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1.  Compounds with a ‘stuffed’ anti-bixbyite-type structure, analysed in terms of the Zintl–Klemm and coordination-defect concepts 
Compounds with a ‘stuffed anti-bixbyite’ structure, such as Li3AlN2, were analysed in terms of both the extended Zintl–Klemm concept and the coordination-defect concept. For the first time, inorganic crystal structures are seen as a set of ‘multiple resonance structures’ (Klemm pseudo-structures) which co-exist as the result of unexpected electron transfers between any species pair comprising either like or unlike atoms, cations or anions. If this is the driving force controlling crystal structures, the conventional oxidation states assigned to cations and anions lose some of their usefulness.
The bixbyite structure (Mn2O3) () is often described as a distorted face-centered cubic (f.c.c.) array of Mn atoms, with O atoms occupying 3/4 of the tetrahedral holes. The empty M 4 tetrahedra are centred at 16c. In anti-bixbyite structures (Mg3N2), cation vacancies are centred in empty N4 tetrahedra. If 16 hypothetical atoms were located at this site they would form the structure of γ-Si. This means that anti-bixbyite structures are ideally prepared to accommodate Si(Ge) atoms at these holes. Several compounds (Li3AlN2 and Li3ScN2) fully satisfy this expectation. They are really anti-bixbyites ‘stuffed’ with Al(Sc). The presence of these atoms in 16c is illuminated in the light of the extended Zintl–Klemm concept (EZKC) [Vegas & García-Baonza (2007 ▶). Acta Cryst. B63, 339–345], from which a compound would be the result of ‘multiple resonance’ pseudo-structures, emerging from electron transfers between any species pair (like or unlike atoms, cations or anions). The coordination-defect (CD) concept [Bevan & Martin (2008) ▶. J. Solid State Chem. 181, 2250–2259] is also consistent with the EZKC description of the pseudo-structures. A more profound insight into crystal structures is gained if one is not restricted to the contemplation of classical anions and cations in their conventional oxidation states.
doi:10.1107/S010876810803423X
PMCID: PMC2628973  PMID: 19155554
Zintl–Klemm concept; coordination-defect concept; multiple resonance structure; electron transfer
2.  Glyceryl Monooleate/Poloxamer 407 Cubic Nanoparticles as Oral Drug Delivery Systems: I. In Vitro Evaluation and Enhanced Oral Bioavailability of the Poorly Water-Soluble Drug Simvastatin 
AAPS PharmSciTech  2009;10(3):960-966.
Glyceryl monooleate (GMO)/poloxamer 407 cubic nanoparticles were investigated as potential oral drug delivery systems to enhance the bioavailability of the water-insoluble model drug simvastatin. The simvastatin-loaded cubic nanoparticles were prepared through fragmentation of the GMO/poloxamer 407 bulk cubic-phase gel using high-pressure homogenization. The internal structure of the cubic nanoparticles was identified by cryo-transmission electron microscopy. The mean diameter of the cubic nanoparticles varied within the range of 100–150 nm, and both GMO/poloxamer 407 ratio and theoretical drug loading had no significant effect on particle size and distribution. Almost complete entrapment with efficiency over 98% was achieved due to the high affinity of simvastatin to the hydrophobic regions of the cubic phase. Release of simvastatin from the cubic nanoparticles was limited both in 0.1 M hydrochloride solution containing 0.2% sodium lauryl sulfate and fasted-state simulated intestinal fluid with a total release of <3.0% at 10 h. Pharmacokinetic profiles in beagle dogs showed sustained plasma levels of simvastatin for cubic nanoparticles over 12 h. The relative oral bioavailability of simvastatin cubic nanoparticles calculated on the basis of area under the curve was 241% compared to simvastatin crystal powder. The enhancement of simvastatin bioavailability was possibly attributable to facilitated absorption by lipids in the formulation rather than improved release.
doi:10.1208/s12249-009-9292-4
PMCID: PMC2802151  PMID: 19636709
cubic nanoparticles; glyceryl monooleate; oral bioavailability; poloxamer 407; simvastatin
3.  Synthesis of Amine-stabilized Aqueous Colloidal Iron Oxide Nanoparticles 
Crystal growth & design  2007;7(3):471-475.
We demonstrate a simple one-step process for the synthesis of iron oxide nanoparticle aqueous colloids using the multifunctional molecule, dodecylamine (DDA), that electrostatically complexes with aqueous iron ions (one precursor Fe2+ from FeCl2), reduces them, and subsequently caps the nanoparticles. The iron oxide particles thus synthesized are of the face-centered cubic (FCC) phase with high degree of monodispersity with appropriate concentration of amine capping molecular layer. The aqueous magnetic nanocrystalline colloids were characterized by TEM, XRD, XPS, TGA/DTA and FTIR spectroscopy techniques. The relaxivity, stability, and hydrodynamic size of the nanoparticles were investigated for potential application in magnetic resonance imaging (MRI). The magnetic properties were also studied by using a superconducting quantum interference device (SQUID) magnetometer at room temperature. We believe that such simple one-step synthesis of biocompatible aqueous nanomagnetic colloids will have viable applications in biomedical imaging, diagnostics and therapeutics.
doi:10.1021/cg060656p
PMCID: PMC2659353  PMID: 19305647
4.  Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron 
Proteins  2008;73(3):730-741.
The orientational geometry of residue packing in proteins was studied in the past by superimposing clusters of neighboring residues with several simple lattices.1,2 In this work, instead of a lattice we use the regular polyhedron, the icosahedron, as the model to describe the orientational distribution of contacts in clusters derived from a high-resolution protein dataset (522 protein structures with high resolution < 1.5Å). We find that the order parameter (orientation function) measuring the angular overlap of directions in coordination clusters with directions of the icosahedron is 0.91, which is a significant improvement in comparison with the value 0.82 for the order parameter with the face-centered cubic (fcc) lattice. Close packing tendencies and patterns of residue packing in proteins is considered in detail and a theoretical description of these packing regularities is proposed.
doi:10.1002/prot.22092
PMCID: PMC3018876  PMID: 18498111
residue packing in proteins; icosahedron; packing pattern
5.  Low-energy structures of clusters supported on metal fcc(110) surfaces 
Nanoscale Research Letters  2011;6(1):633.
The low-energy structures (LESs) of adatom clusters on a series of metal face-centered cubic (fcc) (110) surfaces are systematically studied by the genetic algorithm, and a simplified model based on the atomic interactions is developed to explain the LESs. Two different kinds of LES group mainly caused by the different next nearest-neighbor (NNN) adatom-adatom interaction are distinguished, although the NNN atomic interaction is much weaker than the nearest-neighbor interaction. For a repulsive NNN atomic interaction, only the linear chain is included in the LES group. However, for an attractive one, type of structure in the LES group is various and replace gradually one by one with cluster size increasing. Based on our model, we also predict the shape feature of the large cluster which is found to be related closely to the ratio of NN and NNN bond energies, and discuss the surface reconstruction in the view of atomic interaction. The results are in accordance with the experimental observations.
PACS: 68.43.Hn; 68.43.Fg.
doi:10.1186/1556-276X-6-633
PMCID: PMC3274563  PMID: 22171642
supported cluster; structure; shape; metal surface
6.  Volumetric Interpretation of Protein Adsorption: Interfacial Packing of Protein Adsorbed to Hydrophobic Surfaces from Surface-Saturating Solution Concentrations 
Biomaterials  2010;32(4):969-978.
The maximum capacity of a hydrophobic adsorbent is interpreted in terms of square or hexagonal (cubic and face-centered-cubic, FCC) interfacial packing models of adsorbed blood proteins in a way that accommodates experimental measurements by the solution-depletion method and quartz-crystal-microbalance (QCM) for the human proteins serum albumin (HSA, 66 kDa), immunoglobulin G (IgG, 160 kDa), fibrinogen (Fib, 341 kDa), and immunoglobulin M (IgM, 1000 kDa). A simple analysis shows that adsorbent capacity is capped by a fixed mass/volume (e.g. mg/mL) surface-region (interphase) concentration and not molar concentration. Nearly analytical agreement between the packing models and experiment suggests that, at surface saturation, above-mentioned proteins assemble within the interphase in a manner that approximates a well-ordered array. HSA saturates a hydrophobic adsorbent with the equivalent of a single square-or-hexagonally-packed layer of hydrated molecules whereas the larger proteins occupy two-or-more layers, depending on the specific protein under consideration and analytical method used to measure adsorbate mass (solution depletion or QCM). Square-or-hexagonal (cubic and FCC) packing models cannot be clearly distinguished by comparison to experimental data. QCM measurement of adsorbent capacity is shown to be significantly different than that measured by solution depletion for similar hydrophobic adsorbents. The underlying reason is traced to the fact that QCM measures contribution of both core protein, water of hydration, and interphase water whereas solution depletion measures only the contribution of core protein. It is further shown that thickness of the interphase directly measured by QCM systematically exceeds that inferred from solution-depletion measurements, presumably because the static model used to interpret solution depletion does not accurately capture the complexities of the viscoelastic interfacial environment probed by QCM.
doi:10.1016/j.biomaterials.2010.09.075
PMCID: PMC3040988  PMID: 21035180
Protein adsorption; solution depletion; quartz crystal microbalance; interphase
7.  The Role of Protein Crystallography in Defining the Mechanisms of Biogenesis and Catalysis in Copper Amine Oxidase 
Copper amine oxidases (CAOs) are a ubiquitous group of enzymes that catalyze the conversion of primary amines to aldehydes coupled to the reduction of O2 to H2O2. These enzymes utilize a wide range of substrates from methylamine to polypeptides. Changes in CAO activity are correlated with a variety of human diseases, including diabetes mellitus, Alzheimer’s disease, and inflammatory disorders. CAOs contain a cofactor, 2,4,5-trihydroxyphenylalanine quinone (TPQ), that is required for catalytic activity and synthesized through the post-translational modification of a tyrosine residue within the CAO polypeptide. TPQ generation is a self-processing event only requiring the addition of oxygen and Cu(II) to the apoCAO. Thus, the CAO active site supports two very different reactions: TPQ synthesis, and the two electron oxidation of primary amines. Crystal structures are available from bacterial through to human sources, and have given insight into substrate preference, stereospecificity, and structural changes during biogenesis and catalysis. In particular both these processes have been studied in crystallo through the addition of native substrates. These latter studies enable intermediates during physiological turnover to be directly visualized, and demonstrate the power of this relatively recent development in protein crystallography.
doi:10.3390/ijms13055375
PMCID: PMC3382800  PMID: 22754303
amine oxidase; copper; biogenesis; catalysis; cofactor; protein crystallography
8.  FePt Nanoparticles as Fe Reservoir for Controlled Fe Release and Tumor Inhibition 
Journal of the American Chemical Society  2009;131(42):15346-15351.
Chemically disordered face centered cubic (fcc) FePt nanoparticles (NPs) show the controlled release of Fe in low pH solution. The released Fe catalyzes H2O2 decomposition into reactive oxygen species within cells, causing fast oxidation and deterioration of cellular membrane. Functionalized with luteinizing hormone-releasing hormone (LHRH) peptide via phospholipid, the fcc-FePt NPs can bind preferentially to the human ovarian cancer cell line (A2780) that over-expresses LHRH receptors, and exhibit high toxicity to these tumor cells. In contrast, the fcc-FePt NPs pre-etched in the low pH (4.8) buffer solution show non-appreciable cytotoxicity. The work demonstrates that fcc-FePt NPs may function as a new type of agent for controlled cancer therapy.
doi:10.1021/ja905938a
PMCID: PMC2791709  PMID: 19795861
9.  Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins 
Nucleic Acids Research  2004;32(Web Server issue):W104-W107.
We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html). For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions corresponding to the range of atomic coordinates. This box is then divided into cubic grids of selected size, which now have one or more charged atoms in them. This leaves each grid with a certain amount of charge. Cubic grids with more than a cutoff charge are then clustered using a hierarchical clustering method based on Euclidean distance. A tree diagram made from the resulting clusters indicates the distribution of charged and hydrophobic regions of the protein. Hydrophobic clusters are developed by grouping the positions of Cα atoms of such residues. We propose that such a tree representation will be helpful in detecting protein–protein interfaces, structure similarity and motif detection.
doi:10.1093/nar/gkh363
PMCID: PMC441501  PMID: 15215360
10.  Discrete plasticity in sub-10-nm-sized gold crystals 
Nature Communications  2010;1:144-.
Although deformation processes in submicron-sized metallic crystals are well documented, the direct observation of deformation mechanisms in crystals with dimensions below the sub-10-nm range is currently lacking. Here, through in situ high-resolution transmission electron microscopy (HRTEM) observations, we show that (1) in sharp contrast to what happens in bulk materials, in which plasticity is mediated by dislocation emission from Frank-Read sources and multiplication, partial dislocations emitted from free surfaces dominate the deformation of gold (Au) nanocrystals; (2) the crystallographic orientation (Schmid factor) is not the only factor in determining the deformation mechanism of nanometre-sized Au; and (3) the Au nanocrystal exhibits a phase transformation from a face-centered cubic to a body-centered tetragonal structure after failure. These findings provide direct experimental evidence for the vast amount of theoretical modelling on the deformation mechanisms of nanomaterials that have appeared in recent years.
Deformations in nanocrystals smaller than 10 nm are not well understood. The authors perform compression high-resolution transmission electron microscopy studies of gold nanoparticles, and determine that the nanoparticles deform through the emission of partial dislocations from free surfaces.
doi:10.1038/ncomms1149
PMCID: PMC3105591  PMID: 21266994
11.  Design and In Vitro Evaluation of Capsaicin Transdermal Controlled Release Cubic Phase Gels 
AAPS PharmSciTech  2010;11(3):1405-1410.
The purpose of this study was to design and investigate the transdermal controlled release cubic phase gels containing capsaicin using glycerol monooleate (MO), propylene glycol (1,2-propanediol, PG), and water. Three types of cubic phase gels were designed based on the ternary phase diagram of the MO–PG–water system, and their internal structures were confirmed by polarizing light microscopy (PLM) and small-angle X-ray scattering (SAXS). Release results showed the cubic phase gels could provide a sustained system for capsaicin, while the initial water content in the gels was the major factor affecting the release rate. Release kinetics was determined to fit Higuchi’s square-root equation indicating that the release was under diffusion control. The calculated diffusion exponent showed the release from cubic phase gels was anomalous transport. The unique structure of the cubic phases, capsaicin distributed in the lipid bilayers, and cubic phase gel swelling contributed to the release mechanism. The cubic phase gel may be an interesting application for transdermal delivery system of capsaicin in alleviating the post-incision pain.
doi:10.1208/s12249-010-9481-1
PMCID: PMC2974133  PMID: 20839080
capsaicin; cubic phase gel; kinetics
12.  Synchrotron study of the garnet-type oxide Li6CaSm2Ta2O12  
Hexalithium calcium disamarium(III) ditantalum(V) dodeca­oxide, Li6CaSm2Ta2O12, crystallizes in a cubic garnet-type structure. In the crystal structure, disordered Li atoms occupy two crystallographic sites. One Li has a tetra­hedral coordination environment in the oxide lattice, whereas the other Li atom occupies a significantly distorted octa­hedral site, with site occupancies for the two Li atoms of 0.26 (7) and 0.44 (2), respectively. Ca and Sm atoms are statistically distributed over the same crystallographic position with a occupancy of 2/3 for Sm and of 1/3 for Ca, and are eightfold coordinated by O atoms. The TaO6 octa­hedron is joined to six others via corner-sharing LiO4 tetra­hedra. One Li and the O atoms lie on general positions, while the other atoms are situated on special positions. The Sm/Ca position has 222, Ta has , and the tetra­hedrally coordinated Li atom has site symmetry.
doi:10.1107/S1600536809040008
PMCID: PMC2971154  PMID: 21578033
13.  Pb(core)/ZnO(shell) nanowires obtained by microwave-assisted method 
Nanoscale Research Letters  2011;6(1):553.
In this study, Pb-filled ZnO nanowires [Pb(core)/ZnO(shell)] were synthesized by a simple and novel one-step vapor transport and condensation method by microwave-assisted decomposition of zinc ferrite. The synthesis was performed using a conventional oven at 1000 W and 5 min of treatment. After synthesis, a spongy white cotton-like material was obtained in the condensation zone of the reaction system. HRTEM analysis revealed that product consists of a Pb-(core) with (fcc) cubic structure that preferentially grows in the [111] direction and a hexagonal wurtzite ZnO-(Shell) that grows in the [001] direction. Nanowire length was more than 5 μm and a statistical analysis determined that the shell and core diameters were 21.00 ± 3.00 and 4.00 ± 1.00 nm, respectively. Experimental, structural details, and synthesis mechanism are discussed in this study.
doi:10.1186/1556-276X-6-553
PMCID: PMC3236616  PMID: 21985637
14.  Large amplitude fluxional behaviour of elemental calcium under high pressure 
Scientific Reports  2012;2:372.
Experimental evidences are presented showing unusually large and highly anisotropic vibrations in the “simple cubic” (SC) unit cell adopted by calcium over a broad pressure ranging from 30–90 GPa and at temperature as low as 40 K. X-ray diffraction patterns show a preferential broadening of the (110) Bragg reflection indicating that the atomic displacements are not isotropic but restricted to the [110] plane. The unusual observation can be rationalized invoking a simple chemical perspective. As the result of pressure-induced s → d transition, Ca atoms situated in the octahedral environment of the simple cubic structure are subjected to Jahn-Teller distortions. First-principles molecular dynamics calculations confirm this suggestion and show that the distortion is of dynamical nature as the cubic unit cell undergoes large amplitude tetragonal fluctuations. The present results show that, even under extreme compression, the atomic configuration is highly fluxional as it constantly changes.
doi:10.1038/srep00372
PMCID: PMC3330680  PMID: 22523635
15.  CPSP-web-tools: a server for 3D lattice protein studies 
Bioinformatics  2009;25(5):676-677.
Summary: Studies on proteins are often restricted to highly simplified models to face the immense computational complexity of the associated problems. Constraint-based protein structure prediction (CPSP) tools is a package of very fast algorithms for ab initio optimal structure prediction and related problems in 3D HP-models [cubic and face centered cubic (FCC)]. Here, we present CPSP-web-tools, an interactive online interface of these programs for their immediate use. They include the first method for the direct prediction of optimal energies and structures in 3D HP side-chain models. This newest extension of the CPSP approach is described here for the first time.
Availability and Implementation: Free access at http://cpsp.informatik.uni-freiburg.de
Contact: cpsp@informatik.uni-freiburg.de; cpsp@informatik.uni-freiburg.de
doi:10.1093/bioinformatics/btp034
PMCID: PMC2647832  PMID: 19151096
16.  X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water 
A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å3, and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born–Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from −0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.
doi:10.1021/ct800239q
PMCID: PMC2873214  PMID: 20490369
17.  Poly[[hexa-μ-cyanido-manganese(II)iron(III)] penta­hydrate] 
The structure of the title compound, MnII[FeIII(CN)6]2/3·5H2O, features a face-centered cubic –Mn—NC—Fe– framework with both Mn and Fe having site symmetry m m. Since one-third of the [Fe(CN)6]3− units are missing for a given formula in order to maintain charge neutrality, each Mn atom around such a vacancy is coordinated not only by the N atoms of the CN groups but also by the O atoms of the ligand water mol­ecules. In addition to ligand water mol­ecules, two types of non-coordinated water mol­ecules, so-called zeolitic water mol­ecules, exist in the inter­stitial sites of the –Mn—NC—Fe– framework. The positions of the O atoms of the zeolitic water mol­ecules are fixed by the linkage via hydrogen bonds between ligand water and zeolitic water mol­ecules. The structure is related to a recently reported rubidium manganese hexa­cyano­ferrate. Site occupancy factors for Fe, C, N are 0.67; for two O atoms the value is 0.83 and for one O atom is 0.17.
doi:10.1107/S1600536807068869
PMCID: PMC2960286  PMID: 21201245
18.  The formation of supersaturated solid solutions in Fe–Cu alloys deformed by high-pressure torsion 
Acta Materialia  2012;60(3):860-871.
Fully dense bulk nanocomposites have been obtained by a novel two-step severe plastic deformation process in the immiscible Fe–Cu system. Elemental micrometer-sized Cu and Fe powders were first mixed in different compositions and subsequently high-pressure-torsion-consolidated and deformed in a two-step deformation process. Scanning electron microscopy, X-ray diffraction and atom probe investigations were performed to study the evolving far-from-equilibrium nanostructures which were observed at all compositions. For lower and higher Cu contents complete solid solutions of Cu in Fe and Fe in Cu, respectively, are obtained. In the near 50% regime a solid solution face-centred cubic and solid solution body-centred cubic nanograined composite has been formed. After an annealing treatment, these solid solutions decompose and form two-phase nanostructured Fe–Cu composites with a high hardness and an enhanced thermal stability. The grain size of the composites retained nanocrystalline up to high annealing temperatures.
doi:10.1016/j.actamat.2011.10.044
PMCID: PMC3284766  PMID: 22368454
High-pressure torsion; Solid solubility extension; Fe–Cu alloy
19.  High Resolution Structure of the ba3 Cytochrome c Oxidase from Thermus thermophilus in a Lipidic Environment 
PLoS ONE  2011;6(7):e22348.
The fundamental chemistry underpinning aerobic life on Earth involves reduction of dioxygen to water with concomitant proton translocation. This process is catalyzed by members of the heme-copper oxidase (HCO) superfamily. Despite the availability of crystal structures for all types of HCO, the mode of action for this enzyme is not understood at the atomic level, namely how vectorial H+ and e- transport are coupled. Toward addressing this problem, we report wild type and A120F mutant structures of the ba3-type cytochrome c oxidase from Thermus thermophilus at 1.8 Å resolution. The enzyme has been crystallized from the lipidic cubic phase, which mimics the biological membrane environment. The structures reveal 20 ordered lipid molecules that occupy binding sites on the protein surface or mediate crystal packing interfaces. The interior of the protein encloses 53 water molecules, including 3 trapped in the designated K-path of proton transfer and 8 in a cluster seen also in A-type enzymes that likely functions in egress of product water and proton translocation. The hydrophobic O2-uptake channel, connecting the active site to the lipid bilayer, contains a single water molecule nearest the CuB atom but otherwise exhibits no residual electron density. The active site contains strong electron density for a pair of bonded atoms bridging the heme Fea3 and CuB atoms that is best modeled as peroxide. The structure of ba3-oxidase reveals new information about the positioning of the enzyme within the membrane and the nature of its interactions with lipid molecules. The atomic resolution details provide insight into the mechanisms of electron transfer, oxygen diffusion into the active site, reduction of oxygen to water, and pumping of protons across the membrane. The development of a robust system for production of ba3-oxidase crystals diffracting to high resolution, together with an established expression system for generating mutants, opens the door for systematic structure-function studies.
doi:10.1371/journal.pone.0022348
PMCID: PMC3141039  PMID: 21814577
20.  Role of the conserved distal heme asparagine of coral allene oxide synthase (Asn137) and human catalase (Asn148): mutations affect the rate but not the essential chemistry of the enzymatic transformations 
A catalase-related allene oxide synthase (cAOS) and true catalases that metabolize hydrogen peroxide have similar structure around the heme. One of the distal heme residues considered to help control catalysis is a highly conserved asparagine. Here we addressed the role of this residue in metabolism of the natural substrate 8R-hydroperoxyeicosatetraenoic acid by cAOS and in H2O2 breakdown by catalase. In cAOS, the mutations N137A, N137Q, N137S, N137D, and N137H drastically reduced the rate of reaction (to 0.8–4% of wild-type), yet the mutants all formed the allene oxide as product. This is remarkable because there are many potential heme-catalyzed transformations of fatty acid hydroperoxides and special enzymatic control must be required. In human catalase, the N148A, N148S, or N148D mutations only reduced rates to ~20% of wild-type. The distal heme Asn is not essential in either catalase or cAOS. Its conservation throughout evolution may relate to a role in optimizing catalysis.
doi:10.1016/j.abb.2008.07.011
PMCID: PMC2598388  PMID: 18652800
Peroxidase; Distal heme; Enzyme kinetics; HPETE; Hydroperoxyeicosatetraenoic acid; Hydrogen peroxide; Allene oxide; Allene oxide synthase; Catalase
21.  Anisotropic epitaxial ZnO/CdO core/shell heterostructure nanorods 
Nanoscale Research Letters  2012;7(1):626.
Various surface structures and polarities of one-dimensional nanostructures offer additional control in synthesizing heterostructures suitable for optoelectronic and electronic applications. In this work, we report synthesis and characterization of ZnO-CdO nanorod-based heterostructures grown on a-plane sapphire. The heterojunction formed on the sidewall surface of the nanorod shows that wurtzite ZnO {1010} planes are interfaced with rocksalt CdO {100}. This is evidently different from the heterojunction formed on the nanorod top surface, where a ZnO (0001) top plane is interfaced with a CdO (111) plane. Such anisotropic heterostructures are determined by different surface structures of the nanorods and their polarities. Revelation of such anisotropic heterojunctions will provide a clue for understanding charge transport properties in electronic and optoelectronic nanodevices.
doi:10.1186/1556-276X-7-626
PMCID: PMC3552712  PMID: 23151180
ZnO nanorod; CdO; Heterojunction; Anisotropy
22.  Role of Radical Formation at Tyrosine 193 in the Allene Oxide Synthase Domain of a Lipoxygenase–AOS Fusion Protein from Coral† 
Biochemistry  2003;42(22):6871-6880.
Coral allene oxide synthase (cAOS), a fusion protein with 8R-lipoxygenase in Plexaura homomalla, is a hemoprotein with sequence similarity to catalases. cAOS reacts rapidly with the oxidant peracetic acid to form heme compound I and intermediate II. Concomitantly, an electron paramagnetic resonance (EPR) signal with tyrosyl radical-like features, centered at a g-value of 2.004–2.005, is formed. The radical is identified as tyrosyl by changes in EPR spectra when deuterated tyrosine is incorporated in cAOS. The radical location in cAOS is determined by mutagenesis of Y193 and Y209. Upon oxidation, native cAOS and mutant Y209F exhibit the same radical spectrum, but no significant tyrosine radical forms in mutant Y193H, implicating Y193 as the radical site in native cAOS. Estimates of the side chain torsion angles for the radical at Y193, based on the β-proton isotropic EPR hyperfine splitting, Aiso, are θ1 = 21 to 30° and θ2 = −99 to −90°. The results show that cAOS can cleave nonsubstrate hydroperoxides by a heterolytic path, although a homolytic course is likely taken in converting the normal substrate, 8R-hydroperoxyeicosatetraenoic acid (8R-HpETE), to product. Coral AOS achieves specificity for the allene oxide formed by selection of the homolytic pathway normally, while it inactivates by the heterolytic path with nonoptimal substrates. Accordingly, with the nonoptimal substrate, 13R-hydroperoxyoctadecadienoic acid (13R-HpODE), mutant Y193H is inactivated after turning over significantly fewer substrate molecules than required to inactivate native cAOS or the Y209F mutant because it cannot absorb oxidizing equivalents by forming a radical at Y193.
doi:10.1021/bi027427y
PMCID: PMC1382190  PMID: 12779342
23.  Structural, electronic and vibrational properties of InN under high pressure 
Physica. B, Condensed Matter  2012;407(6):1008-1013.
The structural, electronic and vibrational properties of InN under pressures up to 20 GPa have been investigated using the pseudo-potential plane wave method (PP-PW). The generalized-gradient approximation (GGA) in the frame of density functional theory (DFT) approach has been adopted. It is found that the transition from wurtzite (B4) to rocksalt (B1) phase occurs at a pressure of approximately 12.7 GPa. In addition, a change from a direct to an indirect band gap is observed. The mechanism of these changes is discussed. The phonon frequencies and densities of states (DOS) are derived using the linear response approach and density functional perturbation theory (DFPT). The properties of phonons are described by the harmonic approximation method. Our results show that phonons play an important role in the mechanism of phase transition and in the instability of B4 (wurtzite) just before the pressure of transition. At zero pressure our data agree well with recently reported experimental results.
doi:10.1016/j.physb.2011.12.129
PMCID: PMC3299643  PMID: 22485065
Electronic structure; High pressure; Phase transition
24.  Fabrication and Characterization of Gelatin Stabilized Silver Nanoparticles under UV-Light 
Silver nanoparticles (Ag-NPs) were successfully synthesized using the UV irradiation of aqueous solutions containing AgNO3 and gelatin as a silver source and stabilizer, respectively. The UV irradiation times influence the particles’ diameter of the Ag-NPs, as evidenced from surface plasmon resonance (SPR) bands and transmission electron microscopy (TEM) images. When the UV irradiation time was increased, the mean size of particles continuously decreased as a result of photoinduced Ag-NPs fragmentation. Based on X-ray diffraction (XRD), the UV-irradiated Ag-NPs were a face-centered cubic (fcc) single crystal without any impurity. This study reveals that the UV irradiation-mediated method is a green chemistry and promising route for the synthesis of stable Ag-NPs for several applications (e.g., medical and surgical devices). The important advantages of this method are that it is cheap, easy, and free of toxic materials.
doi:10.3390/ijms12096346
PMCID: PMC3189787  PMID: 22016663
silver nanoparticles; gelatin; UV-light; stabilizer; UV-Vis spectroscopy
25.  Periplasmic Electron Transfer via the c-Type Cytochromes MtrA and FccA of Shewanella oneidensis MR-1 ▿  
Applied and Environmental Microbiology  2009;75(24):7789-7796.
Dissimilatory microbial reduction of insoluble Fe(III) oxides is a geochemically and ecologically important process which involves the transfer of cellular, respiratory electrons from the cytoplasmic membrane to insoluble, extracellular, mineral-phase electron acceptors. In this paper evidence is provided for the function of the periplasmic fumarate reductase FccA and the decaheme c-type cytochrome MtrA in periplasmic electron transfer reactions in the gammaproteobacterium Shewanella oneidensis. Both proteins are abundant in the periplasm of ferric citrate-reducing S. oneidensis cells. In vitro fumarate reductase FccA and c-type cytochrome MtrA were reduced by the cytoplasmic membrane-bound protein CymA. Electron transfer between CymA and MtrA was 1.4-fold faster than the CymA-catalyzed reduction of FccA. Further experiments showing a bidirectional electron transfer between FccA and MtrA provided evidence for an electron transfer network in the periplasmic space of S. oneidensis. Hence, FccA could function in both the electron transport to fumarate and via MtrA to mineral-phase Fe(III). Growth experiments with a ΔfccA deletion mutant suggest a role of FccA as a transient electron storage protein.
doi:10.1128/AEM.01834-09
PMCID: PMC2794085  PMID: 19837833

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