Cavity-Directed Synthesis of Labile Polyoxometalates for Catalysis in Confined Spaces.

The artificial microenvironments inside coordination cages have gained significant attention for performing enzyme-like catalytic reactions by facilitating the formation of labile and complex molecules through a "ship-in-a-bottle" approach. Despite many fascinating examples, this approach remains scarcely explored in the context of synthesizing metallic clusters such as polyoxometalates (POMs). The development of innovative approaches to control and influence the speciation of POMs in aqueous solutions would greatly advance their applicability and could ultimately lead to the formation of elusive clusters that cannot be synthesized by using traditional methods. In this study, we employ host-guest stabilization within a coordination cage to enable a novel cavity-directed synthesis of labile POMs in aqueous solutions under mild conditions. The elusive Lindqvist [M6O19]2- (M=Mo or W) POMs were successfully synthesized at room temperature via the condensation of molybdate or tungstate building blocks within the confined cavity of a robust and water-soluble Pt6L4(NO3)12 coordination cage. Importantly, the encapsulation of these POMs enhances their stability in water, rendering them efficient catalysts for environmentally friendly and selective sulfoxidation reactions using H2O2 as a green oxidant in a pure aqueous medium. The approach developed in this paper offers a means to synthesize and stabilize the otherwise unstable metal-oxo clusters in water, which can broaden the scope of their applications.

Ice crystallization under cryogenic cooling in lipid membrane nanoconfined geometry: Time-resolved structural dynamics.

Time-resolved structural investigations of crystallization of water in lipid/protein/salt mesophases at cryogenic temperatures are significant for comprehension of ice nanocrystal nucleation kinetics in lipid membranous systems and can lead to a better understanding of how to experimentally retard the ice formation that obstructs the protein crystal structure determination. Here, we present a time-resolved synchrotron microfocus X-ray diffraction (TR-XRD) study based on ∼40,000 frames that revealed the dynamics of water-to-ice crystallization in a lipid/protein/salt mesophase subjected to cryostream cooling at 100 K. The monoolein/hemoglobin/salt/water system was chosen as a model composition related to protein-loaded lipid cubic phases (LCP) broadly used for the crystallization of proteins. Under confinement in the nanoscale geometry, metastable short-living cubic ice (Ic) rapidly crystallized well before the formation of hexagonal ice (Ih). The detected early nanocrystalline states of water-to-ice transformation in multicomponent systems are relevant to a broad spectrum of technologies and understanding of natural phenomena, including crystallization, physics of water nanoconfinement, and rational design of anti-freezing and cryopreservation systems.

Structural Variety of Niobium(V) Polyoxo Clusters Obtained from the Reaction with Aromatic Monocarboxylic Acids: Isolation of {Nb2 O}, {Nb4 O4 } and {Nb8 O12 } Cores.

The reactivity of aryl monocarboxylic acids (benzoic, 1- or 2-naphtoic, 4'-methylbiphenyl-4-carboxylic, and anthracene-9-carboxylic acids) as complexing agents for the ethoxide niobium(V) (Nb(OEt)5 precursor has been investigated. A total of eight coordination complexes were isolated with distinct niobium(V) nuclearities as well as carboxylate complexation states. The use of benzoic acid gives a tetranuclear core Nb4 (µ2 -O)4 (L)4 (OEt)8 ] (L=benzoate (1)) with four Nb-(µ2 -O)-Nb linkages in a square plane configuration. A similar tetramer, 7, was obtained with 2-naphtoic acid by using a 55 % humid atmosphere synthetic route. Two types of dinuclear brick were identified with one central Nb-(µ2 -O)-Nb linkage; they differ in their complexation state, with one bridging carboxylate ([Nb2 (µ2 -O)(µ2 -OEt)(L)(OEt)6 ], with L=1-naphtoate (3) or anthracene-9-carboxylate (5)) or two bridging carboxylate groups ([Nb2 (µ2 -O)(L)2 (OEt)6 ], with L=4'-methylbiphenyl-4-carboxylic (4) or anthracene-9-carboxylate (6)). An octanuclear moiety [Nb8 (µ2 -O)12 (L)8 (η1 -L)4-x (OEt)4+x ] (with L=2-naphtoate, x=0 or 2; 8) was obtained by using a solvothermal route in acetonitrile; it has a cubic configuration with niobium centers at each node, linked by 12 µ2 -O groups. The formation of the niobium oxo clusters was characterized by infrared and liquid 1 H NMR spectroscopy in order to analyze the esterification reaction, which induces the release of water molecules that further react through oxolation with niobium atoms, in different {Nb2 O}, {Nb4 O4 } and {Nb8 O12 } nuclearities.

The crystal structure of iC3b-CR3 αI reveals a modular recognition of the main opsonin iC3b by the CR3 integrin receptor.

Complement activation on cell surfaces leads to the massive deposition of C3b, iC3b, and C3dg, the main complement opsonins. Recognition of iC3b by complement receptor type 3 (CR3) fosters pathogen opsonophagocytosis by macrophages and the stimulation of adaptive immunity by complement-opsonized antigens. Here, we present the crystallographic structure of the complex between human iC3b and the von Willebrand A inserted domain of the α chain of CR3 (αI). The crystal contains two composite interfaces for CR3 αI, encompassing distinct sets of contiguous macroglobulin (MG) domains on the C3c moiety, MG1-MG2 and MG6-MG7 domains. These composite binding sites define two iC3b-CR3 αI complexes characterized by specific rearrangements of the two semi-independent modules, C3c moiety and TED domain. Furthermore, we show the structure of iC3b in a physiologically-relevant extended conformation. Based on previously available data and novel insights reported herein, we propose an integrative model that reconciles conflicting facts about iC3b structure and function and explains the molecular basis for iC3b selective recognition by CR3 on opsonized surfaces.

Chaotropic Effect as an Assembly Motif to Construct Supramolecular Cyclodextrin-Polyoxometalate-Based Frameworks.

In aqueous solution, low-charged polyoxometalates (POMs) exhibit remarkable self-assembly properties with nonionic organic matter that have been recently used to develop groundbreaking advances in host-guest chemistry, as well as in soft matter science. Herein, we exploit the affinity between a chaotropic POM and native cyclodextrins (α-, ß-, and γ-CD) to enhance the structural and functional diversity of cyclodextrin-based open frameworks. First, we reveal that the Anderson-Evans type polyoxometalate [AlMo6O18(OH)6]3- represents an efficient inorganic scaffold to design open hybrid frameworks built from infinite cyclodextrin channels connected through the disk-shaped POM. A single-crystal X-ray analysis demonstrates that the resulting supramolecular architectures contain large cavities (up to 2 nm) where the topologies are dictated by the rotational symmetry of the organic macrocycle, generating honeycomb (bnn net) and checkerboard-like (pcu net) networks for α-CD (C6) and γ-CD (C8), respectively. On the other hand, the use of ß-CD, a macrocycle with C7 ideal symmetry, led to a distorted-checkerboard-like network. The cyclodextrin-based frameworks built from an Anderson-Evans type POM are easily functionalizable using the molecular recognition properties of the macrocycle building units. As a proof of concept, we successfully isolated a series of compartmentalized functional frameworks by the entrapment of polyiodides or superchaotropic redox-active polyanions within the macrocyclic host matrix. This set of results paves the way for designing multifunctional supramolecular frameworks whose pore dimensions are controlled by the size of inorganic entities.

Redox-Active 1D Coordination Polymers of Iron-Sulfur Clusters.

Here we describe the combination of an archetypal redox-active metal sulfide cluster, Fe4S4, with an organic linker, 1,4-benzenedithiolate, to prepare coordination polymers containing infinite chains of Fe4S4 clusters. The crystal structures of two solid materials have been solved from synchrotron X-ray powder diffraction data using simulated annealing and refined by a least-squares Rietveld refinement procedure. The electronic properties of these chains have also been characterized by UV-visible and Mössbauer spectroscopies. Additional experiments demonstrated that these chains can be solubilized by variation of the countercation and that the chain structure is maintained in solution. The redox-activity of the Fe4S4 clusters can be accessed with chemical reagents. Introduction of charge carriers by reduction of the Fe4S4 clusters is found to increase the electrical conductivity of the materials by up to 4 orders of magnitude. These results highlight the utility of Fe4S4 clusters as redox-active building blocks in preparing new classes of coordination polymers.

Crystallization and initial X-ray diffraction analysis of the multi-domain Brucella blue light-activated histidine kinase LOV-HK in its illuminated state.

The pathogenic bacterium Brucella abortus codes for a multi-domain dimeric cytoplasmic histidine kinase called LOV-HK, which is a key blue light-activated virulence factor in this microorganism. The structural basis of the light activation mechanism of this protein remains unclear. In this work, full-length LOV-HK was cloned, expressed and purified. The protein was activated by light and crystallized under a controlled illumination environment. The merge of 14 individual native data sets collected on a single crystal resulted in a complete X-ray diffraction data set to a resolution of 3.70 Šwith over 2 million reflections. Crystals belong to space group P212121, with unit-cell parameters a = 95.96, b = 105.30, c = 164.49 Šwith a dimer in the asymmetric unit. Molecular replacement with Phaser using the individual domains as search models allowed for the reconstruction of almost the whole protein. Very recently, improved LOV-HK crystals led to a 3.25-Šresolution dataset. Refinement and model building is underway. This crystal model will represent one of the very few examples of a multi-domain histidine kinase with known structure.

Nonconventional Three-Component Hierarchical Host-Guest Assembly Based on Mo-Blue Ring-Shaped Giant Anion, γ-Cyclodextrin, and Dawson-type Polyoxometalate.

In this communication, we report on a noteworthy hybrid supramolecular assembly built from three functional components hierarchically organized through noncovalent interactions. The one-pot synthesis procedure leads to the formation of large Mo-blue ring-shaped anion {Mo154}, which contains the supramolecular adduct based on the symmetric encapsulation of the Dawson-type [P2W18O62]6- anion by two γ-cyclodextrin units. Such a nanoscopic onion-like structure, noted [P2W18O62]@2γ-CD@{Mo154} has been characterized by single-crystal X-ray diffraction, thus demonstrating the capability of the giant inorganic torus to develop relevant supramolecular chemistry, probing the strong affinity of the inner and outer faces of the γ-CD for the polyoxometalate surfaces. Furthermore, interactions and behavior in solution have been studied by multinuclear NMR spectroscopy, which supports specific interactions between γ-CD and POM units. Finally, the formation of this three-component hybrid assembly from one-pot procedure, in water and using nearly stoichiometric conditions, is discussed in terms of the driving forces orchestrating this highly efficient multilevel recognition process.

Structural and functional characterization of a highly stable endo-ß-1,4-xylanase from Fusarium oxysporum and its development as an efficient immobilized biocatalyst.

BACKGROUND: Replacing fossil fuel with renewable sources such as lignocellulosic biomass is currently a promising alternative for obtaining biofuel and for fighting against the consequences of climate change. However, the recalcitrant structure of lignocellulosic biomass residues constitutes a major limitation for its widespread use in industry. The efficient hydrolysis of lignocellulosic materials requires the complementary action of multiple enzymes including xylanases and ß-xylosidases, which are responsible for cleaving exo- and endoxylan linkages, that release oligocarbohydrates that can be further processed by other enzymes. RESULTS: We have identified the endo-ß-1,4-xylanase Xyl2 from Fusarium oxysporum as a promising glycoside hydrolase family 11 enzyme for the industrial degradation of xylan. To characterize Xyl2, we have cloned the synthetic optimized gene and expressed and purified recombinant Xyl2 to homogeneity, finally obtaining 10 mg pure Xyl2 per liter of culture. The crystal structure of Xyl2 at 1.56 Å resolution and the structure of a methyl-xylopyranoside Xyl2 complex at 2.84 Å resolution cast a highly detailed view of the active site of the enzyme, revealing the molecular basis for the high catalytic efficiency of Xyl2. The kinetic analysis of Xyl2 demonstrates high xylanase activity and non-negligible ß-xylosidase activity under a variety of experimental conditions including alkaline pH and elevated temperature. Immobilizing Xyl2 on a variety of solid supports enhances the enzymatic properties that render Xyl2 a promising industrial biocatalyst, which, together with the detailed structural data, may establish Xyl2 as a platform for future developments of industrially relevant xylanases. CONCLUSIONS: F. oxysporum Xyl2 is a GH11 xylanase which is highly active in free form and immobilized onto a variety of solid supports in a wide pH range. Furthermore, immobilization of Xyl2 on certain supports significantly increases its thermal stability. A mechanistic rationale for Xyl2's remarkable catalytic efficiency at alkaline pH is proposed on the basis of two crystallographic structures. Together, these properties render Xyl2 an attractive biocatalyst for the sustainable industrial degradation of xylan.

The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily.

Cyclic N6-threonylcarbamoyladenosine ('cyclic t6A', ct(6)A) is a non-thiolated hypermodification found in transfer RNAs (tRNAs) in bacteria, protists, fungi and plants. In bacteria and yeast cells ct(6)A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct(6)A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t6A to form ct(6)A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K+ and Na+ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t6A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct(6)A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA.

Recognition determinants of broadly neutralizing human antibodies against dengue viruses.

Dengue disease is caused by four different flavivirus serotypes, which infect 390 million people yearly with 25% symptomatic cases and for which no licensed vaccine is available. Recent phase III vaccine trials showed partial protection, and in particular no protection for dengue virus serotype 2 (refs 3, 4). Structural studies so far have characterized only epitopes recognized by serotype-specific human antibodies. We recently isolated human antibodies potently neutralizing all four dengue virus serotypes. Here we describe the X-ray structures of four of these broadly neutralizing antibodies in complex with the envelope glycoprotein E from dengue virus serotype 2, revealing that the recognition determinants are at a serotype-invariant site at the E-dimer interface, including the exposed main chain of the E fusion loop and the two conserved glycan chains. This 'E-dimer-dependent epitope' is also the binding site for the viral glycoprotein prM during virus maturation in the secretory pathway of the infected cell, explaining its conservation across serotypes and highlighting an Achilles' heel of the virus with respect to antibody neutralization. These findings will be instrumental for devising novel immunogens to protect simultaneously against all four serotypes of dengue virus.

Crystallization and preliminary X-ray characterization of the full-length bacteriophytochrome from the plant pathogen Xanthomonas campestris pv. campestris.

Phytochromes give rise to the largest photosensor family known to date. However, they are underrepresented in the Protein Data Bank. Plant, cyanobacterial, fungal and bacterial phytochromes share a canonical architecture consisting of an N-terminal photosensory module (PAS2-GAF-PHY domains) and a C-terminal variable output module. The bacterium Xanthomonas campestris pv. campestris, a worldwide agricultural pathogen, codes for a single bacteriophytochrome (XccBphP) that has this canonical architecture, bearing a C-terminal PAS9 domain as the output module. Full-length XccBphP was cloned, expressed and purified to homogeneity by nickel-NTA affinity and size-exclusion chromatography and was then crystallized at room temperature bound to its cofactor biliverdin. A complete native X-ray diffraction data set was collected to a maximum resolution of 3.25 Å. The crystals belonged to space group P43212, with unit-cell parameters a = b = 103.94, c = 344.57 Šand a dimer in the asymmetric unit. Refinement is underway after solving the structure by molecular replacement.