Spatial resolution of the variable-period x-ray standing-wave method as applied to model membranes.

A series of model membranes as Langmuir-Blodgett (LB) films composed of long-chain zinc alkanoates (saturated fatty acid salts) was used to evaluate the spatial resolution of the variable-period x-ray standing-wave (XSW) technique. The chain length dependence of the zinc mean position (z) above the supporting substrate demonstrates that it is possible to detect differences in (z) of 1-2 A. Thus 1-2 A is the spatial resolution of the method in the current application. The data show that the chain tilt angle is chain length dependent, varying from 40 degrees to 0 degrees for alkanoates 18 and 24 carbon atoms long, respectively. The spread about the mean position of the zinc in the film, sigma(in), was found to be independent of chain length at 10.0 A for all members of the series. Sigma(in) was shown to be insensitive to the presence of a "spacer" omega-tricosenoic acid (omegaTA) bilayer placed between the zinc alkanoate LB film and the coated gold mirror. However, an overlayer of omegaTA sharpened the zinc ion distribution and lowered the chain tilt angle. This study provides important information regarding sample composition and constitution that facilitates membrane structure determination by XSWs.     

Membrane protein structure determination using paramagnetic tags

The combination of paramagnetic tagging strategies with NMR or EPR spectroscopic techniques can revolutionize de novo structure determination of helical membrane proteins. Leveraging the full potential of this approach requires optimal labeling strategies and prediction of membrane protein topology from sparse and low-resolution distance restraints, as addressed by Chen et?al. (2011).     

One-dimensional acoustic standing waves in rectangular channels for flow cytometry

Flow cytometry has become a powerful analytical tool for applications ranging from blood diagnostics to high throughput screening of molecular assemblies on microsphere arrays. However, instrument size, expense, throughput, and consumable use limit its use in resource poor areas of the world, as a component in environmental monitoring, and for detection of very rare cell populations. For these reasons, new technologies to improve the size and cost-to-performance ratio of flow cytometry are required. One such technology is the use of acoustic standing waves that efficiently concentrate cells and particles to the center of flow channels for analysis. The simplest form of this method uses one-dimensional acoustic standing waves to focus particles in rectangular channels. We have developed one-dimensional acoustic focusing flow channels that can be fabricated in simple capillary devices or easily microfabricated using photolithography and deep reactive ion etching. Image and video analysis demonstrates that these channels precisely focus single flowing streams of particles and cells for traditional flow cytometry analysis. Additionally, use of standing waves with increasing harmonics and in parallel microfabricated channels is shown to effectively create many parallel focused streams. Furthermore, we present the fabrication of an inexpensive optical platform for flow cytometry in rectangular channels and use of the system to provide precise analysis. The simplicity and low-cost of the acoustic focusing devices developed here promise to be effective for flow cytometers that have reduced size, cost, and consumable use. Finally, the straightforward path to parallel flow streams using one-dimensional multinode acoustic focusing, indicates that simple acoustic focusing in rectangular channels may also have a prominent role in high-throughput flow cytometry.     

Membrane structure in isolated and intact myelins.

The biochemical composition of myelin and the topology of its constituent lipids and proteins are typically studied using membranes that have been isolated from whole, intact tissue using procedures involving hypotonic shock and sucrose density gradient centrifugation. To what extent, however, are the structure and intermembrane interactions of isolated myelin similar to those of intact myelin? We have previously reported that intact and isolated myelins do not always show identical myelin periods, indicating a difference in membrane-membrane interactions. The present study addresses the possibility that this is due to altered membrane structure. Because x-ray scattering from isolated myelin sometimes consists of overlapping Bragg reflections or is continuous, we developed nonlinear least squares procedures for analyzing the total intensity distribution after film scaling, background subtraction, and Lorentz correction. We calculated electron density profiles of isolated myelin for comparison with membrane profiles from intact myelin. The change in the width of the extracellular space and the relative invariance of the cytoplasmic space as a function of pH and ionic strength that we previously found for intact nerve was largely paralleled by isolated myelin. There were two exceptions: isolated CNS myelin was resistant to swelling under all conditions, and isolated PNS myelin in hypotonic saline showed indefinite swelling at the extracellular apposition. However, electron density profiles of isolated myelins, calculated to 30 A resolution, did not show any major change in structure compared with intact myelin that could account for the differences in interactions.     

Interdigitated structure of phospholipid-alcohol systems studied by x-ray diffraction.

In the interdigitated structure of phosphatidylcholine/alcohol systems, the one-dimensional electron density profile in the direction normal to the membrane surface is generated from the x-ray diffraction pattern. The membrane thickness for these systems is expressed by the sum of the hydrocarbon chain lengths of phosphatidylcholine and alcohol molecules. For this study, various sets of phosphatidylcholines and 1-alcohols were used; a phosphatidylcholine has a carbon number from 14 to 18 in a hydrocarbon chain, and an alcohol has a carbon number from 1 (methanol) to 4 (1-butanol). Based upon the results, we propose a model for the interdigitated structure in which 1) two alcohol molecules occupy a volume whose surface is surrounded interstitially by the headgroups of phosphatidylcholine molecules, and 2) the methyl ends of both hydrocarbon chains in alcohol and phosphatidylcholine molecules face each other at the bottom of the volume.     

Selection, characterization and x-ray structure of anti-ampicillin single-chain Fv fragments from phage-displayed murine antibody libraries

Single-chain Fv (scFv) antibody libraries were constructed from mice immunized with an ampicillin-bovine serum albumin conjugate. Several antibodies with specificity for intact ampicillin were selected by phage display and characterized. The antibody scFv fragment aL2 binds to intact ampicillin and shows no detectable cross-reactivity with hydrolyzed ampicillin. We determined the X-ray structures of two crystal forms of w.t. aL2, which differ mainly in the side-chain conformation of Trp H109 (according to a new consensus nomenclature Kabat residue number H95) in the extremely short (three residues) CDR H3 and the presence or absence of a well-resolved molecule of 2-methyl-pentane-2,4-diol in the bottom of the binding pocket. Attempts to co-crystallize aL2 with its antigen or to diffuse ampicillin into the wild-type aL2 crystals were unsuccessful, since crystal contacts obstruct the binding pocket. However, a mutant with two point mutations near the N terminus (Gln H6 replaced by Glu and Ala H10 (Kabat H9) replaced by Gly) crystallized in a form compatible with antigen-binding. Although the mutations affect the conformation of framework I, the conformations of the binding pocket of the uncomplexed wild-type aL2 and of the mutant complex were almost identical. The structure explains the specificity of the antibody for intact ampicillin and the degree of cross-reactivity of aL2 with a wide variety of ampicillin analogs. This antibody system will be very useful as a diagnostic reagent for antibiotics use and abuse, as a model for the effect of expression of antibiotic binding molecules in Escherichia coli, and for directed evolution towards high antibiotic resistance.     

Membrane retrieval in the guinea pig neurohypophysis: biochemical characterization of a retrieval structure

[3H]Choline and [35S]methionine injected into the guinea pig hypothalamus in vivo were incorporated into the lipids and proteins, respectively, of secretory vesicles transported to the neural lobe. Prolonged in vivo stimulation of hormone secretion by dehydration decreased the [3H]choline content of secretory vesicles, with a concomitant increase in the [3H]choline content of a membrane fraction isolated on sucrose gradients. After stimulation of neural lobes in vitro in the presence of horseradish peroxidase, this extracellular fluid marker was found in the same membrane fraction. SDS electrophoresis of membrane proteins radiolabelled by [35S]methionine in vivo demonstrated that this fraction contained at least one major protein also present in the secretory vesicle membrane. These results suggest that we have isolated a membrane fraction containing the structure(s) involve in membrane retrieval in the neurohypophysis.     

Membrane binding induces destabilization of cytochrome c structure.

The effect of membranes binding on the structure and stability of ferricytochrome c was studied by Fourier-transform infrared spectroscopy and differential scanning calorimetry. Association of cytochrome c with phospholipid membranes containing phosphatidylglycerol as a model acidic phospholipid results in only slight, if any, perturbation of the protein secondary structure. However, upon membrane binding, there is a considerable increase in the accessibility of protein backbone amide groups to hydrogen-deuterium exchange, which suggests a lipid-mediated loosening and/or destabilization of the protein tertiary structure. A lipid-induced conformational perturbation of ferricytochrome c is also indicated by a marked decrease in the thermodynamic stability of the membrane-bound protein. Upon binding to membranes containing dimyristoylphosphatidylglycerol (DMPG) or dioleoylphosphatidylglycerol (DOPG) as a single lipid component, the denaturation temperature of ferricytochrome c decreases by approximately 30 degrees C. This is accompanied by a decrease in the calorimetric enthalpy of denaturation, particularly for the DMPG-associated protein. With ferricytochrome c bound to membranes containing a mixture of DMPG (or DOPG) and zwitterionic phosphatidylcholine, the extent of structural perturbation depends on the surface density of the negatively charged lipid head groups, becoming smaller with decreasing proportions of acidic phospholipid in the membrane. The observed destabilization of protein structure mediated by acidic phospholipids (and possibly formation of folding intermediates at the membrane surface) may represent a general property of a larger class of water-soluble proteins for which membrane binding is governed by electrostatic forces.