrane of Gram-negative bacteria [l]. LPS are amphiphilic molecules which differ significantly in structure from simple constituents of other biological membranes such as glycerophospholipids. More precisely, the lipid anchor of LPS, termed lipid A, generally harbours 6-7 saturated fatty acid chains, covalently linked to a diglucosamine head group. Thus, a compact hydrophobic domain is formed which is reported to exhibit a high degree of order [2, 31. To the LPS head group, an oligosaccharide portion is linked. The oligosaccharide structures of different bacteria show structural variations which have been useful in the elucidation of LPS physical behaviour and of the role of distinct core portions in the expression of several physiological reactions induced by LPS [4-91. The general architecture of enterobacterial smooth-strain (S form) LPS is shown in Fig. 1. Structures of rough-mutant (R form) LPS (Ra-LPS to Re-LPS) investigated in this study are defined in Table 1.The physicochemical properties of LPS and its molecular conformation have been studied intensively [lo]. However, up to now, it is not clear if a specific aggregation form [8, 111 of the amphiphilic LPS molecules or a specific confor- mation of a single molecule [12] gives rise to the known endotoxicity of LPS. Unfortunately, a precise X-ray-structure determination of LPS is hampered by the fact that suitabl...

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Membrane: A program for simulation and analysis of x‐ray diffraction patterns of thin multilayer films

Cited by 3 publications

References 6 publications

Molecular dynamics simulations of six different fully hydrated monomeric conformers of Escherichia coli re-lipopolysaccharide in the presence and absence of Ca2+

Molecular dynamics simulations of six different fully hydrated monomeric conformers of Escherichia coli re-lipopolysaccharide in the presence and absence of Ca2+

Structural analysis of mixed LB multilayers and superlattice films

Comparison of X‐ray powder‐diffraction data of various bacterial lipopolysaccharide structures with theoretical model conformations

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