Structure determination of lipid bilayers

Refined fibril structures: the hydrophobic core in Alzheimer's amyloid beta-protein and prion as revealed by X-ray diffraction

From the wide-angle, equatorial X-ray data of a beta-amyloid analogue, we previously calculated the electron density of the constituent beta-crystallite, which assembles as multimers (four to six crystallites) in building the amyloid fibre. In the scattering region where the spacing d < approximately 10 A, the observed reflections were indexed by an orthogonal lattice with a unit cell having a = 9.44 A, b = 6.92 A and c = 10.76 A. The phases were initially derived from the atomic coordinates of the beta-keratin backbone and were optimized by including new peaks (as point atom or sphere) in the subsequent Fourier iteration. The R-factor between the observed and calculated amplitudes was refined to 35%. In further developing our analysis, we have now applied an alternative constraint to the optimization by eliminating the negative electron densities, and found that the R-factor decreased to 19% after three iterations. The refined electron density map fits phenylalanine, indicating that the amyloid core likely comes from the hydrophobic Leu-Val-Phe-Phe residues. We have applied the same type of optimization, using beta-silk as an initial phase model, to the hydrophobic H1 domain of the prion protein for which the monoclinic unit cell constants are a = 9.51 A, b = 7.06 A, c = 15.94 A and beta = 88.4 degrees. The R-factor decreased to 11% from 64% after two iterations. The electron density map shows a silk-like quarter-staggered arrangement of beta-sheets which, in the intersheet direction, have circular peaks in one beta-sheet and elongated peaks in the alternating beta-sheet. These peaks were interpreted as arising from the C-terminal alanine-rich domain and N-terminal hydrophobic residues. Skeletal atomic models for these core regions support this interpretation.

Structure and Phase Behavior of Self-Assembled DPPC−DNA−Metal Cation Complexes

Multilamellar liposomes of dipalmitoylphosphatidylcholine (DPPC) in solution with DNA and bivalent metal cations (Ca2+, Mn2+, Mg2+) self-assemble into a ternary DPPC-DNA-Me2+ complex. The supramolecular structure of the complex consists of an ordered multilamellar assembly where hydrated DNA helices are sandwiched between the lipid bilayers and the metal cations bind the phosphate groups of DNA to the lipid polar heads. In the range of explored incubation times, the complex coexists with the uncomplexed DPPC over the whole temperature range investigated (20-55 degrees C). Accordingly, two distinct coexisting lamellar phases are observed, one corresponding to the ternary complex and the other to the uncomplexed lipid. The structure and thermotropic phase behavior of both of these have been investigated by means of synchrotron X-ray diffraction, and the relevant structural data are deduced from experimental electron density profiles. While the uncomplexed lipid exhibits the same phase behavior as pure DPPC, that is, L beta'-P beta'-L alpha, the thermotropic behavior of the bound lipid in the complex is partially altered. This is manifested as an increase in the main transition temperature and the disappearance of the ripple phase leading to the single -phase transition. The role of the different metal cations in promoting and stabilizing the DNA condensation into the ternary complex is also discussed.

Divalent cations affect chain mobility and aggregate structure of lipopolysaccharide from Salmonella minnesota reflected in a decrease of its biological activity

The physicochemical properties and biological activities of rough mutant lipopolysaccharides Re (LPS Re) as preformed divalent cation (Mg2+, Ca2+, Ba2+) salt form or as natural or triethylamine (Ten+)-salt form under the influence of externally added divalent cations were investigated using complementary methods: Differential scanning calorimetry (DSC) and Fourier-transform infrared spectroscopic (FT-IR) measurements for the beta <--> alpha gel to liquid crystalline phase behaviour of the acyl chains of LPS, synchrotron radiation X-ray diffraction studies for their aggregate structures, electron density calculations of the LPS bilayer systems, and LPS-induced cytokine (interleukin-6) production in human mononuclear cells. The divalent cation salt forms of LPS exhibit considerable changes in physicochemical parameters such as acyl chain mobility and aggregate structures as compared to the natural or monovalent cation salt forms. Concomitantly, the biological activity was much lower in particular for the Ca2+- and Ba2+-salt forms. This decrease in activity results mainly from the conversion of the unilamellar/cubic aggregate structure of LPS into a multilamellar one. The reduced activity also clearly correlates with the higher order--lower mobility--of the lipid A acyl chains. Both effects can be understood by an impediment of the interactions of LPS with binding proteins such as lipopolysaccharide-binding protein (LBP) and CD14 due to the action of the divalent cations.

Structure of self-assembled liposome-DNA-metal complexes

We have studied the structural and morphological properties of the triple complex dioleoyl phosphatidylcholine (DOPC)-DNA-Mn2+ by means of synchrotron x-ray diffraction and freeze-fracture transmission electron microscopy. This complex is formed in a self-assembled manner when water solutions of neutral lipid, DNA, and metal ions are mixed, which represents a striking example of supramolecular chemistry. The DNA condensation in the complex is promoted by the metal cations that bind the polar heads of the lipid with the negatively charged phosphate groups of DNA. The complex is rather heterogeneous with respect to size and shape and exhibits the lamellar symmetry of the L(c)(alpha) phase: the structure consists of an ordered multilamellar assembly similar to that recently found in cationic liposome-DNA complexes, where the hydrated DNA helices are sandwiched between the liposome bilayers. The experimental results show that, at equilibrium, globules of the triple complex in the L(c)(alpha) phase coexist with globules of multilamellar vesicles of DOPC in the L(alpha) phase, the volume ratio of the two structures being dependent on the molar ratio of the three components DOPC, DNA, and Mn2+. These complexes are of potential interest for applications as synthetically based nonviral carriers of DNA vectors for gene therapy.

Small-angle x-ray scattering from lipid bilayers is well described by modified Caillé theory but not by paracrystalline theory

X-ray scattering data at high instrumental resolution are reported for multilamellar vesicles of L alpha phase lipid bilayers of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine at 50 degrees C under varying osmotic pressure. The data are fitted to two theories that account for noncrystalline disorder, paracrystalline theory (PT) and modified Caillé theory (MCT). The MCT provides good fits to the data, much better than the PT fits. The particularly important characteristic of MCT is the long power law tails in the scattering. PT fits (as well as ordinary integration with no attempt to account for the noncrystalline disorder) increasingly underestimate this scattering intensity as the order h increases, thereby underestimating the form factors used to obtain electron density profiles.

Bilayer structure and physical dynamics of the cytochrome b5 dimyristoylphosphatidylcholine interaction

Cytochrome b5 is a microsomal membrane protein which provides reducing potential to delta 5-, delta 6-, and delta 9-fatty acid desaturases through its interaction with cytochrome b5 reductase. Low angle x-ray diffraction has been used to determine the structure of an asymmetrically reconstituted cytochrome b5:DMPC model membrane system. Differential scanning calorimetry and fluorescence anisotropy studies were performed to examine the bilayer physical dynamics of this reconstituted system. These latter studies allow us to constrain structural models to those which are consistent with physical dynamics data. Additionally, because the nonpolar peptide secondary structure remains unclear, we tested the sensitivity of our model to different nonpolar peptide domain configurations. In this modeling approach, the nonpolar peptide moiety was arranged in the membrane to meet such chemically determined criteria as protease susceptibility of carboxyl- and amino-termini, tyrosine availability for pH titration and tryptophan 109 location, et cetera. In these studies, we have obtained a reconstituted cytochrome b5:DMPC bilayer structure at approximately 6.3 A resolution and conclude that the nonpolar peptide does not penetrate beyond the bilayer midplane. Structural correlations with calorimetry, fluorescence anisotropy and acyl chain packing data suggest that asymmetric cytochrome b5 incorporation into the bilayer increases acyl chain order. Additionally, we suggest that the heme peptide:bilayer interaction facilitates a discreet heme peptide orientation which would be dependent upon phospholipid headgroup composition.

Direct determination of crystallographic phases for diffraction data from lipid bilayers. I. Reliability and phase refinement

Direct analysis of lipid lamellar packing based on the probabilistic estimate of sigma 1- and sigma 2-triplet phase invariants is evaluated here for a large variety of bilayer structures than examined in an original study of this problem (Dorset, D.L., 1990. Biophys. J. 58:1077-1087). Using x-ray crystal structures of five phospholipids, three glycerides and two cerebrosides, lamellar diffraction data were generated at the approximately 3 A resolution often found experimentally from oriented multilayers. For structures where no significant density occurs at the unit cell origin, the ab initio phase determination is successful for six of the ten structures. A seventh structure can be solved if a limited set of sigma 2-triples are used to determine the initial phase set based on the hierarchy of the A2 values. Bilayers, e.g., with solvent at the origin, can be analyzed if a modified criterion for accepting phase estimates for sigma 1-triples is used, as suggested by the distribution of normalized structure factors and the number of probable single-valued phase domains. In all cases, partial phase determinations can be refined effectively by density modification ("flattening") of the hydrocarbon region in real space. A figure of merit suggested by Luzzati et al. (Luzzati, V., A. Tardieu, and D. Taupin. 1972. J. Mol. Biol. 64:269-286) used to evaluate the success of such refinement can be supplemented by an evaluation of density smoothness, which can also detect the presence of near structure homomorphs not identified by the former test for density flatness.

Direct determination of crystallographic phases for diffraction data from phospholipid multilamellar arrays

Direct determination of crystallographic phases based on probabilistic of sigma 1 and sigma 2 "triplet" structure invariants has been found to be an effective technique for structure analysis with lamellar x-ray or electron diffraction intensity data from phospholipids. In many cases, nearly all phase values are determined, permitting a structure density (electron density for x-ray diffraction; electrostatic potential for electron diffraction) map to be calculated, which is directly interpretable in terms of known bilayer lipid structure. The major source of error is found to be due to the distortion of observed electron diffraction intensity data by incoherent multiple scattering, which can significantly affect the appearance of the electrostatic potential map, but not the success of the phase determination, as long as the observed Patterson function can be interpreted.

Direct determination of phospholipid lamellar structure at 0.34-nm resolution

Low-dose, high-resolution electron microscopy combined with conventional direct-phasing methods based on the estimates of triplet-structure invariants are used to determine phase values for all observed electron-diffraction-structure factor magnitudes from epitaxially oriented multilamellar paracrystals of the phosphospholipid 1,2-dihexadecyl-sn-glycerophosphoethanolamine. The reverse Fourier transform of these phase-structure factors is a one-dimensional electrostatic potential map that strongly resembles the electron-density maps calculated from similar x-ray-diffraction data. Determination of the phase values for the electron-diffraction data with structure invariants alone is nearly as successful as the combined use of two separate methods, assigning values to 13 of the 16 reflections--i.e., the electrostatic potential map closely resembles the one calculated with all data.

The structure of oriented sphingomyelin bilayers

X-ray diffraction from oriented bilayers of sphingomyelin gave up to 14 orders of diffraction of a lamellar repeat of 68.5 A on the merididan and up to eight reflections, including a strong reflection at 4.2 A, on the equator. The diffraction spacings did not change when the sphingomyelin bilayers were exposed to different humidities. A direct analysis of the low resolution X-ray data, using deconvolution is presented. A comparison of the Patterson functions of sphingomyelin with those of phosphatidylcholine and phosphatidylethanolamine suggests that the molecular structure of sphingomyelin in oriented bilayers resembles the structure of both phosphatidylcholine and phosphatidylethanolamine. Molecular model calculations for sphingomyelin bilayers have also been performed. Electron density profiles of sphingomyelin bilayers at resolution of about 6 A and about 2.5 A are presented. Our results indicate that the phosphorylcholine head group of sphingomyelin is in the plane of the membrane and at right angles to the hydrocarbon chains, the hydrocarbon chains are nearly parallel to each other, and there is only a limited, if any, interdigitation of the hydrocarbon chains of the adjacent sphingomyelin molecules in the bilayer.