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Katie H Sizeland,1 Hannah C Wells,2 Nigel M Kirby,3 Adrian Hawley,3 Stephen T Mudie,3 Tim M Ryan,3 Richard G Haverkamp2 1Human Health, ANSTO, Lucas Heights, Sydney, NSW 2234, Australia; 2School of Food and Advanced Technology, Massey University, Palmerston North 4472, New Zealand; 3SAXS/WAXS Beamline, Australian Synchrotron, ANSTO, Clayton, Melbourne, VIC 3168, AustraliaCorrespondence: Richard G HaverkampSchool of Food and Advanced Technology, Massey University, Private Bag 1112, Palmerston North 4472, New ZealandTel +64 6 356 9099Email r.haverkamp@massey.ac.nzBackground: Type I collagen is the major component of the extracellular matrix of the knee’s meniscus and plays a central role in that joint’s biomechanical properties. Repair and reconstruction of tissue damage often requires a scaffold to assist the body to rebuild. The middle zone of bovine meniscus is a material that may be useful for the preparation of extracellular matrix scaffolds.Methods: Here, synchrotron-based small-angle X-ray scattering (SAXS) patterns of bovine meniscus were collected during unconfined compression. Collagen fibril orientation, D-spacing, compression distance and force were measured.Results: The collagen fibrils in middle zone meniscal fibrocartilage become more highly oriented perpendicular to the direction of compression. The D-spacing also increases, from 65.0 to 66.3 nm with compression up to 0.43 MPa, representing a 1.8% elongation of collagen fibrils perpendicular to the compression.Conclusion: The elasticity of the collagen fibrils under tension along their length when the meniscus is compressed, therefore, contributes to the overall elastic response of the meniscus only under loads that exceed those likely to be experienced physiologically.Keywords: collagen, meniscus, compression, SAXS, scaffold

Biomimetic cubic phases can be used for protein encapsulation in a variety of applications such as biosensors and drug delivery. Cubic phases with a high concentration of cholesterol and phospholipids were obtained herein. It is shown that the cubic phase structure can be maintained with a higher concentration of biomimetic membrane additives than has been reported previously. Opposing effects on the curvature of the membrane were observed upon the addition of phospholipids and cholesterol. Furthermore, the coronavirus fusion peptide significantly increased the negative curvature of the biomimetic membrane with cholesterol. We show that the viral fusion peptide can undergo structural changes leading to the formation of hydrophobic α-helices that insert into the lipid bilayer. This is of high importance, as a fusion peptide that induces increased negative curvature as shown by the formation of inverse hexagonal phases allows for greater contact area between two membranes, which is required for viral fusion to occur. The cytotoxicity assay showed that the toxicity toward HeLa cells was dramatically decreased when the cholesterol or peptide level in the nanoparticles increased. This suggests that the addition of cholesterol can improve the biocompatibility of the cubic phase nanoparticles, making them safer for use in biomedical applications. As the results, this work improves the potential for the biomedical end-use applications of the nonlamellar lipid nanoparticles and shows the need of systematic formulation studies due to the complex interplay of all components.

Hypothesis: Dairy proteins and mono- and diglycerides (MDG) are often used in unison to tailor the properties of dairy-based emulsions. However, there are significant gaps in our understanding of how proteins affect lipid crystallisation at the oil-water interface. We have used a unique combination of interfacially-sensitive techniques to elucidate the impact of dairy proteins on interfacial MDG crystal formation., Experiments: The formation temperature of interfacial MDG crystals was assessed through interfacial tension studies via drop shape analysis. Small and Wide-Angle X-ray Scattering measurements were performed on isolated oil-water interfaces, allowing for in-situ interrogation of MDG crystal structure and concentration at and near the interface., Findings: Dairy proteins are seen to reduce the temperature at which MDG crystals form at the oil-water interface. The displacement of proteins upon interfacial crystal formation was also clearly observed in interfacial tension measurements. For the first time, lipid crystals formed at the oil-water interface have been characterised using X-ray scattering. All scattering studies showed no change to the MDG crystal structures at the oil-water interface in the presence of adsorbed proteins. The results demonstrate that informed selection of emulsifier components is critical to controlling interfacial crystallisation with concomitant impact on emulsion stability., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Inc. All rights reserved.)

The casein micelle is a flexible construct, with its key structural components being casein proteins and colloidal calcium phosphate nanoclusters. According to literature, milk from different species exhibits differences in composition and physicochemical properties. X-ray scattering techniques were used to investigate and compare the nanoscale structure of casein micelles present in cow, goat and sheep milk. Although there were differences in the size and density of larger scale protein structures, at an atomic level the protein structures were similar. There were also strong similarities in the structure of the calcium-containing nanoclusters, namely that they had similar sizes and separations within the casein micelle for all three species.

In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.

The zymogen protease plasminogen and its active form plasmin perform key roles in blood clot dissolution, tissue remodeling, cell migration, and bacterial pathogenesis. Dysregulation of the plasminogen/plasmin system results in life-threatening hemorrhagic disorders or thrombotic vascular occlusion. Accordingly, inhibitors of this system are clinically important. Currently, tranexamic acid (TXA), a molecule that prevents plasminogen activation through blocking recruitment to target substrates, is the most widely used inhibitor for the plasminogen/plasmin system in therapeutics. However, TXA lacks efficacy on the active form of plasmin. Thus, there is a need to develop specific inhibitors that target the protease active site. Here we report the crystal structures of plasmin in complex with the novel YO ( trans -4-aminomethylcyclohexanecarbonyl-l-tyrosine- n -octylamide) class of small molecule inhibitors. We found that these inhibitors form key interactions with the S1 and S3' subsites of the catalytic cleft. Here, the TXA moiety of the YO compounds inserts into the primary (S1) specificity pocket, suggesting that TXA itself may function as a weak plasmin inhibitor, a hypothesis supported by subsequent biochemical and biophysical analyses. Mutational studies reveal that F587 of the S' subsite plays a key role in mediating the inhibitor interaction. Taken together, these data provide a foundation for the future development of small molecule inhibitors to specifically regulate plasmin function in a range of diseases and disorders., Competing Interests: Conflict-of-interest disclosure: The authors declare no competing financial interests.

An in-depth, critical review of model-dependent fitting of small-angle X-ray scattering (SAXS) data of bovine skim milk has led us to develop a new mathematical model for interpreting these data. Calcium-edge resonant soft X-ray scattering data provides unequivocal evidence as to the shape and location of the scattering due to colloidal calcium phosphate, which is manifested as a correlation peak centred at q = 0.035 Å(-1). In SAXS data this feature is seldom seen, although most literature studies attribute another feature centred at q = 0.08-0.1 Å(-1) to CCP. This work shows that the major SAXS features are due to protein arrangements: the casein micelle itself; internal regions approximately 20 nm in size, separated by water channels; and protein structures which are inhomogeneous on a 1-3 nm length scale. The assignment of these features is consistent with their behaviour under various conditions, including hydration time after reconstitution, addition of EDTA (a Ca-chelating agent), addition of urea, and reduction of pH.

The proposed mechanism for in meso crystallization of transmembrane proteins suggests that a protein or peptide is initially uniformly dispersed in the lipid self-assembly cubic phase but that crystals grow from a local lamellar phase, which acts as a conduit between the crystal and the bulk cubic phase. However, there is very limited experimental evidence for this theory. We have developed protocols to investigate the lipid mesophase microenvironment during crystal growth using standard procedures readily available in crystallography laboratories. This technique was used to characterize the microenvironment during crystal growth of the DAP12-TM peptide using synchrotron small angle X-ray scattering (SAXS) with a micro-sized X-ray beam. Crystal growth was found to occur from the gyroid cubic mesophase. For one in four crystals, a highly oriented local lamellar phase was observed, providing supporting evidence for the proposed mechanism for in meso crystallization. A new observation of this study was that we can differentiate diffraction peaks from crystals grown in meso, from peaks originating from the surrounding lipid matrix, potentially opening up the possibility of high-throughput SAXS analysis of in meso grown crystals.This article is part of the themed issue 'Soft interfacial materials: from fundamentals to formulation'., (© 2016 The Author(s).)

Plant growth and survival depend upon the activity of membrane transporters that control the movement and distribution of solutes into, around, and out of plants. Although many plant transporters are known, their intrinsic properties make them difficult to study. In barley (Hordeum vulgare), the root anion-permeable transporter Bot1 plays a key role in tolerance to high soil boron, facilitating the efflux of borate from cells. However, its three-dimensional structure is unavailable and the molecular basis of its permeation function is unknown. Using an integrative platform of computational, biophysical, and biochemical tools as well as molecular biology, electrophysiology, and bioinformatics, we provide insight into the origin of transport function of Bot1. An atomistic model, supported by atomic force microscopy measurements, reveals that the protein folds into 13 transmembrane-spanning and five cytoplasmic α-helices. We predict a trimeric assembly of Bot1 and the presence of a Na(+) ion binding site, located in the proximity of a pore that conducts anions. Patch-clamp electrophysiology of Bot1 detects Na(+)-dependent polyvalent anion transport in a Nernstian manner with channel-like characteristics. Using alanine scanning, molecular dynamics simulations, and transport measurements, we show that conductance by Bot1 is abolished by removal of the Na(+) ion binding site. Our data enhance the understanding of the permeation functions of Bot1., (© 2016 American Society of Plant Biologists. All rights reserved.)

The interpretation of milk X-ray and neutron scattering data in relation to the internal structure of the casein micelle is an ongoing debate. We performed resonant X-ray scattering measurements on liquid milk and conclusively identified key scattering features, namely those corresponding to the size of and the distance between colloidal calcium phosphate particles. An X-ray scattering feature commonly assigned to the particle size is instead due to protein inhomogeneities.

The 140 residue intrinsically disordered protein α-synuclein (α-syn) self-associates to form fibrils that are the major constituent of the Lewy body intracellular protein inclusions, and neurotoxic oligomers. Both of these macromolecular structures are associated with a number of neurodegenerative diseases, including Parkinson's disease and dementia with Lewy bodies. Using ensemble optimisation modelling (EOM) and small angle X-ray scattering (SAXS) on a size-exclusion column equipped beamline, we studied how the distribution of structural conformers in α-syn may be influenced by the presence of the familial early-onset mutations A30P, E45K and A53T, by substituting the four methionine residues with alanines and by reaction with copper (Cu2+) or an anti-fibril organic platinum (Pt) complex. We found that the WT had two major conformer groups, representing ensembles of compact and extended structures. The population of the extended group was increased in the more rapidly fibril-forming E45K and A53T mutants, while the compact group was enlarged in the oligomer-forming A30P mutant. Addition of Cu2+ resulted in the formation of an ensemble of compact conformers, while the anti-fibril agent and alanine substitution substantially reduced the population of extended conformers. Since our observations with the mutants suggest that fibrils may be drawn from the extended conformer ensemble, we propose that the compact and extended ensembles represent the beginning of oligomer and fibril formation pathways respectively, both of which have been reported to lead to a toxic gain of function. Manipulating these pathways and monitoring the results by EOM and SAXS may be useful in the development of anti-Parkinson's disease therapies.

We use in situ synchrotron small- and wide-angle X-ray scattering (SAXS/WAXS) to demonstrate that the formation of crystalline siderite (FeCO(3)) during the corrosion of steel in CO(2)-saturated brine - a problem of practical interest relating to the growth of protective scales on the interior surface of oil and gas production pipelines - is preceded by the formation of a colloidal precipitate in the solution and an amorphous surface layer, both assumed to be amorphous ferrous carbonate. Grazing incidence SAXS shows instantaneous film formation upon the application of an anodic potential, followed by development of a separate population of particles at later times, then by the formation of crystalline species, observed by WAXS. These observations can be interpreted in terms of crystal nucleation within the amorphous surface layer. Traces of Cr(3+) in the solution significantly accelerate the precipitation rate of the colloidal precursor and accelerate the appearance of the crystalline scale. We speculate on the significance of these observations for the nucleation, growth and morphology of the corrosion scale and hence its protectiveness.

Small angle X-ray scattering (SAXS) of biomacromolecules in solution has become a prominent technique in structural biology. Whilst the majority of current use is for static measurements, the field is also advancing for measurements where the sample at the beam position changes with time, using high throughput systems, chromatography, high speed mixing and pump-probe techniques in particular. Time resolved work is greatly aided by increasingly sophisticated software for acquiring and analysing data, together with developments in X-ray sources, beamline optics and detectors. The exploitation of spatial coherence is under development, with X-ray free electron lasers aiming to provide major advances in single molecule structure reconstruction and time resolution. Here we provide an overview of current developments advancing time resolved solution SAXS., (Copyright © 2014 Elsevier Ltd. All rights reserved.)