SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Atom

210

The chemistry of hydrogen cyanide (HCN) is believed to be central to the origin of life question. Contradictions between Cassini-Huygens mission measurements of the atmosphere and the surface of Saturn’s moon Titan suggest that HCN-based polymers may have formed on the surface from products of atmospheric chemistry. This makes Titan a valuable “natural laboratory” for exploring potential nonterrestrial forms of prebiotic chemistry. We have used theoretical calculations to investigate the chain conformations of polyimine (pI), a polymer identified as one major component of polymerized HCN in laboratory experiments. Thanks to its flexible backbone, the polymer can exist in several different polymorphs, which are relatively close in energy. The electronic and structural variability among them is extraordinary. The band gap changes over a 3-eV range when moving from a planar sheet-like structure to increasingly coiled conformations. The primary photon absorption is predicted to occur in a window of relative transparency in Titan’s atmosphere, indicating that pI could be photochemically active and drive chemistry on the surface. The thermodynamics for adding and removing HCN from pI under Titan conditions suggests that such dynamics is plausible, provided that catalysis or photochemistry is available to sufficiently lower reaction barriers. We speculate that the directionality of pI’s intermolecular and intramolecular =N-H(…)N hydrogen bonds may drive the formation of partially ordered structures, some of which may synergize with photon absorption and act catalytically. Future detailed studies on proposed mechanisms and the solubility and density of the polymers will aid in the design of future missions to Titan.

Concepts: DNA, Chemistry, Atom, Experiment, Atmosphere, Saturn, Hydrogen cyanide, Titan

185

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

183

Bone loss caused by ionizing radiation is a potential health concern for radiotherapy patients, radiation workers and astronauts. In animal studies, exposure to ionizing radiation increases oxidative damage in skeletal tissues, and results in an imbalance in bone remodeling initiated by increased bone-resorbing osteoclasts. Therefore, we evaluated various candidate interventions with antioxidant or anti-inflammatory activities (antioxidant cocktail, dihydrolipoic acid, ibuprofen, dried plum) both for their ability to blunt the expression of resorption-related genes in marrow cells after irradiation with either gamma rays (photons, 2 Gy) or simulated space radiation (protons and heavy ions, 1 Gy) and to prevent bone loss. Dried plum was most effective in reducing the expression of genes related to bone resorption (Nfe2l2, Rankl, Mcp1, Opg, TNF-α) and also preventing later cancellous bone decrements caused by irradiation with either photons or heavy ions. Thus, dietary supplementation with DP may prevent the skeletal effects of radiation exposures either in space or on Earth.

Concepts: Electron, Bone, Cancer, Ionizing radiation, Bacteria, Skeletal system, Atom, Osteoclast

171

Comparison of the binding sites of proteins is an effective means for predicting protein functions based on their structure information. Despite the importance of this problem and much research in the past, it is still very challenging to predict the binding ligands from the atomic structures of protein binding sites. Here, we designed a new algorithm, TIPSA (Triangulation-based Iterative-closest-point for Protein Surface Alignment), based on the iterative closest point (ICP) algorithm. TIPSA aims to find the maximum number of atoms that can be superposed between two protein binding sites, where any pair of superposed atoms has a distance smaller than a given threshold. The search starts from similar tetrahedra between two binding sites obtained from 3D Delaunay triangulation and uses the Hungarian algorithm to find additional matched atoms. We found that, due to the plasticity of protein binding sites, matching the rigid body of point clouds of protein binding sites is not adequate for satisfactory binding ligand prediction. We further incorporated global geometric information, the radius of gyration of binding site atoms, and used nearest neighbor classification for binding site prediction. Tested on benchmark data, our method achieved a performance comparable to the best methods in the literature, while simultaneously providing the common atom set and atom correspondences.

Concepts: DNA, Proteins, Protein, Prediction, Futurology, Atom, Binding site, Delaunay triangulation

170

In order to endow environmental protection features to dentifrice, hydroxyapatite (HA) was added to ordinary dentifrice. The effects on dentinal tubule occlusion and surface mineralization were compared after brushing dentine discs with dentifrice with or without HA. The two types of dentifrice were then added to 100 µg/ml of hexavalent chromium cation (Cr(6+)) solution in order to evaluate their capacities of adsorbing Cr(6+) from water. Our results showed that the dentifrice containing HA was significantly better than the ordinary dentifrice in occluding the dentinal tubules with a plugging rate greater than 90%. Moreover, the effect of the HA dentifrice was persistent and energy-dispersive spectrometer (EDS) revealed that the atomic percentages of calcium and phosphorus on the surface of dentine discs increased significantly. Adding HA to ordinary dentifrice significantly enhanced the ability of dentifrice to adsorb Cr(6+) from water with the removal rate up to 52.36%. In addition, the sorption was stable. Our study suggests that HA can be added to ordinary dentifrice to obtain dentifrice that has both relieving dentin hypersensitivity benefits and also helps to control environmental pollution.

Concepts: Chemistry, Atom, Adsorption, Pollution, Dentin, Hydroxylapatite, Dentine hypersensitivity, Environmentalism

170

Studies of the interaction between hydrogen and graphene have been increasingly required due to the indispensable modulation of the electronic structure of graphene for device applications and the possibility of using graphene as a hydrogen storage material. Here, we report on the behaviour of molecular hydrogen on graphene using the gate voltage-dependent resistance of single-, bi-, and multi-layer graphene sheets as a function of H(2) gas pressure up to 24 bar from 300 K to 345 K. Upon H(2) exposure, the charge neutrality point shifts toward the negative gate voltage region, indicating n-type doping, and distinct Raman signature changes, increases in the interlayer distance of multi-layer graphene, and a decrease in the d-spacing occur, as determined by TEM. These results demonstrate the occurrence of dissociative H(2) adsorption due to the existence of vacancy defects on graphene.

Concepts: Oxygen, Hydrogen, Catalysis, Atom, Pressure, Gas, Liquid hydrogen, Hydrogen storage

170

The alternate sigma factor sigH of Mycobacterium tuberculosis is expressed under stress and acts as a major regulator of several genes, including some other sigma factors and redox systems. While it is auto-regulated by its own promoter at the transcriptional level, its regulation at the post-translational level is through its cognate protein, an anti-sigma factor, RshA. Hither before RshA was believed to be a zinc-associated anti-sigma factor (ZAS) and the binding of RshA to SigH is redox dependent. Here, we show that RshA coordinates a [2Fe-2S] cluster using cysteines as ligands and native RshA has more affinity to [2Fe-2S] cluster than to zinc. Furthermore, we used amide hydrogen deuterium exchange mass spectrometry (HDX-MS), followed by site-directed mutagenesis in SigH and RshA, to elucidate the interaction mechanism of RshA and SigH and the potential role of metal ion clustering in SigH regulation. Three regions in SigH, comprising of residues 1-25, 58-69, 90-111, 115-132 and 157-196 and residues 35-57 of RshA show decreased deuterium exchange and reflect decreased solvent accessibility upon complexation with SigH. Of the three RshA mutants, created based on the HDX results, the RsHA E37A mutant shows stronger interaction with SigH, relative to WT RshA, while the H49A mutant abolishes interactions and the C(53)XXC(56)AXXA mutant has no effect on complexation with SigH. The D22A, D160A and E162 SigH mutants show significantly decreased binding to RshA and the E168A mutant completely abolished interactions with RshA, indicating that the SigH-RshA interaction is mediated by salt bridges. In addition, SigH-RshA interaction does not require clustering of metal ions. Based on our results, we propose a molecular model of the SigH-RshA interaction.

Concepts: Gene, Gene expression, Mass spectrometry, Hydrogen, Atom, Metal, Zinc, Sigma factor

170

The comparison of volumes of cells and subcellular structures with the pH values reported for them leads to a conflict with the definition of the pH scale. The pH scale is based on the ionic product of water, K(w) = [H(+)]×[OH(-)].We used K(w) [in a reversed way] to calculate the number of undissociated H(2)O molecules required by this equilibrium constant to yield at least one of its daughter ions, H(+) or OH(-) at a given pH. In this way we obtained a formula that relates pH to the minimal volume V(pH) required to provide a physical meaning to K(w), [Formula: see text] (where N(A) is Avogadro’s number). For example, at pH 7 (neutral at 25°C) V(pH) = 16.6 aL. Any deviation from neutral pH results in a larger V(pH) value. Our results indicate that many subcellular structures, including coated vesicles and lysosomes, are too small to contain free H(+) ions at equilibrium, thus the definition of pH based on K(w) is no longer valid. Larger subcellular structures, such as mitochondria, apparently contain only a few free H(+) ions. These results indicate that pH fails to describe intracellular conditions, and that water appears to be dissociated too weakly to provide free H(+) ions as a general source for biochemical reactions. Consequences of this finding are discussed.

Concepts: Acid, Chemistry, Atom, Acid dissociation constant, PH, Activity, PH indicator, Equilibrium constant

168

The structure of a recombinant pineapple cystatin (AcCYS) was determined by NMR with the RMSD of backbone and heavy atoms of twenty lowest energy structures of 0.56 and 1.11 Å, respectively. It reveals an unstructured N-terminal extension and a compact inhibitory domain comprising a four-stranded antiparallel β-sheet wrapped around a central α-helix. The three structural motifs (G(45), Q(89)XVXG, and W(120)) putatively responsible for the interaction with papain-like proteases are located in one side of AcCYS. Significant chemical shift perturbations in two loop regions, residues 45 to 48 (GIYD) and residues 89 to 91 (QVV), of AcCYS strongly suggest their involvement in the binding to papain, consistent with studies on other members of the cystatin family. However, the highly conserved W120 appears not to be involved in the binding with papain as no chemical shift perturbation was observed. Chemical shift index analysis further indicates that the length of the α-helix is shortened upon association with papain. Collectively, our data suggest that AcCYS undergoes local secondary structural rearrangements when papain is brought into close contact. A molecular model of AcCYS/papain complex is proposed to illustrate the interaction between AcCYS and papain, indicating a complete blockade of the catalytic triad by AcCYS.

Concepts: Molecular biology, Enzyme, Structure, Chemistry, Atom, Ananas, Bromeliaceae, Pineapple

166

Platinum-nanoparticle-based catalysts are widely used in many important chemical processes and automobile industries. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their use efficiency, however, very challenging. Here we report a practical synthesis for isolated single Pt atoms anchored to graphene nanosheet using the atomic layer deposition (ALD) technique. ALD offers the capability of precise control of catalyst size span from single atom, subnanometer cluster to nanoparticle. The single-atom catalysts exhibit significantly improved catalytic activity (up to 10 times) over that of the state-of-the-art commercial Pt/C catalyst. X-ray absorption fine structure (XAFS) analyses reveal that the low-coordination and partially unoccupied densities of states of 5d orbital of Pt atoms are responsible for the excellent performance. This work is anticipated to form the basis for the exploration of a next generation of highly efficient single-atom catalysts for various applications.

Concepts: Chemical reaction, Hydrogen, Catalysis, Atom, Ribozyme, Catalytic converter, Solid, Enzyme catalysis