Modern X-ray scattering studies of complex biological systems

The inhibition of fibril formation of lysozyme by sucrose and trehalose

The two disaccharides, trehalose and sucrose, have been compared in many studies due to their structural similarity. Both possess the ability to stabilise and reduce aggregation of proteins. Trehalose has also been shown to inhibit the formation of highly structured protein aggregates called amyloid fibrils. This study aims to compare how the thermal stability of the protein lysozyme at low pH (2.0 and 3.5) is affected by the presence of the two disaccharides. We also address the anti-aggregating properties of the disaccharides and their inhibitory effects on fibril formation. Differential scanning calorimetry confirms that the thermal stability of lysozyme is increased by the presence of trehalose or sucrose. The effect is slightly larger for sucrose. The inhibiting effects on protein aggregation are investigated using small-angle X-ray scattering which shows that the two-component system consisting of lysozyme and water (Lys/H2O) at pH 2.0 contains larger aggregates than the corresponding system at pH 3.5 as well as the sugar containing systems. In addition, the results show that the particle-to-particle distance in the sugar containing systems (Lys/Tre/H2O and Lys/Suc/H2O) at pH 2.0 is longer than at pH 3.5, suggesting larger protein aggregates in the former. Finally, the characteristic distance separating β-strands in amyloid fibrils is observed for the Lys/H2O system at pH 2.0, using wide-angle X-ray scattering, while it is not clearly observed for the sugar containing systems. This study further shows that the two disaccharides stabilise the native fold of lysozyme by increasing the denaturation temperature. However, other factors, such as a weakening of hydrophobic interactions and hydrogen bonding between proteins, might also play a role in their inhibitory effect on amyloid fibril formation.

Modulating hierarchical self-assembly in thermoresponsive intrinsically disordered proteins through high-temperature incubation time

The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this paradigm, some IDPs exhibit large-scale organization, such as liquid-liquid phase separation. In such cases, the structural plasticity has the potential to form numerous self-assembled structures out of thermal equilibrium. Here, we report that high-temperature incubation time is a defining parameter for micro and nanoscale self-assembly of resilin-like IDPs. Interestingly, high-resolution scanning electron microscopy micrographs reveal that an extended incubation time leads to the formation of micron-size rods and ellipsoids that depend on the amino acid sequence. More surprisingly, a prolonged incubation time also induces amino acid composition-dependent formation of short-range nanoscale order, such as periodic lamellar nanostructures. We, therefore, suggest that regulating the period of high-temperature incubation, in the one-phase regime, can serve as a unique method of controlling the hierarchical self-assembly mechanism of structurally disordered proteins.

Bridging attraction of condensed bovine serum albumin solution in the presence of trivalent ions: A SANS study

The bridging attraction of condensed bovine serum albumin (BSA) solution (D2O) in the presence of yttrium chloride (YCl3) was studied by small angle neutron scattering (SANS). With increasing the concentration of YCl3 (cY) from 3 to 15 mM and from 15 to 100 mM, the intensity in low-q region increases and then decreases. Combining the tri-axial ellipsoid (TaE) geometry and the multi-component sticky hard sphere (SHS) potential, a SHS-TaE model was established to quantitatively determine the size and distribution of particles. In this way, the structural mechanism of the aggregation-redissolution process in protein solution was demonstrated and discussed. As cY increases from 3 to 100 mM, the SHS radius rL decreases from ca. 2.97 to 2.50 nm, suggesting that the relatively well dispersed BSAs may form aggregates with various polydispersities. The axis a increases from 1.88 to 2.30 nm, while b and c decrease from 3.53 to 3.23 nm and from 4.12 to 3.55 nm, respectively. (RgTaE decreases from ca. 2.57 to 2.38 nm). Moreover, the scattering length density (SLD) of BSA decreases from 3.67 to 1.56 × 10-6 Å-2. All these results consistently indicate a strengthened attraction and the BSA molecules might shrink and tune out to be more like of oblate ellipsoid with increasing the amount of YCl3.

An atomistic view of rigid crystalline supramolecular polymers derived from short amphiphilic, α,β hybrid peptide

The spontaneous self-association of an amphiphilic α, β-hybrid peptide into supramolecular fibers and atomic details of the fibrillar assembly are reported.

Angular super-resolution retrieval in small-angle X-ray scattering

Small-angle X-ray scattering (SAXS) techniques enable convenient nanoscopic characterization for various systems and conditions. Unlike synchrotron-based setups, lab-based SAXS systems intrinsically suffer from lower X-ray flux and limited angular resolution. Here, we develop a two-step retrieval methodology to enhance the angular resolution for given experimental conditions. Using minute hardware additions, we show that translating the X-ray detector in subpixel steps and modifying the incoming beam shape results in a set of 2D scattering images, which is sufficient for super-resolution SAXS retrieval. The technique is verified experimentally to show superior resolution. Such advantages have a direct impact on the ability to resolve finer nanoscopic structures and can be implemented in most existing SAXS apparatuses both using synchrotron- and laboratory-based sources.

Architectural Change of the Shell-Forming Block from Linear to V-Shaped Accelerates Micellar Disassembly, but Slows the Complete Enzymatic Degradation of the Amphiphiles

Tuning the enzymatic degradation and disassembly rates of polymeric amphiphiles and their assemblies is crucial for designing enzyme-responsive nanocarriers for controlled drug delivery applications. The common methods to control the enzymatic degradation of amphiphilic polymers are to tune the molecular weights and ratios of the hydrophilic and hydrophobic blocks. In addition to these approaches, the architecture of the hydrophilic block can also serve as a tool to tune enzymatic degradation and disassembly. To gain a deeper understanding of the effect of the molecular architecture of the hydrophilic block, we prepared two types of well-defined PEG-dendron amphiphiles bearing linear or V-shaped PEG chains as the hydrophilic blocks. The high molecular precision of these amphiphiles, which emerges from the utilization of dendrons as the hydrophobic blocks, allowed us to study the self-assembly and enzymatic degradation and disassembly of the two types of amphiphiles with high resolution. Interestingly, the micelles of the V-shaped amphiphiles were significantly smaller and disassembled faster than those of the amphiphiles based on linear PEG. However, the complete enzymatic cleavage of the hydrophobic end groups was significantly slower for the V-shaped amphiphiles. Our results show that the V-shaped architecture can stabilize the unimer state and, hence, plays a double role in the enzymatic degradation and the induced disassembly and how it can be utilized to control the release of encapsulated or bound molecular cargo.

Direct Imaging of Superwetting Behavior on Solid-Liquid-Vapor Triphase Interfaces

A solid-liquid-vapor interface dominated by a three-phase contact line usually serves as an active area for interfacial reactions and provides a vital clue to surface behavior. Recently, direct imaging of the triphase interface of superwetting interfaces on the microscale/nanoscale has attracted broad scientific attention for both theoretical research and practical applications, and has gradually become an efficient and intuitive approach to explore the wetting behaviors of various multiphase interfaces. Here, recent progress on characterizing the solid-liquid-vapor triphase interface on the microscale/nanoscale with diverse types of imaging apparatus is summarized. Moreover, the accurate, visible, and quantitative information that can be obtained shows the real interfacial morphology of the wetting behaviors of multiphase interfaces. On the basis of fundamental research, technical innovations in imaging and complicated multiphase interfaces of the superwetting surface are also briefly presented.

Reconstitution of SNARE proteins into solid-supported lipid bilayer stacks and X-ray structure analysis

SNAREs are known as an important family of proteins mediating vesicle fusion. For various biophysical studies, they have been reconstituted into supported single bilayers via proteoliposome adsorption and rupture. In this study we extended this method to the reconstitution of SNAREs into supported multilamellar lipid membranes, i.e. oriented multibilayer stacks, as an ideal model system for X-ray structure analysis (X-ray reflectivity and diffraction). The reconstitution was implemented through a pathway of proteomicelle, proteoliposome and multibilayer. To monitor the structural evolution in each step, we used small-angle X-ray scattering for the proteomicelles and proteoliposomes, followed by X-ray reflectivity and grazing-incidence small-angle scattering for the multibilayers. Results show that SNAREs can be successfully reconstituted into supported multibilayers, with high enough orientational alignment for the application of surface sensitive X-ray characterizations. Based on this protocol, we then investigated the effect of SNAREs on the structure and phase diagram of the lipid membranes. Beyond this application, this reconstitution protocol could also be useful for X-ray analysis of many further membrane proteins.

Phosphorylation-Induced Mechanical Regulation of Intrinsically Disordered Neurofilament Proteins

The biological function of protein assemblies has been conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it has been found that some assemblies contain long flexible regions that adopt multiple structural conformations. These include neurofilament proteins that constitute the stress-responsive supportive network of neurons. Herein, we show that the macroscopic properties of neurofilament networks are tuned by enzymatic regulation of the charge found on the flexible protein regions. The results reveal an enzymatic (phosphorylation) regulation of macroscopic properties such as orientation, stress response, and expansion in flexible protein assemblies. Using a model that explains the attractive electrostatic interactions induced by enzymatically added charges, we demonstrate that phosphorylation regulation is far richer and versatile than previously considered.

Structural Effects of Single Mutations in a Filamentous Viral Capsid Across Multiple Length Scales

Filamentous bacteriophage (phage) are single-stranded DNA viruses that infect bacteria. Single-site mutants of fd phage have been studied by magic-angle spinning nuclear magnetic resonance and by small-angle X-ray scattering. Detailed analysis has been performed that provides insight into structural variations on three length scales. The results, analyzed in conjunction with existing literature data, suggest that a single charge mutation on the capsid surface affects direct interviral interactions but not the structure of individual particles or the macroscale organization. On the other hand, a single hydrophobic mutation located at the hydrophobic interface that stabilizes capsid assembly alters the atomic structure of the phage, mainly affecting intersubunit interactions, affects its macroscale organization, that is, the pitch of the cholesteric liquid crystal formed by the particles, but skips the nanoscale hence does not affect direct interparticle interactions. An X-ray scattering under osmotic pressure assay provides the effective linear charge density of the phage and we obtain values of 0.6 Å^-1 and 0.4 Å^-1 for fd and M13 phage, respectively. These values agree with a simple consideration of a single cylinder with protein and DNA charges spread according to the most recent atomic-resolution models of the phage.

Molecular Precision and Enzymatic Degradation: From Readily to Undegradable Polymeric Micelles by Minor Structural Changes

Studying the enzymatic degradation of synthetic polymers is crucial for the design of suitable materials for biomedical applications ranging from advanced drug delivery systems to tissue engineering. One of the key parameters that governs enzymatic activity is the limited accessibility of the enzyme to its substrates that may be collapsed inside hydrophobic domains. PEG-dendron amphiphiles can serve as powerful tools for the study of enzymatic hydrolysis of polymeric amphiphiles due to the monodispersity and symmetry of the hydrophobic dendritic block, which significantly simplifies kinetic analyses. Using these hybrids, we demonstrate how precise, minor changes in the hydrophobic block are manifested into tremendous changes in the stability of the assembled micelles toward enzymatic degradation. The obtained results emphasize the extreme sensitivity of self-assembly and its great importance in regulating the accessibility of enzymes to their substrates. Furthermore, the demonstration that the structural differences between readily degradable and undegradable micelles are rather minor, points to the critical roles that self-assembly and polydispersity play in designing biodegradable materials.

Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept

Characterizing biomolecular interactions is crucial to the understanding of biological processes. Existing characterization methods have low spatial resolution, poor specificity, and some lack the capability for deep tissue imaging. We describe a novel technique that relies on small-angle X-ray scattering signatures from high-contrast molecular probes that correlate with the presence of biomolecular interactions. We describe a proof-of-concept study that uses a model system consisting of mixtures of monomer solutions of gold nanoparticles (GNPs) as the non-interacting species and solutions of GNP dimers linked with an organic molecule (dimethyl suberimidate) as the interacting species. We report estimates of the interaction fraction obtained with the proposed small-angle X-ray scattering characterization method exhibiting strong correlation with the known relative concentration of interacting and non-interacting species.

Probing the interactions of intrinsically disordered proteins using nanoparticle tags

The structural plasticity of intrinsically disordered proteins serves as a rich area for scientific inquiry. Such proteins lack a fix three-dimensional structure but can interact with multiple partners through numerous weak bonds. Nevertheless, this intrinsic plasticity possesses a challenging hurdle in their characterization. We underpin the intermolecular interactions between intrinsically disordered neurofilaments in various hydrated conditions, using grafted gold nanoparticle (NP) tags. Beyond its biological significance, this approach can be applied to modify the surface interaction of NPs for the creation of future tunable "smart" hybrid biomaterials.

Parallel force assay for protein-protein interactions

Quantitative proteome research is greatly promoted by high-resolution parallel format assays. A characterization of protein complexes based on binding forces offers an unparalleled dynamic range and allows for the effective discrimination of non-specific interactions. Here we present a DNA-based Molecular Force Assay to quantify protein-protein interactions, namely the bond between different variants of GFP and GFP-binding nanobodies. We present different strategies to adjust the maximum sensitivity window of the assay by influencing the binding strength of the DNA reference duplexes. The binding of the nanobody Enhancer to the different GFP constructs is compared at high sensitivity of the assay. Whereas the binding strength to wild type and enhanced GFP are equal within experimental error, stronger binding to superfolder GFP is observed. This difference in binding strength is attributed to alterations in the amino acids that form contacts according to the crystal structure of the initial wild type GFP-Enhancer complex. Moreover, we outline the potential for large-scale parallelization of the assay.

Time resolved SAXS to study the complexation of siRNA with cationic micelles of divalent surfactants

The complexation of siRNA (small interfering RNA) with cationic micelles was studied using time dependent synchrotron SAXS. Micelles were formed by two types of divalent cationic surfactants, i.e. Gemini bis(quaternary ammonium) bromide with variable spacer length (12-3-12, 12-6-12, 12-12-12) and a weak electrolyte surfactant (SH14) with triazine head. Immediately after mixing (t < 50 ms), new large aggregates appeared in solution and the scattering intensity at low q increased. Concomitantly, the presence of a quasi-Bragg peak at q ∼ 1.5 nm(-1) indicated core structuring within the complexes. We hypothesize that siRNA and micelles are alternately arranged into "sandwiches", forming domains with internal structural coherence. The process of complex reorganization followed a first-order kinetics and was completed in less than about 5 minutes, after which a steady state was reached. Aggregates containing Geminis were compact globular structures whose gyration radii Rg depended on the spacer length and were in the order of 7-27 nm. Complexes containing SH14 (Rg = 14-16 nm) were less ordered and possessed a looser internal arrangement. The obtained data, joint with previous structural investigation using Dynamic Light Scattering, Zeta Potential and Small Angle Neutron Scattering, are encouraging evidence for using these systems in biological trials. In fact we showed that transfection agents can be obtained by simply mixing a micelle solution of the cationic surfactant and a siRNA solution, both of which are easily prepared and stable.