BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis

Structure of the G protein chaperone and guanine nucleotide exchange factor Ric-8A bound to Gαi1

Ric-8A is a cytosolic Guanine Nucleotide exchange Factor (GEF) that activates heterotrimeric G protein alpha subunits (Gα) and serves as an essential Gα chaperone. Mechanisms by which Ric-8A catalyzes these activities, which are stimulated by Casein Kinase II phosphorylation, are unknown. We report the structure of the nanobody-stabilized complex of nucleotide-free Gα bound to phosphorylated Ric-8A at near atomic resolution by cryo-electron microscopy and X-ray crystallography. The mechanism of Ric-8A GEF activity differs considerably from that employed by G protein-coupled receptors at the plasma membrane. Ric-8A engages a specific conformation of Gα at multiple interfaces to form a complex that is stabilized by phosphorylation within a Ric-8A segment that connects two Gα binding sites. The C-terminus of Gα is ejected from its beta sheet core, thereby dismantling the GDP binding site. Ric-8A binds to the exposed Gα beta sheet and switch II to stabilize the nucleotide-free state of Gα.

The structural basis of fungal glucuronoyl esterase activity on natural substrates

Structural and functional studies were conducted of the glucuronoyl esterase (GE) from Cerrena unicolor (CuGE), an enzyme catalyzing cleavage of lignin-carbohydrate ester bonds. CuGE is an α/β-hydrolase belonging to carbohydrate esterase family 15 (CE15). The enzyme is modular, comprised of a catalytic and a carbohydrate-binding domain. SAXS data show CuGE as an elongated rigid molecule where the two domains are connected by a rigid linker. Detailed structural information of the catalytic domain in its apo- and inactivated form and complexes with aldouronic acids reveal well-defined binding of the 4-O-methyl-a-D-glucuronoyl moiety, not influenced by the nature of the attached xylo-oligosaccharide. Structural and sequence comparisons within CE15 enzymes reveal two distinct structural subgroups. CuGE belongs to the group of fungal CE15-B enzymes with an open and flat substrate-binding site. The interactions between CuGE and its natural substrates are explained and rationalized by the structural results, microscale thermophoresis and isothermal calorimetry.

S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula

S-adenosylmethionine synthases (MATs) are responsible for production of S-adenosylmethionine, the cofactor essential for various methylation reactions, production of polyamines and phytohormone ethylene, etc. Plants have two distinct MAT types (I and II). This work presents the structural analysis of MATs from Arabidopsis thaliana (AtMAT1 and AtMAT2, both type I) and Medicago truncatula (MtMAT3a, type II), which, unlike most MATs from other domains of life, are dimers where three-domain subunits are sandwiched flat with one another. Although MAT types are very similar, their subunits are differently oriented within the dimer. Structural snapshots along the enzymatic reaction reveal the exact conformation of precatalytic methionine in the active site and show a binding niche, characteristic only for plant MATs, that may serve as a lock of the gate loop. Nevertheless, plants, in contrary to mammals, lack the MAT regulatory subunit, and the regulation of plant MAT activity is still puzzling. Our structures open a possibility of an allosteric activity regulation of type I plant MATs by linear compounds, like polyamines, which would tighten the relationship between S-adenosylmethionine and polyamine biosynthesis.

Mechanism of sequence-based separation of single-stranded DNA in capillary zone electrophoresis

Separation of DNA by length using CGE is a mature field. Separation of DNA by sequence, in contrast, is a more difficult problem. Existing techniques generally rely upon changes in intrinsic or induced differences in conformation. Previous work in our group showed that sets of ssDNA of the same length differing in sequence by as little as a single base could be separated by CZE using simple buffers at high ionic strength. Here, we explore the basis of the separation using circular dichroism spectroscopy, fluorescence anisotropy, and small angle X-ray scattering. The results reveal sequence-dependent differences among the same length strands, but the trends in the differences are not correlated to the migration order of the strands in the CZE separation. They also indicate that the separation is based on intrinsic differences among the strands that do not change with increasing ionic strength; rather, increasing ionic strength has a greater effect on electroosmotic mobility in the normal direction than on electrophoretic mobility of the strands in the reverse direction. This increases the migration time of the strands in the normal direction, allowing more time for the same-length strands to be teased apart based on very small differences in the intrinsic properties of the strands of different sequence. Regression analysis was used to model the intrinsic differences among DNA strands in order to gain insight into the relationship between mobility and sequence that underlies the separation.

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

Prion-like domains (PLDs) can drive liquid-liquid phase separation (LLPS) in cells. Using an integrative biophysical approach that includes nuclear magnetic resonance spectroscopy, small-angle x-ray scattering, and multiscale simulations, we have uncovered sequence features that determine the overall phase behavior of PLDs. We show that the numbers (valence) of aromatic residues in PLDs determine the extent of temperature-dependent compaction of individual molecules in dilute solutions. The valence of aromatic residues also determines full binodals that quantify concentrations of PLDs within coexisting dilute and dense phases as a function of temperature. We also show that uniform patterning of aromatic residues is a sequence feature that promotes LLPS while inhibiting aggregation. Our findings lead to the development of a numerical stickers-and-spacers model that enables predictions of full binodals of PLDs from their sequences.

Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase

Understanding how enzymes achieve their tremendous catalytic power is a major question in biochemistry. Greater understanding is also needed for enzyme engineering applications. In many cases, enzyme efficiency and specificity depend on residues not in direct contact with the substrate, termed remote residues. This work focuses on Escherichia coli ornithine transcarbamoylase (OTC), which plays a central role in amino acid metabolism. OTC has been reported to undergo an induced-fit conformational change upon binding its first substrate, carbamoyl phosphate (CP), and several residues important for activity have been identified. Using computational methods based on the computed chemical properties from theoretical titration curves, sequence-based scores derived from evolutionary history, and protein surface topology, residues important for catalytic activity were predicted. The roles of these residues in OTC activity were tested by constructing mutations at predicted positions, followed by steady-state kinetics assays and substrate binding studies with the variants. First-layer mutations R57A and D231A, second-layer mutation H272L, and third-layer mutation E299Q, result in 57- to 450-fold reductions in k_cat/K_M with respect to CP and 44- to 580-fold reductions with respect to ornithine. Second-layer mutations D140N and Y160S also reduce activity with respect to ornithine. Most variants had decreased stability relative to wild-type OTC, with variants H272L, H272N, and E299Q having the greatest decreases. Variants H272L, E299Q, and R57A also show compromised CP binding. In addition to direct effects on catalytic activity, effects on overall protein stability and substrate binding were observed that reveal the intricacies of how these residues contribute to catalysis.

Structural Modeling Using Solution Small-Angle X-ray Scattering (SAXS)

Small-angle X-ray scattering (SAXS) offers a way to examine the overall shape and oligomerization state of biological macromolecules under quasi native conditions in solution. In the past decades, SAXS has become a standard tool for structure biologists due to the availability of high brilliance X-ray sources and the development of data analysis/interpretation methods. Sample handling robots and software pipelines have significantly reduced the time necessary to conduct SAXS experiments. Presently, most synchrotrons feature beamlines dedicated to biological SAXS, and the SAXS-derived models are deposited into dedicated and accessible databases. The size of macromolecules that may be analyzed ranges from small peptides or snippets of nucleic acids to gigadalton large complexes or even entire viruses. Compared to other structural methods, sample preparation is straightforward, and the risk of inducing preparation artefacts is minimal. Very importantly, SAXS is a method of choice to study flexible systems like unfolded or disordered proteins, providing the structural ensembles compatible with the data. Although it may be utilized stand-alone, SAXS profits a lot from available experimental or predicted high-resolution data and information from complementary biophysical methods. Here, we show the basic principles of SAXS and review latest developments in the fields of hybrid modeling and flexible systems.

Pseudomonas aeruginosa exoenzyme Y directly bundles actin filaments

Pseudomonas aeruginosa uses a type III secretion system (T3SS) to inject cytotoxic effector proteins into host cells. The promiscuous nucleotidyl cyclase, exoenzyme Y (ExoY), is one of the most common effectors found in clinical P. aeruginosa isolates. Recent studies have revealed that the nucleotidyl cyclase activity of ExoY is stimulated by actin filaments (F-actin) and that ExoY alters actin cytoskeleton dynamics in vitro, via an unknown mechanism. The actin cytoskeleton plays an important role in numerous key biological processes and is targeted by many pathogens to gain competitive advantages. We utilized total internal reflection fluorescence microscopy, bulk actin assays, and EM to investigate how ExoY impacts actin dynamics. We found that ExoY can directly bundle actin filaments with high affinity, comparable with eukaryotic F-actin-bundling proteins, such as fimbrin. Of note, ExoY enzymatic activity was not required for F-actin bundling. Bundling is known to require multiple actin-binding sites, yet small-angle X-ray scattering experiments revealed that ExoY is a monomer in solution, and previous data suggested that ExoY possesses only one actin-binding site. We therefore hypothesized that ExoY oligomerizes in response to F-actin binding and have used the ExoY structure to construct a dimer-based structural model for the ExoY-F-actin complex. Subsequent mutational analyses suggested that the ExoY oligomerization interface plays a crucial role in mediating F-actin bundling. Our results indicate that ExoY represents a new class of actin-binding proteins that modulate the actin cytoskeleton both directly, via F-actin bundling, and indirectly, via actin-activated nucleotidyl cyclase activity.

Developing Inhibitors of the p47phox-p22phox Protein-Protein Interaction by Fragment-Based Drug Discovery

Nicotinamide adenine dinucleotide phosphate oxidase isoform 2 is an enzyme complex, which generates reactive oxygen species and contributes to oxidative stress. The p47phox-p22phox interaction is critical for the activation of the catalytical NOX2 domain, and p47phox is a potential target for therapeutic intervention. By screening 2500 fragments using fluorescence polarization and a thermal shift assay and validation by surface plasmon resonance, we found eight hits toward the tandem SH3 domain of p47phox (p47phox^SH3A-B) with K_D values of 400-600 μM. Structural studies revealed that fragments 1 and 2 bound two separate binding sites in the elongated conformation of p47phox^SH3A-B and these competed with p22phox for binding to p47phox^SH3A-B. Chemical optimization led to a dimeric compound with the ability to potently inhibit the p47phox^SH3A-B-p22phox interaction (K_i of 20 μM). Thereby, we reveal a new way of targeting p47phox and present the first report of drug-like molecules with the ability to bind p47phox and inhibit its interaction with p22phox.

Higher-order oligomerization of a chimeric αβγ bifunctional diterpene synthase with prenyltransferase and class II cyclase activities is concentration-dependent

The unusual diterpene (C₂₀) synthase copalyl diphosphate synthase from Penicillium verruculosum (PvCPS) is the first bifunctional terpene synthase identified with both prenyltransferase and class II cyclase activities in a single polypeptide chain with αβγ domain architecture. The C-terminal prenyltransferase α domain generates geranylgeranyl diphosphate which is then cyclized to form copalyl diphosphate at the N-terminal βγ domain interface. We now demonstrate that PvCPS exists as a hexamer at high concentrations - a unique quaternary structure for known αβγ terpene synthases. Hexamer assembly is corroborated by a 2.41 Å-resolution crystal structure of the α domain prenyltransferase obtained from limited proteolysis of full-length PvCPS, as well as the ab initio model of full-length PvCPS derived from small-angle X-ray scattering data. Hexamerization of the prenyltransferase α domain appears to drive the hexamerization of full-length PvCPS. The PvCPS hexamer dissociates into lower-order species at lower concentrations, as evidenced by size-exclusion chromatography in-line with multiangle light scattering, sedimentation velocity analytical ultracentrifugation, and native polyacrylamide gel electrophoresis experiments, suggesting that oligomerization is concentration dependent. Even so, PvCPS oligomer assembly does not affect prenyltransferase activity in vitro.

Structural Basis of Protein Arginine Methyltransferase Activation by a Catalytically Dead Homolog (Prozyme)

Prozymes are pseudoenzymes that stimulate the function of weakly active enzymes through complex formation. The major Trypanosoma brucei protein arginine methyltransferase, TbPRMT1 enzyme (ENZ), requires TbPRMT1 prozyme (PRO) to form an active heterotetrameric complex. Here, we present the X-ray crystal structure of the TbPRMT1 ENZ-Δ52PRO tetrameric complex with the cofactor product S-adenosyl-l-homocysteine (AdoHcy) at 2.4 Å resolution. The individual ENZ and PRO units adopt the highly-conserved PRMT domain architecture and form an antiparallel heterodimer that corresponds to the canonical homodimer observed in all previously reported PRMTs. In turn, two such heterodimers assemble into a tetramer both in the crystal and in solution with twofold rotational symmetry. ENZ is unstable in absence of PRO and incapable of forming a homodimer due to a steric clash of an ENZ-specific tyrosine within the dimerization arm, rationalizing why PRO is required to complement ENZ to form a PRMT dimer that is necessary, but not sufficient for PRMT activity. The PRO structure deviates from other, active PRMTs in that it lacks the conserved η2 3₁₀-helix within the Rossmann fold, abolishing cofactor binding. In addition to its chaperone function for ENZ, PRO substantially contributes to substrate binding. Heterotetramerization is required for catalysis, as heterodimeric ENZ-PRO mutants lack binding affinity and methyltransferase activity toward the substrate protein TbRGG1. Together, we provide a structural basis for TbPRMT1 ENZ activation by PRO heterotetramer formation, which is conserved across all kinetoplastids, and describe a chaperone function of the TbPRMT1 prozyme, which represents a novel mode of PRMT regulation.

Structural Analysis of RNA by Small-Angle X-ray Scattering

Over the past two decades small-angle X-ray scattering (SAXS) has become a popular method to characterize solutions of biomolecules including ribonucleic acid (RNA). In an integrative structural approach, SAXS is complementary to crystallography, NMR, and electron microscopy and provides information about RNA architecture and dynamics. This chapter highlights the practical advantages of combining size-exclusion chromatography and SAXS at synchrotron facilities. It is illustrated by practical case studies of samples ranging from single hairpins and tRNA to a large IRES. The emphasis is also put on sample preparation which is a critical step of SAXS analysis and on optimized protocols for in vitro RNA synthesis ensuring the production of mg amount of pure and homogeneous molecules.

Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-Ray Scattering

Small-angle X-ray scattering (SAXS) is a low-resolution method for the structural characterization of biological macromolecules in solution. Information about the overall structural features provided by SAXS is highly complementary to X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy, which are high-resolution methods. SAXS not only provides the shape, oligomeric state, and quaternary structure of folded proteins and protein complexes but also allows for quantitative analysis of flexible biomolecules. In this chapter, the most relevant SAXS procedures for structural characterization of flexible macromolecules, including intrinsically disordered proteins (IDPs), are presented. The sample requirements for SAXS experiments on protein solutions and the sequence of steps in data collection and processing are described. The use of the advanced data analysis tools to quantitatively characterize flexible proteins is presented in detail. Typical experimental issues and potential problems encountered during SAXS data measurements and analyses are discussed.

Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain

The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate tertiary fold of the RNA domain, with one monovalent and several divalent ions located in specific sites within the structure. Here, we report a new crystal structure of the free GAC that is essentially identical to the L11-bound structure, which retains many common sites of divalent ion occupation. This new structure demonstrates that RNA alone folds into its tertiary structure with bound divalent ions. In solution, we find that this tertiary structure is not static, but rather is best described as an ensemble of states. While L11 protein cannot bind to the GAC until the RNA has adopted its tertiary structure, new experimental data show that L11 binds to Mg²⁺-dependent folded states, which we suggest lie along the folding pathway of the RNA. We propose that L11 stabilizes a specific GAC RNA tertiary state, corresponding to the crystal structure, and that this structure reflects the functionally critical conformation of the rRNA domain in the fully assembled ribosome.

The internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex

The Mixed Lineage Leukemia protein 1 (MLL1) plays an essential role in the maintenance of the histone H3 lysine 4 (H3K4) methylation status for gene expression during differentiation and development. The methyltransferase activity of MLL1 is regulated by three conserved core subunits, WDR5, RBBP5 and ASH2L. Here, we determined the structure of human RBBP5 and demonstrated its role in the assembly and regulation of the MLL1 complex. We identified an internal interaction between the WD40 propeller and the C-terminal distal region in RBBP5, which assisted the maintenance of the compact conformation of the MLL1 complex. We also discovered a vertebrate-specific motif in the C-terminal distal region of RBBP5 that contributed to nucleosome recognition and methylation of nucleosomes by the MLL1 complex. Our results provide new insights into functional conservation and evolutionary plasticity of the scaffold protein RBBP5 in the regulation of KMT2-family methyltransferase complexes.

Salt Dependence of A-Form RNA Duplexes: Structures and Implications

The biological functions of RNA range from gene regulation through catalysis and depend critically on its structure and flexibility. Conformational variations of flexible, non-base-paired components, including RNA hinges, bulges, or single-stranded tails, are well documented. Recent work has also identified variations in the structure of ubiquitous, base-paired duplexes found in almost all functional RNAs. Duplexes anchor the structures of folded RNAs, and their surface features are recognized by partner molecules. To date, no consistent picture has been obtained that describes the range of conformations assumed by RNA duplexes. Here, we apply wide angle, solution X-ray scattering (WAXS) to quantify these variations, by sampling length scales characteristic of helical geometries under different solution conditions. To identify the radius, helical rise, twist, and length of dsRNA helices, we exploit molecular dynamics generated structures, explicit solvent models, and ensemble optimization methods. Our results quantify the substantial and salt-dependent deviations of double-stranded (ds) RNA duplexes from the assumed canonical A-form conformation. Recent experiments underscore the need to properly describe the structures of RNA duplexes when interpreting the salt dependence of RNA conformations.

PET-RAFT and SAXS: High Throughput Tools to Study Compactness and Flexibility of Single-Chain Polymer Nanoparticles

From protein science, it is well understood that ordered folding and 3D structure mainly arises from balanced and noncovalent polar and nonpolar interactions, such as hydrogen bonding. Similarly, it is understood that single-chain polymer nanoparticles (SCNPs) will also compact and become more rigid with greater hydrophobicity and intrachain hydrogen bonding. Here, we couple high throughput photoinduced electron/energy transfer reversible addition-fragmentation chain-transfer (PET-RAFT) polymerization with high throughput small-angle X-ray scattering (SAXS) to characterize a large combinatorial library (>450) of several homopolymers, random heteropolymers, block copolymers, PEG-conjugated polymers, and other polymer-functionalized polymers. Coupling these two high throughput tools enables us to study the major influence(s) for compactness and flexibility in higher breadth than ever before possible. Not surprisingly, we found that many were either highly disordered in solution, in the case of a highly hydrophilic polymer, or insoluble if too hydrophobic. Remarkably, we also found a small group (9/457) of PEG-functionalized random heteropolymers and block copolymers that exhibited compactness and flexibility similar to that of bovine serum albumin (BSA) by dynamic light scattering (DLS), NMR, and SAXS. In general, we found that describing a rough association between compactness and flexibility parameters (R g /R h and Porod Exponent, respectively) with logP, a quantity that describes hydrophobicity, helps to demonstrate and predict material parameters that lead to SCNPs with greater compactness, rigidity, and stability. Future implementation of this combinatorial and high throughput approach for characterizing SCNPs will allow for the creation of detailed design parameters for well-defined macromolecular chemistry.

Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A

Resistance to inhibitors of cholinesterase 8A (Ric8A) protein is an important G protein-coupled receptor (GPCR)-independent regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor (GEF) and a chaperone. Insights into the complex between Ric8A and Gα hold the key to understanding the mechanisms underlying noncanonical activation of G-protein signaling as well as the folding of nascent Gα proteins. Here, we examined the structure of the complex of Ric8A with minimized Gα_i (miniGα_i) in solution by small-angle X-ray scattering (SAXS) and exploited the scattering profile in modeling of the Ric8A/miniGα_i complex by steered molecular dynamics (SMD) simulations. A small set of models of the complex featured minimal clash scores, excellent agreement with the experimental SAXS data, and a large-scale rearrangement of the signal-transducing α5-helix of Gα away from its β-sheet core. The resulting interface involved the Gα α5-helix bound to the concave surface of Ric8A and the Gα β-sheet that wraps around the C-terminal part of the Ric8A armadillo domain, leading to a severe disruption of the GDP-binding site. Further modeling of the flexible C-terminal tail of Ric8A indicated that it interacts with the effector surface of Gα. This smaller interface may enable the Ric8A-bound Gα to interact with GTP. The two-interface interaction with Gα described here distinguishes Ric8A from GPCRs and non-GPCR regulators of G-protein signaling.

SASBDB: Towards an automatically curated and validated repository for biological scattering data

Small-angle scattering (SAS) of X-rays and neutrons is a fundamental tool to study the nanostructural properties, and in particular, biological macromolecules in solution. In structural biology, SAS recently transformed from a specialization into a general technique leading to a dramatic increase in the number of publications reporting structural models. The growing amount of data recorded and published has led to an urgent need for a global SAS repository that includes both primary data and models. In response to this, a small-angle scattering biological data bank (SASBDB) was designed in 2014 and is available for public access at www.sasbdb.org. SASBDB is a comprehensive, free and searchable repository of SAS experimental data and models deposited together with the relevant experimental conditions, sample details and instrument characteristics. SASBDB is rapidly growing, and presently has over 1,000 entries containing more than 1,600 models. We describe here the overall organization and procedures of SASBDB paying most attention to user-relevant information during submission. Perspectives of further developments, in particular, with OneDep system of the Protein Data Bank, and also widening of SASBDB including new types of data/models are discussed.

Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology

Small-angle X-ray scattering (SAXS) has emerged as an enabling integrative technique for comprehensive analyses of macromolecular structures and interactions in solution. Over the past two decades, SAXS has become a mainstay of the structural biologist's toolbox, supplying multiplexed measurements of molecular shape and dynamics that unveil biological function. Here, we discuss evolving SAXS theory, methods, and applications that extend the field of small-angle scattering beyond simple shape characterization. SAXS, coupled with size-exclusion chromatography (SEC-SAXS) and time-resolved (TR-SAXS) methods, is now providing high-resolution insight into macromolecular flexibility and ensembles, delineating biophysical landscapes, and facilitating high-throughput library screening to assess macromolecular properties and to create opportunities for drug discovery. Looking forward, we consider SAXS in the integrative era of hybrid structural biology methods, its potential for illuminating cellular supramolecular and mesoscale structures, and its capacity to complement high-throughput bioinformatics sequencing data. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.

Interaction of the tetratricopeptide repeat domain of aryl hydrocarbon receptor-interacting protein-like 1 with the regulatory Pγ subunit of phosphodiesterase 6

Phosphodiesterase-6 (PDE6) is key to both phototransduction and health of rods and cones. Proper folding of PDE6 relies on the chaperone activity of aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1), and mutations in both PDE6 and AIPL1 can cause a severe form of blindness. Although AIPL1 and PDE6 are known to interact via the FK506-binding protein domain of AIPL1, the contribution of the tetratricopeptide repeat (TPR) domain of AIPL1 to its chaperone function is poorly understood. Here, we demonstrate that AIPL1-TPR interacts specifically with the regulatory Pγ subunit of PDE6. Use of NMR chemical shift perturbation (CSP) mapping technique revealed the interface between the C-terminal portion of Pγ and AIPL1-TPR. Our solution of the crystal structure of the AIPL1-TPR domain provided additional information, which together with the CSP data enabled us to generate a model of this interface. Biochemical analysis of chimeric AIPL1-AIP proteins supported this model and also revealed a correlation between the affinity of AIPL1-TPR for Pγ and the ability of Pγ to potentiate the chaperone activity of AIPL1. Based on these results, we present a model of the larger AIPL1-PDE6 complex. This supports the importance of simultaneous interactions of AIPL1-FK506-binding protein with the prenyl moieties of PDE6 and AIPL1-TPR with the Pγ subunit during the folding and/or assembly of PDE6. This study sheds new light on the versatility of TPR domains in protein folding by describing a novel TPR-protein binding partner, Pγ, and revealing that this subunit imparts AIPL1 selectivity for its client.

Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a

CRISPR-Cas systems provide bacteria and archaea with programmable immunity against mobile genetic elements. Evolutionary pressure by CRISPR-Cas has driven bacteriophage to evolve small protein inhibitors, anti-CRISPRs (Acrs), that block Cas enzyme function by wide-ranging mechanisms. We show here that the inhibitor AcrVA4 uses a previously undescribed strategy to recognize the L. bacterium Cas12a (LbCas12a) pre-crRNA processing nuclease, forming a Cas12a dimer, and allosterically inhibiting DNA binding. The Ac. species Cas12a (AsCas12a) enzyme, widely used for genome editing applications, contains an ancestral helical bundle that blocks AcrVA4 binding and allows it to escape anti-CRISPR recognition. Using biochemical, microbiological, and human cell editing experiments, we show that Cas12a orthologs can be rendered either sensitive or resistant to AcrVA4 through rational structural engineering informed by evolution. Together, these findings explain a new mode of CRISPR-Cas inhibition and illustrate how structural variability in Cas effectors can drive opportunistic co-evolution of inhibitors by bacteriophage.

Flexible Tethering of ASPP Proteins Facilitates PP-1c Catalysis

ASPP (apoptosis-stimulating proteins of p53) proteins bind PP-1c (protein phosphatase 1) and regulate p53 impacting cancer cell growth and apoptosis. Here we determine the crystal structure of the oncogenic ASPP protein, iASPP, bound to PP-1c. The structure reveals a 1:1 complex that relies on interactions of the iASPP SILK and RVxF motifs with PP-1c, plus interactions of the PP-1c PxxPxR motif with the iASPP SH3 domain. Small-angle X-ray scattering analyses suggest that the crystal structure undergoes slow interconversion with more extended conformations in solution. We show that iASPP, and the tumor suppressor ASPP2, enhance the catalytic activity of PP-1c against the small-molecule substrate, pNPP as well as p53. The combined results suggest that PxxPxR binding to iASPP SH3 domain is critical for complex formation, and that the modular ASPP-PP-1c interface provides dynamic flexibility that enables functional binding and dephosphorylation of p53 and other diverse protein substrates.

CHROMIXS: automatic and interactive analysis of chromatography-coupled small-angle X-ray scattering data

Summary

Size-exclusion chromatography (SEC) coupled to small-angle X-ray scattering (SAXS), also known as inline SEC-SAXS, is being increasingly used for the structural analysis of biological macromolecules, complexes and mixtures in solution. A single SEC-SAXS run generates thousands of individual SAXS profiles from the eluting solute and their analysis requires a correct identification of buffer and sample regions, a rather laborous task. We present CHROMIXS (as in CHROMatography Inline X-ray Scattering), a program for rapid reduction and analysis, both automatically and interactively, of SEC-SAXS data.

Availability and implementation

CHROMIXS is freely available to academic users as part of the ATSAS software suite (www.embl-hamburg.de/biosaxs/download.html).

Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor

Resistance to inhibitors of cholinesterase 8A (Ric8A) is an essential regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor and a chaperone. We report two crystal structures of Ric8A, one in the apo form and the other in complex with a tagged C-terminal fragment of Gα. These structures reveal two principal domains of Ric8A: an armadillo-fold core and a flexible C-terminal tail. Additionally, they show that the Gα C-terminus binds to a highly-conserved patch on the concave surface of the Ric8A armadillo-domain, with selectivity determinants residing in the Gα sequence. Biochemical analysis shows that the Ric8A C-terminal tail is critical for its stability and function. A model of the Ric8A/Gα complex derived from crosslinking mass spectrometry and molecular dynamics simulations suggests that the Ric8A C-terminal tail helps organize the GTP-binding site of Gα. This study lays the groundwork for understanding Ric8A function at the molecular level.

Ric8A regulates G protein α-subunits (Gα) by acting as a guanine nucleotide exchange factor (GEF) and a Gα chaperone. Here, the authors solve the crystal structures of free and Gα fragment bound Ric8A, and provide insights into the structural basis for Ric8A’s GEF and chaperone functions.

Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium

Dysfunction of human phenylalanine hydroxylase (hPAH, EC 1.14.16.1) is the primary cause of phenylketonuria, the most common inborn error of amino acid metabolism. The dynamic domain rearrangements of this multimeric protein have thwarted structural study of the full-length form for decades, until now. In this study, a tractable C29S variant of hPAH (C29S) yielded a 3.06 Å resolution crystal structure of the tetrameric resting-state conformation. We used size-exclusion chromatography in line with small-angle X-ray scattering (SEC-SAXS) to analyze the full-length hPAH solution structure both in the presence and absence of Phe, which serves as both substrate and allosteric activators. Allosteric Phe binding favors accumulation of an activated PAH tetramer conformation, which is biophysically distinct in solution. Protein characterization with enzyme kinetics and intrinsic fluorescence revealed that the C29S variant and hPAH are otherwise equivalent in their response to Phe, further supported by their behavior on various chromatography resins and by analytical ultracentrifugation. Modeling of resting-state and activated forms of C29S against SAXS data with available structural data created and evaluated several new models for the transition between the architecturally distinct conformations of PAH and highlighted unique intra- and inter-subunit interactions. Three best-fitting alternative models all placed the allosteric Phe-binding module 8-10 Å farther from the tetramer center than do all previous models. The structural insights into allosteric activation of hPAH reported here may help inform ongoing efforts to treat phenylketonuria with novel therapeutic approaches.

Convergent allostery in ribonucleotide reductase

Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.

Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides, which is an essential step in DNA synthesis. Here the authors use small-angle X-ray scattering, X-ray crystallography, and cryo-electron microscopy to capture active and inactive forms of the Bacillus subtilis RNR and provide mechanistic insights into a convergent form of allosteric regulation.

Cellulose ionic conductors with high differential thermal voltage for low-grade heat harvesting

Converting low-grade heat into useful electricity requires a technology that is efficient and cost effective. Here, we demonstrate a cellulosic membrane that relies on sub-nanoscale confinement of ions in oxidized and aligned cellulose molecular chains to enhance selective diffusion under a thermal gradient. After infiltrating electrolyte into the cellulosic membrane and applying an axial temperature gradient, the ionic conductor exhibits a thermal gradient ratio (analogous to the Seebeck coefficient in thermoelectrics) of 24 mV K^-1-more than twice the highest value reported until now. We attribute the enhanced thermally generated voltage to effective sodium ion insertion into the charged molecular chains of the cellulosic membrane, which consists of type II cellulose, while this process does not occur in natural wood or type I cellulose. With this material, we demonstrate a flexible and biocompatible heat-to-electricity conversion device via nanoscale engineering based on sustainable materials that can enable large-scale manufacture.

A flap motif in human serine hydroxymethyltransferase is important for structural stabilization, ligand binding, and control of product release

Human cytosolic serine hydroxymethyltransferase (hcSHMT) is a promising target for anticancer chemotherapy and contains a flexible "flap motif" whose function is yet unknown. Here, using size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and ligand-binding and enzyme-kinetic analyses, we studied the functional roles of the flap motif by comparing WT hcSHMT with a flap-deleted variant (hcSHMT/Δflap). We found that deletion of the flap results in a mixture of apo-dimers and holo-tetramers, whereas the WT was mostly in the tetrameric form. MD simulations indicated that the flap stabilizes structural compactness and thereby enhances oligomerization. The hcSHMT/Δflap variant exhibited different catalytic properties in (6S)-tetrahydrofolate (THF)-dependent reactions compared with the WT but had similar activity in THF-independent aldol cleavage of β-hydroxyamino acid. hcSHMT/Δflap was less sensitive to THF inhibition than the WT (K_i of 0.65 and 0.27 mm THF at pH 7.5, respectively), and the THF dissociation constant of the WT was also 3-fold lower than that of hcSHMT/Δflap, indicating that the flap is important for THF binding. hcSHMT/Δflap did not display the burst kinetics observed in the WT. These results indicate that, upon removal of the flap, product release is no longer the rate-limiting step, implying that the flap is important for controlling product release. The findings reported here improve our understanding of the functional roles of the flap motif in hcSHMT and provide fundamental insight into how a flexible loop can be involved in controlling the enzymatic reactions of hcSHMT and other enzymes.

Physical methods for studying flavoprotein photoreceptors

Molecular mechanisms of dark-to-light state transitions in flavoprotein photoreceptors have been the subject of intense investigation. Blue-light sensing flavoproteins fall into three general classes that share aspects of their activation processes: LOV domains, BLUF proteins, and cryptochromes. In all cases, light-induced changes in flavin redox, protonation, and bonding states result in hydrogen-bond and conformational rearrangements important for regulation of downstream targets. Physical characterization of these flavoprotein states can provide valuable insights into biological function, but clear conclusions are often challenging to draw owing to complexities of data collection and interpretation. In this chapter, we briefly review the three classes of flavoprotein photoreceptors and provide methods for their recombinant production, reconstitution with flavin cofactor, and characterization. We then relate best practices and special considerations for the application of several types of spectroscopies, redox potential measurements, and X-ray scattering experiments to photosensitive flavoproteins. The methods presented are generally accessible to most laboratories.

A Proteomic Screen of Neuronal Cell-Surface Molecules Reveals IgLONs as Structurally Conserved Interaction Modules at the Synapse

In the developing brain, cell-surface proteins play crucial roles, but their protein-protein interaction network remains largely unknown. A proteomic screen identified 200 interactions, 89 of which were not previously published. Among these interactions, we find that the IgLONs, a family of five cell-surface neuronal proteins implicated in various human disorders, interact as homo- and heterodimers. We reveal their interaction patterns and report the dimeric crystal structures of Neurotrimin (NTRI), IgLON5, and the neuronal growth regulator 1 (NEGR1)/IgLON5 complex. We show that IgLONs maintain an extended conformation and that their dimerization occurs through the first Ig domain of each monomer and is Ca²⁺ independent. Cell aggregation shows that NTRI and NEGR1 homo- and heterodimerize in trans. Taken together, we report 89 unpublished cell-surface ligand-receptor pairs and describe structural models of trans interactions of IgLONs, showing that their structures are compatible with a model of interaction across the synaptic cleft.

A simple adaptation to a protein crystallography station to facilitate difference X-ray scattering studies

The X-ray crystallography station I911-2 at MAXLab II (Lund, Sweden) has been adapted to enable difference small- and wide-angle X-ray scattering (SAXS/WAXS) data to be recorded. Modifications to the beamline included a customized flow cell, a motorized flow cell holder, a helium cone, a beam stop, a sample stage and a sample delivery system. This setup incorporated external devices such as infrared lasers, LEDs and reaction mixers to induce conformational changes in macromolecules. This platform was evaluated through proof-of-principle experiments capturing light-induced conformational changes in phytochromes. A difference WAXS signature of conformational changes in a plant aqua-porin was also demonstrated using caged calcium.

Structural Study of Agmatine Iminohydrolase From Medicago truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants

Plants are unique eukaryotes that can produce putrescine (PUT), a basic diamine, from arginine via a three-step pathway. This process starts with arginine decarboxylase that converts arginine to agmatine. Then, the consecutive action of two hydrolytic enzymes, agmatine iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase, ultimately produces PUT. An alternative route of PUT biosynthesis requires ornithine decarboxylase that catalyzes direct putrescine biosynthesis. However, some plant species lack this enzyme and rely only on agmatine pathway. The scope of this manuscript concerns the structural characterization of AIH from the model legume plant, Medicago truncatula. MtAIH is a homodimer built of two subunits with a characteristic propeller fold, where five αββαβ repeated units are arranged around the fivefold pseudosymmetry axis. Dimeric assembly of this plant AIH, formed by interactions of conserved structural elements from one repeat, is drastically different from that observed in dimeric bacterial AIHs. Additionally, the structural snapshot of MtAIH in complex with 6-aminohexanamide, the reaction product analog, presents the conformation of the enzyme during catalysis. Our structural results show that MtAIH undergoes significant structural rearrangements of the long loop, which closes a tunnel-shaped active site over the course of the catalytic event. This conformational change is also observed in AIH from Arabidopsis thaliana, indicating the importance of the closed conformation of the gate-keeping loop for the catalysis of plant AIHs.

Molecular architecture of the Jumonji C family histone demethylase KDM5B

The full length human histone 3 lysine 4 demethylase KDM5B (PLU-1/Jarid1B) has been studied using Hydrogen/Deuterium exchange mass spectrometry, homology modelling, sequence analysis, small angle X-ray scattering and electron microscopy. This first structure on an intact multi-domain Jumonji histone demethylase reveal that the so-called PLU region, in the central region of KDM5B, has a curved α-helical three-dimensional structure, that acts as a rigid linker between the catalytic core and a region comprising four α-helices, a loop comprising the PHD2 domain, two large intrinsically disordered loops and the PHD3 domain in close proximity. The dumbbell shaped and curved KDM5B architecture observed by electron microscopy is complementary to the nucleosome surface and has a striking overall similarity to that of the functionally related KDM1A/CoREST complex. This could suggest that there are similarities between the demethylation mechanisms employed by the two histone 3 lysine 4 demethylases at the molecular level.

Quantitative Measure of the Size Dispersity in Ultrasmall Fluorescent Organic-Inorganic Hybrid Core-Shell Silica Nanoparticles by Small-angle X-ray Scattering

Small-angle X-ray scattering (SAXS) was performed on dispersions of ultrasmall (d < 10 nm) fluorescent organic-inorganic hybrid core-shell silica nanoparticles synthesized in aqueous solutions (C' dots) by using an oscillating flow cell to overcome beam induced particle degradation. Form factor analysis and fitting was used to determine the size and size dispersity of the internal silica core containing covalently encapsulated fluorophores. The structure of the organic poly(ethylene glycol) (PEG) shell was modelled as a monodisperse corona containing concentrated and semi-dilute regimes of decaying density and as a simple polydisperse shell to determine the bounds of dispersity in the overall hybrid particle. C' dots containing single growth step silica cores have dispersities of 0.19-0.21; growth of additional silica shells onto the core produces a thin, dense silica layer, and increases the dispersity to 0.22-0.23. Comparison to FCS and DLS measures of size shows good agreement with SAXS measured and modelled sizes and size dispersities. Finally, comparison of a set of same sized and purified particles demonstrates that SAXS is sensitive to the skewness of the gel permeation chromatography elugrams of the original as-made materials. These and other insights provided by quantitative SAXS assessments may become useful for generation of robust nanoparticle design criteria necessary for their successful and safe use, for example in nanomedicine and oncology applications.

Molecular Architecture of the Inositol Phosphatase Siw14

Siw14 is a recently discovered inositol phosphatase implicated in suppressing prion propagation in Saccharomyces cerevisiae. In this paper, we used hybrid structural methods to decipher Siw14 molecular architecture. We found the protein exists in solution as an elongated monomer that is ∼140 Å in length, containing an acidic N-terminal domain and a basic C-terminal dual-specificity phosphatase (DSP) domain, structurally similar to the glycogen phosphatase laforin. The two domains are connected by a protease susceptible linker and do not interact in vitro. The crystal structure of Siw14-DSP reveals a highly basic phosphate-binding loop and an ∼10 Å deep substrate-binding crevice that evolved to dephosphorylate pyro-phosphate moieties. A pseudoatomic model of the full-length phosphatase generated from solution, crystallographic, biochemical, and modeling data sheds light on the interesting zwitterionic nature of Siw14, which we hypothesized may play a role in discriminating negatively charged inositol phosphates.

Spermidine Synthase (SPDS) Undergoes Concerted Structural Rearrangements Upon Ligand Binding - A Case Study of the Two SPDS Isoforms From Arabidopsis thaliana

Spermidine synthases (SPDSs) catalyze the production of the linear triamine, spermidine, from putrescine. They utilize decarboxylated S-adenosylmethionine (dc-SAM), a universal cofactor of aminopropyltransferases, as a donor of the aminopropyl moiety. In this work, we describe crystal structures of two SPDS isoforms from Arabidopsis thaliana (AtSPDS1 and AtSPDS2). AtSPDS1 and AtSPDS2 are dimeric enzymes that share the fold of the polyamine biosynthesis proteins. Subunits of both isoforms present the characteristic two-domain structure. Smaller, N-terminal domain is built of the two β-sheets, while the C-terminal domain has a Rossmann fold-like topology. The catalytic cleft composed of two main compartments, the dc-SAM binding site and the polyamine groove, is created independently in each AtSPDS subunits at the domain interface. We also provide the structural details about the dc-SAM binding mode and the inhibition of SPDS by a potent competitive inhibitor, cyclohexylamine (CHA). CHA occupies the polyamine binding site of AtSPDS where it is bound at the bottom of the active site with the amine group placed analogously to the substrate. The crystallographic snapshots show in detail the structural rearrangements of AtSPDS1 and AtSPDS2 that are required to stabilize ligands within the active site. The concerted movements are observed in both compartments of the catalytic cleft, where three major parts significantly change their conformation. These are (i) the neighborhood of the glycine-rich region where aminopropyl moiety of dc-SAM is bound, (ii) the very flexible gate region with helix η6, which interacts with both, the adenine moiety of dc-SAM and the bound polyamine or inhibitor, and (iii) the N-terminal β-hairpin, that limits the putrescine binding grove at the bottom of the catalytic site.

Solution Ensemble of the C-Terminal Domain from the Transcription Factor Pdx1 Resembles an Excluded Volume Polymer

The pancreatic and duodenal homeobox 1 (Pdx1) is an essential pancreatic transcription factor. The C-terminal intrinsically disordered domain of Pdx1 (Pdx1-C) has a heavily biased amino acid composition; most notably, 18 of 83 residues are proline, including a hexaproline cluster near the middle of the chain. For these reasons, Pdx1-C is an attractive target for structure characterization, given the availability of suitable methods. To determine the solution ensembles of disordered proteins, we have developed a suite of ¹³C direct-detect NMR experiments that provide high spectral quality, even in the presence of strong proline enrichment. Here, we have extended our suite of NMR experiments to include four new pulse programs designed to record backbone residual dipolar couplings in a ¹³C,¹⁵N-CON detection format. Using our NMR strategy, in combination with small-angle X-ray scattering measurements and Monte Carlo simulations, we have determined that Pdx1-C is extended in solution, with a radius of gyration and internal scaling similar to that of an excluded volume polymer, and a subtle tendency toward a collapsed structure to the N-terminal side of the hexaproline sequence. This structure leaves Pdx1-C exposed for interactions with trans-regulatory co-factors that contribute with Pdx1 to transcription control in the cell.

SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale

Knowledge of molecular weight, oligomeric states, and quaternary arrangements of proteins in solution is fundamental for understanding their molecular functions and activities. We describe here a program SAXSMoW 2.0 for robust and quick determination of molecular weight and oligomeric state of proteins in dilute solution, starting from a single experimental small-angle scattering intensity curve, I(q), measured on a relative scale. The first version of this calculator has been widely used during the last decade and applied to analyze experimental SAXS data of many proteins and protein complexes. SAXSMoW 2.0 exhibits new features which allow for the direct input of experimental intensity curves and also automatic modes for quick determinations of the radius of gyration, volume, and molecular weight. The new program was extensively tested by applying it to many experimental SAXS curves downloaded from the open databases, corresponding to proteins with different shapes and molecular weights ranging from ~10 kDa up to about ~500 kDa and different shapes from globular to elongated. These tests reveal that the use of SAXSMoW 2.0 allows for determinations of molecular weights of proteins in dilute solution with a median discrepancy of about 12% for globular proteins. In case of elongated molecules, discrepancy value can be significantly higher. Our tests show discrepancies of approximately 21% for the proteins with molecular shape aspect ratios up to 18.

Antibacterial isoamphipathic oligomers highlight the importance of multimeric lipid aggregation for antibacterial potency

Cationic charge and hydrophobicity have long been understood to drive the potency and selectivity of antimicrobial peptides (AMPs). However, these properties alone struggle to guide broad success in vivo, where AMPs must differentiate bacterial and mammalian cells, while avoiding complex barriers. New parameters describing the biophysical processes of membrane disruption could provide new opportunities for antimicrobial optimization. In this work, we utilize oligothioetheramides (oligoTEAs) to explore the membrane-targeting mechanism of oligomers, which have the same cationic charge and hydrophobicity, yet show a unique ~ 10-fold difference in antibacterial potency. Solution-phase characterization reveals little difference in structure and dynamics. However, fluorescence microscopy of oligomer-treated Staphylococcus aureus mimetic membranes shows multimeric lipid aggregation that correlates with biological activity and helps establish a framework for the kinetic mechanism of action. Surface plasmon resonance supports the kinetic framework and supports lipid aggregation as a driver of antimicrobial function.

Joseph Brown et al. use oligothioetheramides (oligo TEAs) to show that multimeric lipid aggregation in Staphylococcus aureus mimetic membranes correlates with the biological activity of oligoTEAs. These results may explain why antimicrobial peptides with identical cationic charge and hydrophobicity show different biological activity.

Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure

Folding of an RNA from secondary to tertiary structure often depends on divalent ions for efficient electrostatic charge screening (nonspecific association) or binding (specific association). To measure how different divalent cations modify folding kinetics of the 60 nucleotide Ecoli rRNA GTPase center, we combined stopped-flow fluorescence in the presence of Mg²⁺, Ca²⁺, or Sr²⁺ together with time-resolved small angle X-ray scattering (SAXS) in the presence of Mg²⁺ to observe the folding process. Immediately upon addition of each divalent ion, the RNA undergoes a transition from an extended state with secondary structure to a more compact structure. Subsequently, specific divalent ions modulate populations of intermediates in conformational ensembles along the folding pathway with transition times longer than 10 msec. Rate constants for the five folding transitions act on timescales from submillisecond to tens of seconds. The sensitivity of RNA tertiary structure to divalent cation identity affects all but the fastest events in RNA folding, and allowed us to identify those states that prefer Mg²⁺ The GTPase center RNA appears to have optimized its folding trajectory to specifically utilize this most abundant intracellular divalent ion.

Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument

Coupling of size-exclusion chromatography with biological solution small-angle X-ray scattering (SEC-SAXS) on dedicated synchrotron beamlines enables structural analysis of challenging samples such as labile proteins and low-affinity complexes. For this reason, the approach has gained increased popularity during the past decade. Transportation of perishable samples to synchrotrons might, however, compromise the experiments, and the limited availability of synchrotron beamtime renders iterative sample optimization tedious and lengthy. Here, the successful setup of laboratory-based SEC-SAXS is described in a proof-of-concept study. It is demonstrated that sufficient quality data can be obtained on a laboratory instrument with small sample consumption, comparable to typical synchrotron SEC-SAXS demands. UV/vis measurements directly on the SAXS exposure cell ensure accurate concentration determination, crucial for direct molecular weight determination from the scattering data. The absence of radiation damage implies that the sample can be fractionated and subjected to complementary analysis available at the home institution after SEC-SAXS. Laboratory-based SEC-SAXS opens the field for analysis of biological samples at the home institution, thus increasing productivity of biostructural research. It may further ensure that synchrotron beamtime is used primarily for the most suitable and optimized samples.

Introducing SEC–SANS for studies of complex self-organized biological systems

Small-angle neutron scattering (SANS) is maturing as a method for studying complex biological structures. Owing to the intrinsic ability of the technique to discern between 1H- and 2H-labelled particles, it is especially useful for contrast-variation studies of biological systems containing multiple components. SANS is complementary to small-angle X-ray scattering (SAXS), in which similar contrast variation is not easily performed but in which data with superior counting statistics are more easily obtained. Obtaining small-angle scattering (SAS) data on monodisperse complex biological structures is often challenging owing to sample degradation and/or aggregation. This problem is enhanced in the D2O-based buffers that are typically used in SANS. In SAXS, such problems are solved using an online size-exclusion chromatography (SEC) setup. In the present work, the feasibility of SEC–SANS was investigated using a series of complex and difficult samples of membrane proteins embedded in nanodisc particles that consist of both phospholipid and protein components. It is demonstrated that SEC–SANS provides data of sufficient signal-to-noise ratio for these systems, while at the same time circumventing aggregation. By combining SEC–SANS and SEC–SAXS data, an optimized basis for refining structural models of the investigated structures is obtained.

Upgraded SSRF BL19U2 beamline for small-angle X-ray scattering of biological macromolecules in solution

The biological small-angle X-ray scattering (BioSAXS) beamline (BL19U2) at the Shanghai Synchrotron Radiation Facility, China, is dedicated exclusively to small-angle scattering experiments for biological macromolecules in solution. With recent advances in data-analysis algorithms and X-ray detectors, SAXS becomes an ideal complementary technique to other structural and biophysical methods, but it can also be applied alone to obtain important structural information. Owing to the increasing interest in solution scattering studies from the biological community, the workload on BL19U2 has steadily risen. A major upgrade of BL19U2 was performed to improve the beamline data quality, to enrich the possible sample environments and to provide a user-friendly interface. These upgrades involved the major components of BL19U2, including the optical system (slits, beamstop), the electronics, the control and acquisition software, and the sample environments, which resulted in improvements to the collected angular range in BL19U2. These upgrades have significantly broadened the scope of macromolecule size (from kilodaltons to gigadaltons) analysed at the beamline. The dedicated BL19U2 BioSAXS beamline now offers fully automated data-collection and remote-control possibilities. These developments have paved the way for high-throughput studies that generate significant quantities of structure information over a short period of time.

Direct observation of conformational dynamics of the PH domain in phospholipases Cϵ and β may contribute to subfamily-specific roles in regulation

Phospholipase C (PLC) enzymes produce second messengers that increase the intracellular Ca2+ concentration and activate protein kinase C (PKC). These enzymes also share a highly conserved arrangement of core domains. However, the contributions of the individual domains to regulation are poorly understood, particularly in isoforms lacking high-resolution information, such as PLCϵ. Here, we used small-angle X-ray scattering (SAXS), EM, and functional assays to gain insights into the molecular architecture of PLCϵ, revealing that its PH domain is conformationally dynamic and essential for activity. We further demonstrate that the PH domain of PLCβ exhibits similar dynamics in solution that are substantially different from its conformation observed in multiple previously reported crystal structures. We propose that this conformational heterogeneity contributes to subfamily-specific differences in activity and regulation by extracellular signals.

Structure-guided disruption of the pseudopilus tip complex inhibits the Type II secretion in Pseudomonas aeruginosa

Pseudomonas aeruginosa utilizes the Type II secretion system (T2SS) to translocate a wide range of large, structured protein virulence factors through the periplasm to the extracellular environment for infection. In the T2SS, five pseudopilins assemble into the pseudopilus that acts as a piston to extrude exoproteins out of cells. Through structure determination of the pseudopilin complexes of XcpVWX and XcpVW and function analysis, we have confirmed that two minor pseudopilins, XcpV and XcpW, constitute a core complex indispensable to the pseudopilus tip. The absence of either XcpV or -W resulted in the non-functional T2SS. Our small-angle X-ray scattering experiment for the first time revealed the architecture of the entire pseudopilus tip and established the working model. Based on the interaction interface of complexes, we have developed inhibitory peptides. The structure-based peptides not only disrupted of the XcpVW core complex and the entire pseudopilus tip in vitro but also inhibited the T2SS in vivo. More importantly, these peptides effectively reduced the virulence of P. aeruginosa towards Caenorhabditis elegans.

The Type II secretion system has been characterized as an important virulence factor translocation machine that secrets various toxic proteins from the periplasm into the extracellular milieu used by a wide spectrum of Gram-negative bacteria. Through the characterization of the structure of the pseudopilus tip complex by protein crystallography and small-angle X-ray scattering, we have identified a critical interaction interface in the core binary complex formed by two minor pseudopilins, XcpV and–W, in Pseudomonas aeruginosa. Based on the interaction interface, two inhibitory peptides were developed, which showed potency of disrupting the entire pseudopilus tip complex and further inhibited the Type II secretion system. When applied to Caenorhabditis elegans, these peptides prevent the killing of worms by the P. aeruginosa. Our work has represented the first successful research on the inhibition of the Type II secretion system based on the structure of the pseudopilus tip complex.

How the Conformations of an Internal Junction Contribute to Fold an RNA Domain

Like proteins, some RNAs fold to compact structures. We can model functional RNAs as a series of short, rigid, base-paired elements, connected by non-base-paired nucleotides that serve as junctions. These connecting regions bend and twist, facilitating the formation of tertiary contacts that stabilize compact states. Here, we explore the roles of salt and junction sequence in determining the structures of a ubiquitous connector: an asymmetric internal loop. We focus on the J5/5a junction from the widely studied P4-P6 domain of the Tetrahymena ribozyme. Following the addition of magnesium ions to fold P4-P6, this junction bends dramatically, bringing the two halves of the RNA domain together for tertiary contact engagement. Using single-molecule fluorescence resonance energy transfer (smFRET), we examine the role of sequence and salt on model RNA constructs that contain these junction regions. We explore the wild-type J5/5a junction as well as two sequence variants. These junctions display distinct, salt-dependent conformations. Small-angle X-ray scattering (SAXS) measurements verify that these effects persist in the full-length P4-P6 domain. These measurements underscore the importance of junction sequence and interactions with ions in facilitating RNA folding.

The dynamic nature of the conserved tegument protein UL37 of herpesviruses

In all herpesviruses, the space between the capsid shell and the lipid envelope is occupied by the unique tegument layer composed of proteins that, in addition to structural roles, play many other roles in the viral replication. UL37 is a highly conserved tegument protein that has activities ranging from virion morphogenesis to directional capsid trafficking to manipulation of the host innate immune response and binds multiple partners. The N-terminal half of UL37 (UL37N) has a compact bean-shaped α-helical structure that contains a surface region essential for neuroinvasion. However, no biochemical or structural information is currently available for the C-terminal half of UL37 (UL37C) that mediates most of its interactions with multiple binding partners. Here, we show that the C-terminal half of UL37 from pseudorabies virus UL37C is a conformationally flexible monomer composed of an elongated folded core and an unstructured C-terminal tail. This elongated structure, along with that of its binding partner UL36, explains the nature of filamentous tegument structures bridging the capsid and the envelope. We propose that the dynamic nature of UL37 underlies its ability to perform diverse roles during viral replication.