Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains.

Dynamic ADP-ribosylation signaling is a crucial pathway that controls fundamental cellular processes, in particular, the response to cellular stresses such as DNA damage, reactive oxygen species, and infection. In some pathogenic microbes, the response to oxidative stress is controlled by a SirTM/zinc-containing macrodomain (Zn-Macro) pair responsible for establishment and removal of the modification, respectively. Targeting this defence mechanism against the host's innate immune response may lead to novel approaches to support the fight against emerging antimicrobial resistance. Earlier studies suggested that Zn-Macros play a key role in the activation of this defence. Therefore, we used phylogenetic, biochemical, and structural approaches to elucidate the functional properties of these enzymes. Using the substrate mimetic asparagine-ADP-ribose as well as the ADP-ribose product, we characterize the catalytic role of the zinc ion in the removal of the ADP-ribosyl modification. Furthermore, we determined structural properties that contribute to substrate selectivity within the different Zn-Macro branches. Together, our data not only give new insights into the Zn-Macro family but also highlight their distinct features that may be exploited for the development of future therapies.

Light-Driven Hexagonal-to-Cubic Phase Switching in Arylazopyrazole Lyotropic Liquid Crystals.

Photoinduced manipulation of the nanoscale molecular structure and organization of soft materials can drive changes in the macroscale properties. Here we demonstrate the first example of a light-induced one- to three-dimensional mesophase transition at room temperature in lyotropic liquid crystals constructed from arylazopyrazole photosurfactants in water. We exploit this characteristic to use light to selectively control the rate of gas (CO2) diffusion across a prototype lyotropic liquid crystal membrane. Such control of phase organization, dimensionality, and permeability unlocks the potential for stimuli-responsive analogues in technologies for controlled delivery.

Developing an in situ LED irradiation system for small-angle X-ray scattering at B21, Diamond Light Source.

Beamline B21 at the Diamond Light Source synchrotron in the UK is a small-angle X-ray scattering (SAXS) beamline that specializes in high-throughput measurements via automated sample delivery systems. A system has been developed whereby a sample can be illuminated by a focused beam of light coincident with the X-ray beam. The system is compatible with the highly automated sample delivery system at the beamline and allows a beamline user to select a light source from a broad range of wavelengths across the UV and visible spectrum and to control the timing and duration of the light pulse with respect to the X-ray exposure of the SAXS measurement. The intensity of the light source has been characterized across the wavelength range enabling experiments where a quantitative measure of dose is important. Finally, the utility of the system is demonstrated via measurement of several light-responsive samples.

Understanding X-ray-induced isomerisation in photoswitchable surfactant assemblies.

Dynamic, responsive materials can be built using photosurfactants (PS) that self-assemble into ordered nanostructures, such as micelles or liquid crystals. These PS contain photoswitchable groups, such as azobenzene (Azo) or, more recently, arylazopyrazoles (AAPs), which change shape and polarity on photoisomerisation between the E and Z states, thus changing the self-assembled structure. Small-angle X-ray scattering (SAXS) is a powerful technique to probe the morphology of PS and can be used to measure the mechanisms of structural changes using in-situ light irradiation with rapid, time-resolved data collection. However, X-ray irradiation has been shown previously to induce Z-to-E isomerisation of Azo-PS, which can lead to inaccuracies in the measured photostationary state. Here, we investigate the effect of light and X-ray irradiation on micelles formed from two different PS, containing either an Azo or AAP photoswitch using SAXS with in-situ light irradiation. The effect of X-ray irradiation on the Z isomer is shown to depend on the photoswitch, solvent, concentration and morphology. We use this to create guidelines for future X-ray experiments using photoswitchable molecules, which can aid more accurate understanding of these materials for application in solar energy storage, catalysis or controlled drug delivery.

A High-Throughput Small-Angle X-ray Scattering Assay to Determine the Conformational Change of Plasminogen.

Plasminogen (Plg) is the inactive form of plasmin (Plm) that exists in two major glycoforms, referred to as glycoforms I and II (GI and GII). In the circulation, Plg assumes an activation-resistant "closed" conformation via interdomain interactions and is mediated by the lysine binding site (LBS) on the kringle (KR) domains. These inter-domain interactions can be readily disrupted when Plg binds to lysine/arginine residues on protein targets or free L-lysine and analogues. This causes Plg to convert into an "open" form, which is crucial for activation by host activators. In this study, we investigated how various ligands affect the kinetics of Plg conformational change using small-angle X-ray scattering (SAXS). We began by examining the open and closed conformations of Plg using size-exclusion chromatography (SEC) coupled with SAXS. Next, we developed a high-throughput (HTP) 96-well SAXS assay to study the conformational change of Plg. This method enables us to determine the Kopen value, which is used to directly compare the effect of different ligands on Plg conformation. Based on our analysis using Plg GII, we have found that the Kopen of ε-aminocaproic acid (EACA) is approximately three times greater than that of tranexamic acid (TXA), which is widely recognized as a highly effective ligand. We demonstrated further that Plg undergoes a conformational change when it binds to the C-terminal peptides of the inhibitor α2-antiplasmin (α2AP) and receptor Plg-RKT. Our findings suggest that in addition to the C-terminal lysine, internal lysine(s) are also necessary for the formation of open Plg. Finally, we compared the conformational changes of Plg GI and GII directly and found that the closed form of GI, which has an N-linked glycosylation, is less stable. To summarize, we have successfully determined the response of Plg to various ligand/receptor peptides by directly measuring the kinetics of its conformational changes.

Light-Responsive Molecular Release from Cubosomes Using Swell-Squeeze Lattice Control.

Stimuli-responsive materials are crucial to advance controlled delivery systems for drugs and catalysts. Lyotropic liquid crystals (LLCs) have well-defined internal structures suitable to entrap small molecules and can be broken up into low-viscosity dispersions, aiding their application as delivery systems. In this work, we demonstrate the first example of light-responsive cubic LLC dispersions, or cubosomes, using photoswitchable amphiphiles to enable external control over the LLC structure and subsequent on-demand release of entrapped guest molecules. Azobenzene photosurfactants (AzoPS), containing a neutral tetraethylene glycol head group and azobenzene-alkyl tail, are combined (from 10-30 wt %) into monoolein-water systems to create LLC phases. Homogenization of the bulk LLC forms dispersions of particles, ∼200 nm in diameter with internal bicontinuous primitive cubic phases, as seen using small-angle X-ray scattering and cryo-transmission electron microscopy. Notably, increasing the AzoPS concentration leads to swelling of the cubic lattice, offering a method to tune the internal nanoscale structure. Upon UV irradiation, AzoPS within the cubosomes isomerizes within seconds, which in turn leads to squeezing of the cubic lattice and a decrease in the lattice parameter. This squeeze mechanism was successfully harnessed to enable phototriggerable release of trapped Nile Red guest molecules from the cubosome structure in minutes. The ability to control the internal structure of LLC dispersions using light, and the dramatic effect this has on the retention of entrapped molecules, suggests that these systems may have huge potential for the next-generation of nanodelivery.

The Role of Lipid Chains as Determinants of Membrane Stability in the Presence of Styrene.

Biofermentative production of styrene from renewable carbon sources is crucially dependent on strain tolerance and viability at elevated styrene concentrations. Solvent-driven collapse of bacterial plasma membranes limits yields and is technologically restrictive. Styrene is a hydrophobic solvent that readily partitions into the membrane interior and alters membrane-chain order and packing. We investigate styrene incorporation into model membranes and the role lipid chains play as determinants of membrane stability in the presence of styrene. MD simulations reveal styrene phase separation followed by irreversible segregation into the membrane interior. Solid state NMR shows committed partitioning of styrene into the membrane interior with persistence of the bilayer phase up to 67 mol % styrene. Saturated-chain lipid membranes were able to retain integrity even at 80 mol % styrene, whereas in unsaturated lipid membranes, we observe the onset of a non-bilayer phase of small lipid aggregates in coexistence with styrene-saturated membranes. Shorter-chain saturated lipid membranes were seen to tolerate styrene better, which is consistent with observed chain length reduction in bacteria grown in the presence of small molecule solvents. Unsaturation at mid-chain position appears to reduce the membrane tolerance to styrene and conversion from cis- to trans-chain unsaturation does not alter membrane phase stability but the lipid order in trans-chains is less affected than cis.

Design of a multipurpose sample cell holder for the Diamond Light Source high-throughput SAXS beamline B21.

The design of a multipurpose sample cell holder for the high-throughput (HT) beamline B21 is presented. The device is compatible with the robot bioSAXS sample changer currently installed on BM29, ESRF, and P12 Petra IV synchrotrons. This work presents an approach that uses 3D-printing to make hardware alterations which can expand the versatility of HT beamlines at low cost.

Palmitic acid sophorolipid biosurfactant: from self-assembled fibrillar network (SAFiN) to hydrogels with fast recovery.

Nanofibres are an interesting phase into which amphiphilic molecules can self-assemble. Described for a large number of synthetic lipids, they were seldom reported for natural lipids like microbial amphiphiles, known as biosurfactants. In this work, we show that the palmitic acid congener of sophorolipids (SLC16:0), one of the most studied families of biosurfactants, spontaneously forms a self-assembled fibre network (SAFiN) at pH below 6 through a pH jump process. pH-resolved in situ small-angle X-ray scattering (SAXS) shows a continuous micelle-to-fibre transition, characterized by an enhanced core-shell contrast between pH 9 and pH 7 and micellar fusion into a flat membrane between pH 7 and pH 6, approximately. Below pH 6, homogeneous, infinitely long nanofibres form by peeling off the membranes. Eventually, the nanofibre network spontaneously forms a thixotropic hydrogel with fast recovery rates after applying an oscillatory strain amplitude out of the linear viscoelastic regime: after being submitted to strain amplitudes during 5 min, the hydrogel recovers about 80% and 100% of its initial elastic modulus after, respectively, 20 s and 10 min. Finally, the strength of the hydrogel depends on the medium's final pH, with an elastic modulus fivefold higher at pH 3 than at pH 6. This article is part of the theme issue 'Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 1)'.

Beamline B21: high-throughput small-angle X-ray scattering at Diamond Light Source.

B21 is a small-angle X-ray scattering (SAXS) beamline with a bending magnet source in the 3 GeV storage ring at the Diamond Light Source Ltd synchrotron in the UK. The beamline utilizes a double multi-layer monochromator and a toroidal focusing optic to deliver 2 × 1012 photons per second to a 34 × 40 µm (FWHM) focal spot at the in-vacuum Eiger 4M (Dectris) detector. A high-performance liquid chromatography system and a liquid-handling robot make it possible to load solution samples into a temperature-controlled in-vacuum sample cell with a high level of automation. Alternatively, a range of viscous or solid materials may be loaded manually using a range of custom sample cells. A default scattering vector range from 0.0026 to 0.34 Å-1 and low instrument background make B21 convenient for measuring a wide range of biological macromolecules. The beamline has run a full user programme since 2013.

Stimuli-Induced Nonequilibrium Phase Transitions in Polyelectrolyte-Surfactant Complex Coacervates.

Polyelectrolyte-surfactant complexes (PESCs) are important soft colloids with applications in the fields of personal care, cosmetics, pharmaceutics, and much more. If their phase diagrams have long been studied under pseudoequilibrium conditions, and often inside the micellar or vesicular regions, understanding the effect of nonequilibrium conditions, applied at phase boundaries, on the structure of PESCs generates an increasing interest. In this work we cross the micelle-vesicle and micelle-fiber phase boundaries in an isocompositional surfactant-polyelectrolyte aqueous system through a continuous and rapid variation of pH. We employ two microbial glycolipid biosurfactants in the presence of polyamines, both systems being characterized by their responsiveness to pH. We show that complex coacervates (Co) are always formed in the micellar region of both glycolipids' phase diagram and that their phase behavior drives the PESC stability and structure. However, for glycolipid forming single-wall vesicles, we observe an isostructural and isodimensional transition between complex coacervates and a multilamellar walls vesicle (MLWV) phase. For the fiber-forming glycolipid, on the contrary, the complex coacervate disassembles into free polyelectrolyte coexisting with the equilibrium fiber phase. Last but not least, this work also demonstrates the use of microbial glycolipid biosurfactants in the development of sustainable PESCs.

Isotopic Control over Self-Assembly in Supramolecular Gels.

It is common to switch between H2O and D2O when examining peptide-based systems, with the assumption being that there are no effects from this change. Here, we describe the effect of changing from H2O to D2O in a number of low-molecular-weight dipeptide-based gels. Gels are formed by decreasing the pH. In most cases, there is little difference in the structures formed at high pH, but this is not universally true. On lowering the pH, the kinetics of gelation are affected and, in some cases, the structures underpinning the gel network are different. Where there are differences in the self-assembled structures, the resulting gel properties are different. We, therefore, show that isotopic control over gel properties is possible.

Light-responsive self-assembly of a cationic azobenzene surfactant at high concentration.

The formation of high-concentration mesophases by a cationic azobenzene photosurfactant is described for the first time. Using a combination of polarised optical microscopy and small-angle X-ray scattering, optically anisotropic, self-assembled structures with long-range order are reported. The mesophases are disrupted or lost upon UV irradiation.

Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase.

Thioesterases catalyze the cleavage of thioester bonds within many activated fatty acids and acyl-CoA substrates. They are expressed ubiquitously in both prokaryotes and eukaryotes and are subdivided into 25 thioesterase families according to their catalytic active site, protein oligomerization, and substrate specificity. Although many of these enzyme families are well-characterized in terms of function and substrate specificity, regulation across most thioesterase families is poorly understood. Here, we characterized a TE6 thioesterase from the bacterium Neisseria meningitidis Structural analysis with X-ray crystallographic diffraction data to 2.0-Å revealed that each protein subunit harbors a hot dog-fold and that the TE6 enzyme forms a hexamer with D3 symmetry. An assessment of thioesterase activity against a range of acyl-CoA substrates revealed the greatest activity against acetyl-CoA, and structure-guided mutagenesis of putative active site residues identified Asn24 and Asp39 as being essential for activity. Our structural analysis revealed that six GDP nucleotides bound the enzyme in close proximity to an intersubunit disulfide bond interactions that covalently link thioesterase domains in a double hot dog dimer. Structure-guided mutagenesis of residues within the GDP-binding pocket identified Arg93 as playing a key role in the nucleotide interaction and revealed that GDP is required for activity. All mutations were confirmed to be specific and not to have resulted from structural perturbations by X-ray crystallography. This is the first report of a bacterial GDP-regulated thioesterase and of covalent linkage of thioesterase domains through a disulfide bond, revealing structural similarities with ADP regulation in the human ACOT12 thioesterase.

MX2: a high-flux undulator microfocus beamline serving both the chemical and macromolecular crystallography communities at the Australian Synchrotron.

MX2 is an in-vacuum undulator-based crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range 4.8-21 keV to a focal spot of 22 × 12 µm FWHM (H × V). At 13 keV the flux at the sample is 3.4 × 1012 photons s-1. The beamline endstation allows robotic handling of cryogenic samples via an updated SSRL SAM robot. This beamline is ideal for weakly diffracting hard-to-crystallize proteins, virus particles, protein assemblies and nucleic acids as well as smaller molecules such as inorganic catalysts and organic drug molecules. The beamline is now mature and has enjoyed a full user program for the last nine years. This paper describes the beamline status, plans for its future and some recent scientific highlights.

Structural and Functional Characterization of the PaaI Thioesterase from Streptococcus pneumoniae Reveals a Dual Specificity for Phenylacetyl-CoA and Medium-chain Fatty Acyl-CoAs and a Novel CoA-induced Fit Mechanism.

PaaI thioesterases are members of the TE13 thioesterase family that catalyze the hydrolysis of thioester bonds between coenzyme A and phenylacetyl-CoA. In this study we characterize the PaaI thioesterase from Streptococcus pneumoniae (SpPaaI), including structural analysis based on crystal diffraction data to 1.8-Å resolution, to reveal two double hotdog domains arranged in a back to back configuration. Consistent with the crystallography data, both size exclusion chromatography and small angle x-ray scattering data support a tetrameric arrangement of thioesterase domains in solution. Assessment of SpPaaI activity against a range of acyl-CoA substrates showed activity for both phenylacetyl-CoA and medium-chain fatty-acyl CoA substrates. Mutagenesis of putative active site residues reveals Asn(37), Asp(52), and Thr(68) are important for catalysis, and size exclusion chromatography analysis and x-ray crystallography confirm that these mutants retain the same tertiary and quaternary structures, establishing that the reduced activity is not a result of structural perturbations. Interestingly, the structure of SpPaaI in the presence of CoA provides a structural basis for the observed substrate specificity, accommodating a 10-carbon fatty acid chain, and a large conformational change of up to 38 Å in the N terminus, and a loop region involving Tyr(38)-Tyr(39). This is the first time PaaI thioesterases have displayed a dual specificity for medium-chain acyl-CoAs substrates and phenylacetyl-CoA substrates, and we provide a structural basis for this specificity, highlighting a novel induced fit mechanism that is likely to be conserved within members of this enzyme family.

The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA.

The pentatricopeptide repeat (PPR) protein family is a large family of RNA-binding proteins that is characterized by tandem arrays of a degenerate 35-amino-acid motif which form an α-solenoid structure. PPR proteins influence the editing, splicing, translation and stability of specific RNAs in mitochondria and chloroplasts ZEA MAYS: PPR10 is amongst the best studied PPR proteins, where sequence-specific binding to two RNA transcripts, ATPH: and PSAJ, HAS BEEN DEMONSTRATED TO FOLLOW: a recognition code where the identity of two amino acids per repeat determines the base-specificity. A recently solved ZmPPR10: PSAJ: complex crystal structure suggested a homodimeric complex with considerably fewer sequence-specific protein-RNA contacts than inferred PREVIOUSLY: Here we describe the solution structure of the ZmPPR10: ATPH: complex using size-exclusion chromatography-coupled synchrotron small-angle X-ray scattering (SEC-SY-SAXS). Our results support prior evidence that PPR10 binds RNA as a monomer, and that it does so in a manner that is commensurate with a canonical and predictable RNA-binding mode across much of the RNA-protein interface.

Cofactor-dependent conformational heterogeneity of GAD65 and its role in autoimmunity and neurotransmitter homeostasis.

The human neuroendocrine enzyme glutamate decarboxylase (GAD) catalyses the synthesis of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) using pyridoxal 5'-phosphate as a cofactor. GAD exists as two isoforms named according to their respective molecular weights: GAD65 and GAD67. Although cytosolic GAD67 is typically saturated with the cofactor (holoGAD67) and constitutively active to produce basal levels of GABA, the membrane-associated GAD65 exists mainly as the inactive apo form. GAD65, but not GAD67, is a prevalent autoantigen, with autoantibodies to GAD65 being detected at high frequency in patients with autoimmune (type 1) diabetes and certain other autoimmune disorders. The significance of GAD65 autoinactivation into the apo form for regulation of neurotransmitter levels and autoantibody reactivity is not understood. We have used computational and experimental approaches to decipher the nature of the holo → apo conversion in GAD65 and thus, its mechanism of autoinactivation. Molecular dynamics simulations of GAD65 reveal coupling between the C-terminal domain, catalytic loop, and pyridoxal 5'-phosphate-binding domain that drives structural rearrangement, dimer opening, and autoinactivation, consistent with limited proteolysis fragmentation patterns. Together with small-angle X-ray scattering and fluorescence spectroscopy data, our findings are consistent with apoGAD65 existing as an ensemble of conformations. Antibody-binding kinetics suggest a mechanism of mutually induced conformational changes, implicating the flexibility of apoGAD65 in its autoantigenicity. Although conformational diversity may provide a mechanism for cofactor-controlled regulation of neurotransmitter biosynthesis, it may also come at a cost of insufficient development of immune self-tolerance that favors the production of GAD65 autoantibodies.

Combined pressure and temperature denaturation of ribonuclease A produces alternate denatured states.

Protein folding, unfolding and misfolding have become critically important to a range of health and industry applications. Increasing high temperature and high pressure are used to control and speed up reactions. A number of studies have indicated that these parameters can have a large effecton protein structure and function. Here we describe the additive effects of these parameters on the small angle scattering behaviour of ribonuclease A. We find that alternate unfolded structures can be obtained with combined high pressure and temperature treatment of the protein.

G-quadruplexes regulate Epstein-Barr virus-encoded nuclear antigen 1 mRNA translation.

Viruses that establish latent infections have evolved unique mechanisms to avoid host immune recognition. Maintenance proteins of these viruses regulate their synthesis to levels sufficient for maintaining persistent infection but below threshold levels for host immune detection. The mechanisms governing this finely tuned regulation of viral latency are unknown. Here we show that mRNAs encoding gammaherpesviral maintenance proteins contain within their open reading frames clusters of unusual structural elements, G-quadruplexes, which are responsible for the cis-acting regulation of viral mRNA translation. By studying the Epstein-Barr virus-encoded nuclear antigen 1 (EBNA1) mRNA, we demonstrate that destabilization of G-quadruplexes using antisense oligonucleotides increases EBNA1 mRNA translation. In contrast, pretreatment with a G-quadruplex-stabilizing small molecule, pyridostatin, decreases EBNA1 synthesis, highlighting the importance of G-quadruplexes within virally encoded transcripts as unique regulatory signals for translational control and immune evasion. Furthermore, these findings suggest alternative therapeutic strategies focused on targeting RNA structure within viral ORFs.