Aggregative adherence fimbriae form compact structures as seen by SAXS.

Bacterial colonization is mediated by fimbriae, which are thin hair-like appendages dispersed from the bacterial surface. The aggregative adherence fimbriae from enteroaggregative E. coli are secreted through the outer membrane and consist of polymerized minor and major pilin subunits. Currently, the understanding of the structural morphology and the role of the minor pilin subunit in the polymerized fimbriae are limited. In this study we use small-angle X-ray scattering to reveal the structural morphology of purified fimbriae in solution. We show that the aggregative fimbriae are compact arrangements of subunit proteins Agg5A + Agg3B which are assembled pairwise on a flexible string rather than extended in relatively straight filaments. Absence of the minor subunit leads to less compact fimbriae, but did not affect the length. The study provides novel insights into the structural morphology and assembly of the aggregative adherence fimbriae. Our study suggests that the minor subunit is not located at the tip of the fimbriae as previously speculated but has a higher importance for the assembled fimbriae by affecting the global structure.

The very small angle neutron scattering instrument at the National Institute of Standards and Technology.

A description and the performance of the very small angle neutron scattering diffractometer at the National Institute of Standards and Technology are presented. The measurement range of the instrument extends over three decades of momentum transfer q from 2 × 10-4 to 0.7 Å-1. The entire scattering angle range from 8 × 10-5 to π/6 rad (30°) can be measured simultaneously using three separate detector carriages on rails holding nine 2D detector arrays. Versatile choices of collimation options and neutron wavelength selection allow the q resolution and beam intensity to be optimized for the needs of the experiment. High q resolution is achieved using multiple converging-beam collimation with circular pinholes combined with refractive lenses and prisms. Relaxed vertical resolution with much higher beam intensity can be achieved with narrow slit collimation and a broad wavelength range chosen by truncating the moderator source distribution below 4 Šwith a Be crystalline filter and above 8 Šwith a supermirror deflector. Polarized beam measurements with full polarization analysis are also provided by a high-performance supermirror polarizer and spin flipper, capable of producing flipping ratios of over 100, along with a high-efficiency 3He polarization analyzer.

Computational Design of Homotetrameric Peptide Bundle Variants Spanning a Wide Range of Charge States.

With the ability to design their sequences and structures, peptides can be engineered to realize a wide variety of functionalities and structures. Herein, computational design was used to identify a set of 17 peptides having a wide range of putative charge states but the same tetrameric coiled-coil bundle structure. Calculations were performed to identify suitable locations for ionizable residues (D, E, K, and R) at the bundle's exterior sites, while interior hydrophobic interactions were retained. The designed bundle structures spanned putative charge states of -32 to +32 in units of electron charge. The peptides were experimentally investigated using spectroscopic and scattering techniques. Thermal stabilities of the bundles were investigated using circular dichroism. Molecular dynamics simulations assessed structural fluctuations within the bundles. The cylindrical peptide bundles, 4 nm long by 2 nm in diameter, were covalently linked to form rigid, micron-scale polymers and characterized using transmission electron microscopy. The designed suite of sequences provides a set of readily realized nanometer-scale structures of tunable charge that can also be polymerized to yield rigid-rod polyelectrolytes.

Colloid-like solution behavior of computationally designed coiled coil bundlemers.

The use of isotropic potential models of simple colloids for describing complex protein-protein interactions is a topic of ongoing debate in the biophysical community. This contention stems from the unavailability of synthetic protein-like model particles that are amenable to systematic experimental characterization. In this article, we test the utility of colloidal theory to capture the solution structure, interactions and dynamics of novel globular protein-mimicking, computationally designed peptide assemblies called bundlemers that are programmable model systems at the intersection of colloids and proteins. Small-angle neutron scattering (SANS) measurements of semi-dilute bundlemer solutions in low and high ionic strength solution indicate that bundlemers interact locally via repulsive interactions that can be described by a screened repulsive potential. We also present neutron spin echo (NSE) spectroscopy results that show high-Q freely-diffusive dynamics of bundlemers. Importantly, formation of clusters due to short-range attractive, inter-bundlemer interactions is observed in SANS even at dilute bundlemer concentrations, which is indicative of the complexity of the bundlemer charged surface. The similarities and differences between bundlemers and simple colloidal as well as complex protein-protein interactions is discussed in detail.

Oligomerization of Pharmaceutically Relevant Insulin Analogues for Varying Concentration and Salinity Revealed by Small-Angle X-ray Scattering.

Two different insulin analogues, insulin degludec and lithocholyl insulin, were studied by small-angle X-ray scattering with respect to their self-assembly and interactions in solution at different concentrations of insulin and salt, NaCl. Very different behavior was observed for the two. Insulin degludec, linked to a hexadecanedioic acid, consistently formed di-hexamers, without any further oligomeric growth upon screening of electrostatic repulsions, indicating a stable di-hexamer unit without further oligomerization, as expected in the presence of phenol. The other insulin analogue, linked to the sterol lithocholic acid, formed n-hexamers with n ranging from 1 to 15, increasing with NaCl concentration and insulin concentration, indicating attractive forces in competition with the electrostatic repulsion and solution entropy. At the highest concentration of insulin and NaCl, a liquid crystal phase was observed, which has not previously been identified, featuring a quadratic structure organized into layers, which might hold interesting properties for pharmaceutical applications.

Compact Thermal Actuation by Water and Flexible Hydrophobic Nanopore.

Efficient and compact energy conversion is at the heart of the sustainable development of humanity. In this work it is demonstrated that hydrophobic flexible nanoporous materials can be used for thermal-to-mechanical energy conversion when coupled with water. In particular, a reversible nonhysteretic wetting-drying (contraction-expansion) cycle provoked by periodic temperature fluctuations was realized for water and a superhydrophobic nanoporous Cu2(tebpz) MOF (tebpz = 3,3',5,5'-tetraethyl-4,4'-bipyrazolate). A thermal-to-mechanical conversion efficiency of ∼30% was directly recorded by high-precision PVT-calorimetry, while the operational cycle was confirmed by in operando neutron scattering. The obtained results provide an alternative approach for compact energy conversion exploiting solid-liquid interfacial energy in nanoscopic flexible heterogeneous systems.

Inflation Negative Compressibility during Intrusion-Extrusion of a Non-Wetting Liquid into a Flexible Nanoporous Framework.

Negative compressibility (NC) is a phenomenon when an object expands/shrinks in at least one of its dimensions upon compression/decompression. NC is very rare and is of great interest for a number of applications. In this work a gigantic (more than one order of magnitude higher compared to the reported values) NC effect was recorded during intrusion-extrusion of a non-wetting liquid into a flexible porous structure. For this purpose, in situ high-pressure neutron scattering, intrusion-extrusion experiments, and DFT calculations were applied to a system consisting of water and a highly hydrophobic Cu2(tebpz) metal-organic framework (MOF), which upon water penetration expands in a and c directions to demonstrate NC coefficients more than order of magnitude higher compared to the highest values ever reported. The proposed approach is not limited to the materials used in this work and can be applied to achieve coefficients of negative linear compressibility of more than 103 TPa-1.

Recombinant expression of computationally designed peptide-bundlemers in Escherichia coli.

Computational design of fully artificial peptides is extensively researched by material scientists and engineers for the construction of novel nanostructures and biomaterials. Such design has yielded a peptide-based building block or bundlemer, a coiled coil peptide assembly that undergoes further physical-covalent interactions to form 1D, 2D and, potentially, 3D hierarchical assemblies and displays targeted and biomimetic material properties. Recombinant expression is a convenient, flexible tool to synthesize such artificial and modified peptides in large quantities while also enabling economical synthesis of isotopically labeled peptides and longer protein-like artificial peptides. This report describes the protocol for recombinant expression of a 31-amino acid, computationally designed bundlemer-forming peptide in Escherichia coli. Peptide yields of 10 mgs per liter of media were achieved which highlights complementary advantages of recombinant expression technique relative to conventional laboratory-scale synthesis, such as solid-phase peptide synthesis.

Giant Negative Compressibility by Liquid Intrusion into Superhydrophobic Flexible Nanoporous Frameworks.

Materials or systems demonstrating negative linear compressibility (NLC), whose size increases (decreases) in at least one of their dimensions upon compression (decompression) are very rare. Materials demonstrating this effect in all their dimensions, negative volumetric compressibility (NVC), are exceptional. Here, by liquid porosimetry and in situ neutron diffraction, we show that one can achieve exceptional NLC and NVC values by nonwetting liquid intrusion in flexible porous media, namely in the ZIF-8 metal-organic framework (MOF). Atomistic simulations show that the volumetric expansion is due to the presence of liquid in the windows connecting the cavities of ZIF-8. This discovery paves the way for designing novel materials with exceptional NLC and NVC at reasonable pressures suitable for a wide range of applications.

Multi-Step Unfolding and Rearrangement of α-Lactalbumin by SDS Revealed by Stopped-Flow SAXS.

Interactions between proteins and surfactants are both of fundamental interest and relevant for applications in food, cosmetics and detergency. The anionic surfactant sodium dodecyl sulfate (SDS) denatures essentially all proteins. Denaturation typically involves a number of distinct steps where growing numbers of SDS molecules bind to the protein, as seen in multidisciplinary approaches combining several complementary techniques. We adopt this approach to study the SDS-induced unfolding of Ca2+-depleted α-lactalbumin (aLA), a protein particularly sensitive toward denaturation by surfactants. By combining stopped-flow mixing of protein and surfactant solutions with stopped-flow synchrotron small-angle X-ray scattering (SAXS), circular dichroism (CD) and Trp fluorescence, together with information from previous calorimetric studies, we construct a detailed picture of the unfolding process at the level of both protein and surfactant. A protein-surfactant complex is formed within the dead time of mixing (2.5 ms). Initially a cluster of SDS molecules binds asymmetrically, i.e., to one side of the protein, after which aLA redistributes around the SDS cluster. This occurs in two kinetic steps where the complex grows in number of both SDS and protein molecules, concomitant with protein unfolding. During these steps, the core-shell complex undergoes changes in shell thickness as well as core shape and radius. The entire process is very sensitive to SDS concentration and completes within 10 s at an SDS:aLA ratio of 9, decreasing to 0.2 s at 60 SDS:aLA. The number of aLA molecules per SDS complex drops from 1.9 to 1.0 over this range of ratios. While both CD and Trp kinetics reveal a fast and a slow conformational transition, only the slow transition is observed by SAXS, indicating that the protein-SDS complex (which is monitored by SAXS) adjusts to the presence of the unfolded protein. We attribute the rapid unfolding of aLA to its predominantly α-helical structure, which persists in SDS (albeit as isolated helices), enabling aLA to unfold without undergoing major secondary structural changes unlike ß-sheet rich proteins. Nevertheless, the overall unfolding steps are broadly similar to those of the more ß-rich protein ß-lactoglobulin, suggesting that this unfolding model is representative of the general process of SDS-unfolding of proteins.

Correlation of the hierarchical structure with rheological behavior of polypseudorotaxane gel composed of pluronic and ß-cyclodextrin.

We have identified the hierarchical (primary, secondary, tertiary and quaternary) structures of a polypseudorotaxane (PPR) gel composed of the Pluronic F108 and ß-cyclodextrin system to be ß-cyclodextrin crystalline, lamellar sheets, lamellar stacks and "grains", respectively. The correlation between the rheological properties and the proposed structures under shear flows was rationalized. Alignment of lamellar stacks and reorganization of grain boundaries under shear flows were investigated by rheo-SANS, small angle X-ray scattering and small-angle light scattering. The relaxation of highly aligned lamellar stacks is slow (>2 h) after flow cessation compared to that of the regrouped grains (a few minutes). The main contribution to thixotropic behavior is likely from the faster relaxation of the reorganized grains containing highly oriented lamellar stacks. The comprehensive understanding of structure-function relationship of the PPR gel will facilitate the rational design for its applications.

Threading-Unthreading Transition of Linear-Ring Polymer Blends in Extensional Flow.

Adding small amounts of ring polymers to a matrix of their linear counterparts is known to increase the zero-shear-rate viscosity because of linear-ring threading. Uniaxial extensional rheology measurements show that, unlike its pure linear and ring constituents, the blend exhibits an overshoot in the stress growth coefficient. By combining these measurements with ex-situ small-angle neutron scattering and nonequilibrium molecular dynamics simulations, this overshoot is shown to be driven by a transient threading-unthreading transition of rings embedded within the linear entanglement network. Prior to unthreading, embedded rings deform affinely with the linear entanglement network and produce a measurably stronger elongation of the linear chains in the blend compared to the pure linear melt. Thus, rings uniquely alter the mechanisms of transient elongation in linear polymers.

Polyelectrolyte character of rigid rod peptide bundlemer chains constructed via hierarchical self-assembly.

Short α-helical peptides were computationally designed to self-assemble into robust coiled coils that are antiparallel, homotetrameric bundles. These peptide bundle units, or 'bundlemers', have been utilized as anisotropic building blocks to construct bundlemer-based polymers via a hierarchical, hybrid physical-covalent assembly pathway. The bundlemer chains were constructed using short linker connections via 'click' chemistry reactions between the N-termini of bundlemer constituent peptides. The resulting bundlemer chains appear as extremely rigid, cylindrical rods in transmission electron microscopy (TEM) images. Small angle neutron scattering (SANS) shows that these bundlemer chains exist as individual rods in solution with a cross-section that is equal to that of a single coiled coil bundlemer building block of ≈20 Å. SANS further confirms that the interparticle solution structure of the rigid rod bundlemer chains is heterogeneous and responsive to solution conditions, such as ionic-strength and pH. Due to their peptidic constitution, the bundlemer assemblies behave like polyelectrolytes that carry an average charge density of approximately 3 charges per bundlemer as determined from SANS structure factor data fitting, which describes the repulsion between charged rods in solution. This repulsion manifests as a correlation hole in the scattering profile that is suppressed by dilution or addition of salt. Presence of rod cluster aggregates with a mass fractal dimension of ≈2.5 is also confirmed across all samples. The formation of such dense, fractal-like cluster aggregates in a solution of net repulsive rods is a unique example of the subtle balance between short-range attraction and long-rage repulsion interactions in proteins and other biomaterials. With computational control of constituent peptide sequences, it is further possible to deconvolute the underlying sequence driven structure-property relationships in the modular bundlemer chains.

Structure of Phospholipid Mixed Micelles (Bicelles) Studied by Small-Angle X-ray Scattering.

Mixed phospholipid micelles (bicelles) are widely applied in nuclear magnetic resonance (NMR) studies of membrane proteins in solution, as they can solubilize these proteins and provide a membrane-like environment. In this work, the structure of bicelles of dihexanoyl phosphatidyl choline (DHPC) and dimyristoyl phosphatidyl choline (DMPC) at different ratios was determined by small-angle X-ray scattering (SAXS) at 37 °C. Samples with concentrations as applied for NMR measurements with 28 wt % lipids were diluted to avoid concentration effects in the SAXS data. The DMPC/DHPC ratio within the bicelles was kept constant by diluting with solutions of finite DHPC concentrations, where the concentration of free DHPC is the same as in the original solution. Absolute-scale modeling of the SAXS data using molecular and concentration constraints reveals a relatively complex set of morphologies of the lipid aggregates as a function of the molar ratio Q of DMPC to DHPC. At Q = 0 (pure DHPC lipids), oblate core-shell micelles are present. At Q = 0.5, the bicelles have a tablet-shaped core-shell cylindrical form with an ellipsoidal cross section. For Q = 1, 2, 3.2, and 4, the bicelles have a rectangular cuboidal structure with a core and a shell, for which the overall length and width increase with Q. At Q = ∞ (pure DMPC), there is coexistence between multilamellar structures and free bilayers. For Q = 1-4, the hydrocarbon core is relatively narrow and the headgroup thickness on the flat areas is larger than that of, respectively, pure DHPC and DMPC, suggesting some mixing of DHPC into these areas and staggering of the molecules. This is further supported by comparisons of the ratio of the areas of rim and flat parts and estimates of the composition of the flat areas.

Effects of multiple scattering encountered for various small-angle scattering model functions.

In small-angle scattering theory and data modeling, it is generally assumed that each scattered ray - photon or neutron - is only scattered once on its path through the sample. This assumption greatly simplifies the interpretation of the data and is valid in many cases. However, it breaks down under conditions of high scattering power, increasing with sample concentration, scattering contrast, sample path length and ray wavelength. For samples with a significant scattering power, disregarding multiple scattering effects can lead to erroneous conclusions on the structure of the investigated sample. In this paper, the impact of multiple scattering effects on different types of scattering pattern are determined, and methods for assessing and addressing them are discussed, including the general implementation of multiple scattering effects in structural model fits. The modification of scattering patterns by multiple scattering is determined for the sphere scattering function and the Gaussian function, as well as for different Sabine-type functions, including the Debye-Andersen-Brumberger (DAB) model and the Lorentzian scattering function. The calculations are performed using the semi-analytical convolution method developed by Schelten & Schmatz [J. Appl. Cryst. (1980 ▸). 13, 385-390], facilitated by analytical expressions for intermediate functions, and checked with Monte Carlo simulations. The results show how a difference in the shape of the scattering function plotted versus momentum transfer q results in different multiple scattering effects at low q, where information on the particle mass and radius of gyration is contained.

Invisible detergents for structure determination of membrane proteins by small-angle neutron scattering.

A novel and generally applicable method for determining structures of membrane proteins in solution via small-angle neutron scattering (SANS) is presented. Common detergents for solubilizing membrane proteins were synthesized in isotope-substituted versions for utilizing the intrinsic neutron scattering length difference between hydrogen and deuterium. Individual hydrogen/deuterium levels of the detergent head and tail groups were achieved such that the formed micelles became effectively invisible in heavy water (D2 O) when investigated by neutrons. This way, only the signal from the membrane protein remained in the SANS data. We demonstrate that the method is not only generally applicable on five very different membrane proteins but also reveals subtle structural details about the sarco/endoplasmatic reticulum Ca2+ ATPase (SERCA). In all, the synthesis of isotope-substituted detergents makes solution structure determination of membrane proteins by SANS and subsequent data analysis available to nonspecialists.

GUB06-046, a novel secretin/glucagon-like peptide 1 co-agonist, decreases food intake, improves glycemic control, and preserves beta cell mass in diabetic mice.

Bariatric surgery is currently the most effective treatment of obesity, which has spurred an interest in developing pharmaceutical mimetics. It is thought that the marked body weight-lowering effects of bariatric surgery involve stimulated secretion of appetite-regulating gut hormones, including glucagon-like peptide 1. We here report that intestinal expression of secretin is markedly upregulated in a rat model of Roux-en-Y gastric bypass, suggesting an additional role of secretin in the beneficial metabolic effects of Roux-en-Y gastric bypass. We therefore developed novel secretin-based peptide co-agonists and identified a lead compound, GUB06-046, that exhibited potent agonism of both the secretin receptor and glucagon-like peptide 1 receptor. Semi-acute administration of GUB06-046 to lean mice significantly decreased cumulative food intake and improved glucose tolerance. Chronic administration of GUB06-046 to diabetic db/db mice for 8 weeks improved glycemic control, as indicated by a 39% decrease in fasting blood glucose and 1.6% reduction of plasma HbA1c levels. Stereological analysis of db/db mice pancreata revealed a 78% increase in beta-cell mass after GUB06-046 treatment, with no impact on exocrine pancreas mass or pancreatic duct epithelial mass. The data demonstrate beneficial effects of GUB06-046 on appetite regulation, glucose homeostasis, and beta-cell mass in db/db mice, without proliferative effects on the exocrine pancreas and the pancreatic duct epithelium. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Recent advances in X-ray compatible microfluidics for applications in soft materials and life sciences.

The increasingly narrow and brilliant beams at X-ray facilities reduce the requirements for both sample volume and data acquisition time. This creates new possibilities for the types and number of sample conditions that can be examined but simultaneously increases the demands in terms of sample preparation. Microfluidic-based sample preparation techniques have emerged as elegant alternatives that can be integrated directly into the experimental X-ray setup remedying several shortcomings of more traditional methods. We review the use of microfluidic devices in conjunction with X-ray measurements at synchrotron facilities in the context of 1) mapping large parameter spaces, 2) performing time resolved studies of mixing-induced kinetics, and 3) manipulating/processing samples in ways which are more demanding or not accessible on the macroscale. The review covers the past 15 years and focuses on applications where synchrotron data collection is performed in situ, i.e. directly on the microfluidic platform or on a sample jet from the microfluidic device. Considerations such as the choice of materials and microfluidic designs are addressed. The combination of microfluidic devices and measurements at large scale X-ray facilities is still emerging and far from mature, but it definitely offers an exciting array of new possibilities.

Transformation from Globular to Cylindrical Mixed Micelles through Molecular Exchange that Induces Micelle Fusion.

Transformations between different micellar morphologies in solution induced by changes in composition, salt, or temperature are well-known phenomena; however, the understanding of the associated kinetic pathways is still limited. Especially for mixed surfactant systems, the micelles can take a very wide range of structures, depending on the surfactant packing parameter and other thermodynamic conditions. Synchrotron-based small-angle X-ray scattering (SAXS) in combination with fast mixing using a stopped-flow apparatus can give direct access to the structural kinetics on a millisecond time scale. Here, this approach is used to study the formation of cylindrical micelles after mixing two solutions with globular micelles of the nonionic surfactant dodecyl maltoside (DDM) and the anionic surfactant sodium dodecyl sulfate (SDS), respectively. Two separate processes were identified: (i) a transition in micellar shell structure, interpreted as exchange of surfactant molecules resulting in mixed globular micelles, and subsequently, (ii) fusion into larger, cylindrical structures.

Tailoring Membrane Nanostructure and Charge Density for High Electrokinetic Energy Conversion Efficiency.

The electrokinetic energy conversion (EKEC) of hydraulic work directly into electrical energy has been investigated in charged polymeric membranes with different pore charge densities and characteristic diameters of the nanoporous network. The membranes were synthesized from blends of nitrocellulose and sulfonated polystyrene (SPS) and were comprehensively characterized with respect to structure, composition, and transport properties. It is shown that the SPS can be used as a sacrificial pore generation medium to tune the pore size and membrane porosity, which in turn highly affects the transport properties of the membranes. Furthermore, it is shown that very high EKEC efficiencies (>35%) are encountered in a rather narrow window of the properties of the nanoporous membrane network, that is, with pore diameters of ca. 10 nm and pore charge densities of 4.6 × 10(2) to 1.5 × 10(3) mol SO3(-) m(-3) for dilute solutions (0.03 M LiCl). The high absolute value of the efficiency combined with the determination of the optimal membrane morphology makes membrane-based EKEC devices a step closer to practical applications and high-performance membrane design less empirical.