Interaction of the full-length Bax protein with biomimetic mitochondrial liposomes: a small-angle neutron scattering and fluorescence study.

In response to apoptotic stimuli, the pro-apoptotic protein Bax inserts in the outer mitochondrial membrane, resulting in the formation of pores and the release of several mitochondrial components, and sealing the cell's fate. To study the binding of Bax to membranes, we used an in vitro system consisting of 50nm diameter liposomes prepared with a lipid composition mimicking that of mitochondrial membranes in which recombinant purified full-length Bax was inserted via activation with purified tBid. We detected the association of the protein with the membrane using fluorescence fluctuation methods, and found that it could well be described by an equilibrium between soluble and membrane-bound Bax and that at a high protein-to-liposome ratio the binding seemed to saturate at about 15 Bax proteins per 50nm diameter liposome. We then obtained structural data for samples in this saturated binding regime using small-angle neutron scattering under different contrast matching conditions. Utilizing a simple model to fit the neutron data, we observed that a significant amount of the protein mass protrudes above the membrane, in contrast to the conjecture that all of the membrane-associated Bax states are umbrella-like. Upon protein binding, we also observed a thinning of the lipid bilayer accompanied by an increase in liposome radius, an effect reminiscent of the action of antimicrobial peptides on membranes.

Development of a Polarizable Interatomic Potential for Molten Lithium, Sodium, and Potassium Nitrate.

A polarizable interatomic potential is developed for atomistic simulations of molten MNO3 (M = Li, Na, K) salts. The potential is parametrized using a force matching method relying on the adjustment of parameters such that density functional theory generated forces, stress tensors, and dipole moments are reproduced. Simulations conducted using the new potential are used to estimate physical parameters of the melt, which are then compared with available experimental results. The average calculated densities of NaNO3 and KNO3 are within 2% of the experimental value within the temperature range studied, while that of LiNO3 is within 3%. Thermal conductivities and viscosities are estimated using equilibrium calculations and the Green-Kubo method. The thermal conductivity values of NaNO3 and KNO3 are found to match well with experimental data, while that of LiNO3 is approximately 20% larger than experimentally determined values throughout the temperature ranges simulated. The calculated viscosities are also in good agreement with experimentally determined values. The (NaxK1-x)NO3 mixture is also investigated, with densities, thermal conductivities, and viscosities determined and compared with experimentally determined values where available. Additionally, radial and angular distribution function data is presented for all salts, revealing details of the atom-level structures present in the melts. We have found that the new interatomic potential is effective for atom scale modeling of the physical properties of molten nitrate salts.

Characterization of anisotropic poly(vinyl alcohol) hydrogel by small- and ultra-small-angle neutron scattering.

Poly(vinyl alcohol) (PVA) hydrogels are formed from PVA solution when physical cross-links form during freeze/thaw cycling. By applying a stress during the freeze/thaw process, PVA hydrogels with anisotropic mechanical properties are produced. We have used small- and ultra-small-angle neutron scattering to study the structure at length scales of 2 nm to 10 mum. By supplementing the neutron data with data from atomic force microscopy, we have probed a large range of length scales within which structural changes responsible for bulk anisotropy occur. We model the gel as interconnected PVA blobs of size 20-50 nm arranged in fractal aggregates extending to micrometers or tens of micrometers. Bulk mechanical anisotropy appears to be due to the alignment of blobs and connections between blobs. This information is essential for tailoring mechanical properties for applications where anisotropy is desirable such as to match the properties of natural tissue in coronary grafts and to control diffusive properties in active wound dressings.

What determines the thickness of a biological membrane.

Membrane thickness is thought to play a key role in protein function. Thus understanding the cell's ability to modulate the thickness of its membranes is essential in elucidating the structure/function relationship in biological membranes. We have investigated the influence of cholesterol on the structure of "thin" (diC14:1PC) and "thick" (diC22:1PC) phospholipid bilayers using oriented multibilayers and small angle neutron diffraction. Neutron contrast variation was used to determine the structure factors and the distribution of water across the bilayers. We found that in response to cholesterol, bilayer thickness changed in a similar fashion in both systems. The thickening of bilayers was rationalized in terms of cholesterol's ordering effect on the lipid's acyl chains, which dominates over the other option of rectifying the hydrophobic mismatch, surprisingly even in the case of diC22:1PC and cholesterol.

Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data.

Quantitative structures were obtained for the fully hydrated fluid phases of dioleoylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC) bilayers by simultaneously analyzing x-ray and neutron scattering data. The neutron data for DOPC included two solvent contrasts, 50% and 100% D(2)O. For DPPC, additional contrast data were obtained with deuterated analogs DPPC_d62, DPPC_d13, and DPPC_d9. For the analysis, we developed a model that is based on volume probability distributions and their spatial conservation. The model's design was guided and tested by a DOPC molecular dynamics simulation. The model consistently captures the salient features found in both electron and neutron scattering density profiles. A key result of the analysis is the molecular surface area, A. For DPPC at 50 degrees C A = 63.0 A(2), whereas for DOPC at 30 degrees C A = 67.4 A(2), with estimated uncertainties of 1 A(2). Although A for DPPC agrees with a recently reported value obtained solely from the analysis of x-ray scattering data, A for DOPC is almost 10% smaller. This improved method for determining lipid areas helps to reconcile long-standing differences in the values of lipid areas obtained from stand-alone x-ray and neutron scattering experiments and poses new challenges for molecular dynamics simulations.

Effect of cations on the structure of bilayers formed by lipopolysaccharides isolated from Pseudomonas aeruginosa PAO1.

The asymmetric outer membrane of Gram-negative bacteria contains lipopolysaccharides (LPSs) which contribute significantly to the bacterium's surface properties and play a crucial role in regulating membrane permeability. We report on neutron diffraction studies performed on aligned, self-assembled bilayers of Na-, Ca-, and Mg-salt forms of LPS isolated from Pseudomonas aeruginosa PAO1. From the one-dimensional neutron scattering length density profiles we find that water penetrates Ca2+-LPS bilayers to a lesser extent than either Na+- or Mg2+-LPS bilayers. This differential water penetration could have implications as to how small molecules permeate the outer membrane of Gram-negative bacteria and, possibly, how nonlamellar phases are formed.

Small-angle neutron scattering to detect rafts and lipid domains.

The detection and characterization of lateral heterogeneities or domains in lipid mixtures has attracted considerable interest, because of the roles that such domains may play in biological function. Studies on both model and cell membranes demonstrate that domains can be formed over a wide range of length scales, as small as nanometers in diameter up to microns. However, although the size and shape of micron-sized domains are readily visualized in freely suspended vesicles, by techniques such as fluorescence microscopy, imaging of nanometer-sized domains has thus far been performed only on substrate-supported membranes (through, e.g., atomic force microscopy), whereas additional evidence for nanodomains has depended on indirect detection (through, e.g., nuclear magnetic resonance or fluorescence resonance energy transfer). Small-angle neutron scattering (SANS) is a technique able to characterize structural features on nanometer length scales and can be used to probe freely suspended membranes. As such, SANS shows promise to characterize nanometer-sized domains in model membranes. The authors have recently demonstrated the efficacy of SANS to detect and characterize nanodomains in freely suspended mixed lipid vesicles.

Bilayer thickness and thermal response of dimyristoylphosphatidylcholine unilamellar vesicles containing cholesterol, ergosterol and lanosterol: a small-angle neutron scattering study.

Small-angle neutron scattering (SANS) measurements are performed on pure dimyristoyl phosphatidylcholine (DMPC) unilamellar vesicles (ULV) and those containing either 20 or 47 mol% cholesterol, ergosterol or lanosterol. From the SANS data, we were able to determine the influence of these sterols on ULV bilayer thickness and vesicle area expansion coefficients. While these parameters have been determined previously for membranes containing cholesterol, to the best of our knowledge, this is the first time such results have been presented for membranes containing the structurally related sterols, ergosterol and lanosterol. At both molar concentrations and at temperatures ranging from 10 to 45 degrees C, the addition of the different sterols leads to increases in bilayer thickness, relative to pure DMPC. We observe large differences in the influence of these sterols on the membrane thermal area expansion coefficient. All three sterols, however, produce very similar changes to membrane thickness.

The influence of curvature on membrane domains.

An interdependence between local curvature and domain formation has been observed in both cell and model membranes. An implication of this observation is that domain formation in model membranes may be modulated by membrane curvature. In this paper, small-angle neutron scattering (SANS) is used to examine the influence of membrane curvature (i.e., vesicle size) on the formation of membrane domains. It is found that, although vesicle size and polydispersity are not significantly altered by the formation of membrane domains, the area fraction occupied by domains depends on the overall vesicle size. In particular, increasing membrane curvature (i.e., decreasing vesicle size) results in increased area fractions of membrane domains.

Curvature effect on the structure of phospholipid bilayers.

High-resolution small-angle X-ray scattering (SAXS), complemented by small-angle neutron scattering (SANS) and dynamic light scattering (DLS) experiments, was used to study the effect of curvature on the bilayer structure of dioleoyl-phosphatidylcholine (DOPC) and dioleoyl-phosphatidylserine (DOPS) unilamellar vesicles (ULVs). Bilayer curvature, as a result of finite vesicle size, was varied as a function of vesicle radius and determined by DLS and SANS measurements. Unilamellarity of large DOPC ULVs was achieved by the addition of small amounts (up to 4 mol %) of the charged lipid, DOPS. A comparison of SANS data over the range of 0.02 < q <0.2 A-1 indicated no change in the overall bilayer thickness as a function of ULV diameter (620 to 1840 A). SANS data were corroborated by high-resolution (0.06 < q <0.6 A-1) SAXS data for the same diameter ULVs and data obtained from planar samples of aligned bilayers. Both the inner and outer leaflets of the bilayer were found to be indistinguishable. This observation agrees well with simple geometric models describing the effect of vesicle curvature. However, 1220-A-diameter pure DOPS ULVs form asymmetric bilayers whose structure can most likely be rationalized in terms of geometrical constraints coupled with electrostatic interactions, rather than curvature alone.

Spontaneously forming ellipsoidal phospholipid unilamellar vesicles and their interactions with helical domains of saposin C.

We have observed a bimodal distribution of ellipsoidal unilamellar vesicles (ULVs) in a phospholipid mixture composed of dioleoyl phosphatidylserine (DOPS) and dipalmitoyl and dihexanoyl phosphatidylcholine, DPPC and DHPC, respectively. Dynamic light scattering and transmission electron microscopy data indicate a bimodal size distribution of these nanoparticles with hydrodynamic radii of approximately 200 and >500 nm, while small-angle neutron scattering data were fit using a model of coexisting monodisperse morphologies, namely, oblate and triaxial ellipsoidal vesicles. Unlike DOPS ULV formed by sonication, which can fuse days after being formed, these ULVs are stable over a period of 12 months at 4 degrees C. We also report on the structure of these ULVs associated with the two helical peptide domains (H1 and H2) of a glucosylprotein, namely, Saposin C, to gain some insight into protein-membrane interactions.

Comparison of solution structures and stabilities of native, partially unfolded and partially refolded pepsin.

A zymogen-derived protein, pepsin, appears to be incapable of folding to the native state without the presence of the prosegment. To better understand the nature of the irreversible denaturation of pepsin, the present study reports on the characterization of the stability and low-resolution tertiary and secondary structures of native, alkaline unfolded and acid refolded porcine pepsin. Through a combination of small-angle neutron scattering (SANS), CD, and DSC, acid refolded pepsin (Rp) was shown to have secondary and tertiary structures intermediate between the alkaline denatured and native forms but was found to be thermodynamically stable relative to the native state. It was also observed that the acid refolded state of pepsin was dependent on the protein concentration during refolding because CD and SANS data revealed that both the secondary and tertiary structures of concentrated-refolded pepsin (>10 mg/mL) (CRp) were native-like, in contrast to the intermediate nature of Rp, refolded under dilute concentration (<10 mg/mL). Despite a native-like conformation, CRp was more stable and had substantially reduced activity compared to that of the native state, suggesting that the protein was misfolded. It is proposed that the stable but misfolded, acid-refolded states are evidence that pepsin in its native conformation was metastable. Furthermore, the disruption of the active site cleft in the denatured states could be discerned by modeling of the SANS data.

"Bicellar" lipid mixtures as used in biochemical and biophysical studies.

Over the past decade "bicellar" lipid mixtures composed of the long-chain dimyristoyl phosphatidylcholine (DMPC) and the short-chain dihexanoyl PC (DHPC) molecules have emerged as a powerful medium for studying membrane associated, biologically relevant macromolecules and assemblies. Depending on temperature, lipid concentration and composition these lipid mixtures can assume a variety of morphologies, some of them alignable in the presence of a magnetic field. This article will examine the biophysical studies that have elucidated the various morphologies assumed by these lipid mixtures, and their use in the biochemical studies of biomolecules.

Spontaneously formed unilamellar vesicles with path-dependent size distribution.

We observe the spontaneous formation of path-dependent monodisperse and polydisperse phospholipid unilamellar vesicles (ULV) from two different equilibrium morphologies specifically, disklike micelles and extended lamellae, respectively. On heating beyond a temperature Tc, low temperature disklike micelles, or so-called bicelles, transform into lamellae. Dilution of the lamellar phase, at a fixed temperature, results in a complete unbinding transition and the formation of polydisperse ULV, demonstrating the instability of the lamellar phase. On the other hand, heating of a dilute bicellar phase above Tc results in monodisperse ULV, which on cooling revert back to bicelles for lipid concentrations phi > or = 0.5 wt % and transform into oblate ellipsoids for phi = 0.1 wt %, a morphology not previously seen in "bicellar" lipid mixtures. Monodisperse ULV reform on heating of the oblate ellipsoids.