Scatter: software for the analysis of nano- and mesoscale small-angle scattering

Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs

PRPF40A plays an important role in the regulation of pre-mRNA splicing by mediating protein-protein interactions in the early steps of spliceosome assembly. By binding to proteins at the 5´ and 3´ splice sites, PRPF40A promotes spliceosome assembly by bridging the recognition of the splices. The PRPF40A WW domains are expected to recognize proline-rich sequences in SF1 and SF3A1 in the early spliceosome complexes E and A, respectively. Here, we combine NMR, SAXS and ITC to determine the structure of the PRPF40A tandem WW domains in solution and characterize the binding specificity and mechanism for proline-rich motifs recognition. Our structure of the PRPF40A WW tandem in complex with a high-affinity SF1 peptide reveals contributions of both WW domains, which also enables tryptophan sandwiching by two proline residues in the ligand. Unexpectedly, a proline-rich motif in the N-terminal region of PRPF40A mediates intramolecular interactions with the WW tandem. Using NMR, ITC, mutational analysis in vitro, and immunoprecipitation experiments in cells, we show that the intramolecular interaction acts as an autoinhibitory filter for proof-reading of high-affinity proline-rich motifs in bona fide PRPF40A binding partners. We propose that similar autoinhibitory mechanisms are present in most WW tandem-containing proteins to enhance binding selectivity and regulation of WW/proline-rich peptide interaction networks.

Characterization of Surfactant Spheroidal Micelle Structure for Pharmaceutical Applications: A Novel Analytical Framework

We introduce an innovative theoretical framework tailored for the analysis of Pair Distribution Function (PDF) data derived from Small-Angle X-ray Scattering (SAXS) measurements of core-shell micelles. The new approach involves the exploitation of the first derivative of the PDF and the derivation of analytical equations to solve the core-shell micelle structure under the hypothesis of a spheroidal shape. These analytical equations enable us to determine the micelle's aggregation number, degree of ellipticity, and contrast in electron density between the core-shell and shell-buffer regions after having determined the whole micelle size and its shell size from the analysis of the first derivative of the PDF. We have formulated an overdetermined system of analytical equations based on the unknowns that characterize the micelle structure. This allows us to establish a Figure of Merit, which is utilized to identify the most reliable solution within the system of equations.

SEB: a computational tool for symbolic derivation of the small-angle scattering from complex composite structures

Analysis of small-angle scattering (SAS) data requires intensive modeling to infer and characterize the structures present in a sample. This iterative improvement of models is a time-consuming process. Presented here is Scattering Equation Builder (SEB), a C++ library that derives exact analytic expressions for the form factors of complex composite structures. The user writes a small program that specifies how the sub-units should be linked to form a composite structure and calls SEB to obtain an expression for the form factor. SEB supports e.g. Gaussian polymer chains and loops, thin rods and circles, solid spheres, spherical shells and cylinders, and many different options for how these can be linked together. The formalism behind SEB is presented and simple case studies are given, such as block copolymers with different types of linkage, as well as more complex examples, such as a random walk model of 100 linked sub-units, dendrimers, polymers and rods attached to the surfaces of geometric objects, and finally the scattering from a linear chain of five stars, where each star is built up of four diblock copolymers. These examples illustrate how SEB can be used to develop complex models and hence reduce the cost of analyzing SAS data.

Structure and function of Campylobacter jejuni polynucleotide phosphorylase (PNPase): Insights into the role of this RNase in pathogenicity

Ribonucleases are in charge of the processing, degradation and quality control of all cellular transcripts, which makes them crucial factors in RNA regulation. This post-transcriptional regulation allows bacteria to promptly react to different stress conditions and growth phase transitions, and also to produce the required virulence factors in pathogenic bacteria. Campylobacter jejuni is the main responsible for human gastroenteritis in the world. In this foodborne pathogen, exoribonuclease PNPase (CjPNP) is essential for low-temperature cell survival, affects the synthesis of proteins involved in virulence and has an important role in swimming, cell adhesion/invasion ability, and chick colonization. Here we report the crystallographic structure of CjPNP, complemented with SAXS, which confirms the characteristic doughnut-shaped trimeric arrangement and evaluates domain arrangement and flexibility. Mutations in highly conserved residues were constructed to access their role in RNA degradation and polymerization. Surprisingly, we found two mutations that altered CjPNP into a protein that is only capable of degrading RNA even in conditions that favour polymerization. These findings will be important to develop new strategies to combat C. jejuni infections.

Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties

A number of intrinsically disordered proteins (IDPs) encoded in stress-tolerant organisms, such as tardigrade, can confer fitness advantage and abiotic stress tolerance when heterologously expressed. Tardigrade-specific disordered proteins including the cytosolic-abundant heat-soluble proteins are proposed to confer stress tolerance through vitrification or gelation, whereas evolutionarily conserved IDPs in tardigrades may contribute to stress tolerance through other biophysical mechanisms. In this study, we characterized the mechanism of action of an evolutionarily conserved, tardigrade IDP, HeLEA1, which belongs to the group-3 late embryogenesis abundant (LEA) protein family. HeLEA1 homologs are found across different kingdoms of life. HeLEA1 is intrinsically disordered in solution but shows a propensity for helical structure across its entire sequence. HeLEA1 interacts with negatively charged membranes via dynamic disorder-to-helical transition, mainly driven by electrostatic interactions. Membrane interaction of HeLEA1 is shown to ameliorate excess surface tension and lipid packing defects. HeLEA1 localizes to the mitochondrial matrix when expressed in yeast and interacts with model membranes mimicking inner mitochondrial membrane. Yeast expressing HeLEA1 shows enhanced tolerance to hyperosmotic stress under nonfermentative growth and increased mitochondrial membrane potential. Evolutionary analysis suggests that although HeLEA1 homologs have diverged their sequences to localize to different subcellular organelles, all homologs maintain a weak hydrophobic moment that is characteristic of weak and reversible membrane interaction. We suggest that such dynamic and weak protein-membrane interaction buffering alterations in lipid packing could be a conserved strategy for regulating membrane properties and represent a general biophysical solution for stress tolerance across the domains of life.

Flexibility and Distributive Synthesis Regulate RNA Priming and Handoff in Human DNA Polymerase α-Primase

DNA replication in eukaryotes relies on the synthesis of a ∼30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C-terminal domain of the primase regulatory subunit (PRIM2C) and is followed by intramolecular handoff of the primer to pol α for extension by ∼20 nucleotides of DNA. Here, we provide evidence that RNA primer synthesis is governed by a combination of the high affinity and flexible linkage of the PRIM2C domain and the surprisingly low affinity of the primase catalytic domain (PRIM1) for substrate. Using a combination of small angle X-ray scattering and electron microscopy, we found significant variability in the organization of PRIM2C and PRIM1 in the absence and presence of substrate, and that the population of structures with both PRIM2C and PRIM1 in a configuration aligned for synthesis is low. Crosslinking was used to visualize the orientation of PRIM2C and PRIM1 when engaged by substrate as observed by electron microscopy. Microscale thermophoresis was used to measure substrate affinities for a series of pol-prim constructs, which showed that the PRIM1 catalytic domain does not bind the template or emergent RNA-primed templates with appreciable affinity. Together, these findings support a model of RNA primer synthesis in which generation of the nascent RNA strand and handoff of the RNA-primed template from primase to polymerase α is mediated by the high degree of inter-domain flexibility of pol-prim, the ready dissociation of PRIM1 from its substrate, and the much higher affinity of the POLA1cat domain of polymerase α for full-length RNA-primed templates.

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.

Stereochemistry-dependent thermotropic liquid crystalline phases of monosaccharide-based amphiphiles

Conformational rigidity controls the bulk self-assembly and liquid crystallinity from amphiphilic block molecules to copolymers. The effects of block stereochemistry on the self-assembly have, however, been less explored. Here, we have investigated amphiphilic block molecules involving eight open-chain monosaccharide-based polyol units possessing different stereochemistries, derived from D-glucose, D-galactose, L-arabinose, D-mannose and L-rhamnose (allylated monosaccharides t-Glc*, e-Glc*, t-Gal*, e-Gal*, t-Ara*, e-Ara*, t-Man*, and t-Rha*), end-functionalized with repulsive tetradecyl alkyl chain blocks to form well-defined amphiphiles with block molecule structures. All compounds studied showed low temperature crystalline phases due to polyol crystallization, and smectic (lamellar) and isotropic phases upon heating in bulk. Hexagonal cylindrical phase was additionally observed for the composition involving t-Man*. Cubic phases were observed for e-Glc*, e-Gal*, e-Ara*, and t-Rha* derived compounds. Therein, the rich array of WAXS-reflections suggested that the crystalline polyol domains are not ultra-confined in spheres as in classic cubic phases but instead show network-like phase continuity, which is rare in bulk liquid crystals. Importantly, the transition temperatures of the self-assemblies were observed to depend strongly on the polyol stereochemistry. The findings underpin that the stereochemistry in carbohydrate-based assemblies involves complexity, which is an important parameter to be considered in material design when developing self-assemblies for different functions.

Heating-Induced Switching to Hierarchical Liquid Crystallinity Combining Colloidal and Molecular Order in Zwitterionic Molecules

Hierarchical self-assemblies of soft matter involving triggerable or switchable structures at different length scales have been pursued toward multifunctional behaviors and complexity inspired by biological matter. They require several and balanced competing attractive and repulsive interactions, which provide a grand challenge in particular in the "bulk" state, i.e., in the absence of plasticizing solvents. Here, we disclose that zwitterionic bis-n-tetradecylphosphobetaine, as a model compound, shows a complex thermally switchable hierarchical self-assembly in the solvent-free state. It shows polymorphism and heating-induced reversible switching from low-temperature molecular-level assemblies to high-temperature hierarchical self-assemblies, unexpectedly combining colloidal and molecular self-assemblies, as inferred by synchrotron small-angle X-ray scattering (SAXS). The high-temperature phase sustains birefringent flow, indicating a new type of hierarchical thermotropic liquid crystallinity. The high-temperature colloidal-level SAXS reflections suggest indexation as a 2D oblique pattern and their well-defined layer separation in the perpendicular direction. We suggest that the colloidal self-assembled motifs are 2D nanoplatelets formed by the lateral packing of the molecules, where the molecular packing frustration between the tightly packed zwitterionic moieties and the coiled alkyl chains demanding more space limits the lateral platelet growth controlled by the alkyl stretching entropy. An indirect proof is provided by the addition of plasticizing ionic liquids, which relieve the ionic dense packings of zwitterions, thus allowing purely smectic liquid crystallinity without the colloidal level order. Thus, molecules with a simple chemical structure can lead to structural hierarchy and tunable complexity in the solvent-free state by balancing the competing long-range electrostatics and short-range nanosegregations.

Strategy to simulate and fit 2D grazing-incidence small-angle X-ray scattering patterns of nanostructured thin films

Grazing-incidence small-angle X-ray scattering (GISAXS) is a widely used method for the characterization of the nanostructure of supported thin films and enables time-resolved in situ measurements. The 2D scattering patterns contain detailed information about the nanostructures within the film and at its surface. However, this information is distorted not only by the reflection of the X-ray beam at the substrate-film interface and its refraction at the film surface but also by scattering of the substrate, the sample holder and other types of parasitic background scattering. In this work, a new, efficient strategy to simulate and fit 2D GISAXS patterns that explicitly includes these effects is introduced and demonstrated for (i) a model case nanostructured thin film on a substrate and (ii) experimental data from a microphase-separated block copolymer thin film. To make the protocol efficient, characteristic linecuts through the 2D GISAXS patterns, where the different contributions dominate, are analysed. The contributions of the substrate and the parasitic background scattering - which ideally are measured separately - are determined first and are used in the analysis of the 2D GISAXS patterns of the nanostructured, supported film. The nanostructures at the film surface and within the film are added step by step to the real-space model of the simulation, and their structural parameters are determined by minimizing the difference between simulated and experimental scattering patterns in the selected linecuts. Although in the present work the strategy is adapted for and tested with BornAgain, it can be easily used with other types of simulation software. The strategy is also applicable to grazing-incidence small-angle neutron scattering.

Fluid-solid transitions in photonic crystals of soft, thermoresponsive microgels

Microgels are often discussed as well-suited model system for soft colloids. In contrast to rigid spheres, the microgel volume and, coupled to this, the volume fraction in dispersion can be manipulated by external stimuli. This behavior is particularly interesting at high packings where phase transitions can be induced by external triggers such as temperature in the case of thermoresponsive microgels. A challenge, however, is the determination of the real volume occupied by these deformable, soft objects and consequently, to determine the boundaries of the phase transitions. Here we propose core-shell microgels with a rigid silica core and a crosslinked, thermoresponsive poly-N-isopropylacrylamide (PNIPAM) shell with a carefully chosen shell-to-core size ratio as ideal model colloids to study fluid-solid transitions that are inducible by millikelvin changes in temperature. Specifically, we identify the temperature ranges where crystallization and melting occur using absorbance spectroscopy in a range of concentrations. Slow annealing from the fluid to the crystalline state leads to photonic crystals with Bragg peaks in the visible wavelength range and very narrow linewidths. Small-angle X-ray scattering is then used to confirm the structure of the fluid phase as well as the long-range order, crystal structure and microgel volume fraction in the solid phase. Thanks to the scattering contrasts and volume ratio of the cores with respect to the shells, the scattering data do allow for form factor analysis revealing osmotic deswelling at volume fractions approaching and also exceeding the hard sphere packing limit.

Phage T3 overcomes the BREX defense through SAM cleavage and inhibition of SAM synthesis by SAM lyase

Bacteriophage T3 encodes a SAMase that, through cleavage of S-adenosyl methionine (SAM), circumvents the SAM-dependent type I restriction-modification (R-M) defense. We show that SAMase also allows T3 to evade the BREX defense. Although SAM depletion weakly affects BREX methylation, it completely inhibits the defensive function of BREX, suggesting that SAM could be a co-factor for BREX-mediated exclusion of phage DNA, similar to its anti-defense role in type I R-M. The anti-BREX activity of T3 SAMase is mediated not just by enzymatic degradation of SAM but also by direct inhibition of MetK, the host SAM synthase. We present a 2.8 Å cryoelectron microscopy (cryo-EM) structure of the eight-subunit T3 SAMase-MetK complex. Structure-guided mutagenesis reveals that this interaction stabilizes T3 SAMase in vivo, further stimulating its anti-BREX activity. This work provides insights in the versatility of bacteriophage counterdefense mechanisms and highlights the role of SAM as a co-factor of diverse bacterial immunity systems.

Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α-primase

DNA replication in eukaryotes relies on the synthesis of a ~30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C-terminal domain of the primase regulatory subunit (PRIM2C) and is followed by intramolecular handoff of the primer to pol α for extension by ~20 nucleotides of DNA. Here we provide evidence that RNA primer synthesis is governed by a combination of the high affinity and flexible linkage of the PRIM2C domain and the low affinity of the primase catalytic domain (PRIM1) for substrate. Using a combination of small angle X-ray scattering and electron microscopy, we found significant variability in the organization of PRIM2C and PRIM1 in the absence and presence of substrate, and that the population of structures with both PRIM2C and PRIM1 in a configuration aligned for synthesis is low. Crosslinking was used to visualize the orientation of PRIM2C and PRIM1 when engaged by substrate as observed by electron microscopy. Microscale thermophoresis was used to measure substrate affinities for a series of pol-prim constructs, which showed that the PRIM1 catalytic domain does not bind the template or emergent RNA-primed templates with appreciable affinity. Together, these findings support a model of RNA primer synthesis in which generation of the nascent RNA strand and handoff of the RNA-primed template from primase to polymerase α is mediated by the high degree of inter-domain flexibility of pol-prim, the ready dissociation of PRIM1 from its substrate, and the much higher affinity of the POLA1cat domain of polymerase α for full-length RNA-primed templates.

Structural basis for different membrane-binding properties of E. coli anaerobic and human mitochondrial β-oxidation trifunctional enzymes

Facultative anaerobic bacteria such as Escherichia coli have two α2β2 heterotetrameric trifunctional enzymes (TFE), catalyzing the last three steps of the β-oxidation cycle: soluble aerobic TFE (EcTFE) and membrane-associated anaerobic TFE (anEcTFE), closely related to the human mitochondrial TFE (HsTFE). The cryo-EM structure of anEcTFE and crystal structures of anEcTFE-α show that the overall assembly of anEcTFE and HsTFE is similar. However, their membrane-binding properties differ considerably. The shorter A5-H7 and H8 regions of anEcTFE-α result in weaker α-β as well as α-membrane interactions, respectively. The protruding H-H region of anEcTFE-β is therefore more critical for membrane-association. Mutational studies also show that this region is important for the stability of the anEcTFE-β dimer and anEcTFE heterotetramer. The fatty acyl tail binding tunnel of the anEcTFE-α hydratase domain, as in HsTFE-α, is wider than in EcTFE-α, accommodating longer fatty acyl tails, in good agreement with their respective substrate specificities.

Improved Route to Linear Triblock Copolymers by Coupling with Glycidyl Ether-Activated Poly(ethylene oxide) Chains

Poly(ethylene oxide) block copolymers (PEO_z BCP) have been demonstrated to exhibit remarkably high lithium ion (Li⁺) conductivity for Li⁺ batteries applications. For linear poly(isoprene)-b-poly(styrene)-b-poly(ethylene oxide) triblock copolymers (PI_xPS_yPEO_z), a pronounced maximum ion conductivity was reported for short PEO_z molecular weights around 2 kg mol^-1. To later enable a systematic exploration of the influence of the PI_x and PS_y block lengths and related morphologies on the ion conductivity, a synthetic method is needed where the short PEO_z block length can be kept constant, while the PI_x and PS_y block lengths could be systematically and independently varied. Here, we introduce a glycidyl ether route that allows covalent attachment of pre-synthesized glycidyl-end functionalized PEO_z chains to terminate PI_xPS_y BCPs. The attachment proceeds to full conversion in a simplified and reproducible one-pot polymerization such that PI_xPS_yPEO_z with narrow chain length distribution and a fixed PEO_z block length of z = 1.9 kg mol^-1 and a Đ = 1.03 are obtained. The successful quantitative end group modification of the PEO_z block was verified by nuclear magnetic resonance (NMR) spectroscopy, gel permeation chromatography (GPC) and differential scanning calorimetry (DSC). We demonstrate further that with a controlled casting process, ordered microphases with macroscopic long-range directional order can be fabricated, as demonstrated by small-angle X-ray scattering (SAXS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). It has already been shown in a patent, published by us, that BCPs from the synthesis method presented here exhibit comparable or even higher ionic conductivities than those previously published. Therefore, this PEO_z BCP system is ideally suitable to relate BCP morphology, order and orientation to macroscopic Li⁺ conductivity in Li⁺ batteries.

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.

Nanoparticle Exsolution from Nanoporous Perovskites for Highly Active and Stable Catalysts

Nanoporosity is clearly beneficial for the performance of heterogeneous catalysts. Although exsolution is a modern method to design innovative catalysts, thus far it is predominantly studied for sintered matrices. A quantitative description of the exsolution of Ni nanoparticles from nanoporous perovskite oxides and their effective application in the biogas dry reforming is here presented. The exsolution process is studied between 500 and 900 °C in nanoporous and sintered La_0.52 Sr_0.28 Ti_0.94 Ni_0.06 O_3±δ . Using temperature-programmed reduction (TPR) and X-ray absorption spectroscopy (XAS), it is shown that the faster and larger oxygen release in the nanoporous material is responsible for twice as high Ni reduction than in the sintered system. For the nanoporous material, the nanoparticle formation mechanism, studied by in situ TEM and small-angle X-ray scattering (SAXS), follows the classical nucleation theory, while on sintered systems also small endogenous nanoparticles form despite the low Ni concentration. Biogas dry reforming tests demonstrate that nanoporous exsolved catalysts are up to 18 times more active than sintered ones with 90% of CO₂ conversion at 800 °C. Time-on-stream tests exhibit superior long-term stability (only 3% activity loss in 8 h) and full regenerability (over three cycles) of the nanoporous exsolved materials in comparison to a commercial Ni/Al₂ O₃ catalyst.

Operando studies reveal active Cu nanograins for CO2 electroreduction

Carbon dioxide electroreduction facilitates the sustainable synthesis of fuels and chemicals¹. Although Cu enables CO₂-to-multicarbon product (C₂₊) conversion, the nature of the active sites under operating conditions remains elusive². Importantly, identifying active sites of high-performance Cu nanocatalysts necessitates nanoscale, time-resolved operando techniques^3-5. Here, we present a comprehensive investigation of the structural dynamics during the life cycle of Cu nanocatalysts. A 7 nm Cu nanoparticle ensemble evolves into metallic Cu nanograins during electrolysis before complete oxidation to single-crystal Cu₂O nanocubes following post-electrolysis air exposure. Operando analytical and four-dimensional electrochemical liquid-cell scanning transmission electron microscopy shows the presence of metallic Cu nanograins under CO₂ reduction conditions. Correlated high-energy-resolution time-resolved X-ray spectroscopy suggests that metallic Cu, rich in nanograin boundaries, supports undercoordinated active sites for C-C coupling. Quantitative structure-activity correlation shows that a higher fraction of metallic Cu nanograins leads to higher C₂₊ selectivity. A 7 nm Cu nanoparticle ensemble, with a unity fraction of active Cu nanograins, exhibits sixfold higher C₂₊ selectivity than the 18 nm counterpart with one-third of active Cu nanograins. The correlation of multimodal operando techniques serves as a powerful platform to advance our fundamental understanding of the complex structural evolution of nanocatalysts under electrochemical conditions.

Using Small-angle X-ray Scattering to Characterize Biological Systems: A General Overview and Practical Tips

Small-angle X-ray Scattering (SAXS) is a versatile and powerful technique with applications in a wide range of fields. The continuous improvements in hardware, data analysis software, and standards for validation significantly contributed to increase its popularity and, nowadays, SAXS is a well-established method. SAXS allows to study flexible and dynamic systems (e.g., proteins and other biomolecules) in solution, providing information about their size and shape. Contrary to other structural characterization methods, SAXS has no limitations on the size of the particle under study and can be used in integrated approaches to reveal important insights otherwise difficult to obtain regarding folding-unfolding, conformational changes, movement of flexible regions, and the formation of complexes.This chapter, in addition to a concise overview on the methodology, intends to systematically enumerate the main steps involved in sample preparation and data collection, processing and analysis including useful practical notes to identify and overcome common bottlenecks. This way, a less experienced user can use the content of the chapter as a starting point to properly design and perform a successful SAXS experiment.

Protein Cage-Stabilized Emulsions: Formulation and Characterization

The formulation of Pickering emulsions using protein cages is gaining interest for applications in molecular delivery. Despite the growing interest, methods to investigate the at the liquid-liquid interface are limited. This chapter describes standard methods to formulate and protocols to characterize protein cage-stabilized emulsions. The characterization methods are dynamic light scattering (DLS), intrinsic fluorescence spectroscopy (TF), circular dichroism (CD), and small angle X-ray scattering (SAXS). Combining these methods allows understanding of the protein cage nanostructure at the oil/water interface.

Updates in SASfit for fitting analytical expressions and numerical models to small-angle scattering patterns

Small-angle scattering is an increasingly common method for characterizing particle ensembles in a wide variety of sample types and for diverse areas of application. SASfit has been one of the most comprehensive and flexible curve-fitting programs for decades, with many specialized tools for various fields. Here, a selection of enhancements and additions to the SASfit program are presented that may be of great benefit to interested and advanced users alike: (a) further development of the technical basis of the program, such as new numerical algorithms currently in use, a continuous integration practice for automated building and packaging of the software, and upgrades on the plug-in system for easier adoption by third-party developers; (b) a selection of new form factors for anisotropic scattering patterns and updates to existing form factors to account for multiple scattering effects; (c) a new type of a very flexible distribution called metalog [Keelin (2016). Decis. Anal. 13, 243-277], and regularization techniques such as the expectation-maximization method [Dempster et al. (1977). J. R. Stat. Soc. Ser. B (Methodological), 39, 1-22; Richardson (1972) J. Opt. Soc. Am. 62, 55; Lucy (1974). Astron. J. 79, 745; Lucy (1994). Astron. Astrophys. 289, 983-994], which is compared with fits of analytical size distributions via the non-linear least-squares method; and (d) new structure factors, especially for ordered nano- and meso-scaled material systems, as well as the Ornstein-Zernike solver for numerical determination of particle interactions and the resulting structure factor when no analytical solution is available, with the aim of incorporating its effects into the small-angle scattering intensity model used for fitting with SASfit.

The Structure of Saccharomyces cerevisiae Arginyltransferase 1 (ATE1)

Eukaryotic post-translational arginylation, mediated by the family of enzymes known as the arginyltransferases (ATE1s), is an important post-translational modification that can alter protein function and even dictate cellular protein half-life. Multiple major biological pathways are linked to the fidelity of this process, including neural and cardiovascular developments, cell division, and even the stress response. Despite this significance, the structural, mechanistic, and regulatory mechanisms that govern ATE1 function remain enigmatic. To that end, we have used X-ray crystallography to solve the crystal structure of ATE1 from the model organism Saccharomyces cerevisiae ATE1 (ScATE1) in the apo form. The three-dimensional structure of ScATE1 reveals a bilobed protein containing a GCN5-related N-acetyltransferase (GNAT) fold, and this crystalline behavior is faithfully recapitulated in solution based on size-exclusion chromatography-coupled small angle X-ray scattering (SEC-SAXS) analyses and cryo-EM 2D class averaging. Structural superpositions and electrostatic analyses point to this domain and its domain-domain interface as the location of catalytic activity and tRNA binding, and these comparisons strongly suggest a mechanism for post-translational arginylation. Additionally, our structure reveals that the N-terminal domain, which we have previously shown to bind a regulatory [Fe-S] cluster, is dynamic and disordered in the absence of metal bound in this location, hinting at the regulatory influence of this region. When taken together, these insights bring us closer to answering pressing questions regarding the molecular-level mechanism of eukaryotic post-translational arginylation.

Controlling the anisotropic self-assembly of polybutadiene-grafted silica nanoparticles by tuning three-body interaction forces

Recently, the significant improvements in polymer composites properties have been mainly attributed to the ability of filler nanoparticles (NPs) to self-assemble into highly anisotropic self-assembled structures. In this work, we investigate the self-assembly of core-shell NPs composed of a silica core grafted with polybutadiene (PB) chains, generating the so-called "hairy" NPs (HNPs), immersed in tetrahydrofuran solvent. While uncoated silica beads aggregate forming uniform compact structures, the presence of a PB shell affects the silica NPs organization to the point that by increasing the polymer density at the corona, they tend to self-assemble into linear chain-like structures. To reproduce the experimental observations, we propose a theoretical model for the two-body that considers the van der Waals attractive energy together with the polymer-induced repulsive steric contribution and includes an additional three-body interaction term. This term arises due to the anisotropic distribution of PB, which increases their concentration near the NPs contact region. The resulting steric repulsion experienced by a third NP approaching the dimer prevents its binding close to the dimer bond and favors the growth of chain-like structures. We find good agreement between the simulated and experimental self-assembled superstructures, confirming that this three-body steric repulsion plays a key role in determining the cluster morphology of these core-shell NPs. The model also shows that further increasing the grafting density leads to low-density gel-like open structures.

Analysis of Plasmodium falciparum myosin B ATPase activity and structure in complex with the calmodulin-like domain of its light chain MLC-B

Myosin B (MyoB) is a class 14 myosin expressed in all invasive stages of the malaria parasite, Plasmodium falciparum. It is not associated with the glideosome complex that drives motility and invasion of host cells. During red blood cell invasion, MyoB remains at the apical tip of the merozoite but is no longer observed once invasion is completed. MyoB is not essential for parasite survival, but when it is knocked out, merozoites are delayed in the initial stages of red blood cell invasion, giving rise to a growth defect that correlates with reduced invasion success. Therefore, further characterization is needed to understand how MyoB contributes to parasite invasion. Here, we have expressed and purified functional MyoB with the help of parasite-specific chaperones Hsp90 and Unc45, characterized its binding to actin and its known light chain MLC-B using biochemical and biophysical methods and determined its low-resolution structure in solution using small angle X-ray scattering. In addition to MLC-B, we found that four other putative regulatory light chains bind to the MyoB IQ2 motif in vitro. The purified recombinant MyoB adopted the overall shape of a myosin, exhibited actin-activated ATPase activity, and moved actin filaments in vitro. Additionally, we determined that the ADP release rate was faster than the ATP turnover number, and thus, does not appear to be rate limiting. This, together with the observed high affinity to actin and the specific localization of MyoB, may point toward a role in tethering and/or force sensing during early stages of invasion.

SAXS Analysis and Characterization of Anticancer Activity of PNP-UDP Family Protein from Putranjiva roxburghii

A class of plant defense and storage proteins, including Putranjiva roxburghii PNP protein (PRpnp), belongs to PNP-UDP family. The PRpnp and related plant proteins contain a disrupted PNP-UDP domain as revealed in previous studies. In PRpnp, the insert disrupting the domain contains the trypsin inhibitory site. In the present work, we analyzed native PRpnp (nPRpnp) complex formation with trypsin and inosine using SAXS experiments and established its dual functionality. Results indicated a relatively compact nPRpnp:Inosine structure, whereas trypsin complex showed conformational changes/flexibility. nPRpnp also exhibited a strong anti-cancer activity toward breast cancer (MCF-7), prostate cancer (DU-145) and hepatocellular carcinoma (HepG2) cell lines. MCF-7 and DU-145 were more sensitive to nPRpnp treatment as compared to HepG2. However, nPRpnp treatment showed no effect on the viability of HEK293 cells indicating that nPRpnp is specific for targeting the viability of only cancer cells. Further, acridine orange, DAPI and DNA fragmentation studies showed that cytotoxic effect of nPRpnp is mediated through induction of apoptosis as evident from the apoptosis-associated morphological changes and nuclear fragmentation observed after PRpnp treatment of cancer cells. These results suggest that PRpnp has the potential to be used as an anticancer agent. This is first report of anticancer activity as well as SAXS-based analysis for a PNP enzyme with trypsin inhibitory activity.

Time-Resolved SAXS Study of Polarity- and Surfactant-Controlled Superlattice Transformations of Oleate-Capped Nanocubes During Solvent Removal

Structural transformations and lattice expansion of oleate-capped iron oxide nanocube superlattices are studied by time-resolved small-angle X-ray scattering (SAXS) during solvent removal. The combination of conductor-like screening model for real solvents (COSMO-RS) theory with computational fluid dynamics (CFD) modeling provides information on the solvent composition and polarity during droplet evaporation. Evaporation-driven poor-solvent enrichment in the presence of free oleic acid results in the formation of superlattices with a tilted face-centered cubic (fcc) structure when the polarity reaches its maximum. The tilted fcc lattice expands subsequently during the removal of the poor solvent and eventually transforms to a regular simple cubic (sc) lattice during the final evaporation stage when only free oleic acid remains. Comparative studies show that both the increase in polarity as the poor solvent is enriched and the presence of a sufficient amount of added oleic acid is required to promote the formation of structurally diverse superlattices with large domain sizes.

Computational design of mechanically coupled axle-rotor protein assemblies

Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry. We find that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo-electron microscopy, we find that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines.

A fusion of the Bacteroides fragilis ferrous iron import proteins reveals a role for FeoA in stabilizing GTP-bound FeoB

Iron is an essential element for nearly all organisms, and under anoxic and/or reducing conditions, Fe²⁺ is the dominant form of iron available to bacteria. The ferrous iron transport (Feo) system is the primary prokaryotic Fe²⁺ import machinery, and two constituent proteins (FeoA and FeoB) are conserved across most bacterial species. However, how FeoA and FeoB function relative to one another remains enigmatic. In this work, we explored the distribution of feoAB operons encoding a fusion of FeoA tethered to the N-terminal, G-protein domain of FeoB via a connecting linker region. We hypothesized that this fusion poises FeoA to interact with FeoB to affect function. To test this hypothesis, we characterized the soluble NFeoAB fusion protein from Bacteroides fragilis, a commensal organism implicated in drug-resistant infections. Using X-ray crystallography, we determined the 1.50-Å resolution structure of BfFeoA, which adopts an SH3-like fold implicated in protein–protein interactions. Using a combination of structural modeling, small-angle X-ray scattering, and hydrogen–deuterium exchange mass spectrometry, we show that FeoA and NFeoB interact in a nucleotide-dependent manner, and we mapped the protein–protein interaction interface. Finally, using guanosine triphosphate (GTP) hydrolysis assays, we demonstrate that BfNFeoAB exhibits one of the slowest known rates of Feo-mediated GTP hydrolysis that is not potassium-stimulated. Importantly, truncation of FeoA from this fusion demonstrates that FeoA–NFeoB interactions function to stabilize the GTP-bound form of FeoB. Taken together, our work reveals a role for FeoA function in the fused FeoAB system and suggests a function for FeoA among prokaryotes.

Gold Nanoprobes Exploring the Ice Structure in the Aqueous Dispersion of Poly(Ethylene Glycol)-Gold Hybrid Nanoparticles

Ice structures and their formation process are fundamentally important to cryobiology, geoscience, and physical chemistry. In this work, we synthesized gold nanoprobes by grafting water-soluble polyethylene glycol (PEG) onto spherical gold nanoparticles and analyzed the structure of ice formation in the vicinity of the resulting hybrid PEG-Au nanoparticles (AuPEGNPs). Temperature-dependent in situ small-angle X-ray scattering (SAXS) indicated that AuPEGNPs, like PEG, caused the formation of bulk spherulite ice. Unlike for PEG, we observed the formation of lamellar ice with a periodicty of 4.6 nm, which is thermodynamically less stable than the bulk form. The lamellar ice formed after AuPEGNP agglomeration during cooling at -19 °C, and it remained during subsequent heating from -20 to -11 °C and melted at around -10 °C, far below the melting temperature of bulk ice. We explain different effects of AuPEGNP and free PEG on ice formation by the topological differences. The highly concentrated PEG chains on the agglomerated Au cores lead to the formation of PEG-hydrates that assemble into lamellar ice with a periodicity of 4.6 nm.

X-ray Characterization of Conformational Changes of Human Apo- and Holo-Transferrin

Human serum transferrin (Tf) is a bilobed glycoprotein whose function is to transport iron through receptor-mediated endocytosis. The mechanism for iron release is pH-dependent and involves conformational changes in the protein, thus making it an attractive system for possible biomedical applications. In this contribution, two powerful X-ray techniques, namely Macromolecular X-ray Crystallography (MX) and Small Angle X-ray Scattering (SAXS), were used to study the conformational changes of iron-free (apo) and iron-loaded (holo) transferrin in crystal and solution states, respectively, at three different pH values of physiological relevance. A crystallographic model of glycosylated apo-Tf was obtained at 3.0 Å resolution, which did not resolve further despite many efforts to improve crystal quality. In the solution, apo-Tf remained mostly globular in all the pH conditions tested; however, the co-existence of closed, partially open, and open conformations was observed for holo-Tf, which showed a more elongated and flexible shape overall.

Self assembling cluster crystals from DNA based dendritic nanostructures

Cluster crystals are periodic structures with lattice sites occupied by several, overlapping building blocks, featuring fluctuating site occupancy, whose expectation value depends on thermodynamic conditions. Their assembly from atomic or mesoscopic units is long-sought-after, but its experimental realization still remains elusive. Here, we show the existence of well-controlled soft matter cluster crystals. We fabricate dendritic-linear-dendritic triblock composed of a thermosensitive water-soluble polymer and nanometer-scale all-DNA dendrons of the first and second generation. Conclusive small-angle X-ray scattering (SAXS) evidence reveals that solutions of these triblock at sufficiently high concentrations undergo a reversible phase transition from a cluster fluid to a body-centered cubic (BCC) cluster crystal with density-independent lattice spacing, through alteration of temperature. Moreover, a rich concentration-temperature phase diagram demonstrates the emergence of various ordered nanostructures, including BCC cluster crystals, birefringent cluster crystals, as well as hexagonal phases and cluster glass-like kinetically arrested states at high densities.

Experimental realization of cluster crystals- periodic structures with lattice sites occupied by several, overlapping building blocks, has been elusive. Here, the authors show the existence of well-controlled soft matter cluster crystals composed of a thermosensitive water-soluble polymer and nanometer-scale all-DNA dendrons.

Silica hairy nanoparticles: a promising material for self-assembling processes

"Hairy" nanoparticles (HNPs), i.e. inorganic NPs functionalized with polymer chains, are promising building blocks for the synthesis of advanced nanocomposite (NC) materials having several technological applications. Recent evidence shows that HNPs self-organize in a variety of anisotropic structures, resulting in an improvement of the functional properties of the materials, in which are embedded. In this paper, we propose a three-step colloidal synthesis of spherical SiO₂-HNPs, with controlled particle morphology and surface chemistry. In detail, the SiO₂ core, synthesized by a modified Stöber method, was first functionalized with a short-chain amino-silane, which acts as an anchor, and then covered by maleated polybutadiene (PB), a rubbery polymer having low glass transition temperature, rarely considered until now. An extensive investigation by a multi-technique analysis demonstrates that the synthesis of SiO₂-HNPs is simple, scalable, and potentially applicable to different kind of NPs and polymers. Morphological analysis shows the overall distribution of SiO₂-HNPs with a certain degree of spatial organization, suggesting that the polymer coating induces a modification of NP-NP interactions. The role of the surface PB brushes in influencing the special arrangement of SiO₂-HNPs was observed also in cis-1,4-polybutadiene (cis-PB), since the resulting NC exhibited the particle packing in "string-like" superstructures. This confirms the tendency of SiO₂-HNPs to self-assemble and create alternative structures in polymer NCs, which may impart them peculiar functional properties.

Structural basis for the inhibition of the Bacillus subtilis c-di-AMP cyclase CdaA by the phosphoglucomutase GlmM

Cyclic-di-adenosine monophosphate (c-di-AMP) is an important nucleotide signaling molecule that plays a key role in osmotic regulation in bacteria. c-di-AMP is produced from two molecules of ATP by proteins containing a diadenylate cyclase (DAC) domain. In Bacillus subtilis, the main c-di-AMP cyclase, CdaA, is a membrane-linked cyclase with an N-terminal transmembrane domain followed by the cytoplasmic DAC domain. As both high and low levels of c-di-AMP have a negative impact on bacterial growth, the cellular levels of this signaling nucleotide are tightly regulated. Here we investigated how the activity of the B. subtilis CdaA is regulated by the phosphoglucomutase GlmM, which has been shown to interact with the c-di-AMP cyclase. Using the soluble B. subtilis CdaA_CD catalytic domain and purified full-length GlmM or the GlmM_F369 variant lacking the C-terminal flexible domain 4, we show that the cyclase and phosphoglucomutase form a stable complex in vitro and that GlmM is a potent cyclase inhibitor. We determined the crystal structure of the individual B. subtilis CdaA_CD and GlmM homodimers and of the CdaA_CD:GlmM_F369 complex. In the complex structure, a CdaA_CD dimer is bound to a GlmM_F369 dimer in such a manner that GlmM blocks the oligomerization of CdaA_CD and formation of active head-to-head cyclase oligomers, thus suggesting a mechanism by which GlmM acts as a cyclase inhibitor. As the amino acids at the CdaA_CD:GlmM interphase are conserved, we propose that the observed mechanism of inhibition of CdaA by GlmM may also be conserved among Firmicutes.

Internal Microstructure Dictates Interactions of Polymer-grafted Nanoparticles in Solution

Understanding the effects of polymer brush architecture on particle interactions in solution is requisite to enable the development of functional materials based on self-assembled polymer-grafted nanoparticles (GNPs). Static and dynamic light scattering of polystyrene-grafted silica particle solutions in toluene reveals that the pair interaction potential, inferred from the second virial coefficient, A 2, is strongly affected by the grafting density, σ, and degree of polymerization, N, of tethered chains. In the limit of intermediate σ (∼0.3 to 0.6 nm-2) and high N, A 2 is positive and increases with N. This confirms the good solvent conditions and can be qualitatively rationalized on the basis of a pair interaction potential derived for grafted (brush) particles. In contrast, for high σ > 0.6 nm-2 and low N, A 2 displays an unexpected reversal to negative values, thus indicating poor solvent conditions. These findings are rationalized by means of a simple analysis based on a coarse-grained brush potential, which balances the attractive core-core interactions and the excluded volume interactions imparted by the polymer grafts. The results suggest that the steric crowding of polymer ligands in dense GNP systems may fundamentally alter the interactions between brush particles in solution and highlight the crucial role of architecture (internal microstructure) on the behavior of hybrid materials. The effect of grafting density also illustrates the opportunity to tailor the physical properties of hybrid materials by altering geometry (or architecture) rather than a variation of the chemical composition.

Structure and dynamics of the quaternary hunchback mRNA translation repression complex

A key regulatory process during Drosophila development is the localized suppression of the hunchback mRNA translation at the posterior, which gives rise to a hunchback gradient governing the formation of the anterior-posterior body axis. This suppression is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for proper Drosophila development. The RNA contacts have been elucidated for the proteins individually in several atomic-resolution structures. However, the interplay of all three proteins during RNA suppression remains a long-standing open question. Here, we characterize the quaternary complex of the RNA-binding domains of Brat, Pum and Nanos with hunchback mRNA by combining NMR spectroscopy, SANS/SAXS, XL/MS with MD simulations and ITC assays. The quaternary hunchback mRNA suppression complex comprising the RNA binding domains is flexible with unoccupied nucleotides functioning as a flexible linker between the Brat and Pum-Nanos moieties of the complex. Moreover, the presence of the Pum-HD/Nanos-ZnF complex has no effect on the equilibrium RNA binding affinity of the Brat RNA binding domain. This is in accordance with previous studies, which showed that Brat can suppress mRNA independently and is distributed uniformly throughout the embryo.

Notch-Jagged signaling complex defined by an interaction mosaic

The Notch signaling system links cellular fate to that of its neighbors, driving proliferation, apoptosis, and cell differentiation in metazoans, whereas dysfunction leads to debilitating developmental disorders and cancers. Other than a five-by-five domain complex, it is unclear how the 40 extracellular domains of the Notch1 receptor collectively engage the 19 domains of its canonical ligand, Jagged1, to activate Notch1 signaling. Here, using cross-linking mass spectrometry (XL-MS), biophysical, and structural techniques on the full extracellular complex and targeted sites, we identify five distinct regions, two on Notch1 and three on Jagged1, that form an interaction network. The Notch1 membrane-proximal regulatory region individually binds to the established Notch1 epidermal growth factor (EGF) 8-EGF13 and Jagged1 C2-EGF3 activation sites as well as to two additional Jagged1 regions, EGF8-EGF11 and cysteine-rich domain. XL-MS and quantitative interaction experiments show that the three Notch1-binding sites on Jagged1 also engage intramolecularly. These interactions, together with Notch1 and Jagged1 ectodomain dimensions and flexibility, determined by small-angle X-ray scattering, support the formation of nonlinear architectures. Combined, the data suggest that critical Notch1 and Jagged1 regions are not distal but engage directly to control Notch1 signaling, thereby redefining the Notch1-Jagged1 activation mechanism and indicating routes for therapeutic applications.

Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae

Rsm22-family proteins are conserved putative SAM-dependent methyltransferases with important functions in mitochondrial translation. Here, the results of a comparative bioinformatics analysis of Rsm22-type proteins are presented, the expression, biophysical characterization and crystallization of Saccharomyces cerevisiae Rsm22 are reported, a low-resolution SAXS structure of the protein is revealed, and SAM-dependent RNA methyl transferase activity of the protein is demonstrated.

The Saccharomyces cerevisiae Rsm22 protein (Sc-Rsm22), encoded by the nuclear RSM22 (systematic name YKL155c) gene, is a distant homologue of Rsm22 from Trypanosoma brucei (Tb-Rsm22) and METTL17 from mouse (Mm-METTL17). All three proteins have been shown to be associated with mitochondrial gene expression, and Sc-Rsm22 has been documented to be essential for mitochondrial respiration. The Sc-Rsm22 protein comprises a polypeptide of molecular weight 72.2 kDa that is predicted to harbor an N-terminal mitochondrial targeting sequence. The precise physiological function of Rsm22-family proteins is unknown, and no structural information has been available for Sc-Rsm22 to date. In this study, Sc-Rsm22 was expressed and purified in monomeric and dimeric forms, their folding was confirmed by circular-dichroism analyses and their low-resolution structures were determined using a small-angle X-ray scattering (SAXS) approach. The solution structure of the monomeric form of Sc-Rsm22 revealed an elongated three-domain arrangement, which differs from the shape of Tb-Rsm22 in its complex with the mitochondrial small ribosomal subunit in T. brucei (PDB entry 6sg9). A bioinformatic analysis revealed that the core domain in the middle (Leu117–Asp462 in Sc-Rsm22) resembles the corresponding region in Tb-Rsm22, including a Rossmann-like methyltransferase fold followed by a zinc-finger-like structure. The latter structure is not present in this position in other methyltransferases and is therefore a unique structural motif for this family. The first half of the C-terminal domain is likely to form an OB-fold, which is typically found in RNA-binding proteins and is also seen in the Tb-Rsm22 structure. In contrast, the N-terminal domain of Sc-Rsm22 is predicted to be fully α-helical and shares no sequence similarity with other family members. Functional studies demonstrated that the monomeric variant of Sc-Rsm22 methylates mitochondrial tRNAs in vitro. These data suggest that Sc-Rsm22 is a new and unique member of the RNA methyltransferases that is important for mitochondrial protein synthesis.

MATSAS: a small-angle scattering computing tool for porous systems

MATSAS analyses X-ray and neutron small-angle scattering data obtained from porous systems. MATSAS delivers a full suite of pore characterizations, including specific surface area, porosity, pore size distribution and fractal dimensions.

MATSAS is a script-based MATLAB program for analysis of X-ray and neutron small-angle scattering (SAS) data obtained from various facilities. The program has primarily been developed for sedimentary rock samples but is equally applicable to other porous media. MATSAS imports raw SAS data from .xls(x) or .csv files, combines small-angle and very small angle scattering data, subtracts the sample background, and displays the processed scattering curves in log–log plots. MATSAS uses the polydisperse spherical (PDSP) model to obtain structural information on the scatterers (scattering objects); for a porous system, the results include specific surface area (SSA), porosity (Φ), and differential and logarithmic differential pore area/volume distributions. In addition, pore and surface fractal dimensions (D_p and D_s, respectively) are obtained from the scattering profiles. The program package allows simultaneous and rapid analysis of a batch of samples, and the results are then exported to .xlsx and .csv files with separate spreadsheets for individual samples. MATSAS is the first SAS program that delivers a full suite of pore characterizations for sedimentary rocks. MATSAS is an open-source package and is freely available at GitHub (https://github.com/matsas-software/MATSAS).

Calmodulin binds to the STAS domain of SLC26A5 prestin with a calcium-dependent, one-lobe, binding mode

SLC26A5 transporter prestin is fundamental for the higher hearing sensitivity and frequency selectivity of mammals. Prestin is a voltage-dependent transporter found in the cochlear outer hair cells responsible for their electromotility. Intracellular chloride binding is considered essential for voltage sensitivity and electromotility. Prestin is composed by a transmembrane domain and by a cytosolic domain called STAS. There is evidence of a calcium/calmodulin regulation of prestin mediated by the STAS domain. Using different biophysical techniques, namely SEC, CD, ITC, MST, NMR and SAXS, here we demonstrate and characterize the direct interaction between calmodulin and prestin STAS. We show that the interaction is calcium-dependent and that involves residues at the N-terminal end of the "variable loop". This is an intrinsically disordered insertion typical of the STAS domains of the SLC26 family of transporters whose function is still unclear. We derive a low-resolution model of the STAS/CaM complex, where only one lobe of calmodulin is engaged in the interaction, and build a model for the entire dimeric prestin in complex with CaM, which can use the unoccupied lobe to interact with other regions of prestin or with other regulatory proteins. We show that also a non-mammalian STAS can interact with calmodulin via the variable loop. These data start to shed light on the regulatory role of the STAS variable loop of prestin.

Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family

The first S-adenosyl methionine (SAM) degrading enzyme (SAMase) was discovered in bacteriophage T3, as a counter-defense against the bacterial restriction-modification system, and annotated as a SAM hydrolase forming 5’-methyl-thioadenosine (MTA) and L-homoserine. From environmental phages, we recently discovered three SAMases with barely detectable sequence similarity to T3 SAMase and without homology to proteins of known structure. Here, we present the very first phage SAMase structures, in complex with a substrate analogue and the product MTA. The structure shows a trimer of alpha–beta sandwiches similar to the GlnB-like superfamily, with active sites formed at the trimer interfaces. Quantum-mechanical calculations, thin-layer chromatography, and nuclear magnetic resonance spectroscopy demonstrate that this family of enzymes are not hydrolases but lyases forming MTA and L-homoserine lactone in a unimolecular reaction mechanism. Sequence analysis and in vitro and in vivo mutagenesis support that T3 SAMase belongs to the same structural family and utilizes the same reaction mechanism.

Bacteria can be infected by viruses known as bacteriophages. These viruses inject their genetic material into bacterial cells and use the bacteria’s own machinery to build the proteins they need to survive and infect other cells. To protect themselves, bacteria produce a molecule called S-adenosyl methionine, or SAM for short, which deposits marks on the bacteria’s DNA. These marks help the bacteria distinguish their own genetic material from the genetic material of foreign invaders: any DNA not bearing the mark from SAM will be immediately broken down by the bacterial cell. This system helps to block many types of bacteriophage infections, but not all. Some bacteriophages carry genes that code for enzymes called SAMases, which can break down SAM, switching off the bacteria’s defenses.

The most well-known SAMase was first discovered in the 1960s in a bacteriophage called T3. Chemical studies of this SAMase suggested that it works as a 'hydrolase', meaning that it uses water to break SAM apart. New SAMases have since been discovered in bacteriophages from environmental water samples, which, despite being able to degrade SAM, are genetically dissimilar to one another and the SAMase in T3. This brings into question whether these enzymes all use the same mechanism to break SAM down.

To gain a better understanding of how these SAMases work, Guo, Söderholm, Kanchugal, Isaksen et al. solved the crystal structure of one of the newly discovered enzymes called Svi3-3. This revealed three copies of the Svi3-3 enzyme join together to form a unit that SAM binds to at the border between two of the enzymes. Computer simulations of this structure suggested that Svi3-3 holds SAM in a position where it cannot interact with water, and that once in the grip of the SAMase, SAM instead reacts with itself and splits into two.

Experiments confirmed these predictions for Svi3-3 and the other tested SAMases. Furthermore, the SAMase from bacteriophage T3 was also found to degrade SAM using the same mechanism. This shows that this group of SAMases are not hydrolases as originally thought, but in fact ‘lyases’: enzymes that break molecules apart without using water.

These findings form a starting point for further investigations into how SAM lyases help bacteriophages evade detection. SAM has various different functions in other living organisms, and these lyases could be used to modulate the levels of SAM in future studies investigating its role.

Comparison of angiopoietin-like protein 3 and 4 reveals structural and mechanistic similarities

Elevated plasma triglycerides are a risk factor for coronary artery disease, which is the leading cause of death worldwide. Lipoprotein lipase (LPL) reduces triglycerides in the blood by hydrolyzing them from triglyceride-rich lipoproteins to release free fatty acids. LPL activity is regulated in a nutritionally responsive manner by macromolecular inhibitors including angiopoietin-like proteins 3 and 4 (ANGPTL3 and ANGPTL4). However, the mechanism by which ANGPTL3 inhibits LPL is unclear, in part due to challenges in obtaining pure protein for study. We used a new purification protocol for the N-terminal domain of ANGPTL3, removing a DNA contaminant, and found DNA-free ANGPTL3 showed enhanced inhibition of LPL. Structural analysis showed that ANGPTL3 formed elongated, flexible trimers and hexamers that did not interconvert. ANGPTL4 formed only elongated flexible trimers. We compared the inhibition of ANGPTL3 and ANGPTL4 using human very-low-density lipoproteins as a substrate and found both were noncompetitive inhibitors. The inhibition constants for the trimeric ANGPTL3 (7.5 ± 0.7 nM) and ANGPTL4 (3.6 ± 1.0 nM) were only 2-fold different. Heparin has previously been reported to interfere with ANGPTL3 binding to LPL, so we questioned if the negatively charged heparin was acting in a similar fashion to the DNA contaminant. We found that ANGPTL3 inhibition is abolished by binding to low-molecular-weight heparin, whereas ANGPTL4 inhibition is not. Our data show new similarities and differences in how ANGPTL3 and ANGPTL4 regulate LPL and opens new avenues of investigating the effect of heparin on LPL inhibition by ANGPTL3.

Defects and plasticity in ultrastrong supercrystalline nanocomposites

Supercrystalline nanocomposites are nanoarchitected materials with a growing range of applications but unexplored in their structural behavior. They typically consist of organically functionalized inorganic nanoparticles arranged into periodic structures analogous to crystalline lattices, including superlattice imperfections induced by processing or mechanical loading. Although featuring a variety of promising functional properties, their lack of mechanical robustness and unknown deformation mechanisms hamper their implementation into devices. We show that supercrystalline materials react to indentation with the same deformation patterns encountered in single crystals. Supercrystals accommodate plastic deformation in the form of pile-ups, dislocations, and slip bands. These phenomena occur, at least partially, also after cross-linking of the organic ligands, which leads to a multifold strengthening of the nanocomposites. The classic shear theories of crystalline materials are found to describe well the behavior of supercrystalline nanocomposites, which result to feature an elastoplastic behavior, accompanied by compaction.

Hierarchically Porous Carbon Materials from Self-Assembled Block Copolymer/Dopamine Mixtures

Hierarchically porous carbon materials with interconnected frameworks of macro- and mesopores are desirable for electrochemical applications in biosensors, electrocatalysis, and supercapacitors. In this study, we report a facile synthetic route to fabricate hierarchically porous carbon materials by controlled macro- and mesophase separation of a mixture of polystyrene-block-poly(ethylene) and dopamine. The morphology of mesopores is tailored by controlling the coassembly of PS-b-PEO and dopamine in the acidic tetrahydrofuran-water cosolvent. HCl addition plays a critical role via enhancing the charge-dipole interactions between PEO and dopamine and suppressing the clustering and chemical reactions of dopamine in solution. As a result, subsequent drying can produce interpenetrated PS-b-PEO/DA mixtures without forming dopamine microsized crystallites. Dopamine oxidative polymerization induced by solvent annealing in NH₄OH vapor enables the formation of percolating macropores. Subsequent pyrolysis to selectively remove the PS-b-PEO template from the complex can produce hierarchically porous carbon materials with interconnected frameworks of macro- and mesopores when pyrolysis is implemented at a low temperature or when DA is a minor component.

Assembly of Capsids from Hepatitis B Virus Core Protein Progresses through Highly Populated Intermediates in the Presence and Absence of RNA

The genetic material of viruses is protected by protein shells that are assembled from a large number of subunits in a process that is efficient and robust. Many of the mechanistic details underpinning efficient assembly of virus capsids are still unknown. The assembly mechanism of hepatitis B capsids has been intensively researched using a truncated core protein lacking the C-terminal domain responsible for binding genomic RNA. To resolve the assembly intermediates of hepatitis B virus (HBV), we studied the formation of nucleocapsids and empty capsids from full-length hepatitis B core proteins, using time-resolved small-angle X-ray scattering. We developed a detailed structural model of the HBV capsid assembly process using a combination of analysis with multivariate curve resolution, structural modeling, and Bayesian ensemble inference. The detailed structural analysis supports an assembly pathway that proceeds through the formation of two highly populated intermediates, a trimer of dimers and a partially closed shell consisting of around 40 dimers. These intermediates are on-path, transient and efficiently convert into fully formed capsids. In the presence of an RNA oligo that binds specifically to the C-terminal domain the assembly proceeds via a similar mechanism to that in the absence of nucleic acids. Comparisons between truncated and full-length HBV capsid proteins reveal that the unstructured C-terminal domain has a significant impact on the assembly process and is required to obtain a more complete mechanistic understanding of HBV capsid formation. These results also illustrate how combining scattering information from different time-points during time-resolved experiments can be utilized to derive a structural model of protein self-assembly pathways.

Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTPσ

Synaptic adhesion molecules play an important role in the formation, maintenance and refinement of neuronal connectivity. Recently, several leucine rich repeat (LRR) domain containing neuronal adhesion molecules have been characterized including netrin G-ligands, SLITRKs and the synaptic adhesion-like molecules (SALMs). Dysregulation of these adhesion molecules have been genetically and functionally linked to various neurological disorders. Here we investigated the molecular structure and mechanism of ligand interactions for the postsynaptic SALM3 adhesion protein with its presynaptic ligand, receptor protein tyrosine phosphatase σ (PTPσ). We solved the crystal structure of the dimerized LRR domain of SALM3, revealing the conserved structural features and mechanism of dimerization. Furthermore, we determined the complex structure of SALM3 with PTPσ using small angle X-ray scattering, revealing a 2:2 complex similar to that observed for SALM5. Solution studies unraveled additional flexibility for the complex structure, but validated the uniform mode of action for SALM3 and SALM5 to promote synapse formation. The relevance of the key interface residues was further confirmed by mutational analysis with cellular binding assays and artificial synapse formation assays. Collectively, our results suggest that SALM3 dimerization is a pre-requisite for the SALM3-PTPσ complex to exert synaptogenic activity.

Molecular assemblies built with the artificial protein Pizza

Recently an artificial protein named Pizza6 was reported, which possesses six identical tandem repeats and adopts a monomeric β -propeller fold with sixfold structural symmetry. Pizza2, a truncated form that consists of a double tandem repeat, self-assembles into a trimer reconstructing the same propeller architecture as Pizza6. The ability of pizza proteins to self-assemble to form complete propellers makes them interesting building blocks to engineer larger symmetrical protein complexes such as symmetric nanoparticles. Here we have explored the self-assembly of Pizza2 fused to homo-oligomerizing peptides. In total, we engineered five different fusion proteins, of which three appeared to assemble successfully into larger complexes. Further characterization of these proteins showed one monodisperse designer protein with a structure close to the intended design. This protein was further fused to eGFP to investigate functionalization of the nanoparticle. The fusion protein was stable and could be expressed in high yield, showing that Pizza-based nanoparticles may be further decorated with functional domains.

Architecture and functional dynamics of the pentafunctional AROM complex

The AROM complex is a multifunctional metabolic machine with ten enzymatic domains catalyzing the five central steps of the shikimate pathway in fungi and protists. We determined its crystal structure and catalytic behavior, and elucidated its conformational space using a combination of experimental and computational approaches. We derived this space in an elementary approach, exploiting an abundance of conformational information from its monofunctional homologs in the Protein Data Bank. It demonstrates how AROM is optimized for spatial compactness while allowing for unrestricted conformational transitions and a decoupled functioning of its individual enzymatic entities. With this architecture, AROM poses a tractable test case for the effects of active site proximity on the efficiency of both natural metabolic systems and biotechnological pathway optimization approaches. We show that a mere colocalization of enzymes is not sufficient to yield a detectable improvement of metabolic throughput.

Human aminolevulinate synthase structure reveals a eukaryotic-specific autoinhibitory loop regulating substrate binding and product release

5'-aminolevulinate synthase (ALAS) catalyzes the first step in heme biosynthesis, generating 5'-aminolevulinate from glycine and succinyl-CoA. Inherited frameshift indel mutations of human erythroid-specific isozyme ALAS2, within a C-terminal (Ct) extension of its catalytic core that is only present in higher eukaryotes, lead to gain-of-function X-linked protoporphyria (XLP). Here, we report the human ALAS2 crystal structure, revealing that its Ct-extension folds onto the catalytic core, sits atop the active site, and precludes binding of substrate succinyl-CoA. The Ct-extension is therefore an autoinhibitory element that must re-orient during catalysis, as supported by molecular dynamics simulations. Our data explain how Ct deletions in XLP alleviate autoinhibition and increase enzyme activity. Crystallography-based fragment screening reveals a binding hotspot around the Ct-extension, where fragments interfere with the Ct conformational dynamics and inhibit ALAS2 activity. These fragments represent a starting point to develop ALAS2 inhibitors as substrate reduction therapy for porphyria disorders that accumulate toxic heme intermediates.