Uridine as a new scavenger for synchrotron-based structural biology techniques.

Macromolecular crystallography (MX) and small-angle X-ray scattering (SAXS) studies on proteins at synchrotron light sources are commonly limited by the structural damage produced by the intense X-ray beam. Several effects, such as aggregation in protein solutions and global and site-specific damage in crystals, reduce the data quality or even introduce artefacts that can result in a biologically misguiding structure. One strategy to reduce these negative effects is the inclusion of an additive in the buffer solution to act as a free radical scavenger. Here the properties of uridine as a scavenger for both SAXS and MX experiments on lysozyme at room temperature are examined. In MX experiments, upon addition of uridine at 1 M, the critical dose D1/2 is increased by a factor of ∼1.7, a value similar to that obtained in the presence of the most commonly used scavengers such as ascorbate and sodium nitrate. Other figures of merit to assess radiation damage show a similar trend. In SAXS experiments, the scavenging effect of 40 mM uridine is similar to that of 5% v/v glycerol, and greater than 2 mM DTT and 1 mM ascorbic acid. In all cases, the protective effect of uridine is proportional to its concentration.

Continuous One-Step Synthesis of Porous M-XF6 -Based Metal-Organic and Hydrogen-Bonded Frameworks.

Metal-organic frameworks (MOFs) built up from connecting M-XF6 pillars through N-donor ligands are among the most attractive adsorbents and separating agents for CO2 and hydrocarbons today. The continuous, one-step spray-drying synthesis of several members of this isoreticular MOF family varying the anionic pillar (XF6 =[SiF6 ]2- and [TiF6 ]2- ), the N-donor organic ligand (pyrazine and 4,4'-bipyridine) and the metal ion (M=Co, Cu and Zn) is demonstrated here. This synthetic method allows them to be obtained in the form of spherical superstructures assembled from nanosized crystals. As confirmed by CO2 and N2 sorption studies, most of the M-XF6 -based MOFs synthesised through spray-drying can be considered "ready-to-use" sorbents as they do not need additional purification and time consuming solvent exchange steps to show comparable porosity and sorption properties with the bulk/single-crystal analogues. Stability tests of nanosized M-SiF6 -based MOFs confirm their low stability in most solvents, including water and DMF, highlighting the importance of protecting them once synthesised. Finally, for the first time it was shown that the spray-drying method can also be used to assemble hydrogen-bonded open networks, as evidenced by the synthesis of MPM-1-TIFSIX.

Narrowing the Zero-Field Tunneling Resonance by Decreasing the Crystal Symmetry of Mn12 Acetate.

We report the discovery of a less symmetric crystalline phase of Mn12 acetate, a triclinic phase, resulting from recrystallizing the original tetragonal phase reported by Lis in acetonitrile and toluene. This new phase exhibits the same structure of Mn12 acetate clusters and the same positions of tunneling resonances on the magnetic field as the conventional tetragonal phase. However, the width of the zero-field resonance is at least 1 order of magnitude smaller-can be as low as 50 Oe-indicating very small inhomogeneous broadening due to dipolar and nuclear fields.

pH-Responsive Relaxometric Behaviour of Coordination Polymer Nanoparticles Made of a Stable Macrocyclic Gadolinium Chelate.

Lanthanide-containing nanoscale particles have been widely explored for various biomedical purposes, however, they are often prone to metal leaching. Here we have created a new coordination polymer (CP) by applying, for the first time, a stable Gd(III) chelate as building block in order to prevent any fortuitous release of free lanthanide(III) ion. The use of the Gd-DOTA-4AmP complex as a design element in the CP allows not only for enhanced relaxometric properties (maximum r1 =16.4 mm(-1) s(-1) at 10 MHz), but also for a pH responsiveness (Δr1 =108 % between pH 4 and 6.5), beyond the values obtained for the low molecular weight Gd-DOTA-4AmP itself. The CP can be miniaturised to the nanoscale to form colloids that are stable in physiological saline solution and in cell culture media and does not show cytotoxicity.

Current advances in synchrotron radiation instrumentation for MX experiments.

Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choice for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing.

Switchable Surface Hydrophobicity-Hydrophilicity of a Metal-Organic Framework.

Materials with surfaces that can be switched from high/superhydrophobicity to superhydrophilicity are useful for myriad applications. Herein, we report a metal-organic framework (MOF) assembled from ZnII ions, 1,4-benzenedicarboxylate, and a hydrophobic carborane-based linker. The MOF crystal-surface can be switched between hydrophobic and superhydrophilic through a chemical treatment to remove some of the building blocks.

Developments in optics and performance at BL13-XALOC, the macromolecular crystallography beamline at the ALBA synchrotron.

BL13-XALOC is currently the only macromolecular crystallography beamline at the 3 GeV ALBA synchrotron near Barcelona, Spain. The optics design is based on an in-vacuum undulator, a Si(111) channel-cut crystal monochromator and a pair of KB mirrors. It allows three main operation modes: a focused configuration, where both mirrors can focus the beam at the sample position to 52 µm × 5.5 µm FWHM (H × V); a defocused configuration that can match the size of the beam to the dimensions of the crystals or to focus the beam at the detector; and an unfocused configuration, where one or both mirrors are removed from the photon beam path. To achieve a uniform defocused beam, the slope errors of the mirrors were reduced down to 55 nrad RMS by employing a novel method that has been developed at the ALBA high-accuracy metrology laboratory. Thorough commissioning with X-ray beam and user operation has demonstrated an excellent energy and spatial stability of the beamline. The end-station includes a high-accuracy single-axis diffractometer, a removable mini-kappa stage, an automated sample-mounting robot and a photon-counting detector that allows shutterless operation. The positioning tables of the diffractometer and the detector are based on a novel and highly stable design. This equipment, together with the operation flexibility of the beamline, allows a large variety of types of crystals to be tackled, from medium-sized crystals with large unit-cell parameters to microcrystals. Several examples of data collections measured during beamline commissioning are described. The beamline started user operation on 18 July 2012.

Crystallization and preliminary X-ray diffraction analysis of vaccinia virus H1L phosphatase.

The cysteine-based protein phosphatase H1L was the first reported dual-specificity protein phosphatase. H1L is encapsidated within the vaccinia virus and is required for successful host infection and for the production of viable vaccinia progeny. H1L has therefore been proposed as a target candidate for antiviral compounds. Recombinant H1L has been expressed in a catalytically inactive form using an Escherichia coli host, leading to purification and crystallization by the microbatch method. The crystals diffract to 2.1 A resolution using synchrotron radiation. These crystals belong to space group P422, with unit-cell parameters a = b = 98.31, c = 169.15 A, and are likely to contain four molecules in the asymmetric unit. A sulfur SAD data set was collected to 2.8 A resolution on beamline BM14 at the ESRF to facilitate structure determination. Attempts to derivatize these crystals with xenon gas changed the space group to I422, with unit-cell parameters a = b = 63.28, c = 169.68 A and a single molecule in the asymmetric unit. The relationship between these two crystal forms is discussed.

Leucine zipper motif inspiration: a two-dimensional leucine Velcro-like array in peptide coordination polymers generates hydrophobicity.

Here, we show that the well-known hydrophobic leucine (Leu) zipper motif (also known as the coiled-coil or Leu scissors motif), typically found in proteins, can be used as a source of inspiration in coordination polymers built from Leu-containing dipeptides or tripeptides. We demonstrate that this motif can be extended to form Velcro-like layers of Leu, and that the hydrophobicity of these layers is transferred to coordination polymers, thereby enabling the development of a new type of hydrophobic materials.

Structural and functional analysis of Oceanobacillus iheyensis macrodomain reveals a network of waters involved in substrate binding and catalysis.

Macrodomains are ubiquitous conserved domains that bind or transform ADP-ribose (ADPr) metabolites. In humans, they are involved in transcription, X-chromosome inactivation, neurodegeneration and modulating PARP1 signalling, making them potential targets for therapeutic agents. Unfortunately, some aspects related to the substrate binding and catalysis of MacroD-like macrodomains still remain unclear, since mutation of the proposed catalytic aspartate does not completely abolish enzyme activity. Here, we present a functional and structural characterization of a macrodomain from the extremely halotolerant and alkaliphilic bacterium Oceanobacillus iheyensis (OiMacroD), related to hMacroD1/hMacroD2, shedding light on substrate binding and catalysis. The crystal structures of D40A, N30A and G37V mutants, and those with MES, ADPr and ADP bound, allowed us to identify five fixed water molecules that play a significant role in substrate binding. Closure of the ß6-α4 loop is revealed as essential not only for pyrophosphate recognition, but also for distal ribose orientation. In addition, a novel structural role for residue D40 is identified. Furthermore, it is revealed that OiMacroD not only catalyses the hydrolysis of O-acetyl-ADP-ribose but also reverses protein mono-ADP-ribosylation. Finally, mutant G37V supports the participation of a substrate-coordinated water molecule in catalysis that helps to select the proper substrate conformation.

Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin.

The Gram-positive anaerobic human pathogenic bacterium Atopobium vaginae causes most diagnosed cases of bacterial vaginosis as well as opportunistic infections in immunocompromised patients. In addition to its well-established role in carbohydrate metabolism, D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Streptococcus pyogenes and S. pneumoniae have been reported to act as extracellular virulence factors during streptococcal infections. Here, we report the crystal structure of GAPDH from A. vaginae (AvGAPDH) at 2.19 Å resolution. The refined model has a crystallographic Rfree of 22.6%. AvGAPDH is a homotetramer wherein each subunit is bound to a nicotinamide adenine dinucleotide (NAD+) molecule. The AvGAPDH enzyme fulfills essential glycolytic as well as moonlight (non-glycolytic) functions, both of which might be targets of chemotherapeutic intervention. We report that AvGAPDH interacts in vitro with the human C5a anaphylatoxin and inhibits C5a-specific granulocyte chemotaxis, thereby suggesting the participation of AvGAPDH in complement-targeted immunoevasion in a context of infection. The availability of high-quality structures of AvGAPDH and other homologous virulence factors from Gram-positive pathogens is critical for drug discovery programs. In this study, sequence and structural differences between AvGAPDH and related bacterial and eukaryotic GAPDH enzymes are reported in an effort to understand how to subvert the immunoevasive properties of GAPDH and evaluate the potential of AvGAPDH as a druggable target.

Single-crystal and humidity-controlled powder diffraction study of the breathing effect in a metal-organic framework upon water adsorption/desorption.

Herein we report a study on water adsorption/desorption-triggered single-crystal to single-crystal transformations in a MOF, by single-crystal and humidity-controlled powder X-ray diffraction and water-sorption measurements. We identified a gate-opening effect at a relative humidity of 85% upon water adsorption, and a gate-closure effect at a relative humidity of 55 to 77% upon water desorption. This reversible breathing effect between the "open" and the "closed" structures of the MOF involves the cleavage and formation of several coordination bonds.

Hetero-bimetallic paddlewheel clusters in coordination polymers formed by a water-induced single-crystal-to-single-crystal transformation.

Herein we report a water-induced single-crystal to single-crystal transformation that involves the formation of hetero-bimetallic paddlewheel clusters in coordination polymers. Through this transformation, which involves the cleavage and formation of different coordination bonds, two different Cu(ii)-Zn(ii) and Cu(ii)-Ni(ii) paddlewheel units exhibiting a 1 : 1 metal ratio were created.

Sponge-like molecular cage for purification of fullerenes.

Since fullerenes are available in macroscopic quantities from fullerene soot, large efforts have been geared toward designing efficient strategies to obtain highly pure fullerenes, which can be subsequently applied in multiple research fields. Here we present a supramolecular nanocage synthesized by metal-directed self-assembly, which encapsulates fullerenes of different sizes. Direct experimental evidence is provided for the 1:1 encapsulation of C60, C70, C76, C78 and C84, and solid state structures for the host-guest adducts with C60 and C70 have been obtained using X-ray synchrotron radiation. Furthermore, we design a washing-based strategy to exclusively extract pure C60 from a solid sample of cage charged with a mixture of fullerenes. These results showcase an attractive methodology to selectively extract C60 from fullerene mixtures, providing a platform to design tuned cages for selective extraction of higher fullerenes. The solid-phase fullerene encapsulation and liberation represent a twist in host-guest chemistry for molecular nanocage structures.

The crystal structure of the globular head of complement protein C1q provides a basis for its versatile recognition properties.

C1q is a versatile recognition protein that binds to an amazing variety of immune and non-immune ligands and triggers activation of the classical pathway of complement. The crystal structure of the C1q globular domain responsible for its recognition properties has now been solved and refined to 1.9 A of resolution. The structure reveals a compact, almost spherical heterotrimeric assembly held together mainly by non-polar interactions, with a Ca2+ ion bound at the top. The heterotrimeric assembly of the C1q globular domain appears to be a key factor of the versatile recognition properties of this protein. Plausible three-dimensional models of the C1q globular domain in complex with two of its physiological ligands, C-reactive protein and IgG, are proposed, highlighting two of the possible recognition modes of C1q. The C1q/human IgG1 model suggests a critical role for the hinge region of IgG and for the relative orientation of its Fab domain in C1q binding.