A SAXS and USAXS study of the influence of pH on the casein micelle structure

Changes in milk pH significantly influence the behavior and physical properties of casein micelles; however, the effects of these changes on casein micelle structures are still unclear. The aim of this study was to elucidate the effect of changes in pH range from 5.9 to 7.1 on the structure of casein micelles in milk using small-angle X-ray scattering (SAXS) and ultra small-angle X-ray scattering (USAXS). The casein micelles formed one-dimensional aggregates. The micelle radius decreased with decreasing pH, whereas the size of the water domain increased. The distance between colloidal calcium phosphates (CCP) remained unchanged, whereas the CCP radius decreased with decreasing pH. Voluminosity, which was calculated from scattering intensities, increased at increased pH. In conclusion, the micelle structure changed significantly in response to changes in pH. Our findings help to understand the changes in the physical properties of milk at various pH levels in terms of the microscopic structure.

Small-angle scattering of complex fluids in flow

Complex fluids encompass a significant proportion of the materials that we use today from feedstocks such as cellulose fibre dispersions, materials undergoing processing or formulation, through to consumer end products such as shampoo. Such systems exhibit intricate behaviour due to their composition and microstructure, particularly when analysing their texture and response to flow (rheology). In particular, these fluids when flowing may undergo transitions in their nano- to microstructure, potentially aligning with flow fields, breaking and reassembling or reforming, or entirely changing phase. This manifests as macroscopic changes in material properties, such as core-annular flow of concentrated emulsions in pipelines or the favourable texture of liquid soaps. Small-angle scattering provides a unique method for probing underlying changes in fluid nano- to microstructure, from a few angströms to several microns, of complex fluids under flow. In particular, the alignment of rigid components or shape changes of soft components can be explored, along with local inter-particle ordering and global alignment with macroscopic flow fields. This review highlights recent important developments in the study of such complex fluid systems that couple flow or shear conditions with small-angle scattering measurements, and highlights the physical insight obtained by these experiments. Recent results from neutron scattering measurements made using a simple flow cell are presented, offering a facile method to explore alignment of complex fluids in an easily accessible geometry, and contextualised within existing and potential future research questions.

Small-angle X-ray and neutron scattering applied to lipid-based nanoparticles: Recent advancements across different length scales

Lipid-based nanoparticles (LNPs), ranging from nanovesicles to non-lamellar assemblies, have gained significant attention in recent years, as versatile carriers for delivering drugs, vaccines, and nutrients. Small-angle scattering methods, employing X-rays (SAXS) or neutrons (SANS), represent unique tools to unveil structure, dynamics, and interactions of such particles on different length scales, spanning from the nano to the molecular scale. This review explores the state-of-the-art on scattering methods applied to unveil the structure of lipid-based nanoparticles and their interactions with drugs and bioactive molecules, to inform their rational design and formulation for medical applications. We will focus on complementary information accessible with X-rays or neutrons, ranging from insights on the structure and colloidal processes at a nanoscale level (SAXS) to details on the lipid organization and molecular interactions of LNPs (SANS). In addition, we will review new opportunities offered by Time-resolved (TR)-SAXS and -SANS for the investigation of dynamic processes involving LNPs. These span from real-time monitoring of LNPs structural evolution in response to endogenous or external stimuli (TR-SANS), to the investigation of the kinetics of lipid diffusion and exchange upon interaction with biomolecules (TR-SANS). Finally, we will spotlight novel combinations of SAXS and SANS with complementary on-line techniques, recently enabled at Large Scale Facilities for X-rays and neutrons. This emerging technology enables synchronized multi-method investigation, offering exciting opportunities for the simultaneous characterization of the structure and chemical or mechanical properties of LNPs.

Insights on the dynamic behavior of protein disulfide isomerase in the solution environment through the SAXS technique

The dynamic behavior of Protein Disulfide Isomerase (PDI) in an aqueous solution environment under physiologically active pH has been experimentally verified in this study using Small Angle X-ray Scattering (SAXS) technique. The structural mechanism of dimerization for full-length PDI molecules and co-complex with two renowned substrates has been comprehensively discussed. The structure models obtained from the SAXS data of PDI purified from bovine liver display behavior duality between unaccompanied-enzyme and after engaged with substrates. The analysis of SAXS data revealed that PDI exists as a homo-dimer in the solution environment, and substrate induction provoked its segregation into monomer to enable the enzyme to interact systematically with incoming clients.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00198-0.

Solvation Structure of Methanol-in-Salt Electrolyte Revealed by Small-Angle X-ray Scattering and Simulations

The solvation structure of water-in-salt electrolytes was thoroughly studied, and two competing structures─anion solvated structure and anion network─were well-defined in recent publications. To further reveal the solvation structure in those highly concentrated electrolytes, particularly the influence of solvent, methanol was chosen as the solvent for this proposed study. In this work, small-angle X-ray scattering, small-angle neutron scattering, Fourier-transform infrared spectroscopy, and Raman spectroscopy were utilized to obtain the global and local structural information. With the concentration increment, the anion network formed by TFSI- became the dominant structure. Meanwhile, the hydrogen bonds among methanol were interrupted by the TFSI- anion and formed a new connection with them. Molecular dynamic simulations with two different force fields (GAFF and OPLS-AA) are tested, and GAFF agreed with synchrotron small-angle X-ray scattering/wide-angle X-ray scattering (SAXS/WAXS) results well and provided insightful information about molecular/ion scale solvation structure. This article not only deepens the understanding of the solvation structure in highly concentrated solutions, but more importantly, it provides additional strong evidence for utilizing SAXS/WAXS to validate molecular dynamics simulations.

Recent advances in synchrotron scattering methods for probing the structure and dynamics of colloids

Recent progress in synchrotron based X-ray scattering methods applied to colloid science is reviewed. An important figure of merit of these techniques is that they enable in situ investigations of colloidal systems under the desired thermophysical and rheological conditions. An ensemble averaged simultaneous structural and dynamical information can be derived albeit in reciprocal space. Significant improvements in X-ray source brilliance and advances in detector technology have overcome some of the limitations in the past. Notably coherent X-ray scattering techniques have become more competitive and they provide complementary information to laboratory based real space methods. For a system with sufficient scattering contrast, size ranges from nm to several μm and time scales down to μs are now amenable to X-ray scattering investigations. A wide variety of sample environments can be combined with scattering experiments further enriching the science that could be pursued by means of advanced X-ray scattering instruments. Some of these recent progresses are illustrated via representative examples. To derive quantitative information from the scattering data, rigorous data analysis or modeling is required. Development of powerful computational tools including the use of artificial intelligence have become the emerging trend.

Structure-function analyses reveal Arabidopsis thaliana HDA7 to be an inactive histone deacetylase

Histone deacetylases (HDACs), responsible for the removal of acetyl groups from histone tails, are important epigenetic factors. They play a critical role in the regulation of gene expression and are significant in the context of plant growth and development. The Rpd3/Hda1 family of HDACs is reported to regulate key biological processes in plants, such as stress response, seed, embryonic, and floral development. Here, we characterized Arabidopsis thaliana HDA7, a Class I, Rpd3/Hda1 family HDAC. SAXS and AUC results show that the recombinantly expressed and purified histone deacetylase domain of AtHDA7 exists as a monomer in solution. Further, the crystal structure showed AtHDA7 to fold into the typical α/β arginase fold, characteristic of Rpd3/Hda1 family HDACs. Sequence analysis revealed that the Asp and His residues of the catalytic 'XDXH' motif present in functional Rpd3/Hda1 family HDACs are mutated to Gly and Pro, respectively, in AtHDA7, suggesting that it might be catalytically inactive. The Asp and His residues are important for Zn2+-binding. Not surprisingly, the crystal structure did not have Zn2+ bound in the catalytic pocket, which is essential for the HDAC activity. Further, our in vitro activity assay revealed AtHDA7 to be inactive as an HDAC. A search in the sequence databases suggested that homologs of AtHDA7 are found exclusively in the Brassicaceae family to which Arabidopsis belongs. It is possible that HDA7 descended from HDA6 through whole genome duplication and triplication events during evolution, as suggested in a previous phylogenetic study.

SAXS/WAXS data of conformationally flexible ribose binding protein

Modern artificial intelligence-based protein structure prediction methods, such as Alphafold2, can predict structures of folded proteins with reasonable accuracy. However, Alphafold2 provides a static view of a protein, which does not show the conformational variability of the protein, domain movement in a multi-domain protein, or ligand-induced conformational changes it might undergo in solution. Small-angle X-ay scattering (SAXS) and wide-angle X-ray scattering (WAXS) are solution techniques that can aid in integrative modeling of conformationally flexible proteins, or in validating their predicted ensemble structures. While SAXS is sensitive to global structural features, WAXS can expand the scope of structural modeling by including information about local structural changes. We present SAXS and WAXS datasets obtained from conformationally flexible d-ribose binding protein (RBP) from Escherichia coli in the ribose bound and unbound forms. SAXS/WAXS datasets of RBP provided here may aid in method development efforts for more accurate prediction of structural ensembles of conformationally flexible proteins, and their conformational changes.

Dual thermoresponsive polysaccharide derivative - water system. Partially substituted amylose butylcarbamate in water

Partially substituted amylose n-butylcarbamate (ABC) samples were synthesized with weight-average molar mass Mw ranging between 40 kg mol-1 and 220 kg mol-1 with different degree of substitution DS. When DS was between 0.17 and 0.33, the ABC samples were soluble in water. Furthermore, both LCST and UCST type phase separations were observed for the ABC samples in water when DS is >0.26. The closed-loop phase diagrams for the dual thermoresponsive ABC samples in water were constructed by turbidity measurement. The UCST ranged from 70 °C to 77 °C and the LCST ranged from 13 °C to 17 °C. SAXS measurements were performed for dilute aqueous ABC solutions to determine the chain conformation of ABC at various temperatures. The resulting form factor at the polymer mass concentration of 3 mg mL-1 indicated that the chain conformation is almost independent of temperature, except for the chain diameter, which is influenced by the temperature-dependent hydration behavior. This result suggests that the attractive interactions between ABC chains are not very significant even between UCST and LCST, where higher concentrated polymer solutions show macroscopic phase separation.

Structural analysis of polyglycerol fatty acid ester-coenzyme Q10 aggregates in solution

Polyglycerol fatty acid esters (PGFEs) are common food additives. PGFE-based formulations exhibit high structural stability, however, the stability mechanism of the micellar structures has not been yet elucidated. In this study, nanostructural analysis was performed using small-angle neutron and X-ray scattering (SANS and SAXS) measurements to reveal the mechanism of the structural stability of PGFE-coenzyme Q10 (CoQ10) mixtures as a CoQ10 formulation. Pure PGFE formed multilamellar vesicles, whereas PGFE-CoQ10 formed spherical micelles. Furthermore, when the amount of added water increased, the PGFE-CoQ10 micellar size and the amount of water in the micelles remained unchanged. A model-fitting analysis of the SANS results suggested that the CoQ10 molecules were introduced between the surfactants, forming a palisade-type structure. The high structural stability of the PGFE-CoQ10 micelles was attributed to two factors: proper spreading of the hydrophilic head chains and inhibition of the change of the amount of water inside the micelles by the PGFE heads and quinone ring of CoQ10. This indicates that PGFE-CoQ10 can function in water while maintaining the micellar structure formed in the storage solution. The findings of this study are important for the safety and nano-hazard aspects of PGFE-CoQ10 formulations.

Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids

Ions are important to modulate protein properties, including solubility and stability, through specific ion effects. Ionic liquids (ILs) are designer salts with versatile ion combinations with great potential to control protein properties. Although protein-ion binding of common metals is well-known, the IL effect on proteins is not well understood. Here, we employ the model protein lysozyme in dilute and concentrated IL solutions to determine the specific ion binding effect on protein phase behaviour, activity, size and conformational change, aggregation and intermolecular interactions. A combination of spectroscopic techniques, activity assays, small-angle X-ray scattering, and crystallography highlights that ILs, particularly their anions, bind to specific sites in the protein hydration layer via polar contacts on charged, polar and aromatic residues. The specific ion binding can induce more flexible loop regions in lysozyme, while the ion binding in the bulk phase can be more dynamic in solution. Overall, the protein behaviour in ILs depends on the net effect of nonspecific interactions and specific ion binding. Compared to formate, the nitrate anion induced high protein solubility, low activity, elongated shape and aggregation, which is largely owing to its higher propensity for ion binding. These findings provide new insights into protein-IL binding interactions and using ILs to modulate protein properties.

The intrinsically disordered protein glue of the myelin major dense line: Linking AlphaFold2 predictions to experimental data

Numerous human proteins are classified as intrinsically disordered proteins (IDPs). Due to their physicochemical properties, high-resolution structural information about IDPs is generally lacking. On the other hand, IDPs are known to adopt local ordered structures upon interactions with e.g. other proteins or lipid membrane surfaces. While recent developments in protein structure prediction have been revolutionary, their impact on IDP research at high resolution remains limited. We took a specific example of two myelin-specific IDPs, the myelin basic protein (MBP) and the cytoplasmic domain of myelin protein zero (P0ct). Both of these IDPs are crucial for normal nervous system development and function, and while they are disordered in solution, upon membrane binding, they partially fold into helices, being embedded into the lipid membrane. We carried out AlphaFold2 predictions of both proteins and analysed the models in light of experimental data related to protein structure and molecular interactions. We observe that the predicted models have helical segments that closely correspond to the membrane-binding sites on both proteins. We furthermore analyse the fits of the models to synchrotron-based X-ray scattering and circular dichroism data from the same IDPs. The models are likely to represent the membrane-bound state of both MBP and P0ct, rather than the conformation in solution. Artificial intelligence-based models of IDPs appear to provide information on the ligand-bound state of these proteins, instead of the conformers dominating free in solution. We further discuss the implications of the predictions for mammalian nervous system myelination and their relevance to understanding disease aspects of these IDPs.

Nonlinear viscoelasticity and crystallization behavior of anhydrous milk fat/palm stearin/oleogel blends

The crystallization behavior of anhydrous milk fat (AMF)/palm stearin (POs)/diacetyl tartaric acid ester of mono(di)glycerides (DATEM) oleogel blends was investigated, moreover, the linear and nonlinear rheological behavior of systems was analyzed by small amplitude oscillatory shear (SAOS) and large amplitude oscillatory shear (LAOS). The addition of DATEM oleogels inhibited the growth rate of crystals of blends at 4 °C and reduced the average size of crystalline nanoplatelet. Moreover, the DATEM oleogels promoted the transition of blends to more stable β polymorphism. The nonlinear rheological response of blends was qualitatively analyzed by normalized Lissajous-Bowditch curves. The addition of DATEM oleogels made blends more resistant to large deformations and slowed down viscous losses while reducing the rearrangement behavior of the crystal microstructure under high strain. These findings could open up the possibility of developing low-saturated fat products and further broaden the application of oleogels.

Modeling of flexible membrane-bound biomolecular complexes for solution small-angle scattering

Recent advances in protein expression protocols, sample handling, and experimental set up of small-angle scattering experiments have allowed users of the technique to structurally investigate biomolecules of growing complexity and structural disorder. Notable examples include intrinsically disordered proteins, multi-domain proteins and membrane proteins in suitable carrier systems. Here, we outline a modeling scheme for calculating the scattering profiles from such complex samples. This kind of modeling is necessary for structural information to be refined from the corresponding data. The scheme bases itself on a hybrid of classical form factor based modeling and the well-known spherical harmonics-based formulation of small-angle scattering amplitudes. Our framework can account for flexible domains alongside other structurally elaborate components of the molecular system in question. We demonstrate the utility of this modeling scheme through a recent example of a structural model of the growth hormone receptor membrane protein in a phospholipid bilayer nanodisc which is refined against experimental SAXS data. Additionally we investigate how the scattering profiles from the complex would appear under different scattering contrasts. For each contrast situation we discuss what structural information is contained and the related consequences for modeling of the data.

Rheological and microstructural properties of polysaccharide obtained from the gelatinous Tremella fuciformis fungus

The gelatinous feature of Tremella fuciformis polysaccharide (TFP) has attracted growing interest in its application as a thickening agent in the food industry. This study aims to reveal the microstructure and rheological properties of TFP. Results showed that TFP randomly distributed in aqueous solutions in an irregular worm-like morphology and formed a more extensive entangled network and stiffer chains at higher concentration solutions. The further rheological study indicated that the TFP solutions exhibited a shear-thinning behavior. Multiple results of dynamic oscillation tests confirmed the viscoelastic properties of TFP. Frequency sweep data display that TFP solutions exhibit solid-like behavior at high frequencies, showing the oscillatory behavior of entangled polymers. The temperature sweep demonstrated that the rheological behavior of TFP is thermally reversible. These results enriched the understanding of the rheology-microstructure relationship of TFP solution and were beneficial to expanding the application of TFP in food processing.

Structure of Polymer-Grafted Nanocellulose in the Colloidal Dispersion System

Clarifying the primary structure of nanomaterials is invaluable to understand how the nanostructures lead to macroscopic material functions. Nanocellulose is attracting attention as a sustainable building block in materials science. The surface of nanocellulose is often chemically modified by polymer grafting to tune the material properties, such as the viscoelastic properties in rheology modifiers and the reinforcement effect in composites. However, the structure, such as molecular conformation of the grafted polymer and the twist of the core nanocellulose, is not well understood. Here, we investigated the structure of polymer-grafted nanocellulose in the colloidal dispersion system by combining small-angle X-ray scattering measurement and all-atom molecular dynamics simulation. We demonstrated formation of the polymer brush layer on the nanocellulose surface in solvents, which explains the excellent colloidal stability. We also found that twisting of the nanocellulose in the core is suppressed by the existence of the polymer brush layer.

Nanoscale characterization of collagen structural responses to in situ loading in rat Achilles tendons

The specific viscoelastic mechanical properties of Achilles tendons are highly dependent on the structural characteristics of collagen at and between all hierarchical levels. Research has been conducted on the deformation mechanisms of positional tendons and single fibrils, but knowledge about the coupling between the whole tendon and nanoscale deformation mechanisms of more commonly injured energy-storing tendons, such as Achilles tendons, remains sparse. By exploiting the highly periodic arrangement of tendons at the nanoscale, in situ loading of rat Achilles tendons during small-angle X-ray scattering acquisition was used to investigate the collagen structural response during load to rupture, cyclic loading and stress relaxation. The fibril strain was substantially lower than the applied tissue strain. The fibrils strained linearly in the elastic region of the tissue, but also exhibited viscoelastic properties, such as an increased stretchability and recovery during cyclic loading and fibril strain relaxation during tissue stress relaxation. We demonstrate that the changes in the width of the collagen reflections could be attributed to strain heterogeneity and not changes in size of the coherently diffracting domains. Fibril strain heterogeneity increased with applied loads and after the toe region, fibrils also became increasingly disordered. Additionally, a thorough evaluation of radiation damage was performed. In conclusion, this study clearly displays the simultaneous structural response and adaption of the collagen fibrils to the applied tissue loads and provide novel information about the transition of loads between length scales in the Achilles tendon.

Supramolecular structure of quinoa starch affected by nonenyl succinic anhydride (NSA) substitution

Quinoa starch granular structure as affected by nonenyl succinic anhydride (NSA) substitution was investigated by multiple approaches, including scattering, spectroscopic, and microscopic techniques. The modification had little impact on the morphology of starch granules. The NSA substitution was found mainly in the amorphous lamellae and amorphous growth rings. The NSA modification increased the thickness of the amorphous lamellae. The homogeneity of the ordered structure in the granules was improved, probably because the NSA modification reduced the amount of defects in the semi-crystalline growth ring. Compared to other chemical modifications such as acylation, succinylation was more effective in modifying the starch lamellar structure. A possible reaction pattern of NSA modification on quinoa starch is proposed, in which the NSA modification may follow the sequence of amorphous growth rings, the amorphous matrices among blocklets, amorphous and crystalline lamellae in semi-crystalline growth rings. This study provides new insights on the structural changes of starch granules induced by succinylation on the supramolecular level.

Recombinant AcnB, NrdR and RibD of Acinetobacter baumannii and their potential interaction with DNA adenine methyltransferase AamA

In the last decades Acinetobacter baumannii developed into an increasingly challenging nosocomial pathogen. A. baumannii ATCC 17978 harbors a DNA-(adenine N6)-methyltransferase termed AamA. Previous studies revealed a low specific activity of AamA in vitro despite proven folding, which led us to speculate about possible interaction partners assisting AamA in targeting methylation sites. Here, applying a pulldown assay with subsequent mass spectrometry we identified aconitate hydratase 2 (AcnB) as possible interaction partner. In addition, we considered the putative transcriptional regulator gene nrdR (A1S_0220) and the pyrimidine deaminase/reductase gene ribD (A1S_0221) of A. baumannii strain ATCC 17978 to encode additional potential interaction partners due to their vicinity to the aamA gene (A1S_0222). Proteins were recombinantly produced in the milligram scale, purified to near homogeneity, and interactions with AamA were studied applying blue native gel electrophoreses, electrophoretic mobility shift assay, chemical cross-linking and co-immunoprecipitation. These analyses did not provide evidence of interaction between AamA and purified proteins. Solution structures of RibD, NrdR and AcnB were studied by small-angle X-ray scattering (SAXS) alone and in combination with AamA. While in the case of RibD and AcnB no evidence of an interaction with AamA was produced, addition of AamA to NrdR resulted in dissociation of long and rod-shaped polymeric NrdR structures, implying a specific but transient interaction. Moreover, we identified a molecular crowding effect possibly impeding the DNA methyltransferase activity in vivo and a sequence-independent DNA binding activity of AamA calling for continued efforts to identify the interaction network of AamA.

Solution structure of the type I polyketide synthase Pks13 from Mycobacterium tuberculosis

BACKGROUND

Type I polyketide synthases (PKSs) are multifunctional enzymes responsible for the biosynthesis of a group of diverse natural compounds with biotechnological and pharmaceutical interest called polyketides. The diversity of polyketides is impressive despite the limited set of catalytic domains used by PKSs for biosynthesis, leading to considerable interest in deciphering their structure-function relationships, which is challenging due to high intrinsic flexibility. Among nineteen polyketide synthases encoded by the genome of Mycobacterium tuberculosis, Pks13 is the condensase required for the final condensation step of two long acyl chains in the biosynthetic pathway of mycolic acids, essential components of the cell envelope of Corynebacterineae species. It has been validated as a promising druggable target and knowledge of its structure is essential to speed up drug discovery to fight against tuberculosis.

RESULTS

We report here a quasi-atomic model of Pks13 obtained using small-angle X-ray scattering of the entire protein and various molecular subspecies combined with known high-resolution structures of Pks13 domains or structural homologues. As a comparison, the low-resolution structures of two other mycobacterial polyketide synthases, Mas and PpsA from Mycobacterium bovis BCG, are also presented. This study highlights a monomeric and elongated state of the enzyme with the apo- and holo-forms being identical at the resolution probed. Catalytic domains are segregated into two parts, which correspond to the condensation reaction per se and to the release of the product, a pivot for the enzyme flexibility being at the interface. The two acyl carrier protein domains are found at opposite sides of the ketosynthase domain and display distinct characteristics in terms of flexibility.

CONCLUSIONS

The Pks13 model reported here provides the first structural information on the molecular mechanism of this complex enzyme and opens up new perspectives to develop inhibitors that target the interactions with its enzymatic partners or between catalytic domains within Pks13 itself.

Elucidation of critical pH-dependent structural changes in Botulinum Neurotoxin E

Botulinum Neurotoxins (BoNT) are the most potent toxins currently known. However, they also have therapeutic applications for an increasing number of motor related conditions due to their specificity, and low diffusion into the system. Although the start- and end- points for the BoNT mechanism of action are well-studied, a critical step remains poorly understood. It is theorised that BoNTs undergo a pH-triggered conformational shift, activating the neurotoxin by priming it to form a transmembrane (TM) channel. To test this hypothesis, we combined molecular dynamics (MD) simulations and small-angle x-ray scattering (SAXS), revealing a new conformation of serotype E (BoNT/E). This conformation was exclusively observed in simulations below pH 5.5, as determined by principal component analysis (PCA), and its theoretical SAXS profile matched an experimental SAXS profile obtained at pH 4. Additionally, a localised secondary structural change was observed in MD simulations below pH 5.5, in a region previously identified as instrumental for membrane insertion for serotype A (BoNT/A). These changes were found at a critical pH value for BoNTs in vivo, and may be relevant for their therapeutic use.

Interdigitation-Induced Order and Disorder in Asymmetric Membranes

We studied the transleaflet coupling of compositionally asymmetric liposomes in the fluid phase. The vesicles were produced by cyclodextrin-mediated lipid exchange and contained dipalmitoyl phosphatidylcholine (DPPC) in the inner leaflet and different mixed-chain phosphatidylcholines (PCs) as well as milk sphingomyelin (MSM) in the outer leaflet. In order to jointly analyze the obtained small-angle neutron and X-ray scattering data, we adapted existing models of trans-bilayer structures to measure the overlap of the hydrocarbon chain termini by exploiting the contrast of the terminal methyl ends in X-ray scattering. In all studied systems, the bilayer-asymmetry has large effects on the lipid packing density. Fully saturated mixed-chain PCs interdigitate into the DPPC-containing leaflet and evoke disorder in one or both leaflets. The long saturated acyl chains of MSM penetrate even deeper into the opposing leaflet, which in turn has an ordering effect on the whole bilayer. These results are qualitatively understood in terms of a balance of entropic repulsion of fluctuating hydrocarbon chain termini and van der Waals forces, which is modulated by the interdigitation depth. Monounsaturated PCs in the outer leaflet also induce disorder in DPPC despite vestigial or even absent interdigitation. Instead, the transleaflet coupling appears to emerge here from a matching of the inner leaflet lipids to the larger lateral lipid area of the outer leaflet lipids.

Structure and function of an atypical homodimeric actin capping protein from the malaria parasite

Apicomplexan parasites, such as Plasmodium spp., rely on an unusual actomyosin motor, termed glideosome, for motility and host cell invasion. The actin filaments are maintained by a small set of essential regulators, which provide control over actin dynamics in the different stages of the parasite life cycle. Actin filament capping proteins (CPs) are indispensable heterodimeric regulators of actin dynamics. CPs have been extensively characterized in higher eukaryotes, but their role and functional mechanism in Apicomplexa remain enigmatic. Here, we present the first crystal structure of a homodimeric CP from the malaria parasite and compare the homo- and heterodimeric CP structures in detail. Despite retaining several characteristics of a canonical CP, the homodimeric Plasmodium berghei (Pb)CP exhibits crucial differences to the canonical heterodimers. Both homo- and heterodimeric PbCPs regulate actin dynamics in an atypical manner, facilitating rapid turnover of parasite actin, without affecting its critical concentration. Homo- and heterodimeric PbCPs show partially redundant activities, possibly to rescue actin filament capping in life cycle stages where the β-subunit is downregulated. Our data suggest that the homodimeric PbCP also influences actin kinetics by recruiting lateral actin dimers. This unusual function could arise from the absence of a β-subunit, as the asymmetric PbCP homodimer lacks structural elements essential for canonical barbed end interactions suggesting a novel CP binding mode. These findings will facilitate further studies aimed at elucidating the precise actin filament capping mechanism in Plasmodium.

Structural Information on Bacterial Amyloid and Amyloid-DNA Complex Obtained by Small-Angle Neutron or X-Ray Scattering

Small-angle scattering is a powerful technique to obtain structural information on biomacromolecules in aqueous solution at the sub-nanometer and nanometer length scales. It provides the sizes and overall shapes of the scattering particles. While small-angle X-ray scattering (SAXS) has often been used for structural analysis of a single-component system, small-angle neutron scattering (SANS) has been used to reveal the internal organization of a multicomponent system such as protein-protein and protein-DNA complexes. This is due to the fact that the neutron scattering length is largely different between hydrogen and deuterium, and thus it allows to make a specific component in complexes "invisible" to neutrons by changing the H₂O/D₂O ratio in the solvent with or without molecular deuteration. In this chapter, we describe a method to characterize the biomolecular structures using SANS and SAXS, in particular, focusing on fibrillar proteins such as bacterial amyloids and their complexes with nucleic acids.

Kinetics of denaturation and renaturation processes of double-stranded helical polysaccharide, xanthan in aqueous sodium chloride

Circular dichroism (CD) and small-angle X-ray scattering (SAXS) measurements were made for three xanthan samples, a double helical polysaccharide, in 5 or 10 mM aqueous NaCl after rapid temperature change to investigate the kinetics of the conformational change between the ordered and disordered states. After the rapid heating, the CD signal mainly reflecting the carbonyl groups on the side chains quickly changed (<150 s) while the scattering intensity from SAXS around q (magnitude of the scattering vector) = 1 nm^-1 changed more gradually, reflecting the main-chain conformation. The difference between CD and SAXS implies us the intermediate conformation which can be regarded as a loose double helix. The SAXS profile in the rapid cooling process showed that the loose double helical structure was constructed within 150 s, but the CD signal slowly changed with around 2 days to recover the native tight double helix.

Monitoring Nuclease Activity by X-Ray Scattering Interferometry Using Gold Nanoparticle-Conjugated DNA

The biologically critical, exquisite specificity and efficiency of nucleases, such as those acting in DNA repair and replication, often emerge in the context of multiple other macromolecules. The evolved complexity also makes biologically relevant nuclease assays challenging and low-throughput. Meiotic recombination 11 homolog 1 (MRE11) is an exemplary nuclease that initiates DNA double-strand break (DSB) repair and processes stalled DNA replication forks. Thus, DNA resection by MRE11 nuclease activity is critical for multiple DSB repair pathways as well as in replication. Traditionally, in vitro nuclease activity of purified enzymes is studied either through gel-based assays or fluorescence-based assays like fluorescence resonance energy transfer (FRET). However, adapting these methods for a high-throughput application such as inhibitor screening can be challenging. Gel-based approaches are slow, and FRET assays can suffer from interference and distance limitations. Here we describe an alternative methodology to monitor nuclease activity by measuring the small-angle X-ray scattering (SAXS) interference pattern from gold nanoparticles (Au NPs) conjugated to 5'-ends of dsDNA using X-ray scattering interferometry (XSI). In addition to reporting on the enzyme activity, XSI can provide insight into DNA-protein interactions, aiding in the development of inhibitors that trap enzymes on the DNA substrate. Enabled by efficient access to synchrotron beamlines, sample preparation, and the feasibility of high-throughput XSI data collection and processing pipelines, this method allows for far greater speeds with less sample consumption than conventional SAXS techniques. The reported metrics and methods can be generalized to monitor not only other nucleases but also most other DNA-protein interactions.

Fiber Diffraction and Small-Angle Scattering for Structural Investigation of Bacterial Amyloids

X-ray/neutron fiber diffraction and small-angle X-ray/neutron scattering are widely used to investigate the molecular structure of fibrous proteins, including amyloid fibrils. However, there is sometimes confusion between these two techniques despite the fact that sample conditions and the content of the information obtained are not the same. In this brief chapter, we present the differences in sample conditions between these two methods, and their effects on experimentally obtained diffraction or scattering patterns, emphasizing the degree of disorder in the samples.

Spectroscopic and Small-angle X-ray scattering analysis of binding between Copper(II) -1-allylimidazole complex, a potential anti-tumor agent, and bovine serum albumin

Interactions between transport proteins and compounds with therapeutic potential are pharmacologically important. In this study, using fluorescence, circular dichroism (CD), and small-angle X-ray Scattering (SAXS), we investigated the interaction between bovine serum albumin (BSA) and a copper(II)-1-allylimidazole complex with potential anti-cancer properties. The results revealed dynamic fluorescence quenching of the model carrier protein BSA by the copper(II) complex. The enthalpy change (ΔH), free energy (ΔG), and entropy change (ΔS) were calculated to be 108 kJ/mol, -16.47 kJ/mol, and 419 J/mol K, respectively, according to the Van't Hoff equation. The reaction was an endothermic and spontaneous process, and hydrophobic interactions played a major role in binding. The results indicate a much lower affinity (K_b ∼ 10²-10³) for the metal complex compared with similar compounds (K_b ∼ 10³-10⁵). CD showed that the studied copper(II) complex does not change the secondary structure of the protein, while SAXS showed that the this compound may attach to the protein surface and stimulate interactions between proteins. The results suggest that the copper(II) complex with 1-allylimidazole binds weakly to BSA, leading to aggregation of albumin in solution, thereby altering its pharmacokinetic properties. The findings are pertinent to drug design.

Structural Characterization of Silk Fibers by Small-Angle X-Ray Scattering

Nature is rich in all kinds of unbelievably designed microstructures, which endows the natural materials with various fantastic performances. Unveiling the mystery of the sophisticated configurations and the relationship between those microstructures and the corresponding functions is helpful for the manufacture of artificial functional materials. Small-angle X-ray scattering (SAXS) is an advanced tool to gain the microstructural features of materials within a spatial scale much larger than the atomic scale (1000 nm), which can be carried out along with WAXS to conduct more systematic investigation over different kinds of materials. With the help of SAXS/WAXS, one may generate an insightful understanding of the mechanisms of structure-property evolution (which is efficient guidance for the artificial material designs). This chapter will introduce the mathematics and the methodologies used by SAXS when investigating the microstructure of natural materials.

Mechanistic insights into the formation of polyion complex aggregates from cationic thermoresponsive diblock copolymers

HYPOTHESIS

The formation of polyion complexes (PICs) comprising thermoresponsive polymers is intended to result in the formation of aggregates that undergo significant structural changes with temperature. Moreover the observed modifications might be critically affected by polymer structure and PICs composition.

EXPERIMENTS

Different block copolymers based on cationic poly(3-acrylamidopropyltrimethylammonium chloride) and thermoresponsive poly(N-isopropylacrylamide) were synthesized by aqueous RAFT/MADIX polymerization at room temperature. Addition of poly(acrylic acid) in a controlled fashion led to the formation of PICs aggregates. The structural changes induced by temperature were characterized by differential scanning calorimetry, Nuclear Magnetic Resonance spectroscopy and scattering methods.

FINDINGS

Thermoresponsive PICs undergo significant structural changes when increasing temperature above the cloud point of the thermoresponsive block. The reversibility of these phenomena depends strongly on the structural parameters of the block copolymers and on PICs composition.

Influence of polysorbates (Tweens) on structural and antimicrobial properties for microemulsions

Polysorbates (Tweens) are one of the most used excipients for essential oils encapsulation. In this work, the polysorbate based microemulsions (PMEs) for R-(+)-limonene (LMN) encapsulation were investigated for the structural and antimicrobial properties. PMEs were constructed using the pseudoternary phase diagrams, and then characterized for electrical conductivity, rheology, size distribution and particle geometry. Conductivity and rheological measurement results showed that Tween 80 and Tween 60 based microemulsions have identical phase transitions. Dynamic light scattering demonstrated that hydrodynamic diameters of oil-in-water microemulsions decreased from 30 nm to 25 nm during the dilution, while small-angle X-ray scattering indicated that their spherical geometries were maintained. PMEs exhibited enhanced antimicrobial efficiencies in vitro against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. Interestingly, when Tween 80 was replaced by Tween 60, PME was observed more effective against S. aureus. The two PMEs structural analogues exhibited different antimicrobial efficiencies corresponding to the bioactivity of polysorbates. In conclusion, PMEs can be considered as a desirable system for LMN encapsulation to enhance its solubility and antimicrobial efficiency. Furthermore, the difference in the antimicrobial efficiency suggested that the choice of emulsifiers should be concerned to improve further applications.

Emulsions containing optimum cow milk fat and canola oil mixtures replicate the lipid self-assembly of human breast milk during digestion

HYPOTHESIS

The digestion of different milks and milk substitutes leads to the formation of a variety of self-assembled lipid structures, with the structuring of human milk being paramount for infant nutrition. It was hypothesised that mixing cow milk fat rich in medium/long-chain lipids with canola oil rich in long-chain unsaturated lipids would replicate the structuring of human milk by balancing lipid chain lengths and saturation levels.

EXPERIMENTS

Emulsions of cow milk fat/canola oil mixtures were prepared in two ways - by pre-mixing ghee and canola oil before dispersing them and by dispersing canola oil directly into commercial cow milk. Small angle X-ray scattering combined with titration of the fatty acids produced during digestion allowed for the correlation of dynamic lipid self-assembly with the extent of lipid digestion. Laser light scattering was used to show that the particle sizes in the digesting mixtures were similar and coherent anti-Stokes Raman spectroscopy (CARS) microscopy was used to confirm the mixing of canola oil into cow milk fat globules.

FINDINGS

As the amount of long-chain unsaturated canola oil lipids in the mixtures increased, the lipid self-assembly tended towards colloidal structures of greater interfacial curvature. When the ratio of cow milk fat to canola oil lipids was 1:1 (w/w), the digesting lipids assembled themselves into the same liquid crystalline structures as human breast milk. This observation was independent of the method used to mix the lipids, with CARS microscopy indicating uniform mixing of the canola oil into cow milk upon ultrasonication.

Human cathepsin X/Z is a biologically active homodimer

Human cathepsin X belongs to the cathepsin family of 11 lysosomal cysteine proteases. We expressed recombinant procathepsin X in Pichia pastoris in vitro and cleaved it into its active mature form using aspartic cathepsin E. We found, using size exclusion chromatography, X-ray crystallography, and small-angle X-ray scattering, that cathepsin X is a biologically active homodimer with a molecular weight of ~53 kDa. The novel finding that cathepsin X is a dimeric protein opens new horizons in the understanding of its function and the underlying pathophysiological mechanisms of various diseases including neurodegenerative disorders in humans.

Computational modeling and small-angle X-ray scattering based structure analysis and identifying ligand cleavage mechanism by processive endocellulase of family 9 glycoside hydrolase (HtGH9) from Hungateiclostridium thermocellum ATCC 27405

The cellulases of family 9 glycoside hydrolase with subtle difference in amino acid sequence have shown different types of catalytic activities such as endo-, exo- or processive endocellulase. However, the reason behind the different types of catalytic activities still unclear. In this study, the processive endocellulase, HtGH9 of family 9 GH from Hungateiclostridium thermocellum was modeled by homology modeling. The catalytic module (HtGH9t) of HtGH9 modeled structure displayed the (α/α)₆ barrel topology and associated family 3 carbohydrate binding module (HtCBM3c) displayed β-sandwich fold. Ramachandran plot of HtGH9 modeled structure displayed all the amino acid residues in allowed region except Asn225 and Asp317. Secondary structure analysis of modeled HtGH9 showed the presence of 41.3% α-helices and 11.0% β-strands which was validated through circular dichroism analysis that showed the presence of 42.6% α-helices and 14.5% β-strands. Molecular Dynamic (MD) simulation of HtGH9 structure for 50 ns showed Root Mean Square Deviation (RMSD), 0.84 nm and radius of gyration (Rg) 3.1 nm. The Small-angle X-ray scattering of HtGH9 confirmed the monodisperse state. The radius of gyration for globular shape (Rg) was 5.50 ± 0.15 nm and for rod shape (Rc) by Guinier plot was 2.0 nm. The loop formed by amino acid residues, 264-276 towards one end of the catalytic site of HtGH9 forms a barrier, that blocks the non-reducing end of the cellulose chain causing the processive cleavage resulting in the release of cellotetraose. The position of the corresponding loop in cellulases of family 9 GH is responsible for different types of cleavage patterns.

Recombinant expression, purification and SAXS analysis of Arabidopsis thaliana ClpC1

Caseinolytic protease-associated chaperones (Clp chaperones) are HSP100 proteins belonging to the family of ATPases having diverse cellular functions, and they occur in various organisms ranging from bacteria to plants and mammals. Most Clp chaperones have a hexameric organization and associate with tetradecameric Clp proteases to recognize and unfold protein substrates that get degraded within the cellular milieu. Vascular plants have a diverse family of Clp chaperones compared to other organisms; wherein, the chloroplasts of Arabidopsis thaliana alone contain four distinct Clp chaperones, such as ClpC1, ClpC2, ClpD, and ClpB3. The paralogs AtClpC1 and AtClpC2 are more than 90% identical, though the extent of functional overlap between the two is not clear. Moreover, in vitro characterization reports are available only for AtClpC2, as AtClpC1 could not be expressed in recombinant form in the past. Herein, using a bacterial expression system, we have successfully expressed and purified AtClpC1 with a short N-terminal truncation, employing a three-step chromatographic purification strategy. We show that AtClpC1 exists as a hexamer in the presence of ATP and MgCl₂, as known for other functional Clp chaperones. Further, our SAXS analyses provide a low-resolution envelope structure for the hexameric AtClpC1, which very well fits a ClpC hexamer model.

Solvents, CO2 and biopolymers: Structure formation in chitosan aerogel

The functionality of biopolymer aerogels is inherently linked to its microstructure, which in turn depends on the synthesis protocol. Detailed investigations on the macroscopic size change and nanostructure formation during chitosan aerogel synthesis reveal a new aspect of biopolymer aerogels that increases process flexibility. Formaldehyde-cross-linked chitosan gels retain a significant fraction of their original volume after solvent exchange into methanol (50.3 %), ethanol (47.1 %) or isopropanol (26.7 %), but shrink dramatically during subsequent supercritical CO₂ processing (down to 4.9 %, 3.5 % and 3.7 %, respectively). In contrast, chitosan gels shrink more strongly upon exchange into n-heptane (7.2 %), a low affinity solvent, and retain this volume during CO₂ processing. Small-angle X-ray scattering confirms that the occurrence of the volumetric changes correlates with mesoporous network formation through physical coagulation in CO₂ or n-heptane. The structure formation step can be controlled by solvent-polymer and polymer-drying interactions, which would be a new tool to tailor the aerogel structure.

Toward reliable low-density lipoprotein ultrastructure prediction in clinical conditions: A small-angle X-ray scattering study on individuals with normal and high triglyceride serum levels

Atherosclerosis is the main killer in the west and therefore a major health challenge today. Total serum cholesterol and lipoprotein concentrations, used as clinical markers, fail to predict the majority of cases, especially between the risk scale extremes, due to the high complexity in lipoprotein structure and composition. In particular, low-density lipoprotein (LDL) plays a key role in atherosclerosis development, with LDL size being a parameter considered for determining the risk for cardiovascular diseases. Determining LDL size and structural parameters is challenging to address experimentally under physiological-like conditions. This article describes the biochemistry and ultrastructure of normolipidemic and hypertriglyceridemic LDL fractions and subfractions using small-angle X-ray scattering. Our results conclude that LDL particles of hypertriglyceridemic compared to healthy individuals 1) have lower LDL core melting temperature, 2) have lower cholesteryl ester ordering in their core, 3) are smaller, rounder and more spherical below melting temperature, and 4) their protein-containing shell is thinner above melting temperature.

Spatio-temporal evolution of hydroxyapatite crystal thickness at the bone-implant interface

A better understanding of bone nanostructure around the bone-implant interface is essential to improve longevity of clinical implants and decrease failure risks. This study investigates the spatio-temporal evolution of mineral crystal thickness and plate orientation in newly formed bone around the surface of a metallic implant. Standardized coin-shaped titanium implants designed with a bone chamber were inserted into rabbit tibiae for 7 and 13 weeks. Scanning measurements with micro-focused small-angle X-ray scattering (SAXS) were carried out on newly formed bone close to the implant and in control mature cortical bone. Mineral crystals were thinner close to the implant (1.8 ± 0.45 nm at 7 weeks and 2.4 ± 0.57 nm at 13 weeks) than in the control mature bone tissue (2.5 ± 0.21 nm at 7 weeks and 2.8 ± 0.35 nm at 13 weeks), with increasing thickness over healing time (+30 % in 6 weeks). These results are explained by younger bone close to the implant, which matures during osseointegration. Thinner mineral crystals parallel to the implant surface within the first 100 µm indicate that the implant affects the ultrastructure of neighbouring bone , potentially due to heterogeneous interfacial stresses, and suggest a longer maturation process of bone tissue and difficulty in binding to the metal. The bone growth kinetics within the bone chamber was derived from the spatio-temporal evolution of bone tissue's nanostructure, coupled with microtomographic imaging. The findings indicate that understanding mineral crystal thickness or plate orientation can improve our knowledge of osseointegration.

Structures and mechanisms of formation of liprotides

Many proteins form complexes called liprotides with oleic acid and other cis-fatty acids under conditions where the protein is partially unfolded. The complexes vary in structure depending on the ratio of protein and lipid, but the most common structural organization is the core-shell structure, in which a layer of dynamic, partially unfolded and extended proteins surrounds a micelle-like fatty acid core. This structure, first reported for α-lactalbumin together with OA, resembles complexes formed between proteins and anionic surfactants like SDS. Liprotides first rose to fame through their anti-carcinogenic properties which still remains promising for topical applications though not yet implemented in the clinic. In addition, liprotides show potential in drug delivery thanks to the ability of the micelle core to solubilize and stabilize hydrophobic compounds, though applications are challenged by their sensitivity to acidic pH and dynamic exchange of lipids which makes them easy prey for serum "hoovers" such as albumin. However, liprotides are also of fundamental interest as a generic "protein complex structure", demonstrating the many and varied structural consequences of protein-lipid interactions. Here we provide an overview of the different types of liprotide complexes, ranging from quasi-native complexes via core-shell structures to multi-layer structures, and discuss the many conditions under which they form. Given the many variable types of complexes that can form, rigorous biophysical analysis (stoichiometry, shape and structure of the complexes) remains crucial for a complete understanding of the mechanisms of action of this fascinating group of protein-lipid complexes both in vitro and in vivo.

Inhibition, crystal structures, and in-solution oligomeric structure of aldehyde dehydrogenase 9A1

Aldehyde dehydrogenase 9A1 (ALDH9A1) is a human enzyme that catalyzes the NAD⁺-dependent oxidation of the carnitine precursor 4-trimethylaminobutyraldehyde to 4-N-trimethylaminobutyrate. Here we show that the broad-spectrum ALDH inhibitor diethylaminobenzaldehyde (DEAB) reversibly inhibits ALDH9A1 in a time-dependent manner. Possible mechanisms of inhibition include covalent reversible inactivation involving the thiohemiacetal intermediate and slow, tight-binding inhibition. Two crystal structures of ALDH9A1 are reported, including the first of the enzyme complexed with NAD⁺. One of the structures reveals the active conformation of the enzyme, in which the Rossmann dinucleotide-binding domain is fully ordered and the inter-domain linker adopts the canonical β-hairpin observed in other ALDH structures. The oligomeric structure of ALDH9A1 was investigated using analytical ultracentrifugation, small-angle X-ray scattering, and negative stain electron microscopy. These data show that ALDH9A1 forms the classic ALDH superfamily dimer-of-dimers tetramer in solution. Our results suggest that the presence of an aldehyde substrate and NAD⁺ promotes isomerization of the enzyme into the active conformation.

Low-resolution molecular shape, biochemical characterization and emulsification properties of a halotolerant esterase from Bacillus licheniformis

Bacterial esterases are highly versatile enzymes, currently widely used in detergents, biosurfactants, bioemulsifiers and as biocatalysts in paper and food industries. Present work describes heterologous expression, purification, and biophysical and biochemical characterization of a halotolerant esterase from Bacillus licheniformis (BlEstA). BlEstA preferentially cleaves pNP-octanoate and both activity and stability of the enzyme increased in the presence of 2 M NaCl, and also with several organic solvents (ethanol, methanol and DMSO). Furthermore, BlEstA has considerable emulsifying properties, particularly with olive oil as substrate. Our studies also show that the enzyme is monomeric in solution and its small-angle X-ray scattering low-resolution molecular envelope fits well its high-resolution homology model.

Real-time monitoring of oil-induced micellar transitions in viscoelastic surfactants by small-angle X-ray scattering

HYPOTHESIS

Viscoelastic surfactant solutions with entangled wormlike micelles (WLMs) display dramatic changes in rheological properties when exposed to hydrophobic substances. This change is key in the oil and gas industry and for drug delivery. The changes in viscoelastic properties are believed to be a result of changes in micellar shape due to the oil solubilization. The time dependence of the process has practical importance, yet its mechanism is unknown. We set out to map the structural changes with time using small-angle x-ray scattering (SAXS).

EXPERIMENT

A surfactant system with erucamidopropyl hydroxypropyl sulfobetaine as the active ingredient was homogenized with three concentrations of n-decane (70 mM, 140 mM, 280 mM) in 600 mM CaCl₂. The samples were monitored with time using SAXS. Model fits were used to determine the structures present in the sample at each time interval.

FINDINGS

The entangled WLMs disappeared while spherical decane-swollen micelles formed with time, explaining the sharp decrease in viscosity. It was shown that the time at which the spherical swollen micelles appeared depends on the concentration of n-decane. This insight allows control of the spherical micelle appearance time, which is important for the successful application of WLMs in sectors that require WLMs to persist for a set time before they transform.

High-intensity ultrasound-assisted extraction of phenolic compounds from cowpea pods and its encapsulation in hydrogels

Currently and according to the growing worldwide interest in the revaluation of agricultural by-products, the use of legumes waste presents great potential to obtain bioactive compounds. In this context, an extract rich in phenolic compounds was obtained from Vigna unguiculata (cowpea) pods by optimizing the high-intensity ultrasound conditions (10 min and 36% of amplitude) using response surface methodology. Then, the extract was encapsulated in Ca(II)-alginate beads with the addition of arabic or guar gums or cowpea isolated proteins. A complete morphological study by image analysis and microstructural evaluation by SAXS has been carried out. Results showed that beads containing alginate and alginate-guar gum have the highest loading efficiency of total phenolic compounds (47 ± 5%) and antioxidant activity (44 ± 3%). However, the coupled effect of the cowpea extract and the isolated proteins (at it higher concentration) increased the antioxidant capacity of the beads due to the contribution of the phenolic compounds and the amino acids with anti-radical activity, reaching a value of 67 ± 3 % of inhibition of ABTS.+. Finally, the microstructural analyses revealed that cowpea pod extract increased the interconnectivity of the rods due to the presence of trivalent cations, conferring versatility, and larger coordination to the network. Also, it was observed that the addition of cowpea proteins produced more interconnected bigger and fewer compacts rods than beads containing only alginate, increasing 12 and 49 % the interconnection and the size, respectively, and decreasing 10 % their compactness. This research demonstrated the use of cowpea sub-products as a source of bioactive compounds that further modulate the microstructure of the hydrogel network, and the outstanding potential for being incorporated in techno-functional foods by using Ca(II)-alginate as a carrier.

Influence of TMAO as co-solvent on the gelation of silica-PNIPAm core-shell nanogels at intermediate volume fractions

We study the structure and dynamics of poly(N-isopropylacrylamide) (PNIPAm) core-shell nanogels dispersed in aqueous trimethylamine N-oxide (TMAO) solutions by means of small-angle X-ray scattering and X-ray photon correlation spectroscopy (XPCS). Upon increasing the temperature above the lower critical solution temperature of PNIPAm at 33 °C, a colloidal gel is formed as identified by an increase of I(q) at small q as well as a slowing down of sample dynamics by various orders of magnitude. With increasing TMAO concentration the gelation transition shifts linearly to lower temperatures. Above a TMAO concentration of approximately 0.40 mol/L corresponding to a 1 : 1 ratio of TMAO and NIPAm groups, collapsed PNIPAm states are found for all temperatures without any gelation transition. This suggests that reduction of PNIPAm-water hydrogen bonds due to the presence of TMAO results in a stabilisation of the collapsed PNIPAm state and suppresses gelation of the nanogel.

Mineralization of cortical bone during maturation and growth in rabbits

INTRODUCTION

The composite nature of bone as a material governs its structure and mechanical behavior. How the collagenous matrix mineralizes, in terms of both mineral deposition and structure of the mineral crystals, is highly interesting when trying to elucidate the complex structural changes that occur during bone growth and maturation. We have previously looked at mineral deposition and structural evolution of the collagenous matrix, linking both to changes in mechanics. The purpose of this study was to provide specific information on changes in crystal size and organization as a function of growth and maturation.

MATERIALS AND METHODS

Using micro-computed tomography (µCT) and micro-focused scanning small-angle X-ray scattering (SAXS) we investigated cortical bone in two orthogonal directions relative to the long axis of the humeri of New Zealand White rabbits spanning from new-born to 6-months of age. We also investigated the changes with tissue age by looking at radial profiles of osteonal structures in the 6-months old rabbits. The findings were compared to our previous compositional, structural and mechanical data on the same sample cohort.

RESULTS

µCT showed a continuous mineral deposition up until 3-months of age, whilst the SAXS data showed an increase in both crystal thickness and degree of orientation up until 6-months of age. The osteonal profiles showed no statistically significant changes in crystal thickness.

CONCLUSIONS

Comparison to previously collected mechanical data suggests that changes are not only explained by amount of mineral in the tissue but also by the crystal dimensions.

Peptide-Modified Gemini Surfactants: Preparation and Characterization for Gene Delivery

Diquaternary ammonium-based gemini surfactants have been investigated widely as nonviral gene delivery systems. These unique cationic lipids have versatility in their chemical structure, show relatively low toxicity, are able to compact genetic material (pDNA, RNA) into nano-sized lipoplexes, and can be easily produced. In addition, the gemini surfactants show significant improvement in the transfection activity and biocompatibility compared to other cationic lipids used as nonviral gene delivery agents. The successful applications of gemini surfactant-based lipoplexes as topical gene delivery systems in animal models indicate their potential as noninvasive carriers for genetic immunization, theranostic agents, and in other gene therapy treatments. Detailed physicochemical characterization of gemini surfactant lipoplexes is a key factor in terms of formulation optimization and elucidation of the cellular uptake and stability of the lipoplexes system. In this chapter, we describe in detail different formulation methods to prepare gemini surfactant lipoplexes and comprehensive physicochemical characterization. In addition, we illustrate general protocols for in vitro evaluations.

Expanding crystallization tools for nucleic acid complexes using U1A protein variants

The major bottlenecks in structure elucidation of nucleic acids are crystallization and phasing. Co-crystallization with proteins is a straight forward approach to overcome these challenges. The human RNA-binding protein U1A has previously been established as crystallization module, however, the absence of UV-active residues and the predetermined architecture in the asymmetric unit constitute clear limitations of the U1A system. Here, we report three crystal structures of tryptophan-containing U1A variants, which expand the crystallization toolbox for nucleic acids. Analysis of the structures complemented by SAXS, NMR spectroscopy, and optical spectroscopy allow for insights into the potential of the U1A variants to serve as crystallization modules for nucleic acids. In addition, we report a fast and efficient protocol for crystallization of RNA by soaking and present a fluorescence-based approach for detecting RNA-binding in crystallo. Our results provide a new tool set for the crystallization of RNA and RNA:DNA complexes.

Monomeric and homotrimeric solution structures of truncated human peroxidasin 1 variants

Human peroxidasin 1 is a multidomain peroxidase situated in the basement membrane. The iron enzyme with covalently bound heme oxidizes bromide to hypobromous acid which facilitates the formation of distinct sulfilimine cross-links in the collagen IV network and therefore contributes to its mechanical stability. Additional to the catalytically active peroxidase domain peroxidasin comprises a leucine rich repeat domain, four Ig domains and a C-terminal von Willebrand factor type C module (VWC). Peroxidasin has been shown to form homotrimers involving two redox-sensitive cysteine residues and to undergo posttranslational C-terminal proteolytic cleavage. The present study on several recombinantly produced truncated peroxidasin variants showed that the VWC is not required for trimer formation whereas the alpha-helical linker region located between the peroxidase domain and the VWC is crucial for trimerization. Our data furthermore implies that peroxidasin oligomerization occurs intracellularly before C-terminal cleavage. For the first time we present overall solution structures of monomeric and trimeric truncated peroxidasin variants which were determined by rotary shadowing combined with transmission electron microscopy and by small-angle X-ray scattering (SAXS). A triangular arrangement of the peroxidase domains to each other within the homotrimer was revealed and this structure was confirmed by a model of trimeric peroxidase domains. Our SAXS data showed that the Ig domains are highly flexible and interact with the peroxidase domain and that within the homotrimer each alpha-helical linker region interacts with the respective adjacent peroxidase domain. The implications of our findings on the structure-function relationship of peroxidasin are discussed.

Changes in the orientations of cellulose microfibrils during the development of collenchyma cell walls of celery (Apium graveolens L.)

During development, cellulose microfibrils in collenchyma walls become increasingly longitudinal, as determined by small-angle X-ray scattering, despite the walls maintaining a fine structure indicative of a crossed-polylamellate structure. Collenchyma cells have thickened primary cell walls and provide mechanical support during plant growth. During their development, these cells elongate and their walls thicken considerably. We used microscopy and synchrotron small-angle X-ray scattering to study changes in the orientations of cellulose microfibrils that occur during development in the walls of collenchyma cells present in peripheral strands in celery (Apium graveolens) petioles. Transmission electron microscopy showed that the walls consisted of many lamellae (polylamellate), with lamellae containing longitudinally oriented cellulose microfibrils alternating with microfibrils oriented at higher angles. The lamellae containing longitudinally oriented microfibrils predominated at later stages of development. Nevertheless, transmission electron microscopy of specially stained, oblique sections provided evidence that the cellulose microfibrils were ordered throughout development as crossed-polylamellate structures. These results are consistent with our synchrotron small-angle X-ray scattering results that showed the cellulose microfibrils become oriented increasingly longitudinally during development. Some passive reorientation of cellulose microfibrils may occur during development, but extensive reorientation throughout the wall would destroy ordered structures. Atomic force microscopy and field emission scanning electron microscopy were used to determine the orientations of newly deposited cellulose microfibrils. These were found to vary widely among different cells, which could be consistent with the formation of crossed-polylamellate structures. These newly deposited cellulose microfibrils are deposited in a layer of pectic polysaccharides that lies immediately outside the plasma membrane. Overall, our results show that during development of collenchyma walls, the cellulose microfibrils become increasingly longitudinal in orientation, yet organized, crossed-polylamellate structures are maintained.

Design and structural characterisation of olfactomedin-1 variants as tools for functional studies

BACKGROUND

Olfactomedin-1 (Olfm1; also known as Noelin or Pancortin) is a highly-expressed secreted brain and retina protein and its four isoforms have different roles in nervous system development and function. Structural studies showed that the long Olfm1 isoform BMZ forms a disulfide-linked tetramer with a V-shaped architecture. The tips of the Olfm1 "V" each consist of two C-terminal β-propeller domains that enclose a calcium binding site. Functional characterisation of Olfm1 may be aided by new biochemical tools derived from these core structural elements.

RESULTS

Here we present the production, purification and structural analysis of three novel monomeric, dimeric and tetrameric forms of mammalian Olfm1 for functional studies. We characterise these constructs structurally by high-resolution X-ray crystallography and small-angle X-ray scattering. The crystal structure of the Olfm1 β-propeller domain (to 1.25 Å) represents the highest-resolution structure of an olfactomedin family member to date, revealing features such as a hydrophilic tunnel containing water molecules running into the core of the domain where the calcium binding site resides. The shorter Olfactomedin-1 isoform BMY is a disulfide-linked tetramer with a shape similar to the corresponding region in the longer BMZ isoform.

CONCLUSIONS

These recombinantly-expressed protein tools should assist future studies, for example of biophysical, electrophysiological or morphological nature, to help elucidate the functions of Olfm1 in the mature mammalian brain. The control over the oligomeric state of Olfm1 provides a firm basis to better understand the role of Olfm1 in the (trans-synaptic) tethering or avidity-mediated clustering of synaptic receptors such as post-synaptic AMPA receptors and pre-synaptic amyloid precursor protein. In addition, the variation in domain composition of these protein tools provides a means to dissect the Olfm1 regions important for receptor binding.