SciCombinator

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Concept: Mineralogy

187

Murine noroviruses have emerged as a valuable tool for investigating the molecular basis of infection and pathogenesis of the closely related human noroviruses, which are the major cause of non-bacterial gastroenteritis. The replication of noroviruses relies on the proteolytic processing of a large polyprotein precursor into six non-structural proteins (NS1-2, NS3, NS4, NS5, NS6(pro), NS7(pol)) by the virally-encoded NS6 protease. We report here the crystal structure of MNV NS6(pro), which has been determined to a resolution of 1.6 Å. Adventitiously, the crystal contacts are mediated in part by the binding of the C-terminus of NS6(pro) within the peptide-binding cleft of a neighbouring molecule. This insertion occurs for both molecules in the asymmetric unit of the crystal in a manner that is consistent with physiologically-relevant binding, thereby providing two independent views of a protease-peptide complex. Since the NS6(pro) C-terminus is formed in vivo by NS6(pro) processing, these crystal contacts replicate the protease-product complex that is formed immediately following cleavage of the peptide bond at the NS6-NS7 junction. The observed mode of binding of the C-terminal product peptide yields new insights into the structural basis of NS6(pro) specificity.

Concepts: Scientific method, Protein, Amino acid, Crystal, Molecule, Atom, Norovirus, Mineralogy

25

SerpinA12 (vaspin) is thought to be mainly expressed in adipose tissue and has multiple beneficial effects on metabolic, inflammatory and atherogenic processes related to obesity. Kallikrein 7 (KLK7) is the only known protease target of vaspin to date and is inhibited with a moderate inhibition rate. In the crystal structure, the cleavage site (P1-P1') of the vaspin reactive center loop is fairly rigid compared to the flexible residues before P2, possibly supported by an ionic interaction of P1' glutamate (Glu(379)) with an arginine residue (Arg(302)) of the β-sheet C. A P1' glutamate seems highly unusual and unfavorable for the protease KLK7. We characterized vaspin mutants to investigate the roles of these two residues in protease inhibition and recognition by vaspin. RCL mutations changing the P1' residue or altering RCL conformation significantly increased inhibition parameters while removal of the positive charge within β-sheet C impeded the serpin-protease interaction. Arg(302) is a crucial contact to enable vaspin recognition by KLK7 and it supports moderate inhibition of the serpin despite the presence of the detrimental P1' Glu(379), which clearly represents a major limiting factor for vaspin inhibitory activity. We also show that the vaspin inhibition rate for KLK7 can be modestly increased by heparin and demonstrate that vaspin is a heparin-binding serpin. Noteworthy, we observed vaspin as a remarkably thermostable serpin and found residues Glu(379) and Arg(302) influencing heat-induced polymerization. These structural and functional results reveal the mechanistic basis of how reactive center loop sequence and exosite interaction in vaspin enable KLK7 recognition and regulate protease inhibition as well as stability of this adipose tissue derived serpin.

Concepts: Amino acid, Obesity, Insulin resistance, Adipose tissue, Ionic bond, Mineralogy, Adiponectin, Antithrombin

25

The recent re-emergence of the halide perovskites, of the type AMX3, derives from a sea-changing breakthrough in the field of photovoltaics that has led to a whole new generation of solar devices with remarkable power conversion efficiency. The success in the field of photovoltaics has led to intense, combined research efforts to better understand these materials both from the fundamental chemistry and physics points of view and for the improvement of applied functional device engineering. This groundswell of activity has breathed new life into this long-known but largely “forgotten” class of perovskites. The impressive achievements of halide perovskites in photovoltaics, as well as other optoelectronic applications, stem from an unusually favorable combination of optical and electronic properties, with the ability to be solution processed into films. This defines them as a brand new class of semiconductors that can rival or exceed the performance of the venerable classes of III-V and II-IV semiconductors, which presently dominate the industries of applied optoelectronics. Our aim in this Account is to highlight the basic pillars that define the chemistry of the halide perovskites and their unconventional electronic properties through the prism of structure-property relationships. We focus on the synthetic requirements under which a halide perovskite can exist and emphasize how the synthetic conditions can determine the structural integrity and the bulk properties of the perovskites. Then we proceed to discuss the origins of the optical and electronic phenomena, using the perovskite crystal structure as a guide. Some of the most remarkable features of the perovskites dealt with in this Account include the evolution of a unique type of defect, which gives rise to superlattices. These can enhance or diminish the fluorescence properties of the perovskites. For example, the exotic self-doping ability of the Sn-based perovskites allows them to adopt electrical properties from semiconducting to metallic. We attempt to rationalize how these properties can be tuned and partially controlled through targeted synthetic procedures for use in electronic and optical devices. In addition, we address open scientific questions that pose big obstacles in understanding the fundamentals of perovskites. We anticipate that the answers to these questions will provide the impetus upon which future research directions will be founded.

Concepts: Crystal structure, Semiconductor, Solar cell, Photovoltaics, Diode, Perovskite, Mineralogy, Optoelectronics

19

Meteorites exposed to high pressures and temperatures during impact-induced shock often contain minerals whose occurrence and stability normally confine them to the deeper portions of Earth’s mantle. One exception has been MgSiO3 in the perovskite structure, which is the most abundant solid phase in Earth. Here we report the discovery of this important phase as a mineral in the Tenham L6 chondrite and approved by the International Mineralogical Association (specimen IMA 2014-017). MgSiO3-perovskite is now called bridgmanite. The associated phase assemblage constrains peak shock conditions to ~ 24 gigapascals and 2300 kelvin. The discovery concludes a half century of efforts to find, identify, and characterize a natural specimen of this important mineral.

Concepts: Crystal structure, Ice, Mineral, Mineralogy, Triple point, Meteorite, Olivine, International Mineralogical Association

4

Ocean acidification, a product of increasing atmospheric carbon dioxide, may already have affected calcified organisms in the coastal zone, such as bivalves and other shellfish. Understanding species' responses to climate change requires the context of long-term dynamics. This can be particularly difficult given the longevity of many important species in contrast with the relatively rapid onset of environmental changes. Here, we present a unique archival dataset of mussel shells from a locale with recent environmental monitoring and historical climate reconstructions. We compare shell structure and composition in modern mussels, mussels from the 1970s, and mussel shells dating back to 1000-2420 years BP. Shell mineralogy has changed dramatically over the past 15 years, despite evidence for consistent mineral structure in the California mussel, Mytilus californianus, over the prior 2500 years. We present evidence for increased disorder in the calcium carbonate shells of mussels and greater variability between individuals. These changes in the last decade contrast markedly from a background of consistent shell mineralogy for centuries. Our results use an archival record of natural specimens to provide centennial-scale context for altered minerology and variability in shell features as a response to acidification stress and illustrate the utility of long-term studies and archival records in global change ecology. Increased variability between individuals is an emerging pattern in climate change responses, which may equally expose the vulnerability of organisms and the potential of populations for resilience.

Concepts: Carbon dioxide, Mineral, Calcium carbonate, Mineralogy, Mussel, Calcite, Mytilidae, California mussel

4

Reconstruction of enamel-like materials is a central topic of research in dentistry and material sciences. The importance of precise proteolytic mechanisms in amelogenesis to form a hard tissue with more than 95% mineral content has already been reported. A mutation in the Matrix Metalloproteinase-20 (MMP-20) gene results in hypomineralized enamel that is thin, disorganized and breaks from the underlying dentin. We hypothesized that the absence of MMP-20 during amelogenesis results in the occlusion of amelogenin in the enamel hydroxyapatite crystals. We used spectroscopy and electron microscopy techniques to qualitatively and quantitatively analyze occluded proteins within the isolated enamel crystals from MMP-20 null and Wild type (WT) mice. Our results showed that the isolated enamel crystals of MMP-20 null mice had more organic macromolecules occluded inside them than enamel crystals from the WT. The crystal lattice arrangements of MMP-20 null enamel crystals analyzed by High Resolution Transmission Electron Microscopy (HRTEM) were found to be significantly different from those of the WT. Raman studies indicated that the crystallinity of the MMP-20 null enamel crystals was lower than that of the WT. In conclusion, we present a novel functional mechanism of MMP-20, specifically prevention of unwanted organic material entrapped in the forming enamel crystals, which occurs as the result of precise amelogenin cleavage. MMP-20 action guides the growth morphology of the forming hydroxyapatite crystals and enhances their crystallinity. Elucidating such molecular mechanisms can be applied in the design of novel biomaterials for future clinical applications in dental restoration or repair.

Concepts: Protein, Gene, Crystal, Materials science, Teeth, Dental caries, Tooth enamel, Mineralogy

4

Crystallization is a fundamental and ubiquitous process much studied over the centuries. But although the crystallization of atoms is fairly well understood, it remains challenging to predict reliably the outcome of molecular crystallization processes that are complicated by various molecular interactions and solvent involvement. This difficulty also applies to nanoparticles: high-quality three-dimensional crystals are mostly produced using drying and sedimentation techniques that are often impossible to rationalize and control to give a desired crystal symmetry, lattice spacing and habit (crystal shape). In principle, DNA-mediated assembly of nanoparticles offers an ideal opportunity for studying nanoparticle crystallization: a well-defined set of rules have been developed to target desired lattice symmetries and lattice constants, and the occurrence of features such as grain boundaries and twinning in DNA superlattices and traditional crystals comprised of molecular or atomic building blocks suggests that similar principles govern their crystallization. But the presence of charged biomolecules, interparticle spacings of tens of nanometres, and the realization so far of only polycrystalline DNA-interconnected nanoparticle superlattices, all suggest that DNA-guided crystallization may differ from traditional crystal growth. Here we show that very slow cooling, over several days, of solutions of complementary-DNA-modified nanoparticles through the melting temperature of the system gives the thermodynamic product with a specific and uniform crystal habit. We find that our nanoparticle assemblies have the Wulff equilibrium crystal structure that is predicted from theoretical considerations and molecular dynamics simulations, thus establishing that DNA hybridization can direct nanoparticle assembly along a pathway that mimics atomic crystallization.

Concepts: Crystal, Crystal structure, Crystallography, Solid, Materials science, Mineralogy, Crystal growth, Crystal habit

3

Microbial induced concrete corrosion (MICC) is recognized as one of the main degradation mechanisms of subsurface infrastructure worldwide, raising the demand for sustainable construction materials in corrosive environments. This review aims to summarize the key research progress acquired during the last decade regarding the understanding of MICC reaction mechanisms and the development of durable materials from an interdisciplinary perspective. Special focus was laid on aspects governing concrete - micoorganisms interaction since being the central process steering biogenic acid corrosion. The insufficient knowledge regarding the latter is proposed as a central reason for insufficient progress in tailored material development for aggressive wastewater systems. To date no cement-based material exists, suitable to withstand the aggressive conditions related to MICC over its entire service life. Research is in particular needed on the impact of physiochemical material parameters on microbial community structure, growth characteristics and limitations within individual concrete speciation. Herein an interdisciplinary approach is presented by combining results from material sciences, microbiology, mineralogy and hydrochemistry to stimulate the development of novel and sustainable materials and mitigation strategies for MICC. For instance, the application of antibacteriostatic agents is introduced as an effective instrument to limit microbial growth on concrete surfaces in aggressive sewer environments. Additionally, geopolymer concretes are introduced as highly resistent in acid environments, thus representing a possible green alternative to conventional cement-based construction materials.

Concepts: Microbiology, Chemistry, Physical chemistry, Materials science, Material, Mineralogy, Construction, Concrete

3

Helictites-an enigmatic type of mineral structure occurring in some caves-differ from classical speleothems as they develop with orientations that defy gravity. While theories for helictite formation have been forwarded, their genesis remains equivocal. Here, we show that a remarkable suite of helictites occurring in Asperge Cave (France) are formed by biologically-mediated processes, rather than abiotic processes as had hitherto been proposed. Morphological and petro-physical properties are inconsistent with mineral precipitation under purely physico-chemical control. Instead, microanalysis and molecular-biological investigation reveals the presence of a prokaryotic biofilm intimately associated with the mineral structures. We propose that microbially-influenced mineralization proceeds within a gliding biofilm which serves as a nucleation site for CaCO3, and where chemotaxis influences the trajectory of mineral growth, determining the macroscopic morphology of the speleothems. The influence of biofilms may explain the occurrence of similar speleothems in other caves worldwide, and sheds light on novel biomineralization processes.

Concepts: Bacteria, Microbiology, Mineral, Mineralogy, Cave, Crystal growth, Speleothem, Helictite

2

Understanding and predicting crystal growth is fundamental to the control of functionality in modern materials. Despite investigations for more than one hundred years, it is only recently that the molecular intricacies of these processes have been revealed by scanning probe microscopy. To organize and understand this large amount of new information, new rules for crystal growth need to be developed and tested. However, because of the complexity and variety of different crystal systems, attempts to understand crystal growth in detail have so far relied on developing models that are usually applicable to only one system. Such models cannot be used to achieve the wide scope of understanding that is required to create a unified model across crystal types and crystal structures. Here we describe a general approach to understanding and, in theory, predicting the growth of a wide range of crystal types, including the incorporation of defect structures, by simultaneous molecular-scale simulation of crystal habit and surface topology using a unified kinetic three-dimensional partition model. This entails dividing the structure into ‘natural tiles’ or Voronoi polyhedra that are metastable and, consequently, temporally persistent. As such, these units are then suitable for re-construction of the crystal via a Monte Carlo algorithm. We demonstrate our approach by predicting the crystal growth of a diverse set of crystal types, including zeolites, metal-organic frameworks, calcite, urea and l-cystine.

Concepts: Crystal, Crystal structure, Crystallography, Materials science, Monte Carlo, Microscopy, Mineralogy, Scanning probe microscopy