A multipurpose instrument for time-resolved ultra-small-angle and coherent X-ray scattering

E+: Software for Hierarchical Modeling of Electron Scattering from Complex Structures

In modern nanobeam transmission electron microscopy methods, such as 4D-STEM, a converged electron nanobeam is scanned across a sample. Its 2D scattering pattern is recorded at each sample position, mapping the local sample structure. One of the bottlenecks in electron scattering is the analysis of the scattering data obtained from complex atomic or molecular structures. On the basis of D+ software, we developed the software E+ for analyzing electron scattering data, enabling us to model the 2D scattering pattern from any complex structure in a single orientation or a fiber. In addition, the azimuthally integrated 1D scattering curve of isotropically oriented structures (as in solutions or powders), or any other distribution of orientations, can also be computed. E+ allows the docking of geometric and/or molecular atomic models into their assembly symmetry. The assembly symmetry contains the rotations and translations of repeating subunits within a large structure. This process can be repeated hierarchically, using a bottom-up approach, adding as many subunits as needed. This procedure can be used to model the scattering data from any complex supramolecular structure at any spatial resolution, down to atomic resolution. In addition, the contribution from the solvation layers of structures in solutions can be computed in a scalable manner for large complexes. Furthermore, the Python API of E+ can be used for advanced modeling of structure factor and pair distribution functions, taking into account various effects, including thermal fluctuations, polydispersity of any structural parameters, or the intermolecular interactions between subunits. We validate E+ against the abTEM software and show a few examples, demonstrating how E+ can be used to analyze 4D-STEM electron scattering data.

Temperature-Enhanced Ordering in Plate-like Semicrystalline Block Copolymer Single-Crystal Suspensions Studied by Real-Time SAXS/WAXS

Self-assembly of hard platelet colloids into liquid crystalline phases is typically driven by entropy, making them less sensitive to temperature changes. However, soft interaction potentials often exist in real colloidal systems, which can lead to temperature-sensitive phase transitions. Despite significant progress in understanding phase behavior in the past 2 decades, studies on temperature-dependent phase behavior remain rare, and there is limited knowledge about how soft interactions influence phase transitions upon temperature changes. In this work, we investigated a platelet colloid system in isotropic and nematic phases using small- and wide-angle X-ray scattering techniques (SAXS/WAXS) and polarized optical microscopy (POM). The system consisted of polystyrene-block-poly(l-lactide) (PS-b-PLLA) block copolymer single crystals (BCSCs) with varying sizes dispersed in p-xylene. These crystals were truncated lozenge-shaped with effective diameters of 500 and 1000 nm and a uniform dry thickness of 18.0 nm. The ordering behaviors of BCSC500 in the isotropic phase and BCSC1000 in the N phase were monitored through SAXS/WAXS during heating, quenching, self-seeding, crystal growth, and final quenching. Enhanced ordering, specifically face-to-face correlation, was observed during heating prior to crystal melting. For BCSC500, ordering emerged at 105 °C during heating. In the case of BCSC1000 in the N phase, ordering was enhanced with increased heating and reached up to the ninth order of correlation peaks, indicating the formation of lamellar domains within the N phase. After seeding and crystal growth, both systems exhibited ordering. However, during the final cooling to room temperature, ordering disappeared for BCSC500 but persisted for BCSC1000. POM observations revealed that for both systems, initial heating resulted in a decrease in overall brightness; however, enhanced nematic domains or tactoids emerged prior to melting. Subsequent thermal treatments did not induce noticeable changes in the observed order. While both techniques revealed increased order, discrepancies were noted. SAXS indicated intensified short-range correlations, while POM showed the formation of local nematic domains or tactoids. We propose three distinct ordering regimes to reconcile these observations: large-scale nematic order, enhanced short-range order, and short-range clusters. We attributed the temperature-enhanced ordering phenomenon to lateral interactions between the BCSCs, annealing, and memory effects during melting and crystallization.

An integrated picture of the structural pathways controlling the heart performance

The regulation of heart function is attributed to a dual filament mechanism: i) the Ca2+-dependent structural changes in the regulatory proteins of the thin, actin-containing filament making actin available for myosin motor attachment, and ii) the release of motors from their folded (OFF) state on the surface of the thick filament allowing them to attach and pull the actin filament. Thick filament mechanosensing is thought to control the number of motors switching ON in relation to the systolic performance, but its molecular basis is still controversial. Here, we use high spatial resolution X-ray diffraction data from electrically paced rat trabeculae and papillary muscles to provide a molecular explanation of the modulation of heart performance that calls for a revision of the mechanosensing hypothesis. We find that upon stimulation, titin-mediated structural changes in the thick filament switch motors ON throughout the filament within ~½ the maximum systolic force. These structural changes also drive Myosin Binding Protein-C (MyBP-C) to promote first motor attachments to actin from the central 1/3 of the half-thick filament. Progression of attachments toward the periphery of half-thick filament with increase in systolic force is carried on by near-neighbor cooperative thin filament activation by attached motors. The identification of the roles of MyBP-C, titin, thin and thick filaments in heart regulation enables their targeting for potential therapeutic interventions.

Morphology and intervesicle distances in condensates of synaptic vesicles and synapsin

Synaptic vesicle clusters or pools are functionally important constituents of chemical synapses. In the so-called reserve and the active pools, neurotransmitter-loaded synaptic vesicles (SVs) are stored and conditioned for fusion with the synaptic membrane and subsequent neurotransmitter release during synaptic activity. Vesicle clusters can be considered as so-called membraneless compartments, which form by liquid-liquid phase separation. Synapsin as one of the most abundant synaptic proteins has been identified as a major driver of pool formation. It has been shown to induce liquid-liquid phase separation and form condensates on its own in solution, but also has been shown to integrate vesicles into condensates in vitro. In this process, the intrinsically disordered region of synapsin is believed to play a critical role. Here, we first investigate the solution structure of synapsin and SVs separately by small-angle x-ray scattering. In the limit of low momentum transfer q, the scattering curve for synapsin gives clear indication for supramolecular aggregation (condensation). We then study mixtures of SVs and synapsin-forming condensates, aiming at the morphology and intervesicle distances, i.e., the structure of the condensates in solution. To obtain the structure factor S(q) quantifying intervesicle correlation, we divide the scattering curve of condensates by that of pure SV suspensions. Analysis of S(q) in combination with numerical simulations of cluster aggregation indicates a noncompact fractal-like vesicular fluid with rather short intervesicle distances at the contact sites.

Load-dependence of the activation of myosin filaments in heart muscle

Contraction of heart muscle requires activation of both the actin and myosin filaments. The mechanism of myosin filament activation is unknown, but the leading candidate hypothesis is direct mechano-sensing by the filaments. Here, we tested this hypothesis by activating intact trabeculae from rat heart by electrical stimulation under different loads and measuring myosin filament activation by X-ray diffraction. Unexpectedly, we found that the distinct structural changes in the myosin filament associated with activation had different dependences on the load. In early activation, all the structural changes indicated faster activation at higher load, as expected from the mechano-sensing hypothesis, but, at later times, the helical order of the myosin motors characteristic of the inactivated state was lost even at very low load. We conclude that mechano-sensing does operate in heart muscle, but it is supplemented by a previously undescribed mechanism that links myosin filament activation to actin filament activation. KEY POINTS: Myosin filament activation controls the strength and speed of contraction in heart muscle. Early activation of the myosin filament is determined by the filament load. At later times, myosin filament activation is controlled by a load independent pathway. This load independent pathway provides new targets and assays for drug development.

Synchrotron Radiation: A Key Tool for Drug Discovery

Synchrotron radiation is extensively utilized in the domains of materials science, physical chemistry, and life science, resulting from its high intensity, exceptional monochromaticity, superior collimation, and broad wave spectrum. This top-notch light source has also made significant contributions to the progress of biomedicine. The advancement of synchrotron radiation-based X-ray and protein crystallography technologies has created new prospects for drug discovery. These innovative techniques have opened up exciting avenues in the field. The investigation of protein crystal structures and the elucidation of the spatial configuration of biological macromolecules have revealed intricate details regarding the modes of protein binding. Furthermore, the screening of crystal polymorphs and ligands has laid the groundwork for rational drug modification and the improvement of drug physicochemical properties. As science and technology continue to advance, the techniques for analyzing structures using synchrotron radiation sources and the design of corresponding crystallographic beamline stations are undergoing continuous enhancement. These cutting-edge tools and facilities are expected to expedite the drug development process and rectify the current situation of a lack of targeted drugs.

Bridging length scales in hard materials with ultra-small angle X-ray scattering - a critical review

Owing to their exceptional properties, hard materials such as advanced ceramics, metals and composites have enormous economic and societal value, with applications across numerous industries. Understanding their microstructural characteristics is crucial for enhancing their performance, materials development and unleashing their potential for future innovative applications. However, their microstructures are unambiguously hierarchical and typically span several length scales, from sub-ångstrom to micrometres, posing demanding challenges for their characterization, especially for in situ characterization which is critical to understanding the kinetic processes controlling microstructure formation. This review provides a comprehensive description of the rapidly developing technique of ultra-small angle X-ray scattering (USAXS), a nondestructive method for probing the nano-to-micrometre scale features of hard materials. USAXS and its complementary techniques, when developed for and applied to hard materials, offer valuable insights into their porosity, grain size, phase composition and inhomogeneities. We discuss the fundamental principles, instrumentation, advantages, challenges and global status of USAXS for hard materials. Using selected examples, we demonstrate the potential of this technique for unveiling the microstructural characteristics of hard materials and its relevance to advanced materials development and manufacturing process optimization. We also provide our perspective on the opportunities and challenges for the continued development of USAXS, including multimodal characterization, coherent scattering, time-resolved studies, machine learning and autonomous experiments. Our goal is to stimulate further implementation and exploration of USAXS techniques and inspire their broader adoption across various domains of hard materials science, thereby driving the field toward discoveries and further developments.

Multiscale analysis of triglycerides using X-ray scattering: implementing a shape-dependent model for CNP characterization

In the last decade, research has focused on examining the fundamental interactions occurring in triglycerides, aiming to comprehend the self-assembly of crystalline nanoplatelets (CNPs) and their role in forming larger hierarchical structures essential for fat functionality. Microscopy research on CNPs frequently requires disruptive preparatory techniques, such as deoiling and sonication, to achieve quantitative outcomes. Conversely, X-ray scattering has proven to be an advantageous method for studying triglycerides, as little sample is needed to quantify the system's hierarchical structures. Specifically, ultra-small-angle X-ray scattering (USAXS) has emerged as a fitting technique for studying CNPs, owing to its length scale range falling between 25 nm and 3.49 μm. In this study, we characterized four different 30% fat dilutions of stearic acid-based fats in triolein, with various purities and preparation protocols. Samples were characterized by combining diverse microscopy techniques (cryo-SEM, TEM, polarized light and phase contrast microscopy) with synchrotron-radiation X-ray scattering (WAXS, SAXS, and USAXS). A shape-dependent model for the interpretation of USAXS data is proposed, overcoming some of the drawbacks linked to previously utilized models. CNPs are modeled as polydisperse parallelepipeds, and the aggregates are characterized by fractal dimensionality. This model offers novel insights into CNP cross-section, as well as aggregation. In the long run, we hope that the model will increase our understanding of CNP conformation and interactions, helping us design new fat systems on the mesoscale.

Guanidine Hydrochloride-Induced Hepatitis B Virus Capsid Disassembly Hysteresis

Hepatitis B virus (HBV) displays remarkable self-assembly capabilities that interest the scientific community and biotechnological industries as HBV is leading to an annual mortality of up to 1 million people worldwide (especially in Africa and Southeast Asia). When the ionic strength is increased, hepatitis B virus-like particles (VLPs) can assemble from dimers of the first 149 residues of the HBV capsid protein core assembly domain (Cp149). Using solution small-angle X-ray scattering, we investigated the disassembly of the VLPs by titrating guanidine hydrochloride (GuHCl). Measurements were performed with and without 1 M NaCl, added either before or after titrating GuHCl. Fitting the scattering curves to a linear combination of atomic models of Cp149 dimer (the subunit) and T = 3 and T = 4 icosahedral capsids revealed the mass fraction of the dimer in each structure in all the titration points. Based on the mass fractions, the variation in the dimer-dimer association standard free energy was calculated as a function of added GuHCl, showing a linear relation between the interaction strength and GuHCl concentration. Using the data, we estimated the energy barriers for assembly and disassembly and the critical nucleus size for all of the assembly reactions. Extrapolating the standard free energy to [GuHCl] = 0 showed an evident hysteresis in the assembly process, manifested by differences in the dimer-dimer association standard free energy obtained for the disassembly reactions compared with the equivalent assembly reactions. Similar hysteresis was observed in the energy barriers for assembly and disassembly and the critical nucleus size. The results suggest that above 1.5 M, GuHCl disassembled the capsids by attaching to the protein and adding steric repulsion, thereby weakening the hydrophobic attraction.

Small-angle X-ray scattering unveils the internal structure of lipid nanoparticles

Lipid nanoparticles own a remarkable potential in nanomedicine, only partially disclosed. While the clinical use of liposomes and cationic lipid-nucleic acid complexes is well-established, liquid lipid nanoparticles (nanoemulsions), solid lipid nanoparticles, and nanostructured lipid carriers have even greater possibilities. However, they face obstacles in being used in clinics due to a lack of understanding about the molecular mechanisms controlling their drug loading and release, interactions with the biological environment (such as the protein corona), and shelf-life stability. To create effective drug delivery carriers and successfully translate bench research to clinical settings, it is crucial to have a thorough understanding of the internal structure of lipid nanoparticles. Through synchrotron small-angle X-ray scattering experiments, we determined the spatial distribution and internal structure of the nanoparticles' lipid, surfactant, and the bound water in them. The nanoparticles themselves have a barrel-like shape that consists of coplanar lipid platelets (specifically cetyl palmitate) that are covered by loosely spaced polysorbate 80 surfactant molecules, whose polar heads retain a large amount of bound water. To reduce the interface cost of bound water with unbound water without stacking, the platelets collapse onto each other. This internal structure challenges the classical core-shell model typically used to describe solid lipid nanoparticles and could play a significant role in drug loading and release, biological fluid interaction, and nanoparticle stability, making our findings valuable for the rational design of lipid-based nanoparticles.

Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies

Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems and treating disease. Despite the deposition of over 215 000 macromolecular structures in the Protein Data Bank and the advent of AI-based structure prediction tools such as AlphaFold2, RoseTTAFold, and ESMFold, static representations are typically produced, which fail to fully capture macromolecular motion. Here, we discuss the importance of integrating experimental structures with computational clustering to explore the conformational landscapes that manifest protein function. We describe the method developed by the Protein Data Bank in Europe - Knowledge Base to identify distinct conformational states, demonstrate the resource's primary use cases, through examples, and discuss the need for further efforts to annotate protein conformations with functional information. Such initiatives will be crucial in unlocking the potential of protein dynamics data, expediting drug discovery research, and deepening our understanding of macromolecular mechanisms.

Structure of symmetric and asymmetric lipid membranes from joint SAXS/SANS

Small-angle X-ray and neutron scattering (SAXS/SANS) techniques excel in unveiling intricate details of the internal structure of lipid membranes under physiologically relevant temperature and buffer conditions, all without the need to resort to bulky labels. By concurrently conducting and analyzing neutron and X-ray data, these methods harness the complete spectrum of contrast and resolution from various components constituting lipid membranes. Despite this, the literature exhibits only a sparse presence of applications compared to other techniques in membrane biophysics. This chapter serves as a primer for conducting joint SAXS/SANS analyses on symmetric and asymmetric large unilamellar vesicles, elucidating fundamental elements of the analysis process. Specifically, we introduce the basics of interactions of X-rays and neutrons with matter that lead to the scattering contrast and a description of membrane structure in terms of scattering length density profiles. These profiles allow fitting of the experimentally observed scattering intensity. We further integrate practical insights, unveiling strategies for successful data acquisition and providing a comprehensive assessment of the technique's advantages and drawbacks. By amalgamating theoretical underpinnings with practical considerations, this chapter aims to dismantle barriers hindering the adoption of joint SAXS/SANS approaches, thereby encouraging an influx of studies in this domain.

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.

Regulating Striated Muscle Contraction: Through Thick and Thin

Force generation in striated muscle is primarily controlled by structural changes in the actin-containing thin filaments triggered by an increase in intracellular calcium concentration. However, recent studies have elucidated a new class of regulatory mechanisms, based on the myosin-containing thick filament, that control the strength and speed of contraction by modulating the availability of myosin motors for the interaction with actin. This review summarizes the mechanisms of thin and thick filament activation that regulate the contractility of skeletal and cardiac muscle. A novel dual-filament paradigm of muscle regulation is emerging, in which the dynamics of force generation depends on the coordinated activation of thin and thick filaments. We highlight the interfilament signaling pathways based on titin and myosin-binding protein-C that couple thin and thick filament regulatory mechanisms. This dual-filament regulation mediates the length-dependent activation of cardiac muscle that underlies the control of the cardiac output in each heartbeat.

A synchrotron X-ray scattering study of the crystallization behavior of mixtures of confectionary triacylglycerides: Effect of chemical composition and shear on polymorphism and kinetics

Cocoa butter equivalents (CBE) are mixtures of triglycerides from multiple sources (e.g., sunflower oil, mango kernel and sal), which resemble cocoa butter (CB) in both physical and chemical properties. Despite being widely used to replace CB in chocolate products, the crystallization behavior of many CBEs is still poorly understood. The aim of this work was to develop a fundamental understanding, at the molecular level, of the crystallization behavior of selected CBEs, and compare it with that of CB. Chromatography was used to determine the composition of CBEs, in terms of fatty acids and triacylglycerides (TAGs), while their thermodynamic behavior and crystallization kinetics were studied using polarized microscopy, differential calorimetry and three different synchrotron X-ray scattering setups. CBEs of different origin and chemical composition (e.g., different ratios of the main CB TAGs, namely POP, SOS and POS) crystallized in different polymorphs and with different kinetics of nucleation, growth and polymorphic transformation. SOS rich CBEs presented showed more polymorphs than CB and POP rich samples; whereas, CBEs with high concentration of POP showed slow kinetic of polymorphic transformation towards the stable β(3L) form. Additionally, it was observed that the presence of small amounts (<1% w/w) of specific TAGs, such as OOO, PPP or SSS, could significantly affect the crystallization behavior of CBEs and CBs in terms of kinetics of polymorphic transformation and number of phases detected (multiple high melting β(2L) polymorphs were identified in all samples studied). Finally, it was found that, regardless of the CBE composition, the presence of shear could promote the formation of stable β polymorphs over metastable β' and γ forms, and reduced the size of the crystal agglomerates formed due to increased secondary nucleation.

Sarcomere level mechanics of the fast skeletal muscle of the medaka fish larva

The medaka fish (Oryzias latipes) is a vertebrate model used in developmental biology and genetics. Here we explore its suitability as a model for investigating the molecular mechanisms of human myopathies caused by mutations in sarcomeric proteins. To this end, the relevant mechanical parameters of the intact skeletal muscle of wild-type medaka are determined using the transparent tail at larval stage 40. Tails were mounted at sarcomere length of 2.1 μm in a thermoregulated trough containing physiological solution. Tetanic contractions were elicited at physiological temperature (10°C-30°C) by electrical stimulation, and sarcomere length changes were recorded with nanometer-microsecond resolution during both isometric and isotonic contractions with a striation follower. The force output has been normalized for the actual fraction of the cross section of the tail occupied by the myofilament lattice, as established with transmission electron microscopy (TEM), and then for the actual density of myofilaments, as established with X-ray diffraction. Under these conditions, the mechanical performance of the contracting muscle of the wild-type larva can be defined at the level of the half-thick filament, where ∼300 myosin motors work in parallel as a collective motor, allowing a detailed comparison with the established performance of the skeletal muscle of different vertebrates. The results of this study point out that the medaka fish larva is a suitable model for the investigation of the genotype/phenotype correlations and therapeutic possibilities in skeletal muscle diseases caused by mutations in sarcomeric proteins.NEW & NOTEWORTHY The suitability of the medaka fish as a model for investigating the molecular mechanisms of human myopathies caused by mutations of sarcomeric proteins is tested by combining structural analysis and sarcomere-level mechanics of the skeletal muscle of the tail of medaka larva. The mechanical performance of the medaka muscle, scaled at the level of the myosin-containing thick filament, together with its reduced genome duplication makes this model unique for investigations of the genotype/phenotype correlations in human myopathies.

Orientational ordering and assembly of silica-nickel Janus particles in a magnetic field

The orientation ordering and assembly behavior of silica-nickel Janus particles in a static external magnetic field were probed by ultra small-angle X-ray scattering (USAXS). Even in a weak applied field, the net magnetic moments of the individual particles aligned in the direction of the field, as indicated by the anisotropy in the recorded USAXS patterns. X-ray photon correlation spectroscopy (XPCS) measurements on these suspensions revealed that the corresponding particle dynamics are primarily Brownian diffusion [Zinn, Sharpnack & Narayanan (2023). Soft Matter, 19, 2311-2318]. At higher fields, the magnetic forces led to chain-like configurations of particles, as indicated by an additional feature in the USAXS pattern. A theoretical framework is provided for the quantitative interpretation of the observed anisotropic scattering diagrams and the corresponding degree of orientation. No anisotropy was detected when the magnetic field was applied along the beam direction, which is also replicated by the model. The method presented here could be useful for the interpretation of oriented scattering patterns from a wide variety of particulate systems. The combination of USAXS and XPCS is a powerful approach for investigating asymmetric colloidal particles in external fields.

Improvement of ultra-small-angle XPCS with the Extremely Brilliant Source

Recent technical developments and the performance of the X-ray photon correlation spectroscopy (XPCS) method over the ultra-small-angle range with the Extremely Brilliant Source (EBS) at the ESRF are described. With higher monochromatic coherent photon flux (∼1012 photons s-1) provided by the EBS and the availability of a fast pixel array detector (EIGER 500K detector operating at 23000 frames s-1), XPCS has become more competitive for probing faster dynamics in relatively dilute suspensions. One of the goals of the present development is to increase the user-friendliness of the method. This is achieved by means of a Python-based graphical user interface that enables online visualization and analysis of the processed data. The improved performance of XPCS on the Time-Resolved Ultra-Small-Angle X-ray Scattering instrument (ID02 beamline) is demonstrated using dilute model colloidal suspensions in several different applications.

Dependence of myosin filament structure on intracellular calcium concentration in skeletal muscle

Contraction of skeletal muscle is triggered by an increase in intracellular calcium concentration that relieves the structural block on actin-binding sites in resting muscle, potentially allowing myosin motors to bind and generate force. However, most myosin motors are not available for actin binding because they are stabilized in folded helical tracks on the surface of myosin-containing thick filaments. High-force contraction depends on the release of the folded motors, which can be triggered by stress in the thick filament backbone, but additional mechanisms may link the activation of the thick filaments to that of the thin filaments or to intracellular calcium concentration. Here, we used x-ray diffraction in combination with temperature-jump activation to determine the steady-state calcium dependence of thick filament structure and myosin motor conformation in near-physiological conditions. We found that x-ray signals associated with the perpendicular motors characteristic of isometric force generation had almost the same calcium sensitivity as force, but x-ray signals associated with perturbations in the folded myosin helix had a much higher calcium sensitivity. Moreover, a new population of myosin motors with a longer axial periodicity became prominent at low levels of calcium activation and may represent an intermediate regulatory state of the myosin motors in the physiological pathway of filament activation.

Insight into structural biophysics from solution X-ray scattering

The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.

Freeze-Induced Phase Transition and Local Pressure in a Phospholipid/Water System: Novel Insights Were Obtained from a Time/Temperature Resolved Synchrotron X-ray Diffraction Study

Water-to-ice transformation results in a 10% increase in volume, which can have a significant impact on biopharmaceuticals during freeze-thaw cycles due to the mechanical stresses imparted by the growing ice crystals. Whether these stresses would contribute to the destabilization of biopharmaceuticals depends on both the magnitude of the stress and sensitivity of a particular system to pressure and sheer stresses. To address the gap of the "magnitude" question, a phospholipid, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), is evaluated as a probe to detect and quantify the freeze-induced pressure. DPPC can form several phases under elevated pressure, and therefore, the detection of a high-pressure DPPC phase during freezing would be indicative of a freeze-induced pressure increase. In this study, the phase behavior of DPPC/water suspensions, which also contain the ice nucleation agent silver iodide, is monitored by synchrotron small/wide-angle X-ray scattering during the freeze-thaw transition. Cooling the suspensions leads to heterogeneous ice nucleation at approximately -7 °C, followed by a phase transition of DPPC between -11 and -40 °C. In this temperature range, the initial gel phase of DPPC, Lβ', gradually converts to a second phase, tentatively identified as a high-pressure Gel III phase. The Lβ'-to-Gel III phase transition continues during an isothermal hold at -40 °C; a second (homogeneous) ice nucleation event of water confined in the interlamellar space is detected by differential scanning calorimetry (DSC) at the same temperature. The extent of the phase transition depends on the DPPC concentration, with a lower DPPC concentration (and therefore a higher ice fraction), resulting in a higher degree of Lβ'-to-Gel III conversion. By comparing the data from this study with the literature data on the pressure/temperature Lβ'/Gel III phase boundary and the lamellar lattice constant of the Lβ' phase, the freeze-induced pressure is estimated to be approximately 0.2-2.6 kbar. The study introduces DPPC as a probe to detect a pressure increase during freezing, therefore addressing the gap between a theoretical possibility of protein destabilization by freeze-induced pressure and the current lack of methods to detect freeze-induced pressure. In addition, the observation of a freeze-induced phase transition in a phospholipid can improve the mechanistic understanding of factors that could disrupt the structure of lipid-based biopharmaceuticals, such as liposomes and mRNA vaccines, during freezing and thawing.

Effect of ionic strength on the assembly of simian vacuolating virus capsid protein around poly(styrene sulfonate)

Virus-like particles (VLPs) are noninfectious nanocapsules that can be used for drug delivery or vaccine applications. VLPs can be assembled from virus capsid proteins around a condensing agent, such as RNA, DNA, or a charged polymer. Electrostatic interactions play an important role in the assembly reaction. VLPs assemble from many copies of capsid protein, with a combinatorial number of intermediates. Hence, the mechanism of the reaction is poorly understood. In this paper, we combined solution small-angle X-ray scattering (SAXS), cryo-transmission electron microscopy (TEM), and computational modeling to determine the effect of ionic strength on the assembly of Simian Vacuolating Virus 40 (SV40)-like particles. We mixed poly(styrene sulfonate) with SV40 capsid protein pentamers at different ionic strengths. We then characterized the assembly product by SAXS and cryo-TEM. To analyze the data, we performed Langevin dynamics simulations using a coarse-grained model that revealed incomplete, asymmetric VLP structures consistent with the experimental data. We found that close to physiological ionic strength, [Formula: see text] VLPs coexisted with VP1 pentamers. At lower or higher ionic strengths, incomplete particles coexisted with pentamers and [Formula: see text] particles. Including the simulated structures was essential to explain the SAXS data in a manner that is consistent with the cryo-TEM images.

Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA

RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA-regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy can provide high-resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small-angle X-ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large-sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.

New Lyotropic Complex Fluid Structured in Sheets of Ellipsoidal Micelles Solubilizing Fragrance Oils

New lyotropic, fragranced, viscoelastic fluid with a complex structure is obtained from fragranced microemulsions by the addition of a fatty acid. Nonhomogeneous mixing of an appropriate nonionic surfactant, a fatty acid, and a fragrance oil led to the formation of anisotropically shaped and highly oriented micelles in aqueous solution. The nano- and microstructures, and consequently the viscosity, are controlled by the balance of fatty acids used as a cosurfactant and fragrance molecules, which partly behave as a cosurfactant and partly segregate in the micelles of the hydrophilic nonionic surfactant. The transition from isotropic microemulsion to a more structured viscoelastic solution is characterized by X-ray scattering and rheological methods. Considering our X-ray scattering results, we propose a structure composed of planar sheets of ellipsoidal micelles arranged in a lamellar type of stacking. The complex structured, low viscous, transparent fluid is capable of solubilizing a fragrance inside the ellipsoidal micelles, as well as retaining microparticles containing fragrance, without the addition of a polymeric thickener or another gelator. These features allow the creation of a 2-in-1 fragrance-solubilizing liquid product compatible with all types of home and body care consumer products.

Multiscale investigation of viscoelastic properties of aqueous solutions of sodium alginate and evaluation of their biocompatibility

In order to get better knowledge of mechanical properties from microscopic to macroscopic scale of biopolymers, viscoelastic bulk properties of aqueous solutions of sodium alginate were studied at different scales by combining macroscopic shear rheology (Hz), diffusing-wave spectroscopy microrheology (kHz-MHz) and Brillouin spectroscopy (GHz). Structural properties were also directly probed by small-angle X-ray scattering (SAXS). The results demonstrate a change from polyelectrolyte behavior to neutral polymer behavior by increasing polymer concentration with the determination of characteristic sizes (persistence length, correlation length). The viscoelastic properties probed at the phonon wavelength much higher than the ones obtained at low frequency reflect the variation of microscopic viscosity. First experiments obtained by metabolic activity assays with mouse embryonic fibroblasts showed biocompatibility of sodium alginate aqueous solutions in the studied range of concentrations (2.5-10 g L-1) and consequently their potential biomedical applications.

Small-angle X-ray scattering in the era of fourth-generation light sources

Recently, fourth-generation synchrotron sources with several orders of magnitude higher brightness and higher degree of coherence compared with third-generation sources have come into operation. These new X-ray sources offer exciting opportunities for the investigation of soft matter and biological specimens by small-angle X-ray scattering (SAXS) and related scattering methods. The improved beam properties together with the advanced pixel array detectors readily enhance the angular resolution of SAXS and ultra-small-angle X-ray scattering in the pinhole collimation. The high degree of coherence is a major boost for the X-ray photon correlation spectroscopy (XPCS) technique, enabling the equilibrium dynamics to be probed over broader time and length scales. This article presents some representative examples illustrating the performance of SAXS and XPCS with the Extremely Brilliant Source at the European Synchrotron Radiation Facility. The rapid onset of radiation damage is a significant challenge with the vast majority of samples, and appropriate protocols need to be adopted for circumventing this problem.

In Situ Ultra-Small- and Small-Angle X-ray Scattering Study of ZnO Nanoparticle Formation and Growth through Chemical Bath Deposition in the Presence of Polyvinylpyrrolidone

ZnO inverse opals combine the outstanding properties of the semiconductor ZnO with the high surface area of the open-porous framework, making them valuable photonic and catalysis support materials. One route to produce inverse opals is to mineralize the voids of close-packed polymer nanoparticle templates by chemical bath deposition (CBD) using a ZnO precursor solution, followed by template removal. To ensure synthesis control, the formation and growth of ZnO nanoparticles in a precursor solution containing the organic additive polyvinylpyrrolidone (PVP) was investigated by in situ ultra-small- and small-angle X-ray scattering (USAXS/SAXS). Before that, we studied the precursor solution by in-house SAXS at T = 25 °C, revealing the presence of a PVP network with semiflexible chain behavior. Heating the precursor solution to 58 °C or 63 °C initiates the formation of small ZnO nanoparticles that cluster together, as shown by complementary transmission electron microscopy images (TEM) taken after synthesis. The underlying kinetics of this process could be deciphered by quantitatively analyzing the USAXS/SAXS data considering the scattering contributions of particles, clusters, and the PVP network. A nearly quantitative description of both the nucleation and growth period could be achieved using the two-step Finke-Watzky model with slow, continuous nucleation followed by autocatalytic growth.

SpatDistCalib: a GUI Python software for spatial-distortion correction of 2D detectors using splines

CCD-based X-ray detector systems often suffer from spatial distortions. Reproducible distortions can be quantitatively measured with a calibration grid and described as a displacement matrix or as spline functions. The measured distortion can be used afterwards to undistort raw images or to refine the actual position of each pixel, e.g. for azimuthal integration. This article describes a method using a regular grid, not necessarily orthogonal, to measure the distortions. The graphical user interface (GUI) Python software that is used to implement this method is available under a GPLv3 license on ESRF GitLab, and produces a spline file that is usable with data-reduction software such as FIT2D or pyFAI.

Selected advances in small-angle scattering and applications they serve in manufacturing, energy and climate change

Innovations in small-angle X-ray and neutron scattering (SAXS and SANS) at major X-ray and neutron facilities offer new characterization tools for researching materials phenomena relevant to advanced applications. For SAXS, the new generation of diffraction-limited storage rings, incorporating multi-bend achromat concepts, dramatically decrease electron beam emittance and significantly increase X-ray brilliance over previous third-generation sources. This results in intense X-ray incident beams that are more compact in the horizontal plane, allowing significantly improved spatial resolution, better time resolution, and a new era for coherent-beam SAXS methods such as X-ray photon correlation spectroscopy. Elsewhere, X-ray free-electron laser sources provide extremely bright, fully coherent, X-ray pulses of <100 fs and can support SAXS studies of material processes where entire SAXS data sets are collected in a single pulse train. Meanwhile, SANS at both steady-state reactor and pulsed spallation neutron sources has significantly evolved. Developments in neutron optics and multiple detector carriages now enable data collection in a few minutes for materials characterization over nanometre-to-micrometre scale ranges, opening up real-time studies of multi-scale materials phenomena. SANS at pulsed neutron sources is becoming more integrated with neutron diffraction methods for simultaneous structure characterization of complex materials. In this paper, selected developments are highlighted and some recent state-of-the-art studies discussed, relevant to hard matter applications in advanced manufacturing, energy and climate change.

Sterically Stabilized Diblock Copolymer Nanoparticles Enable Efficient Preparation of Non-Aqueous Pickering Nanoemulsions

We report the first example of a non-aqueous Pickering nanoemulsion, which comprises glycerol droplets dispersed in mineral oil. The droplet phase is stabilized by hydrophobic sterically stabilized poly(lauryl methacrylate)-poly(benzyl methacrylate) nanoparticles which are prepared directly in mineral oil using polymerization-induced self-assembly. First, a glycerol-in-mineral oil Pickering macroemulsion with a mean droplet diameter of 2.1 ± 0.9 μm is prepared via high-shear homogenization using excess nanoparticles as an emulsifier. Then, this precursor macroemulsion is subjected to high-pressure microfluidization (a single pass at an applied pressure of 20,000 psi) to produce glycerol droplets of approximately 200-250 nm diameter. Transmission electron microscopy studies indicate preservation of the distinctive superstructure produced by nanoparticle adsorption at the glycerol/mineral oil interface, thus confirming the Pickering nature of the nanoemulsion. Glycerol is sparingly soluble in mineral oil, thus such nanoemulsions are rather susceptible to destabilization via Ostwald ripening. Indeed, substantial droplet growth occurs within 24 h at 20 °C, as judged by dynamic light scattering. However, this problem can be suppressed by dissolving a non-volatile solute (sodium iodide) in glycerol prior to formation of the nanoemulsion. This reduces diffusional loss of glycerol molecules from the droplets, with analytical centrifugation studies indicating much better long-term stability for such Pickering nanoemulsions (up to 21 weeks). Finally, the addition of just 5% water to the glycerol phase prior to emulsification enables the refractive index of the droplet phase to be matched to that of the continuous phase, leading to relatively transparent nanoemulsions.

Dynamics of magnetic Janus colloids studied by ultra small-angle X-ray photon correlation spectroscopy

The orientation behavior and the translational dynamics of spherical magnetic silica-nickel Janus colloids in an external magnetic field have been studied by small-angle X-ray scattering and X-ray photon correlation spectroscopy at ultra small-angles. For weak applied fields and at low volume fractions, the particle dynamics is dominated by Brownian motion even though the net magnetic moments of the individual particles are aligned in the direction of the field as indicated by the anisotropy in the small-angle scattering patterns. For higher fields the magnetic forces result in more complex structural changes with nickel caps of Janus particles pointing predominantly along the applied magnetic field. The alignment ultimately leads to chain-like configurations and the intensity-intensity autocorrelation functions, g₂(q,t), show a second slower decay which becomes more pronounced at higher volume fractions. A direction dependent analysis of g₂(q,t) revealed a faster than exponential decay perpendicular to the field which is related to the sedimentation of magnetically ordered domains. The corresponding velocity fluctuations could be decoupled from the diffusion of particles by decomposing g₂(q,t) into advective and diffusive contributions. Finally, the particle dynamics becomes anisotropic at higher volume fractions and strong magnetic fields. The derived translational diffusion coefficients indicate slower particle dynamics perpendicular to the field as compared to the parallel direction.

Titin activates myosin filaments in skeletal muscle by switching from an extensible spring to a mechanical rectifier

Titin is a molecular spring in parallel with myosin motors in each muscle half-sarcomere, responsible for passive force development at sarcomere length (SL) above the physiological range (>2.7 μm). The role of titin at physiological SL is unclear and is investigated here in single intact muscle cells of the frog (Rana esculenta), by combining half-sarcomere mechanics and synchrotron X-ray diffraction in the presence of 20 μM para-nitro-blebbistatin, which abolishes the activity of myosin motors and maintains them in the resting state even during activation of the cell by electrical stimulation. We show that, during cell activation at physiological SL, titin in the I-band switches from an SL-dependent extensible spring (OFF-state) to an SL-independent rectifier (ON-state) that allows free shortening while resisting stretch with an effective stiffness of ~3 pN nm^-1 per half-thick filament. In this way, I-band titin efficiently transmits any load increase to the myosin filament in the A-band. Small-angle X-ray diffraction signals reveal that, with I-band titin ON, the periodic interactions of A-band titin with myosin motors alter their resting disposition in a load-dependent manner, biasing the azimuthal orientation of the motors toward actin. This work sets the stage for future investigations on scaffold and mechanosensing-based signaling functions of titin in health and disease.

2023 update of template tables for reporting biomolecular structural modelling of small-angle scattering data

In 2017, guidelines were published for reporting structural modelling of small-angle scattering (SAS) data from biomolecules in solution that exemplified best-practice documentation of experiments and analysis. Since then, there has been significant progress in SAS data and model archiving, and the IUCr journal editors announced that the IUCr biology journals will require the deposition of SAS data used in biomolecular structure solution into a public archive, as well as adherence to the 2017 reporting guidelines. In this context, the reporting template tables accompanying the 2017 publication guidelines have been reviewed with a focus on making them both easier to use and more general. With input from the SAS community via the IUCr Commission on SAS and attendees of the triennial 2022 SAS meeting (SAS2022, Campinas, Brazil), an updated reporting template table has been developed that includes standard descriptions for proteins, glycosylated proteins, DNA and RNA, with some reorganization of the data to improve readability and interpretation. In addition, a specialized template has been developed for reporting SAS contrast-variation (SAS-cv) data and models that incorporates the additional reporting requirements from the 2017 guidelines for these more complicated experiments. To demonstrate their utility, examples of reporting with these new templates are provided for a SAS study of a DNA-protein complex and a SAS-cv experiment on a protein complex. The examples demonstrate how the tabulated information promotes transparent reporting that, in combination with the recommended figures and additional information best presented in the main text, enables the reader of the work to readily draw their own conclusions regarding the quality of the data and the validity of the models presented.

Effect of tubulin self-association on GTP hydrolysis and nucleotide exchange reactions

We investigated how the self-association of isolated tubulin dimers affects the rate of GTP hydrolysis and the equilibrium of nucleotide exchange. Both reactions are relevant for microtubule (MT) dynamics. We used HPLC to determine the concentrations of GDP and GTP and thereby the GTPase activity of SEC-eluted tubulin dimers in assembly buffer solution, free of glycerol and tubulin aggregates. When GTP hydrolysis was negligible, the nucleotide exchange mechanism was studied by determining the concentrations of tubulin-free and tubulin-bound GTP and GDP. We observed no GTP hydrolysis below the critical conditions for MT assembly (either below the critical tubulin concentration and/or at low temperature), despite the assembly of tubulin 1D curved oligomers and single-rings, showing that their assembly did not involve GTP hydrolysis. Under conditions enabling spontaneous slow MT assembly, a slow pseudo-first-order GTP hydrolysis kinetics was detected, limited by the rate of MT assembly. Cryo-TEM images showed that GTP-tubulin 1D oligomers were curved also at 36 °C. Nucleotide exchange depended on the total tubulin concentration and the molar ratio between tubulin-free GDP and GTP. We used a thermodynamic model of isodesmic tubulin self-association, terminated by the formation of tubulin single-rings to determine the molar fractions of dimers with exposed and buried nucleotide exchangeable sites (E-sites). Our analysis shows that the GDP to GTP exchange reaction equilibrium constant was an order-of-magnitude larger for tubulin dimers with exposed E-sites than for assembled dimers with buried E-sites. This conclusion may have implications on the dynamics at the tip of the MT plus end.

Fast X-ray diffraction (XRD) tomography for enhanced identification of materials

X-ray computed tomography (CT) is a commercially established modality for imaging large objects like passenger luggage. CT can provide the density and the effective atomic number, which is not always sufficient to identify threats like explosives and narcotics, since they can have a similar composition to benign plastics, glass, or light metals. In these cases, X-ray diffraction (XRD) may be better suited to distinguish the threats. Unfortunately, the diffracted photon flux is typically much weaker than the transmitted one. Measurement of quality XRD data is therefore slower compared to CT, which is an economic challenge for potential customers like airports. In this article we numerically analyze a novel low-cost scanner design which captures CT and XRD signals simultaneously, and uses the least possible collimation to maximize the flux. To simulate a realistic instrument, we propose a forward model that includes the resolution-limiting effects of the polychromatic spectrum, the detector, and all the finite-size geometric factors. We then show how to reconstruct XRD patterns from a large phantom with multiple diffracting objects. We include a reasonable amount of photon counting noise (Poisson statistics), as well as measurement bias (incoherent scattering). Our XRD reconstruction adds material-specific information, albeit at a low resolution, to the already existing CT image, thus improving threat detection. Our theoretical model is implemented in GPU (Graphics Processing Unit) accelerated software which can be used to further optimize scanner designs for applications in security, healthcare, and manufacturing quality control.

Controlling the rotation modes of hematite nanospindles using dynamic magnetic fields

The magnetic field-induced actuation of colloidal nanoparticles has enabled tremendous recent progress towards microrobots, suitable for a variety of applications including targeted drug delivery, environmental remediation, or minimally invasive surgery. Further size reduction to the nanoscale requires enhanced control of orientation and locomotion to overcome dominating viscous properties. Here, control of the coherent precession of hematite spindles via a dynamic magnetic field is demonstrated using nanoscale particles. Time-resolved small-angle scattering and optical transmission measurements reveal a clear frequency-dependent variation of orientation and rotation of an entire ensemble of non-interacting hematite nanospindles. The different motion mechanisms by nanoscale spindles in bulk dispersion resemble modes that have been observed for much larger, micron-sized elongated particles near surfaces. The dynamic rotation modes promise hematite nanospindles as a suitable model system for field-induced locomotion in nanoscale magnetic robots.

Mechanism of the Initial Tubulin Nucleation Phase

Tubulin nucleation is a highly frequent event in microtubule (MT) dynamics but is poorly understood. In this work, we characterized the structural changes during the initial nucleation phase of dynamic tubulin. Using size-exclusion chromatography-eluted tubulin dimers in an assembly buffer solution free of glycerol and tubulin aggregates enabled us to start from a well-defined initial thermodynamic ensemble of isolated dynamic tubulin dimers and short oligomers. Following a temperature increase, time-resolved X-ray scattering and cryo-transmission electron microscopy during the initial nucleation phase revealed an isodesmic assembly mechanism of one-dimensional (1D) tubulin oligomers (where dimers were added and/or removed one at a time), leading to sufficiently stable two-dimensional (2D) dynamic nanostructures, required for MT assembly. A substantial amount of tubulin octamers accumulated before two-dimensional lattices appeared. Under subcritical assembly conditions, we observed a slower isodesmic assembly mechanism, but the concentration of 1D oligomers was insufficient to form the multistranded 2D nucleus required for MT formation.

Tools shaping drug discovery and development

Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.

Neurotransmitter uptake of synaptic vesicles studied by X-ray diffraction

The size, polydispersity, and electron density profile of synaptic vesicles (SVs) can be studied by small-angle X-ray scattering (SAXS), i.e. by X-ray diffraction from purified SV suspensions in solution. Here we show that size and shape transformations, as they appear in the functional context of these important synaptic organelles, can also be monitored by SAXS. In particular, we have investigated the active uptake of neurotransmitters, and find a mean vesicle radius increase of about 12% after the uptake of glutamate, which indicates an unusually large extensibility of the vesicle surface, likely to be accompanied by conformational changes of membrane proteins and rearrangements of the bilayer. Changes in the electron density profile (EDP) give first indications for such a rearrangement. Details of the protein structure are screened, however, by SVs polydispersity. To overcome the limitations of large ensemble averages and heterogeneous structures, we therefore propose serial X-ray diffraction by single free electron laser pulses. Using simulated data for realistic parameters, we show that this is in principle feasible, and that even spatial distances between vesicle proteins could be assessed by this approach.

Ultra-/Small Angle X-ray Scattering (USAXS/SAXS) and Static Light Scattering (SLS) Modeling as a Tool to Determine Structural Changes and Effect on Growth in S. epidermidis

Usually, to characterize bacterial cells' susceptibility to antimicrobials, basic microbiology techniques such as serial dilutions or disk assays are used. In this work, we present an approach focused on combining static light scattering (SLS) and ultra-/small angle X-ray scattering (USAXS/SAXS). This approach was used to support microbiology techniques, with the aim of understanding the structural changes caused to bacteria when they are exposed to different stresses like pH, oxidation, and surfactants. Using USAXS/SAXS and SLS data, we developed a detailed multiscale model for a Gram-positive bacterium, S. epidermidis, and we extracted information regarding changes in the overall size and cell thickness induced by different stresses (i.e., pH and hydrogen peroxide). Increasing the concentration of hydrogen peroxide leads to a progressive reduction in cell wall thickness. Moreover, the concomitant use of pH and hydrogen peroxide provides evidence for a synergy in inhibiting the S. epidermidis growth. These promising results will be used as a starting base to further investigate more complex formulations and improve/refine the data modeling of bacteria in the small angle scattering regime.

Mechanism of Tubulin Oligomers and Single-Ring Disassembly Catastrophe

Cold tubulin dimers coexist with tubulin oligomers and single rings. These structures are involved in microtubule assembly; however, their dynamics are poorly understood. Using state-of-the-art solution synchrotron time-resolved small-angle X-ray scattering, we discovered a disassembly catastrophe (half-life of ∼0.1 s) of tubulin rings and oligomers upon dilution or addition of guanosine triphosphate. A slower disassembly (half-life of ∼38 s) was observed following an increase in temperature. Our analysis showed that the assembly and disassembly processes were consistent with an isodesmic mechanism, involving a sequence of reversible reactions in which dimers were rapidly added or removed one at a time, terminated by a 2 order-of-magnitude slower ring-closing/opening step. We revealed how assembly conditions varied the mass fraction of tubulin in each of the coexisting structures, the rate constants, and the standard Helmholtz free energies for closing a ring and for longitudinal dimer-dimer associations.

Lactoferricins impair the cytosolic membrane of Escherichia coli within a few seconds and accumulate inside the cell

We report the real-time response of Escherichia coli to lactoferricin-derived antimicrobial peptides (AMPs) on length scales bridging microscopic cell sizes to nanoscopic lipid packing using millisecond time-resolved synchrotron small-angle X-ray scattering. Coupling a multiscale scattering data analysis to biophysical assays for peptide partitioning revealed that the AMPs rapidly permeabilize the cytosolic membrane within less than 3 s-much faster than previously considered. Final intracellular AMP concentrations of ∼80-100 mM suggest an efficient obstruction of physiologically important processes as the primary cause of bacterial killing. On the other hand, damage of the cell envelope and leakage occurred also at sublethal peptide concentrations, thus emerging as a collateral effect of AMP activity that does not kill the bacteria. This implies that the impairment of the membrane barrier is a necessary but not sufficient condition for microbial killing by lactoferricins. The most efficient AMP studied exceeds others in both speed of permeabilizing membranes and lowest intracellular peptide concentration needed to inhibit bacterial growth.

Persistent nucleation and size dependent attachment kinetics produce monodisperse PbS nanocrystals

Modern syntheses of colloidal nanocrystals yield extraordinarily narrow size distributions that are believed to result from a rapid "burst of nucleation" (La Mer, JACS, 1950, 72(11), 4847-4854) followed by diffusion limited growth and size distribution focusing (Reiss, J. Chem. Phys., 1951, 19, 482). Using a combination of in situ X-ray scattering, optical absorption, and 13C nuclear magnetic resonance (NMR) spectroscopy, we monitor the kinetics of PbS solute generation, nucleation, and crystal growth from three thiourea precursors whose conversion reactivity spans a 2-fold range. In all three cases, nucleation is found to be slow and continues during >50% of the precipitation. A population balance model based on a size dependent growth law (1/r) fits the data with a single growth rate constant (k G) across all three precursors. However, the magnitude of the k G and the lack of solvent viscosity dependence indicates that the rate limiting step is not diffusion from solution to the nanoparticle surface. Several surface reaction limited mechanisms and a ligand penetration model that fits data our experiments using a single fit parameter are proposed to explain the results.

Polished diamond X-ray lenses

High-quality bi-concave 2D focusing diamond X-ray lenses of apex-radius R = 100 µm produced via laser-ablation and improved via mechanical polishing are presented here. Both for polished and unpolished individual lenses and for stacks of ten lenses, the remaining figure errors determined using X-ray speckle tracking are shown and these results are compared with those of commercial R = 50 µm beryllium lenses that have similar focusing strength and physical aperture. For two stacks of ten diamond lenses (polished and unpolished) and a stack of eleven beryllium lenses, this paper presents measured 2D beam profiles out of focus and wire scans to obtain the beam size in the focal plane. These results are complemented with small-angle X-ray scattering (SAXS) measurements of a polished and an unpolished diamond lens. Again, this is compared with the SAXS of a beryllium lens. The polished X-ray lenses show similar figure errors to commercially available beryllium lenses. While the beam size in the focal plane is comparable to that of the beryllium lenses, the SAXS signal of the polished diamond lenses is considerably lower.

Performance of the new biological small- and wide-angle X-ray scattering beamline 13A at the Taiwan Photon Source

A new endstation for biological small- and wide-angle X-ray scattering is detailed, which provides development opportunities for studying correlated local and global structures of biomolecules in solution.

Recent developments in the instrumentation and data analysis of synchrotron small-angle X-ray scattering (SAXS) on biomolecules in solution have made biological SAXS (BioSAXS) a mature and popular tool in structural biology. This article reports on an advanced endstation developed at beamline 13A of the 3.0 GeV Taiwan Photon Source for biological small- and wide-angle X-ray scattering (SAXS–WAXS or SWAXS). The endstation features an in-vacuum SWAXS detection system comprising two mobile area detectors (Eiger X 9M/1M) and an online size-exclusion chromatography system incorporating several optical probes including a UV–Vis absorption spectrometer and refractometer. The instrumentation and automation allow simultaneous SAXS–WAXS data collection and data reduction for high-throughput biomolecular conformation and composition determinations. The performance of the endstation is illustrated with the SWAXS data collected for several model proteins in solution, covering a scattering vector magnitude q across three orders of magnitude. The crystal-model fittings to the data in the q range ∼0.005–2.0 Å⁻¹ indicate high similarity of the solution structures of the proteins to their crystalline forms, except for some subtle hydration-dependent local details. These results open up new horizons of SWAXS in studying correlated local and global structures of biomolecules in solution.

Cooling intact and demembranated trabeculae from rat heart releases myosin motors from their inhibited conformation

Myosin filament–based regulation supplements actin filament–based regulation to control the strength and speed of contraction in heart muscle. In diastole, myosin motors form a folded helical array that inhibits actin interaction; during contraction, they are released from that array. A similar structural transition has been observed in mammalian skeletal muscle, in which cooling below physiological temperature has been shown to reproduce some of the structural features of the activation of myosin filaments during active contraction. Here, we used small-angle x-ray diffraction to characterize the structural changes in the myosin filaments associated with cooling of resting and relaxed trabeculae from the right ventricle of rat hearts from 39°C to 7°C. In intact quiescent trabeculae, cooling disrupted the folded helical conformation of the myosin motors and induced extension of the filament backbone, as observed in the transition from diastole to peak systolic force at 27°C. Demembranation of trabeculae in relaxing conditions induced expansion of the filament lattice, but the structure of the myosin filaments was mostly preserved at 39°C. Cooling of relaxed demembranated trabeculae induced changes in motor conformation and filament structure similar to those observed in intact quiescent trabeculae. Osmotic compression of the filament lattice to restore its spacing to that of intact trabeculae at 39°C stabilized the helical folded state against disruption by cooling. The myosin filament structure and motor conformation of intact trabeculae at 39°C were largely preserved in demembranated trabeculae at 27°C or above in the presence of Dextran, allowing the physiological mechanisms of myosin filament–based regulation to be studied in those conditions.