Hydrothermal synthesis, structure and rare ferromagnetic property of a 3-D Nd(III) metal-organic framework based on mixed pyridine-2,5-dicarboxylic acid/nicotinic acid ligands

A novel 3-D metal-organic framework Nd(2,5-pydc)(nic)(H₂O) (1, 2,5-pydc = pyridine-2,5-dicarboxylic acid, nic = nicotinic acid) has been hydrothermally synthesized and characterized by elemental analyses, IR, and X-ray single-crystal diffraction. Compound 1 is the first MOF based on mixed 2,5-pydc/nic ligands. The title compound displays an interseting 3-D (6,3)-connected network with the topology of (4.6²)₂(4² × 6¹⁰ × 8³). Magnetic susceptibility measurements show that compound1 presents a rare ferromagnetic interaction between two adjacent Nd(III) ions.     

Synthesis and characterization of a novel photoluminescent three-dimensional metal-organic framework

A novel metal-organic framework containing one-dimensional channels of formula [Zn₃(Aco)₂(H₂O)₆]_n (H₃Aco = aconitic acid) has been synthesized and characterized by FT-IR spectroscopy, thermogravimetric analysis (TG), X-ray analysis, and solid state photoluminescence spectra. X-ray crystallographic studies reveal that there are two kinds of crystallographically independent Zn atoms in the title complex. The most interesting feature of the structure is an unprecedented 3D MOF containing infinite Zn(1) linear chains and heterochiral Zn(2) single-stranded helices. The linear chains and helices happen to be perpendicular to each other. Photoluminescence properties of the title compound have been examined in the solid state at room temperature.     

Synthesis of copper-zinc bimetallic imidazolate framework compounds and the structure of Cu(I)-containing Cu2Zn(N2C3H3)4

Copper(II)-zinc(II) bimetallic imidazolate metal-organic framework compounds of composition Cu_aZn_bIm_2(a + b) (Im = C₃H₃N₂), including Cu₂ZnIm₆ (1), were prepared in high yields from the metal oxides under mild aqueous conditions using a novel acid catalysis method. Mild acidic hydrothermal treatment of paramagnetic 1 (≥120 °C) gave diamagnetic Cu(I)-containing Cu₂ZnIm₄ (2) in high yield. The formation mechanism of 2 involves electron transfer from Im⁻ to Cu(II), with concomitant formation of the unusual cyclotriimidazole, C₉H₆N₆. Air-stable 2, characterized by single-crystal X-ray diffraction, crystallized in the tetragonal space group , with a = b = 10.9623(3), c = 6.3231(4) Å, α = β = γ = 90°, V = 759.86(6) Å³, and Z = 1.     

Understanding diversity in coral-algal symbiosis: a cluster-based approach to interpreting fine-scale genetic variation in the genus <Emphasis Type="Italic">Symbiodinium</Emphasis>

Reef corals associate with an extraordinary diversity of dinoflagellate endosymbionts (genus Symbiodinium), and this diversity has become critical to understanding how corals respond to environmental changes. A popular molecular marker for Symbiodinium diversity, the Internal Transcribed Spacer-2 (ITS-2) region of ribosomal DNA, has revealed hundreds of distinct variants that are generally interpreted as representing different species, even though many have not been systematically tested for functional or ecological differentiation. Many of these variants are only minimally divergent from one another (1 bp or less), and others occupy basal nodes of traditional species phylogenies (“living ancestors”), indicating that some Symbiodinium ITS-2 diversity may represent intraspecific sequence variation. This hypothesis was tested for Symbiodinium clades A–D (the dominant symbionts of reef corals) through the construction of statistical parsimony networks of ITS-2 sequence diversity, and identification of clusters of closely related sequences within these networks. Initial assessments indicated that ecological differentiation exists between, but not within, these clusters. This approach, although imperfect in its ability to identify species boundaries in all cases, nevertheless dramatically reduces “species” diversity in Symbiodinium (from ~175 to 35). This testable alternative hypothesis indicates that, in Symbiodinium, “species” consist of clusters of closely related ITS-2 sequences diverging from ancestral variants that are typically ecologically dominant. A cluster-based view of Symbiodinium ITS-2 diversity improves our ability to: (1) construct well-supported symbiont phylogenies; (2) establish functional niches for symbiont species; and (3) understand flexibility and specificity within coral-algal symbioses. This cluster-based approach can ultimately be integrated with emerging population-level datasets (microsatellites and microsatellite flanking regions) to improve understanding of species diversity in Symbiodinium. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Communicated by Biology Editor Dr Ruth Gates     

Union of Geometric Constraint-Based Simulations with Molecular Dynamics for Protein Structure Prediction

Although proteins are a fundamental unit in biology, the mechanism by which proteins fold into their native state is not well understood. In this work, we explore the assembly of secondary structure units via geometric constraint-based simulations and the effect of refinement of assembled structures using reservoir replica exchange molecular dynamics. Our approach uses two crucial features of these methods: i), geometric simulations speed up the search for nativelike topologies as there are no energy barriers to overcome; and ii), molecular dynamics identifies the low free energy structures and further refines these structures toward the actual native conformation. We use eight α-, β-, and α/β-proteins to test our method. The geometric simulations of our test set result in an average RMSD from native of 3.7 Å and this further reduces to 2.7 Å after refinement. We also explore the question of robustness of assembly for inaccurate (shifted and shortened) secondary structure. We find that the RMSD from native is highly dependent on the accuracy of secondary structure input, and even slightly shifting the location of secondary structure along the amino acid sequence can lead to a rapid decrease in RMSD to native due to incorrect packing.     

Dissection of the IgNAR V Domain: Molecular Scanning and Orthologue Database Mining Define Novel IgNAR Hallmarks and Affinity Maturation Mechanisms

The shark antigen-binding V_NAR domain has the potential to provide an attractive alternative to traditional biotherapeutics based on its small size, advantageous physiochemical properties, and unusual ability to target clefts in enzymes or cell surface molecules. The V_NAR shares many of the properties of the well-characterised single-domain camelid V_HH but is much less understood at the molecular level. We chose the hen-egg-lysozyme-specific archetypal Type I V_NAR 5A7 and used ribosome display in combination with error-prone mutagenesis to interrogate the entire sequence space. We found a high level of mutational plasticity across the V_NAR domain, particularly within the framework 2 and hypervariable region 2 regions. A number of residues important for affinity were identified, and a triple mutant combining A1D, S61R, and G62R resulted in a K_D of 460 pM for hen egg lysozyme, a 20-fold improvement over wild-type 5A7, and the highest K_D yet reported for V_NAR-antigen interactions. These findings were rationalised using structural modelling and indicate the importance of residues outside the classical complementarity determining regions in making novel antigen contacts that modulate affinity. We also located two solvent-exposed residues (G15 and G42), distant from the V_NAR paratope, which retain function upon mutation to cysteine and have the potential to be exploited as sites for targeted covalent modification. Our findings with 5A7 were extended to all known NAR structures using an in-depth bioinformatic analysis of sequence data available in the literature and a newly generated V_NAR database. This study allowed us to identify, for the first time, both V_NAR-specific and V_NAR/Ig V_L/TCR V_α overlapping hallmark residues, which are critical for the structural and functional integrity of the single domain. Intriguingly, each of our designated V_NAR-specific hallmarks align precisely with previously defined mutational ‘cold spots’ in natural nurse shark cDNA sequences. These findings will aid future V_NAR engineering and optimisation studies towards the development of V_NAR single-domain proteins as viable biotherapeutics.