PDBe: Protein Data Bank in Europe.

The Protein Data Bank in Europe (PDBe; pdbe.org) is a partner in the Worldwide PDB organization (wwPDB; wwpdb.org) and as such actively involved in managing the single global archive of biomacromolecular structure data, the PDB. In addition, PDBe develops tools, services and resources to make structure-related data more accessible to the biomedical community. Here we describe recently developed, extended or improved services, including an animated structure-presentation widget (PDBportfolio), a widget to graphically display the coverage of any UniProt sequence in the PDB (UniPDB), chemistry- and taxonomy-based PDB-archive browsers (PDBeXplore), and a tool for interactive visualization of NMR structures, corresponding experimental data as well as validation and analysis results (Vivaldi).

PDBe: Protein Data Bank in Europe.

The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive of bio-macromolecular structure data, the Protein Data Bank (PDB). PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new database infrastructure based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The group has developed new services that allow users to carry out simple textual queries or more complex 3D structure-based queries. The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe database. PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.

Properties of plasma membranes of Phsp 70-ipt transformed tobacco (Nicotiana tabacum).

Application of 10 successive daily heat shocks reduced the growth of control tobacco (Nicotiana tabacum L. cv. Petit Havana SR1) plants by about 15%; for Phsp 70-ipt transformed plants this is about 48%. The shoot diameter of these ipt-transformed plants increased by about 75%. In addition, in heat shock treated ipt-plants (IPT-HS) the upper lateral buds grew out due to a reduction of apical dominance. The older leaves of IPT-HS plants had a higher chlorophyll content. In spite of the observed effects due to a higher endogenous cytokinin content in the IPT-HS plants, no significant changes were observed on the plasma membrane fatty acid composition, nor on its fluidity as determined from the steady-state fluorescence anisotropy of DPH. Only a minor change in the plasma membrane free sterol composition was found as evidenced by a 20% decrease in the stigmasterol to sitosterol ratio in IPT-HS, indicative for a possible anti-senescence effect of enhanced endogenous cytokinins, but without significant effects on the plasma membrane function.

Physical effects of biologically formed cholesterol oxidation products on lipid membranes investigated with fluorescence depolarization spectroscopy and electron spin resonance.

Planar oriented membranes of 1-palmitoyl, 2-oleoyl-phosphatidylcholine (POPC) containing cholesterol, 19-hydroxycholesterol, 22S-hydroxycholesterol, or 25-hydroxycholesterol in concentrations up to 5 mol % were investigated with angle-resolved fluorescence depolarization and electron spin resonance measurements. Analyses of the data with the Brownian diffusion model show that the oxysterols have structural effects similar to those of cholesterol: an increase in molecular order and no change in the rotational diffusion coefficients of the probe molecules. Time-resolved fluorescence anisotropy measurements on diphenylhexatriene (DPH) in small unilamellar vesicles of POPC and DOPC were performed using oxysterols commonly found in oxidized low density lipoproteins (LDL) in comparison to membranes containing cholesterol or no sterols. Analyses using the Brownian rotational diffusion model show that most LDL-oxysterols affect the vesicle physical structure in a manner similar to cholesterol, viz. an increase in molecular order and a decrease in the dynamics. Cholesterol-alpha-epoxide has a much smaller ordering effect than cholesterol in POPC-vesicles. A similar effect was found for 7 beta-hydroxycholesterol in DOPC-vesicles. The tendency of the oxysterols to influence the molecular order as compared to pure cholesterol may contribute to cell membrane permeability changes affecting crucial cell functions and events leading to vascular cell injury. Increased LDL oxysterol levels may account for some of the structural changes noted for oxidatively modified LDL as well as its toxicity to vascular cells.

Effect of lipid molecular structure and gramicidin A on the core of lipid vesicle bilayers. A time-resolved fluorescence depolarization study.

We have investigated the molecular orientational order and reorientational dynamics of the fluorescent probe 1,6-diphenyl-1,3,5-hexatriene (DPH) in the core of the membrane bilayer. Vesicles of lipids of varying unsaturation and headgroup (POPC, DOPC, DLPC, DLLPC, EGGPG, DOPG, DGDG, and SQDG) were studied using the time-resolved fluorescence anisotropy of DPH. Generally, values of the second order parameter for DPH are found to be very small. However, this should not be interpreted as DPH having low orientational order as witnessed by large values of the next relevant order parameter . This implies considerable transverse populations of DPH molecules within the bilayer. In phosphatidylcholines with an acyl chain of 18 carbon atoms, the value of for DPH decreases with increasing lipid unsaturation and even attains negative values. No effect of the lipid headgroup on the order and dynamics of DPH is detected. Furthermore, we study the peptide-lipid interaction of the hydrophobic antibiotic gramicidin A (gA) in DOPC vesicles using DPH. The nonchannel conformation has an ordering effect on DPH in the bilayer core, which the channel confirmation lacks. This can be understood in terms of the geometrical shape of the gA dimer, as shown previously with the probes TMA-DPH and DPHPC [Muller, J. M., et al. (1995) Biochemistry 34, 3092]. We find that for DPH data the conventional Brownian rotational diffusion (BRD) model and the compound motion model (CMM) give equivalent fits. In this respect, DPH differs from TMA-DPH and DPHPC, for which probes only the CMM allowed a consistent interpretation of the molecular orientation.

Effect of gramicidin A on structure and dynamics of lipid vesicle bilayers. A time-resolved fluorescence depolarization study.

We investigated the effects of the hydrophobic small peptide antibiotic gramicidin A (gA) on the properties of vesicle bilayers in the liquid crystalline state. Time-resolved fluorescence anisotropy experiments were performed with unilamellar vesicles of the lipids DMPC, POPC, DOPC, EGGPC, DLPC, DOPG, and SQDG containing various concentrations of gA in two different conformations using TMA-DPH and DPHPC as fluorescent probes. These analogues of DPH were taken to study the gA induced change in the structural and dynamical properties of the lipid bilayer in different portions of the hydrophobic region. The time-resolved anisotropy data were analyzed using the recently introduced compound motion model [van der Sijs, D. A., et al. (1993) Chem. Phys. Lett. 216, 559; Muller, J. M., et al. (1994) Chem. Phys. 185, 393]. In general, gA raises the order and reduces the rotational diffusion coefficient for the probes in the bilayer. In DOPC vesicles this ordering effect of gA on the bilayer is found to depend on both the conformation of the peptide and the depth in the bilayer at which the order is probed. This significant effect of gA conformation on the lipid order parameter profile suggests that the shape of the gA dimer in the bilayer, which is determined by its conformation, affects the order of the adjacent DOPC lipid acyl chains.

The interpretation of the time-resolved fluorescence anisotropy of diphenylhexatriene-phosphatidylcholine using the compound motion model.

Time-resolved fluorescence anisotropy experiments on lipid membranes can provide estimates of the molecular order and motion on microscopic scales. For the analysis of anisotropy data the so-called compound motion model was recently introduced to overcome problems with conventional models. We show that this novel model gives good fits for the time-resolved anisotropy of the fluorescent probe diphenylhexatriene-phosphatidylcholine (DPHPC) and can be successfully used to interpret experiments with DPHPC embedded in small unilamellar vesicles of the lipids DMPC, POPC, DOPC, DLPC, DERPC, DOPE, POPE, EGGPG and SQDG. The lifetime and order parameters are found to be intermediate between those found for the related DPH and TMA-DPH fluorescent probes, while the rotational diffusion of DPHPC is much slower. These findings can be rationalised in terms of the position of the DPH-fluorophore of DPHPC in the bilayer.

Determination of the directions of the transition dipoles in tetrabutylperylene in stretched polymers.

The directions of the transition dipole moments of 2,5,8,11,-tetra-butylperylene were determined from angle-resolved fluorescence depolarization experiments on molecules embedded in a stretched anhydrous nitrocellulose matrix. The absorption transition moments lies almost parallel to the elongated axis of the molecule, but the emission transition moment makes an angle of 20° with the axis. The orientational distribution of the molecules in the polymer indicates significant deviations from a circular form.

On the interpretation of fluorescence anisotropy decays from probe molecules in lipid vesicle systems.

Measurements of fluorescence depolarization decays are widely used to obtain information about the molecular order and rotational dynamics of fluorescent probe molecules in membrane systems. This information is obtained by least-squares fits of the experimental data to the predictions of physical models for motion. Here we present a critical review of the ways and means of the data analysis and address the question how and why totally different models such as Brownian rotational diffusion and "wobble-in-cone" provide such convincing fits to the fluorescence anistropy decay curves. We show that while these models are useful for investigating the general trends in the behavior of the probe molecules, they fail to describe the underlying motional processes. We propose to remedy this situation with a model in which the probe molecules undergo fast, though restricted local motions within a slowly rotating cage in the lipid bilayer structure. The cage may be envisaged as a free volume cavity between the lipid molecules, so that its position and orientation change with the internal conformational motions of the lipid chains. This approach may be considered to be a synthesis of the wobble-in-cone and Brownian rotational diffusion models. Importantly, this compound motion model appears to provide a consistent picture of fluorescent probe behavior in both oriented lipid bilayers and lipid vesicle systems.

Structural and dynamic effects of oxidatively modified phospholipids in unsaturated lipid membranes.

Phospholipid hydroperoxides and phospholipid alcohols are two of the major forms of oxidatively modified phospholipids produced during oxidant stress and lipid peroxidation. The process of lipid peroxidation is known to affect the physiological function of membranes. We, therefore, investigated the effects of lipid peroxidation products on the molecular interactions in membranes. Our study was specifically focused on the effects of lipid peroxidation products on static membrane structure (molecular orientational order) and on the reorientational dynamics of the probe molecules in lipid bilayers. The study was done by performing angle-resolved fluorescence depolarization measurements (AFD) on the fluorescent probe diphenylhexatriene (DPH) and by performing angle-resolved electron spin resonance (A-ESR) measurements on cholestane (CSL) nitroxide spin probes embedded in macroscopically oriented planar bilayers consisting of 2-10% 1-palmitoyl-2-(9/13-hydroperoxylinoleoyl)phosphatidylcholine (PLPC-OOH) or 1-palmitoyl-2-(9/13-hydroxylinoleoyl)phosphatidylcholine (PLPC-OH) in 1-palmitoyl-2-linoleoylphosphatidylcholine (PLPC) or dilinoleoylphosphatidylcholine (DLPC). Both probe molecules have rigid cylindrical geometries and report on the overall molecular order and dynamics. However, being more polar, the nitroxide spin probe CSL is preferentially located near the surface of the membrane, while the less polar fluorescent probe DPH reports preferentially near the central hydrophobic region of the lipid bilayers. The results show that the presence of relatively small amounts of oxidatively modified phospholipids within the PLPC or DLPC membranes causes pronounced structural effects as the molecular orientational order of the probe molecules is strongly decreased. In contrast, the effect on membrane reorientational dynamics is minimal.

Effects of steroid molecules on the dynamical structure of dioleoylphosphatidylcholine and digalactosyldiacylglycerol bilayers.

The ESR spectra of cholestane spin labels (CSL) in dioleoylphosphatidylcholine (DOPC) bilayers containing 20 wt% of cholesterol, 7-dehydrocholesterol, beta-sitosterol, stigmasterol and lanosterol exhibit a marked similarity, thus indicating that these steroids induced the same effects on the lipid bilayer over the temperature range 21-55 degrees C. The incorporation of these steroids into the DOPC bilayers enhances the orientational order of the CSL molecules at every temperature studied, but only induces a pronounced slow-down in their rotational motions at temperatures above 35 degrees C. Similar results were obtained in DOPC/ergosterol multilamellar liposomes, but the changes are now less pronounced than in the other five DOPC/steroid systems. In contrast, the addition of stigmasterol to digalactosyldiacylglycerol (DGDG) bilayers appears to increase the order parameter mean value of P2, without affecting the diffusion coefficients. Furthermore, the incorporation of 7-dehydrocholesterol to DGDG bilayers causes a large enhancement in the orientational order, but has only a small effect on D perpendicular of the CSL molecules. Importantly, this latter effect appears to be independent of temperature. The marked changes in the rates of the rotational motion brought about by the addition of steroids, contrasts with the lack of a significant effect of unsaturation on the bilayer dynamics reported by us previously (Korstanje et al. (1989), Biochim. Biophys. Acta 980, 225-233, and 982, 196-204).

Order and dynamics in the lamellar L alpha and in the hexagonal HII phase. Dioleoylphosphatidylethanolamine studied with angle-resolved fluorescence depolarization.

Fluorescence depolarization techniques are used to determine the molecular order and reorientational dynamics of the probe molecule TMA-DPH embedded in the lamellar L alpha and the hexagonal HII phases of lipid/water mixtures. The thermotropically induced L alpha----HII phase transition of the lipid DOPE is used to obtain macroscopically aligned samples in the hexagonal HII phase at 45 degrees C from samples prepared in the lamellar L alpha phase at 7 degrees C. The interpretation of angle-resolved fluorescence depolarization experiments on these phases, within the framework of the rotational diffusion model, yields the order parameters (P2) and (P4), and the diffusion constants for the reorientational motions. The reorientational motion rates of the TMA-DPH molecules in the hexagonal HII phase are comparable with those in the lamellar L alpha phase. Furthermore, the lateral diffusion of the probe molecule on the surface of the lipid/water cylinder in the hexagonal phase is found to be considerably slower than the reorientational motion.

The membrane fluidity concept revisited by polarized fluorescence spectroscopy on different model membranes containing unsaturated lipids and sterols.

Quantitative analysis of time-resolved anisotropy measurements of DPH or TMA-DPH in lipid vesicles yields more than one mathematically correct solution. The solutions differ with respect to the average orientation and to the reorientational dynamics of the probe molecules in the bilayer. This leads to quite opposite results regarding the effects of cholesterol on membrane fluidity. One solution predicts an increase in fluidity, the other a decrease. Angle-resolved fluorescence depolarization (AFD) measurements of probes in oriented lipid bilayers enable determination of the average orientation of the probes in the bilayer and, if the fluorescence decay function is known, of the reorientational dynamics. Analysis of AFD measurements of DPH and TMA-DPH show that increasing unsaturation leads to a decrease in molecular order and a decrease in reorientational dynamics (= fluidity) of the probes. At temperatures above the phase transition of the lipids, the addition of cholesterol causes an increase in molecular order and an increase in reorientational dynamics (= fluidity). The plant sterol stigmaterol, which is structurally closely related to cholesterol, has different effects than cholesterol. The effects vary with the structure of the surrounding lipids. The membrane fluidity concept as it was originally proposed by Chapman attempts to describe the structural and dynamic properties of lipids in a membrane using one single parameter indicated as 'membrane fluidity'. Our results show that it is necessary to distinguish between structural parameters describing molecular order and motion parameters describing molecular dynamics, thus supporting a similar suggestion by Seelig and Seelig. In order to be useful, the membrane fluidity concept has to be limited to the parameters describing molecular dynamics.

The fidelity of response by 1-[4-(trimethylammonio)phenyl]-6-phenyl-1,3,5-hexatriene in time-resolved fluorescence anisotropy measurements on lipid vesicles. Effects of unsaturation, headgroup and cholesterol on orientational order and reorientational dynamics.

Time-resolved fluorescence anisotropy measurements on 1-[4-(tri-methylammonio)phenyl]-6-phenyl-1,3,5-hexatriene (TMA-DPH) molecules in lipid vesicles of palmitoyloleoylphosphatidylcholine (POPC), PC extracted from egg yolk (EggPC), dioleoyl-PC (DOPC), dilinoleoyl-PC (DLPC), phosphatidylglycerol extracted from egg yolk (EggPG), dioleoyl-PG (DOPG), sulfoquinovosyldiacylglycerol (SQDG) and digalactosyl-DG (DGDG) with and without cholesterol are presented. The observed intensity decay curves are analyzed simultaneously in terms of the Brownian rotational diffusion model. The analysis thus yields the isotropic fluorescence decay, the initial anisotropy r (0), the order parameters mean value of P2 and mean value of P4 as well as the diffusion coefficient of the long molecular axis. It is shown that increasing unsaturation in the acyl chains of the PC lipids results in an increase in the rotational diffusion rates of the probes and a decrease in the order parameter mean value of P2. However, the value of mean value of P4 remains unchanged. The corresponding orientational distribution function of the probes is bimodal, with fractions lying preferentially parallel and perpendicular to the local vesicle surface. Surprisingly, the fraction of probe molecules lying with their long axes parallel to the bilayer surface increases with increasing unsaturation with a concomitant narrowing in the width of the distribution of the fraction lying perpendicular to it. As expected, cholesterol is found to increase the order parameters in all the systems and to suppress the tendency of the molecules to lie parallel to the bilayer surface. Furthermore, the rotational diffusion coefficients of the probes is found to increase in all the systems except for DLPC. Interestingly, the effects of unsaturation on the reorientational dynamics of TMA-DPH molecules in the vesicle systems are opposite to those found in the corresponding planar multibilayers (Deinum et al. 1988), whereas the same cholesterol effect is observed for the two systems. Nevertheless, the TMA-DPH molecules exhibit higher diffusion coefficients in the vesicle than in the planar multibilayer systems. In addition, a unimodal distribution of the probe molecules is found in the multibilayer systems. The differences between the two systems are ascribed to the differences in the radius of curvature and the hydration of the bilayers. Lastly we rationalize the bimodal distribution of the TMA-DPH molecules in the vesicles in terms of their observed partition between the lipid and aqueous phases.

Orientational properties of biological pigments in ordered systems studied with polarized light: photosynthetic pigment-protein complexes in membranes.

A discussion is presented of the problems involved in the interpretation of linear dichroism and fluorescence depolarization experiments on macroscopically ordered membrane systems. Particular attention has been paid to ordered membranes containing photosynthetic pigment-protein complexes, but the mathematical treatment can equally well be applied to other systems. The information about the orientational properties of the pigments is obtained by the application of the theories developed for the characterization of the molecular orientational order in liquid-crystalline materials. It is shown that while linear dichroism only yields the order parameter S mu of the absorption transition moment, fluorescence depolarization experiments yield in addition the order parameter Sv of the emission transition moment as well as three orientational correlation functions of the two transition moments. It is argued that in general the latter information can only be obtained on utilizing a number of experimental scattering geometries. In particular, the merits of angle-resolved experiments are illustrated.

Molecular order and dynamics in planar lipid bilayers: effects of unsaturation and sterols.

Angle-resolved fluorescence depolarization experiments were carried out on 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-[4-(trimethylammonio)phenyl]-6-phenyl-1,3,5-hexatriene (TMA-DPH) molecules embedded in macroscopically oriented multilayers of saturated [dimyristoylphosphatidylcholine (DMPC)] and unsaturated [palmitoyloleoylphosphatidylcholine (POPC), dioleoylphosphatidylcholine (DOPC), dilineoylphosphatidylcholine (DLPC), plant digalactosyldiglyceride (DGDG)] lipids with and without cholesterol. In all the lipid systems studied the order parameter (P2) of TMA-DPH molecules was found to be higher than that for DPH. Considerations of the order parameter (P4), however, indicate that DPH molecules have a heterogeneous distribution in bilayers of unsaturated lipids, with a significant fraction of the molecules lying with their long axes parallel to the bilayer planes. Both the DPH and TMA-DPH molecules exhibit a decrease in the molecular order as well as a decrease in their rates of motion on increasing the unsaturation of the hydrocarbon chains. The addition of cholesterol tends to reverse this effect, with an increase in both the order and dynamics. Bilayers of DOPC, however, exhibit a somewhat different result. It is suggested that the discrepancies between these observations and findings with lipid vesicle systems simply reflect the effects of curvature on the behavior of the probe molecules. The results indicate that the concept of membrane fluidity must be used with great caution.

Angle resolved fluorescence depolarisation of 1,6-diphenyl-1,3,5 hexatriene (DPH) in unsaturated digalactosyl diacylglycerol (DGDG) lipid bilayers.

The orientational ordering and dynamics of DPH molecules embedded in macroscopically ordered bilayers of the unsaturated galactolipid digalactosyl diacylglycerol (DGDG) were studied by angle-resolved fluorescence depolarisation at room temperature. The depolarisation ratios exhibited a weaker angular dependence than those observed for DPH incorporated in multi-bilayers of saturated lecithins above their phase transition. The results reflect the differences in the modes of reorientational motion of the DPH molecules in these systems while a similar orientational order is found. It is suggested that DPH molecules in bilayers of DGDG cannot be considered to possess an effective cylindrical symmetry in contrast to DPH in bilayers of saturated lecithins.

Study of the orientational ordering of carotenoids in lipid bilayers by resonance-Raman spectroscopy.

The orientational ordering of beta-carotene and crocetin embedded in lamellar model membranes has been investigated by angle-resolved resonance Raman scattering at a temperature well above the phase transition of the lipid chains. It is shown that the ordering of the carotenoids is dependent on the chemical composition of the lipid bilayers. The orientational distribution functions found clearly show that beta-carotene is oriented parallel to the bilayer plane (dioleoyl lecithin) or perpendicular to it (soybean lecithin). For dimyristoyl lecithin at 40 degrees C, egg-lecithin, and digalactosyl diacylglycerol two maxima were found in the orientational distribution: one parallel and one perpendicular to the bilayer surface. Crocetin embedded in soybean lecithin bilayers yields a similar bimodal distribution function. Because of rapid photodegradation no results could be obtained for spirilloxanthin.

Angle resolved depolarised resonance Raman studies of beta-carotene in lipid/water mixtures.

The orientational ordering of beta-carotene incorporated in lamellar model membranes above their main phase transitions has been studied by angle resolved depolarised Resonance Raman scattering. The ordering strongly depends on the chemical composition of the lipid bilayers: in di-oleoyl lecithin (DOPC) the carotenoid molecules lie parallel to the bilayer plane, while in di-galactosyl diglyceride ( DGDG ) a bimodal distribution was found with molecules lying both parallel and perpendicular to the membrane phase.