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.

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.

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.

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.

Soft interactions at nanoparticles alter protein function and conformation in a size dependent manner.

Weak protein-nanoparticle (NP) interactions are studied in a low binding regime as a model for the soft protein corona around nanoparticles in complex biological fluids. Noncovalent, reversible interactions between Subtilisin Carlsberg (SC) and silica NPs shows significant alteration in conformation and enzymatic activity in a NP-size dependent manner. Very weak interactions between SC and silica NPs were revealed by centrifugation-based separations and further supported by small-angle X-ray scattering, while bovine serum albumin was used as a strongly interacting reference. Secondary and tertiary structure changes of SC were studied via circular dichroism and correlated to enzymatic activity where the enzyme kinetics showed a critical role for nanoparticle size.

SAXS investigation of a cubic to a sponge (L3) phase transition in self-assembled lipid nanocarriers.

The encapsulation and release of peptides, proteins, nucleic acids, and drugs in nanostructured lipid carriers depend on the type of the self-assembled liquid-crystalline organization and the structural dimensions of the aqueous and membraneous compartments, which can be tuned by the multicomponent composition of the systems. In this work, small-angle X-ray scattering (SAXS) investigation is performed on the 'melting' transition of the bicontinuous double diamond cubic phase, formed by pure glycerol monooleate (MO), upon progressive inclusion of varying fractions of pharmaceutical-grade glycerol monooleate (GO) in the hydrated system. The self-assembled MO/GO mixtures are found to form diamond (Pn3m) inverted cubic, inverted hexagonal (H(II)), and sponge (L(3)) phases at ambient temperature in excess of aqueous medium without heat treatment. Mixing of the inverted-cubic-phase-forming MO and the sponge-phase-forming GO components, in equivalent proportions (50/50 w/w), yields an inverted hexagonal (H(II)) phase nanostructured carrier. Scattering models are applied for fitting of the experimental SAXS patterns and identification of the structural changes in the aqueous and lipid bilayer subcompartments. The possibility of transforming, at ambient temperature (20 °C), the bicontinuous cubic nanostructures into inverted hexagonal (H(II)) or sponge (L(3)) mesophases may facilitate novel biomedical applications of the investigated liquid crystalline self-assemblies.