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Find video protocols related to scientific articles indexed in Pubmed.
[Adaptive EEMD residue related baseline correction algorithm].
Guang Pu Xue Yu Guang Pu Fen Xi
PUBLISHED: 11-01-2014
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Baseline correction is an important part of spectral analysis; the existing algorithms usually need to set the key parameters and does not have adaptability. The spectral baseline is fitted by the residue according to the feature of ensemble empirical mode decomposition (EEMD for short). The correlation between residual and original signal, the self-correlation and the cross-correlation of residual form the residual related rule. The residual related rule is proposed to judge whether the residual is a component of baseline, based on which adaptive EEMD residual related base line algorithm is proposed. With experiment on the simulated spectrum data of superimposing curve background and the linear background, the results showed that in the case of known baseline mathematical assumption: EEMD residual related method is not so good for polynomial fitting, it is almost no difference from linear fitting, but is better than the wavelet decomposition. In the absence of spectral background knowledge, the real Raman spectrum data are tested. The model is established between Raman spectra treated by the procedure above and chlorophyll, and the model corrected by EEMD residual related baseline method has the biggest correlation coefficient and prediction coefficient, but the smallest root mean square error of cross validation and relative prediction deviation. The effect of EEMD residual related baseline method effects on the peak position, peak intensity and peak width is the smallest in all kinds of baseline correction methods. EEMD residual method has the best baseline correction effect. Experiments show that this algorithm can be used for Raman spectra baseline correction, without prior knowledge of the sample composition analysis, and there is no need to select appropriate fitting function, fitting data points, fitting order as well as basis function and decomposition levels, also there is no need of mathematical hypothesis of baseline signal distribution, so the adaptability is very strong.
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Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 10-22-2014
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Coenzyme Q (CoQ) is an isoprenylated quinone that is essential for cellular respiration and is synthesized in mitochondria by the combined action of at least nine proteins (COQ1-9). Although most COQ proteins are known to catalyze modifications to CoQ precursors, the biochemical role of COQ9 remains unclear. Here, we report that a disease-related COQ9 mutation leads to extensive disruption of the CoQ protein biosynthetic complex in a mouse model, and that COQ9 specifically interacts with COQ7 through a series of conserved residues. Toward understanding how COQ9 can perform these functions, we solved the crystal structure of Homo sapiens COQ9 at 2.4 Å. Unexpectedly, our structure reveals that COQ9 has structural homology to the TFR family of bacterial transcriptional regulators, but that it adopts an atypical TFR dimer orientation and is not predicted to bind DNA. Our structure also reveals a lipid-binding site, and mass spectrometry-based analyses of purified COQ9 demonstrate that it associates with multiple lipid species, including CoQ itself. The conserved COQ9 residues necessary for its interaction with COQ7 comprise a surface patch around the lipid-binding site, suggesting that COQ9 might serve to present its bound lipid to COQ7. Collectively, our data define COQ9 as the first, to our knowledge, mammalian TFR structural homolog and suggest that its lipid-binding capacity and association with COQ7 are key features for enabling CoQ biosynthesis.
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Racemosin C, a novel minor bisindole alkaloid with protein tyrosine phosphatase-1B inhibitory activity from the green alga Caulerpa racemosa.
J Asian Nat Prod Res
PUBLISHED: 10-09-2014
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A novel minor bisindole alkaloid, racemosin C (1), characterized by a naturally unprecedented 8-hydroxy-2,4,6-cyclooctatrienone ring fused with two indole systems, was isolated from the green alga Caulerpa racemosa, together with one known related metabolite, caulersin (2). The structure of 1 was elucidated on the basis of extensive spectroscopic analysis, and by comparison with the data of related known compounds. A plausible biosynthetic pathway of 1 was proposed. Compounds 1 and 2 exhibited significant PTP1B inhibitory activity with IC50 values of 5.86 ± 0.57 and 7.14 ± 1.00 ?M, respectively, compared with the positive control oleanolic acid (IC50 = 3.03 ± 0.20 ?M). On the basis of the data obtained, the Caulerpa bisindole alkaloids may be considered as a new class of PTP1B inhibitors.
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Structural modulation in two Cu(II)-based MOFs by synergistic assembly involving the mixed-ligand synthetic strategy and the solvent effect.
Dalton Trans
PUBLISHED: 09-20-2014
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Two Cu(II)-based MOFs have been constructed by synergistic assembly involving the mixed-ligand synthetic strategy and the solvent effect. Compound is a 3D structure and represents a cds topology, while compound displays a rare structure built by three distinct {Cu4} clusters as SBUs. Moreover, the magnetic properties of have been thoroughly investigated.
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Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 09-08-2014
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Methylation of the N6 position of selected internal adenines (m(6)A) in mRNAs and noncoding RNAs is widespread in eukaryotes, and the YTH domain in a collection of proteins recognizes this modification. We report the crystal structure of the splicing factor YT521-B homology (YTH) domain of Zygosaccharomyces rouxii MRB1 in complex with a heptaribonucleotide with an m(6)A residue in the center. The m(6)A modification is recognized by an aromatic cage, being sandwiched between a Trp and Tyr residue and with the methyl group pointed toward another Trp residue. Mutations of YTH domain residues in the RNA binding site can abolish the formation of the complex, confirming the structural observations. These residues are conserved in the human YTH proteins that also bind m(6)A RNA, suggesting a conserved mode of recognition. Overall, our structural and biochemical studies have defined the molecular basis for how the YTH domain functions as a reader of methylated adenines.
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Targeted structure modulation of "pillar-layered" metal-organic frameworks for CO? capture.
Inorg Chem
PUBLISHED: 08-15-2014
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Two new zinc MOFs with similar "pillar-layered" framework structures based on 1,1'-biphenyl-2,2',6,6'-tetracarboxylic acid (H4bpta) and two different bipyridine pillar ligands, namely {[Zn4(bpta)2(4-pna)2(H2O)2]·4DMF·3H2O}n (1) and {[Zn2(bpta)(bpy-ea)(H2O)]·2DMF·H2O}n (2) (4-pna = N-(4-pyridyl)isonicotinamide and bpy-ea = 1,2-bis(4-pyridyl)ethane), have been synthesized and investigated with their CO2 adsorption properties. By analysis of the structure properties and the CO2 adsorption performances of these two MOFs, it was found that the introduction of polar acylamide groups via 4-pna resulted in 1 with enhanced CO2 capacity and CO2/CH4 selectivity at low pressure. In contrast, the framework of 2 shows flexible properties originating from the flexibility of the ethanediylidene group in the bpy-ea ligand, which benefits the sieve effect of pores to give higher CO2/CH4 selectivity at a relatively high pressure range.
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Zn(II)-benzotriazolate clusters based amide functionalized porous coordination polymers with high CO? adsorption selectivity.
Inorg Chem
PUBLISHED: 08-13-2014
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Two new porous coordination polymers (PCPs) based on different nanosized C3 symmetry ligands and Zn(II)-benzotriazolate clusters have been synthesized solvothermally. Both of the desolvated complexes show selective uptake of CO2 over CH4 and N2 at ambient temperature.
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Structure-Guided Functional Characterization of Enediyne Self-Sacrifice Resistance Proteins, CalU16 and CalU19.
ACS Chem. Biol.
PUBLISHED: 08-13-2014
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Calicheamicin ?1(I) (1) is an enediyne antitumor compound produced by Micromonospora echinospora spp. calichensis, and its biosynthetic gene cluster has been previously reported. Despite extensive analysis and biochemical study, several genes in the biosynthetic gene cluster of 1 remain functionally unassigned. Using a structural genomics approach and biochemical characterization, two proteins encoded by genes from the 1 biosynthetic gene cluster assigned as "unknowns", CalU16 and CalU19, were characterized. Structure analysis revealed that they possess the STeroidogenic Acute Regulatory protein related lipid Transfer (START) domain known mainly to bind and transport lipids and previously identified as the structural signature of the enediyne self-resistance protein CalC. Subsequent study revealed calU16 and calU19 to confer resistance to 1, and reminiscent of the prototype CalC, both CalU16 and CalU19 were cleaved by 1 in vitro. Through site-directed mutagenesis and mass spectrometry, we identified the site of cleavage in each protein and characterized their function in conferring resistance against 1. This report emphasizes the importance of structural genomics as a powerful tool for the functional annotation of unknown proteins.
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Gadolinium oxalate derivatives with enhanced magnetocaloric effect via ionothermal synthesis.
Inorg Chem
PUBLISHED: 08-12-2014
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Two new oxalate-bridged Gd(III) coordination polymers, namely, (choline)[Gd(C2O4)(H2O)3Cl]Cl·H2O (1) and [Gd(C2O4)(H2O)3Cl] (2), were first obtained ionothermally by using a deep eutectic solvent (DES). The magnetic studies and heat capacity measurements reveal that the two-dimensional Gd(III)-based coordination polymer of 2 has the higher magnetic density and exhibits a larger cryogenic magnetocaloric effect (MCE) (?S(m) = 48 J kg(-1) K(-1) for ?H = 7 T at 2.2 K).
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Solvent induced rapid modulation of micro/nano structures of metal carboxylates coordination polymers: mechanism and morphology dependent magnetism.
Sci Rep
PUBLISHED: 08-12-2014
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Rational modulation of morphology is very important for functional coordination polymers (CPs) micro/nanostructures, and new strategies are still desired to achieve this challenging target. Herein, organic solvents have been established as the capping agents for rapid modulating the growth of metal-carboxylates CPs in organic solvent/water mixtures at ambient conditions. Co-3,5-pyridinedicarboxylate (pydc) CPs was studied here as the example. During the reaction, the organic solvents exhibited three types of modulation effect: anisotropic growth, anisotropic growth/formation of new crystalline phase and the formation of new crystalline phase solely, which was due to the variation of their binding ability with metal cations. The following study revealed that the binding ability was critically affected by their functional groups and molecular size. Moreover, their modulation effect could be finely tuned by changing volume ratios of solvent mixtures. Furthermore, they could be applied for modulating other metal-carboxylates CPs: Co-1,3,5-benzenetricarboxylic (BTC), Zn-pydc and Eu-pydc etc. Additionally, the as-prepared Co-pydc CPs showed a fascinating morphology-dependent antiferromagnetic behavior.
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Effectiveness of contrast-enhanced ultrasound in the classification and emergency management of abdominal trauma.
Eur Radiol
PUBLISHED: 08-09-2014
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To analyse the correlation between contrast-enhanced ultrasound (CEUS)-based classification of the severity of abdominal parenchymal organ trauma and clinical outcomes, and to explore CEUS in classifying patients with such trauma, expecting that the use of CEUS will potentially enhance the quality and speed of the emergency management of abdominal trauma.
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A Heterometallic Fe(II) -Dy(III) Single-Molecule Magnet with a Record Anisotropy Barrier.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 07-31-2014
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A record anisotropy barrier (319?cm(-1) ) for all d-f complexes was observed for a unique Fe(II) -Dy(III) -Fe(II) single-molecule magnet (SMM), which possesses two asymmetric and distorted Fe(II) ions and one quasi-D5h Dy(III) ion. The frozen magnetization of the Dy(III) ion leads to the decreased Fe(II) relaxation rates evident in the Mössbauer spectrum. Ab initio calculations suggest that tunneling is interrupted effectively thanks to the exchange doublets.
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Enhanced spin-crossover behavior mediated by supramolecular cooperative interactions.
Inorg Chem
PUBLISHED: 07-14-2014
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Three one-dimensional (1D) hetereobimetallic coordination polymers [Fe(II)(L)2(AgCN)2]·Solv (L = bpt(-), 1; L = Mebpt(-), Solv = 1.75EtOH, 2; L = bpzt(-), 3) with in situ generated AgCN species were synthesized by solvothermal reactions of Fe(II) salt, K[Ag(CN)2], and the corresponding ligands [bptH = 3,5-bis(pyridin-2-yl)-1,2,4-triazole, MebptH = 3-(3-methyl-2-pyridyl)-5-(2-pyridyl)-1,2,4-triazole, and bpztH = 3,5-bis(pyrazin-2-yl)-1,2,4-triazole]. They were further characterized by X-ray crystallography, magnetic and photomagnetic measurements, and differential scanning calorimetry. Single-crystal X-ray analyses show that they are isostructural with 1D zigzag chain structures with rhombus {Fe2Ag2} units, in which the substituted bpt(-) ligand connects the Fe(II) ion and AgCN species in a cis bridging mode. Then the zigzag chains are packed into three-dimensional supramolecular structures by ?···? interactions. Most importantly, weak Ag···N interactions (2.750 Å at 150 K) between the ?-stacked neighboring chains present in complex 3. Magnetic susceptibility measurements exhibit that complex 1 displays characteristic paramagnetic behavior in the temperature range investigated. Complex 2 undergoes a gradual spin-crossover (SCO) with critical temperatures T(1/2)? = 232 K and T(1/2)? = 235 K, whereas 3 exhibits an abrupt SCO with critical temperatures T(1/2)? = 286 K and T(1/2)? = 292 K. The magnetostructural relationships suggest that the magnetic behaviors can be modulated from paramagnetic behavior to abrupt and hysteretic SCO near room temperature through adjustment of the electronic substituent effect and intermolecular interactions.
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[Study on plasma temperature of a large area surface discharge by optical emission spectrum].
Guang Pu Xue Yu Guang Pu Fen Xi
PUBLISHED: 07-11-2014
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A large area surface discharge was realized in air/argon gas mixture by designing a discharge device with water electrodes. By using optical emission spectrum, the variations of the molecular vibrational temperature, the mean energy of electron, and the electronic excitation temperature as a function of the gas pressure were studied. The nitrogen molecular vibrational temperature was calculated according to the emission line of the second positive band system of the nitrogen molecule (C3 pi(u) --> B 3 pi(g)). The electronic excitation temperature was obtained by using the intensity ratio of Ar I 763.51 nm (2P(6) --> 1S(5)) to Ar I 772.42 nm (2P(2) --> 1S(3)). The changes in the mean energy of electron were studied by the relative intensity ratio of the nitrogen molecular ion 391.4 nm to nitrogen 337.1 nm. It was found that the intensity of emission spectral line increases with the increase in the gas pressure, meanwhile, the outline and the ratios of different spectral lines intensity also change. The molecular vibrational temperature, the mean energy of electron, and the electronic excitation temperature decrease as the gas pressure increases from 0.75 x 10(5) Pa to 1 x 10(5) Pa.
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A human mitochondrial poly(A) polymerase mutation reveals the complexities of post-transcriptional mitochondrial gene expression.
Hum. Mol. Genet.
PUBLISHED: 07-09-2014
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The p.N478D missense mutation in human mitochondrial poly(A) polymerase (mtPAP) has previously been implicated in a form of spastic ataxia with optic atrophy. In this study, we have investigated fibroblast cell lines established from family members. The homozygous mutation resulted in the loss of polyadenylation of all mitochondrial transcripts assessed; however, oligoadenylation was retained. Interestingly, this had differential effects on transcript stability that were dependent on the particular species of transcript. These changes were accompanied by a severe loss of oxidative phosphorylation complexes I and IV, and perturbation of de novo mitochondrial protein synthesis. Decreases in transcript polyadenylation and in respiratory chain complexes were effectively rescued by overexpression of wild-type mtPAP. Both mutated and wild-type mtPAP localized to the mitochondrial RNA-processing granules thereby eliminating mislocalization as a cause of defective polyadenylation. In vitro polyadenylation assays revealed severely compromised activity by the mutated protein, which generated only short oligo(A) extensions on RNA substrates, irrespective of RNA secondary structure. The addition of LRPPRC/SLIRP, a mitochondrial RNA-binding complex, enhanced activity of the wild-type mtPAP resulting in increased overall tail length. The LRPPRC/SLIRP effect although present was less marked with mutated mtPAP, independent of RNA secondary structure. We conclude that (i) the polymerase activity of mtPAP can be modulated by the presence of LRPPRC/SLIRP, (ii) N478D mtPAP mutation decreases polymerase activity and (iii) the alteration in poly(A) length is sufficient to cause dysregulation of post-transcriptional expression and the pathogenic lack of respiratory chain complexes.
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Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 07-07-2014
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Replication-dependent histone mRNAs end with a conserved stem loop that is recognized by stem-loop-binding protein (SLBP). The minimal RNA-processing domain of SLBP is phosphorylated at an internal threonine, and Drosophila SLBP (dSLBP) also is phosphorylated at four serines in its 18-aa C-terminal tail. We show that phosphorylation of dSLBP increases RNA-binding affinity dramatically, and we use structural and biophysical analyses of dSLBP and a crystal structure of human SLBP phosphorylated on the internal threonine to understand the striking improvement in RNA binding. Together these results suggest that, although the C-terminal tail of dSLBP does not contact the RNA, phosphorylation of the tail promotes SLBP conformations competent for RNA binding and thereby appears to reduce the entropic penalty for the association. Increased negative charge in this C-terminal tail balances positively charged residues, allowing a more compact ensemble of structures in the absence of RNA.
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Doping cobalt into a [Zn?] cluster-based MOF to tune magnetic behaviour and induce fluorescence signal mutation.
Dalton Trans
PUBLISHED: 06-24-2014
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An in situ doping strategy was successfully applied to tune the magnetic behaviour and induce fluorescence signal mutation of a spindle heptanuclear zinc cluster-based MOF, by only modifying its structural composition. The Co(II)-doped Zn(II)-MTV-M'MOF exhibits canted antiferromagnetism and weaker fluorescence properties.
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Disklike hepta- and tridecanuclear cobalt clusters. Synthesis, structures, magnetic properties, and DFT calculations.
Inorg Chem
PUBLISHED: 05-14-2014
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The synthesis, structure and magnetic properties are reported of two disklike mixed-valence cobalt clusters [Co(III)Co(II)6(thmp)2(acac)6(ada)3] (1) and [Co(III)2Co(II)11(thmp)4(Me3CCOO)4(acac)6(OH)4(H2O)4](Me3CCOO)2·H2O (2). Heptanuclear complex 1 was prepared by solvothermal reaction of cobalt(II) acetylacetonate (Co(acac)2), 1,1,1-tris(hydroxymethyl)-propane (H3thmp), and adamantane-1-carboxylic acid (Hada), whereas by substituting Hada with Me3CCO2H, tridecanuclear complex 2 was obtained with an unexpected [Co(III)2Co(II)11] core. The core structures of 1 and 2 are related to each other: that of 1 arranges as a centered hexagon of a central Co(III) ion surrounded by a [Co(II)6] hexagon, while that of 2 can be described as a larger oligomer based on two vertex-sharing [Co(III)Co(II)6] clusters. Variable-temperature direct-current magnetic susceptibility measurements demonstrated overall ferromagnetic coupling between the Co(II) ions within both clusters. The magnetic exchange (J) and magnetic anisotropy (D) values were quantified with appropriate spin-Hamiltonian models and were also supported by density functional theory calculations. The presence of frequency-dependent out-of-phase (?M?) alternating current susceptibility signals at temperatures below 3 K suggested that 2 might be a single-molecule magnet.
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Structure and function of a single-chain, multi-domain long-chain acyl-CoA carboxylase.
Nature
PUBLISHED: 05-04-2014
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Biotin-dependent carboxylases are widely distributed in nature and have important functions in the metabolism of fatty acids, amino acids, carbohydrates, cholesterol and other compounds. Defective mutations in several of these enzymes have been linked to serious metabolic diseases in humans, and acetyl-CoA carboxylase is a target for drug discovery in the treatment of diabetes, cancer and other diseases. Here we report the identification and biochemical, structural and functional characterizations of a novel single-chain (120 kDa), multi-domain biotin-dependent carboxylase in bacteria. It has preference for long-chain acyl-CoA substrates, although it is also active towards short-chain and medium-chain acyl-CoAs, and we have named it long-chain acyl-CoA carboxylase. The holoenzyme is a homo-hexamer with molecular mass of 720 kDa. The 3.0 Å crystal structure of the long-chain acyl-CoA carboxylase holoenzyme from Mycobacterium avium subspecies paratuberculosis revealed an architecture that is strikingly different from those of related biotin-dependent carboxylases. In addition, the domains of each monomer have no direct contact with each other. They are instead extensively swapped in the holoenzyme, such that one cycle of catalysis involves the participation of four monomers. Functional studies in Pseudomonas aeruginosa suggest that the enzyme is involved in the utilization of selected carbon and nitrogen sources.
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Self-assembled conjugated polymer spheres as fluorescent microresonators.
Sci Rep
PUBLISHED: 04-28-2014
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Confinement of light inside an active medium cavity can amplify emission. Whispering gallery mode (WGM) is one of mechanisms that amplifies light effectively by confining it inside high-refractive-index microstructures, where light propagates along the circumference of a sphere via total internal reflection. Here we show that isolated single microspheres of 2-10??m diameter, formed from self-assembly of ?-conjugated alternating copolymers, display WGM photoemission induced by laser pumping. The wavelengths of the emission peaks depend sensitively on the sphere size, position of the excitation spot and refractive index of each polymer. The Q-factor increases with increasing sphere diameter and displays a linear correlation with the reciprocal radius, indicating that the small curvature increases the efficacy of the total internal reflection. WGM photoemission from ?-conjugated polymer microspheres is unprecedented and may be of high technological impact since the microspheres fulfill the role of fluorophores, high-refractive-index media and resonators simultaneously, in addition to their simple fabrication process.
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The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA.
Nat. Struct. Mol. Biol.
PUBLISHED: 04-28-2014
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A conserved stem-loop motif of the constitutive decay element (CDE) in the 3' UTR of mRNAs is recognized by the ROQ domain of Roquin, which mediates mRNA degradation. Here we report two crystal structures of the Homo sapiens ROQ domain in complex with CDE RNA. The ROQ domain has an elongated shape with three subdomains. The 19-nt Hmgxb3 CDE is bound as a stem-loop to domain III. The 23-nt TNF RNA is bound as a duplex to a separate site at the interface between domains I and II. Mutagenesis studies confirm that the ROQ domain has two separate RNA-binding sites, one for stem-loop RNA (A site) and the other for double-stranded RNA (B site). Mutation in either site perturbs the Roquin-mediated degradation of HMGXB3 and IL6 mRNAs in human cells, demonstrating the importance of both sites for mRNA decay.
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Guest-effected spin-crossover in a novel three-dimensional self-penetrating coordination polymer with permanent porosity.
Inorg Chem
PUBLISHED: 03-31-2014
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Porous and nonporous 3D heterobimetallic coordination polymers based on the 1,4-di(pyridin-4-yl)benzene ligand (dpb), [Fe(dpb){Ag(CN)2}{Ag2(CN)3}]·nSolv (1·nSolv; nSolv = DMF·EtOH, 2DMF·MeCN) and [Fe(dpb)2{Ag(CN)2}2] (2), have been synthesized by diffusion technique, respectively. Single-crystal X-ray analysis shows that 1·nSolv consists of a 3D self-penetrating network with in-situ-generated [Ag2(CN)3](-) species and displays one of the largest volume values of porosity (299 Å(3) per iron atom) after desolvation for the Hoffman-like porous SCO coordination polymers to date. In contrast, nonporous compound 2 is composed of two independent interpenetrated 3D nets with in-situ-generated [Ag(dpb)(CN)2](-) species. Their significant distinctions of structural architectures lead to dramatically different magnetic properties: 1·nSolv displays two-step guest-effected SCO with hysteresis, whereas 2 presents characteristic paramagnetic behavior.
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Functional conformations for pyruvate carboxylase during catalysis explored by cryoelectron microscopy.
Structure
PUBLISHED: 03-21-2014
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The tetrameric enzyme pyruvate carboxylase (PC), a biotin-dependent carboxylase, produces oxaloacetate by two consecutive reactions that take place in distant active sites. Previous crystal structures revealed two different configurations for PC tetramers, the so-called symmetric and asymmetric, which were understood as characteristic molecular architectures for PC from different organisms. We have analyzed PC samples from Staphylococcus aureus while the enzyme generates oxaloacetate, expecting PC tetramers to display the conformational landscape relevant for its functioning. Using cryoelectron microscopy (cryo-EM) and sorting techniques, we detect previously defined symmetric and asymmetric architectures, demonstrating that PC maps both arrangements by large conformational changes. Furthermore, we observe that each configuration is coupled to one of the two consecutive enzymatic reactions. The findings describe the structural transitions relevant for the allosteric control of the multifunctional PC and demonstrate that by cryo-EM and classification, we can characterize freely working macromolecules.
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The cyclic dinucleotide c-di-AMP is an allosteric regulator of metabolic enzyme function.
Cell
PUBLISHED: 03-20-2014
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Cyclic di-adenosine monophosphate (c-di-AMP) is a broadly conserved second messenger required for bacterial growth and infection. However, the molecular mechanisms of c-di-AMP signaling are still poorly understood. Using a chemical proteomics screen for c-di-AMP-interacting proteins in the pathogen Listeria monocytogenes, we identified several broadly conserved protein receptors, including the central metabolic enzyme pyruvate carboxylase (LmPC). Biochemical and crystallographic studies of the LmPC-c-di-AMP interaction revealed a previously unrecognized allosteric regulatory site 25 Å from the active site. Mutations in this site disrupted c-di-AMP binding and affected catalytic activity of LmPC as well as PC from pathogenic Enterococcus faecalis. C-di-AMP depletion resulted in altered metabolic activity in L. monocytogenes. Correction of this metabolic imbalance rescued bacterial growth, reduced bacterial lysis, and resulted in enhanced bacterial burdens during infection. These findings greatly expand the c-di-AMP signaling repertoire and reveal a central metabolic regulatory role for a cyclic dinucleotide.
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Structure and function of pre-mRNA 5'-end capping quality control and 3'-end processing.
Biochemistry
PUBLISHED: 03-20-2014
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Messenger RNA precursors (pre-mRNAs) are produced as the nascent transcripts of RNA polymerase II (Pol II) in eukaryotes and must undergo extensive maturational processing, including 5'-end capping, splicing, and 3'-end cleavage and polyadenylation. This review will summarize the structural and functional information reported over the past few years on the large machinery required for the 3'-end processing of most pre-mRNAs, as well as the distinct machinery for the 3'-end processing of replication-dependent histone pre-mRNAs, which have provided great insights into the proteins and their subcomplexes in these machineries. Structural and biochemical studies have also led to the identification of a new class of enzymes (the DXO family enzymes) with activity toward intermediates of the 5'-end capping pathway. Functional studies demonstrate that these enzymes are part of a novel quality surveillance mechanism for pre-mRNA 5'-end capping. Incompletely capped pre-mRNAs are produced in yeast and human cells, in contrast to the general belief in the field that capping always proceeds to completion, and incomplete capping leads to defects in splicing and 3'-end cleavage in human cells. The DXO family enzymes are required for the detection and degradation of these defective RNAs.
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A methionine-restricted diet and endurance exercise decrease bone mass and extrinsic strength but increase intrinsic strength in growing male rats.
J. Nutr.
PUBLISHED: 03-19-2014
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Dietary methionine restriction (MR) has been suggested to be comparable to endurance exercise with respect to its beneficial effects on health. To further investigate the effects of MR and endurance exercise on growing bone, 7-wk-old male Sprague-Dawley rats were fed different l-methionine (Met)-containing diets with or without endurance exercise intervention (Ex; 0.86% Met, 0.52% Met, 0.17% Met, 0.86% Met-Ex, 0.52% Met-Ex, and 0.17% Met-Ex groups). After an 8-wk intervention period, exercise-trained rats had a 9.2% lower body weight (BW) than did sedentary rats (P < 0.05). Additionally, 0.17% Met-fed rats had 32% lower BW when compared with rats fed the other 2 diets (P < 0.05). Serum osteocalcin was lower in the 0.17% Met-Ex group compared with the other 2 exercise groups and the 0.17% Met group (P < 0.05). Serum concentrations of C-terminal telopeptide of type 1 collagen were lower in exercise-trained and 0.17% Met-fed rats than in sedentary rats and rats fed the other 2 diets (P < 0.05 for both). Rats fed the 0.17% Met diet had lower trabecular bone volume, bone mineralization activities, and bone mineral content (BMC; e.g., total, cortical, and spongy BMC) and bone mineral density (BMD; e.g., total and spongy BMD) indices compared with rats fed the other 2 diets (P < 0.05). Exercise-trained rats also had lower bone mineralization activity, trabecular osteoclast density, total BMC, cortical BMC, and total BMD compared with sedentary rats (P < 0.05). In total BMD, only the 0.17% Met-Ex group had values lower than the other 2 exercise groups and the 0.17% Met group (P < 0.05). Compared with rats fed the other 2 diets and sedentary rats, the femora of 0.17% Met-fed and exercise-trained rats, respectively, had smaller size and/or lower extrinsic strength but enhanced intrinsic biomechanical properties (P < 0.05). The results indicate that MR and endurance exercise caused lower whole bone mass, size, and/or strength but might enhance intrinsic bone strength.
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A chiral spin crossover metal-organic framework.
Chem. Commun. (Camb.)
PUBLISHED: 03-07-2014
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A chiral metal-organic framework exhibiting spin crossover (SCO) property, [Fe(II)(mptpy)2]·EtOH·0.2DMF (·solv), has been solvothermally synthesized through spontaneous resolution. It displays remarkable stability and two-step SCO at (Tc1 = 200 K) and above (Tc2 = 357 K) room temperature.
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Delineating the structural blueprint of the pre-mRNA 3'-end processing machinery.
Mol. Cell. Biol.
PUBLISHED: 03-03-2014
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Processing of mRNA precursors (pre-mRNAs) by polyadenylation is an essential step in gene expression. Polyadenylation consists of two steps, cleavage and poly(A) synthesis, and requires multiple cis elements in the pre-mRNA and a megadalton protein complex bearing the two essential enzymatic activities. While genetic and biochemical studies remain the major approaches in characterizing these factors, structural biology has emerged during the past decade to help understand the molecular assembly and mechanistic details of the process. With structural information about more proteins and higher-order complexes becoming available, we are coming closer to obtaining a structural blueprint of the polyadenylation machinery that explains both how this complex functions and how it is regulated and connected to other cellular processes.
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The cytoplasmic domain of rat synaptotagmin I enhances synaptic transmission.
Cell. Mol. Neurobiol.
PUBLISHED: 02-22-2014
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Synaptotagmin, an integral membrane protein of synaptic vesicles, functions as a calcium sensor in the temporal control of neurotransmitter release. Although synaptotagmin facilitates lipid membrane fusion in biochemical experiments, overexpression of synaptotagmin inhibits neurotransmission. A facilitatory effect of synaptotagmin on synaptic transmission was never observed. To determine whether synaptotagmin may accelerate synaptic transmission in vivo, we injected the cytoplasmic domain of rat synaptotagmin I (CD-syt) into crayfish motor axons and tested the effect of CD-syt on synaptic response. We confirmed that CD-syt accelerates neuromuscular transmission. The injected preparation had larger synaptic potentials with shorter rise time. Experiments with varying calcium concentrations showed that CD-syt increased the maximum synaptic response of the neuromuscular synapses. Further tests on short-term plasticity of neuromuscular synapses revealed that CD-syt increases the release probability of the release-ready vesicles.
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Switching of the magnetocaloric effect of Mn(II) glycolate by water molecules.
Chemistry
PUBLISHED: 02-13-2014
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The transformation of Mn(II) glycolates (glc) between the three-dimensional coordination polymer [Mn(glc)2]n (1) and discrete mononuclear phase [Mn(glc)2 (H2O)2] (2) can be reversibly switched by water molecules, which dramatically change the magnetocaloric effect (MCE) of Mn(II) glycolates from the maximum of 6.9?J?kg(-1) ?K(-1) in 1 to 60.3?J?kg(-1) ?K(-1) in 2. This case example reveals that the effect of magnetic coupling on MCE plays a dominant role over that of other factors such as magnetic density for 3d-type magnetic refrigerants.
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Structure of the Arabidopsis thaliana TOP2 oligopeptidase.
Acta Crystallogr F Struct Biol Commun
PUBLISHED: 02-10-2014
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Thimet oligopeptidase (TOP) is a zinc-dependent metallopeptidase. Recent studies suggest that Arabidopsis thaliana TOP1 and TOP2 are targets for salicylic acid (SA) binding and participate in SA-mediated plant innate immunity. The crystal structure of A. thaliana TOP2 has been determined at 3.0 Å resolution. Comparisons to the structure of human TOP revealed good overall structural conservation, especially in the active-site region, despite their weak sequence conservation. The protein sample was incubated with the photo-activated SA analog 4-azido-SA and exposed to UV irradiation before crystallization. However, there was no conclusive evidence for the binding of SA based on the X-ray diffraction data. Further studies are needed to elucidate the molecular mechanism of how SA regulates the activity of A. thaliana TOP1 and TOP2.
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Emergency contrast-enhanced ultrasonography for pancreatic injuries in blunt abdominal trauma.
Radiol Med
PUBLISHED: 02-03-2014
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The purpose of this study was to retrospectively investigate the application of emergency contrast-enhanced ultrasonography (CEUS) in blunt pancreatic trauma.
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Allosteric regulation and substrate activation in cytosolic nucleotidase II from Legionella pneumophila.
FEBS J.
PUBLISHED: 01-21-2014
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Cytosolic nucleotidase II (cN-II) from Legionella pneumophila (Lp) catalyzes the hydrolysis of GMP and dGMP displaying sigmoidal curves, whereas catalysis of IMP hydrolysis displayed a biphasic curve in the initial rate versus substrate concentration plots. Allosteric modulators of mammalian cN-II did not activate LpcN-II although GTP, GDP and the substrate GMP were specific activators. Crystal structures of the tetrameric LpcN-II revealed an activator-binding site at the dimer interface. A double mutation in this allosteric-binding site abolished activation, confirming the structural observations. The substrate GMP acting as an activator, partitioning between the allosteric and active site, is the basis for the sigmoidicity of the initial velocity versus GMP concentration plot. The LpcN-II tetramer showed differences in subunit organization upon activator binding that are absent in the activator-bound human cN-II structure. This is the first observation of a structural change induced by activator binding in cN-II that may be the molecular mechanism for enzyme activation.
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Molecular mechanism for self-protection against the type VI secretion system in Vibrio cholerae.
Acta Crystallogr. D Biol. Crystallogr.
PUBLISHED: 01-17-2014
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VgrG proteins form the spike of the type VI secretion system (T6SS) syringe-like complex. VgrG3 of Vibrio cholerae degrades the peptidoglycan cell wall of rival bacteria via its C-terminal region (VgrG3C) through its muramidase activity. VgrG3C consists of a peptidoglycan-binding domain (VgrG3C(PGB)) and a putative catalytic domain (VgrG3C(CD)), and its activity can be inhibited by its immunity protein partner TsiV3. Here, the crystal structure of V. cholerae VgrG3C(CD) in complex with TsiV3 is presented at 2.3?Å resolution. VgrG3C(CD) adopts a chitosanase fold. A dimer of TsiV3 is bound in the deep active-site groove of VgrG3C(CD), occluding substrate binding and distorting the conformation of the catalytic dyad. Gln91 and Arg92 of TsiV3 are located in the centre of the interface and are important for recognition of VgrG3C. Mutation of these residues destabilized the complex and abolished the inhibitory activity of TsiV3 against VgrG3C toxicity in cells. Disruption of TsiV3 dimerization also weakened the complex and impaired the inhibitory activity. These structural, biochemical and functional data define the molecular mechanism underlying the self-protection of V. cholerae and expand the understanding of the role of T6SS in bacterial competition.
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Structure of the DNA-binding and RNA-polymerase-binding region of transcription antitermination factor ?Q.
Structure
PUBLISHED: 01-16-2014
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The bacteriophage ? Q protein is a transcription antitermination factor that controls expression of the phage late genes as a stable component of the transcription elongation complex. To join the elongation complex, ?Q binds a specific DNA sequence element and interacts with RNA polymerase that is paused during early elongation. ?Q binds to the paused early-elongation complex through interactions between ?Q and two regions of RNA polymerase: region 4 of the ?(70) subunit and the flap region of the ? subunit. We present the 2.1 Å resolution crystal structure of a portion of ?Q containing determinants for interaction with DNA, interaction with region 4 of ?(70), and interaction with the ? flap. The structure provides a framework for interpreting prior genetic and biochemical analysis and sets the stage for future structural studies to elucidate the mechanism by which ?Q alters the functional properties of the transcription elongation complex.
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[Influence of pressure on plasma temperature of octagon structure in dielectric barrier discharge].
Guang Pu Xue Yu Guang Pu Fen Xi
PUBLISHED: 12-28-2013
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Octagon structure consisting of the spots and lines was firstly observed in discharge in argon and air mixture by using a dielectric barrier discharge device with water electrodes. Plasma temperatures of the spots and lines in octagon structure at different gas pressure were studied by using optical emission spectra. The emission spectra of the N2 second positive band (C3IIu-->B3IIg)were measured, and the molecule vibrational temperatures of the spots and lines were calculated by the emission intensities. Based on the relative intensity of the line at 391.4 nm and the N2 line at 394.1 nm, the average electron energy of the spots and lines were investigated. The spectral lines of Ar I 763.26 nm ((2)P6-1Ss) and 772.13 nm ((2)P2-->1S3) were chosen to estimate electron excitation temperature of the spots and lines by the relative intensity ratio method. The molecule vibrational temperature, average electron energy, and electron excitation temperature of the lines are higher than those of the spots at the same pressure. The molecule vibrational temperature, average electron energy, and electron excitation temperature of the spots and lines decrease with pressure increasing from 40 to 60 kPa.
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Spin-Crossover Behavior in Two New Supramolecular Isomers.
Inorg Chem
PUBLISHED: 12-23-2013
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Two spin-crossover (SCO) supramolecular isomers formulated as [Fe(Mebpt){Au(CN)2}]n·xH2O (1, x = 0, and 2·H2O, x = n, MebptH = 3-(5-methyl-2-pyridyl)-5-(2-pyridyl)-1,2,4-triazole) have been successfully isolated and characterized by single-crystal X-ray crystallography, thermogravimetric analysis, differential scanning calorimetry, variable-temperature powder X-ray diffraction, and magnetic measurements. Structural analysis reveals that 1 is a two-dimensional coordination layer and 2·H2O is a one-dimensional coordination ladder structure, in which the Mebpt(-) ligands are coordinated in trans and cis bridging mode in 1 and 2·H2O, respectively. Dramatically, their SCO properties are further influenced by the octahedral coordination configuration of Fe(II). In 1, only the Fe(II) centers in trans configuration exhibit spin transition (Tc = 303 K), while in 2·H2O and the dehydrated 2, gradual two-step SCO (Tc1 = 235 K, Tc2 = 313 K) and one-step SCO behaviors (Tc = 315 K) occur, respectively.
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Enzymatic Basis for N-Glycan Sialylation: STRUCTURE OF RAT ?2,6-SIALYLTRANSFERASE (ST6GAL1) REVEALS CONSERVED AND UNIQUE FEATURES FOR GLYCAN SIALYLATION.
J. Biol. Chem.
PUBLISHED: 10-23-2013
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Glycan structures on glycoproteins and glycolipids play critical roles in biological recognition, targeting, and modulation of functions in animal systems. Many classes of glycan structures are capped with terminal sialic acid residues, which contribute to biological functions by either forming or masking glycan recognition sites on the cell surface or secreted glycoconjugates. Sialylated glycans are synthesized in mammals by a single conserved family of sialyltransferases that have diverse linkage and acceptor specificities. We examined the enzymatic basis for glycan sialylation in animal systems by determining the crystal structures of rat ST6GAL1, an enzyme that creates terminal ?2,6-sialic acid linkages on complex-type N-glycans, at 2.4 ? resolution. Crystals were obtained from enzyme preparations generated in mammalian cells. The resulting structure revealed an overall protein fold broadly resembling the previously determined structure of pig ST3GAL1, including a CMP-sialic acid-binding site assembled from conserved sialylmotif sequence elements. Significant differences in structure and disulfide bonding patterns were found outside the sialylmotif sequences, including differences in residues predicted to interact with the glycan acceptor. Computational substrate docking and molecular dynamics simulations were performed to predict and evaluate the CMP-sialic acid donor and glycan acceptor interactions, and the results were compared with kinetic analysis of active site mutants. Comparisons of the structure with pig ST3GAL1 and a bacterial sialyltransferase revealed a similar positioning of donor, acceptor, and catalytic residues that provide a common structural framework for catalysis by the mammalian and bacterial sialyltransferases.
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Fluorous Metal-Organic Frameworks with Enhanced Stability and High H2/CO2 Storage Capacities.
Sci Rep
PUBLISHED: 09-20-2013
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A new class of metal-organic frameworks (MOFs) has been synthesized by ligand-functionalization strategy. Systematic studies of their adsorption properties were performed at low and high pressure. Importantly, when fluorine was introduced into the framework via the functionalization, both the framework stabilities and adsorption capacities towards H2/CO2 were enhanced significantly. This consequence can be well interpreted by theoretical studies of these MOFs structures. In addition, one of these MOFs TKL-107 was used to fabricate mixed matrix membranes, which exhibit great potential for the application of CO2 separation.
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MGARP Regulates Mouse Neocortical Development via Mitochondrial Positioning.
Mol. Neurobiol.
PUBLISHED: 09-18-2013
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Neocortical development is an extremely complicated process that critically depends on the proper migration, distribution, and positioning of neural cells. Here, we identified mitochondria-localized glutamic acid-rich protein (MGARP) as a negative regulator of neocortical development. In the developing neocortex, the overexpression of MGARP by in utero electroporation impedes the radial migration of neocortical cells to their final destination. These neocortical cells failed to be normally polarized, leading to shortened axons and compromised axonal bundles. The number of dendrites was also attenuated in cells with MGARP overexpression and was expanded in MGARP-knockdown or knockout cells. Mechanistic studies indicated that overexpression of MGARP caused alterations in the structural integrity, subcellular distribution, and motility of mitochondria. The mitochondria in MGARP-overexpressing cells became "fatty" with a round morphology, and the total number of mitochondria in MGARP-overexpressing cells was also decreased in the cell body and dendrites as well as in the axons. Time lapse studies showed that the ratio of motile mitochondria was remarkably decreased in the axons of MGARP-overexpressing cells. Together, our findings suggest that MGARP negatively mediates neocortical development by regulating mitochondrial distribution and motility in neocortical neurons.
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Structural evidence: a single charged residue affects substrate binding in cytochrome P450 BM-3.
Biochemistry
PUBLISHED: 09-16-2013
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Cytochrome P450 BM-3 is a bacterial enzyme with sequence similarity to mammalian P450s that catalyzes the hydroxylation of fatty acids with high efficiency. Enzyme-substrate binding and dynamics has been an important topic of study for cytochromes P450 because most of the crystal structures of substrate-bound structures show the complex in an inactive state. We have determined a new crystal structure for cytochrome P450 BM-3 in complex with N-palmitoylglycine (NPG), which unexpectedly showed a direct bidentate ion pair between NPG and arginine 47 (R47). We further explored the role of R47, the only charged residue in the binding pocket in cytochrome P450 BM-3, through mutagenesis and crystallographic studies. The mutations of R47 to glutamine (R47Q), glutamic acid (R47E), and lysine (R47K) were designed to investigate the role of its charge in binding and catalysis. The oppositely charged R47E mutation had the greatest effect on activity and binding. The crystal structure of R47E BMP shows that the glutamic acid side chain is blocking the entrance to the binding pocket, accounting for NPGs low binding affinity and charge repulsion. For R47Q and R47K BM-3, the mutations caused only a slight change in kcat and a large change in Km and Kd, which suggests that R47 mostly is involved in binding and that our crystal structure, 4KPA , represents an initial binding step in the P450 cycle.
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Unprecedented ferromagnetic dipolar interaction in a dinuclear holmium(III) complex: a combined experimental and theoretical study.
Chem. Commun. (Camb.)
PUBLISHED: 09-04-2013
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A ferromagnetic intramolecular dipolar interaction is observed and verified by both experimental studies and ab initio calculations on a dinuclear holmium(III) complex [Ho2(H2cht)2Cl4(H2O)(MeCN)]·MeCN.
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Structural insights into the functions of the FANCM-FAAP24 complex in DNA repair.
Nucleic Acids Res.
PUBLISHED: 09-03-2013
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Fanconi anemia (FA) is a genetically heterogeneous disorder associated with deficiencies in the FA complementation group network. FA complementation group M (FANCM) and FA-associated protein 24 kDa (FAAP24) form a stable complex to anchor the FA core complex to chromatin in repairing DNA interstrand crosslinks. Here, we report the first crystal structure of the C-terminal segment of FANCM in complex with FAAP24. The C-terminal segment of FANCM and FAAP24 both consist of a nuclease domain at the N-terminus and a tandem helix-hairpin-helix (HhH)2 domain at the C-terminus. The FANCM-FAAP24 complex exhibits a similar architecture as that of ApXPF. However, the variations of several key residues and the electrostatic property at the active-site region render a catalytically inactive nuclease domain of FANCM, accounting for the lack of nuclease activity. We also show that the first HhH motif of FAAP24 is a potential binding site for DNA, which plays a critical role in targeting FANCM-FAAP24 to chromatin. These results reveal the mechanistic insights into the functions of FANCM-FAAP24 in DNA repair.
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Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy.
J. Am. Chem. Soc.
PUBLISHED: 08-29-2013
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Genetically encoded unnatural amino acids could facilitate the design of proteins and enzymes of novel function, but correctly specifying sites of incorporation and the identities and orientations of surrounding residues represents a formidable challenge. Computational design methods have been used to identify optimal locations for functional sites in proteins and design the surrounding residues but have not incorporated unnatural amino acids in this process. We extended the Rosetta design methodology to design metalloproteins in which the amino acid (2,2-bipyridin-5yl)alanine (Bpy-Ala) is a primary ligand of a bound metal ion. Following initial results that indicated the importance of buttressing the Bpy-Ala amino acid, we designed a buried metal binding site with octahedral coordination geometry consisting of Bpy-Ala, two protein-based metal ligands, and two metal-bound water molecules. Experimental characterization revealed a Bpy-Ala-mediated metalloprotein with the ability to bind divalent cations including Co(2+), Zn(2+), Fe(2+), and Ni(2+), with a Kd for Zn(2+) of ?40 pM. X-ray crystal structures of the designed protein bound to Co(2+) and Ni(2+) have RMSDs to the design model of 0.9 and 1.0 Å respectively over all atoms in the binding site.
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A bidirectional system for the dynamic small molecule control of intracellular fusion proteins.
ACS Chem. Biol.
PUBLISHED: 08-26-2013
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Small molecule control of intracellular protein levels allows temporal and dose-dependent regulation of protein function. Recently, we developed a method to degrade proteins fused to a mutant dehalogenase (HaloTag2) using small molecule hydrophobic tags (HyTs). Here, we introduce a complementary method to stabilize the same HaloTag2 fusion proteins, resulting in a unified system allowing bidirectional control of cellular protein levels in a temporal and dose-dependent manner. From a small molecule screen, we identified N-(3,5-dichloro-2-ethoxybenzyl)-2H-tetrazol-5-amine as a nanomolar HALoTag2 Stabilizer (HALTS1) that reduces the Hsp70:HaloTag2 interaction, thereby preventing HaloTag2 ubiquitination. Finally, we demonstrate the utility of the HyT/HALTS system in probing the physiological role of therapeutic targets by modulating HaloTag2-fused oncogenic H-Ras, which resulted in either the cessation (HyT) or acceleration (HALTS) of cellular transformation. In sum, we present a general platform to study protein function, whereby any protein of interest fused to HaloTag2 can be either degraded 10-fold or stabilized 5-fold using two corresponding compounds.
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Cu(II) ?Gd(III) Cryogenic Magnetic Refrigerants and Cu8 Dy9 Single-Molecule Magnet Generated by In Situ Reactions of Picolinaldehyde and Acetylpyridine: Experimental and Theoretical Study.
Chemistry
PUBLISHED: 08-20-2013
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A series of heterometallic [Ln(III) x Cu(II) y ] complexes, [Gd2 Cu2 ]n (1), [Gd4 Cu8 ] (2), [Ln9 Cu8 ] (Ln=Gd, 3?Gd; Ln=Dy, 3?Dy), were successfully synthesized by a one-pot route at room temperature with three kinds of in situ carbonyl-related reactions: Cannizzaro reaction, aldol reaction, and oxidation. This strategy led to dysprosium analogues that behaved as single-molecule magnets (SMMs) and gadolinium analogues that showed significant magnetocaloric effect (MCE). In this study a numerical DFT approach is proposed by using pseudopotentials to calculate the exchange coupling constants in three polynuclear [Gdx Cuy ] complexes; with these values exact diagonalization or quantum Monte Carlo simulations have been performed to calculate the variation of the magnetic entropy involved in the MCE. For the [Dy9 Cu8 ] complexes, local magnetic properties of the Dy(III) centers have been determined by using the CASSCF+RASSI method.
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Wheel-shaped nanoscale 3d-4f {Co(II)16Ln(III)24} clusters (Ln = Dy and Gd).
Chem. Commun. (Camb.)
PUBLISHED: 08-02-2013
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Two unprecedented wheel-shaped nanoscale clusters {Co(II)16Ln(III)24} (Ln = Dy and Gd), with a diameter and a thickness of 3.0 nm and 2.0 nm, respectively, were obtained from the self-assembly of Co(NO3)2, Ln(NO3)3 and a pyridyl-functionalized ?-diketone ligand. Notably, the gadolinium species exhibited a relatively large magnetocaloric effect.
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Ionothermal synthesis of two oxalate-bridged lanthanide(III) chains with slow magnetization relaxation by using a deep eutectic solvent.
Dalton Trans
PUBLISHED: 08-01-2013
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Two novel isostructural oxalate-bridged lanthanide(III) chains, (choline)[Ln(ox)(H2O)3Cl]Cl·H2O (Ln = Dy/Er), were first obtained ionothermally by using a choline chloride-oxalic acid eutectic mixture as both solvent and structure-directing agent, both of which show field-induced slow relaxation of magnetization.
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A new ditopic ratiometric receptor for detecting zinc and fluoride ions in living cells.
Analyst
PUBLISHED: 07-29-2013
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The synthesis, characterization and ion binding properties of a new ditopic ratiometric receptor (1), based on 2-(4,5-dihydro-1H-imidazol-2-yl)phenol and crown ether moieties, have been described. The ditopic ratiometric receptor has been studied in sensing both F(-) and Zn(2+) ions, exhibiting different fluorescent colour changes from cyan green to blue/black observable by the naked eye under UV-light. The addition of Zn(2+) to the solution of 1 induced the formation of a 2?:?2 ligand-metal complex 1-Zn(2+), which displays a remarkable blue shift of the emission maxima of 1 from 455 nm to 400 nm due to the inhibition of excited-state intramolecular proton transfer (ESIPT) mechanism. The sensing processes were monitored by fluorescence/absorption titrations, and further confirmed by Jobs plot and (1)H NMR titrations. The crystal structure of 1-Zn(2+) reveals that 1 binds Zn(2+) in four-coordinated modes. Furthermore, 1 is cell permeable and may be applied to detect trace Zn(2+) and F(-) during the development of a living organism.
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Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design.
J. Mol. Biol.
PUBLISHED: 07-27-2013
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Designed retroaldolases have utilized a nucleophilic lysine to promote carbon-carbon bond cleavage of ?-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff base and to function as a general acid/base. Here we investigate an alternative active-site design in which the catalytic water molecule was replaced by the side chain of a glutamic acid. Five out of seven designs expressed solubly and exhibited catalytic efficiencies similar to previously designed retroaldolases for the conversion of 4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone to 6-methoxy-2-naphthaldehyde and acetone. After one round of site-directed saturation mutagenesis, improved variants of the two best designs, RA114 and RA117, exhibited among the highest kcat (>10(-3)s(-1)) and kcat/KM (11-25M(-1)s(-1)) values observed for retroaldolase designs prior to comprehensive directed evolution. In both cases, the >10(5)-fold rate accelerations that were achieved are within 1-3 orders of magnitude of the rate enhancements reported for the best catalysts for related reactions, including catalytic antibodies (kcat/kuncat=10(6) to 10(8)) and an extensively evolved computational design (kcat/kuncat>10(7)). The catalytic sites, revealed by X-ray structures of optimized versions of the two active designs, are in close agreement with the design models except for the catalytic lysine in RA114. We further improved the variants by computational remodeling of the loops and yeast display selection for reactivity of the catalytic lysine with a diketone probe, obtaining an additional order of magnitude enhancement in activity with both approaches.
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A controllable gate effect in cobalt(II) organic frameworks by reversible structure transformations.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 07-19-2013
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With H2 O or NH3 stimuli, the blue cobalt-based metal-organic framework (MOF) BP can reversibly transform to red RP. The removal/recovery of terephthalate ligands accompanied by the transformation leads to a gate effect, which allows the encapsulation and release of small solvent molecules under certain conditions. This is the first example of topology transformation from a self-penetrating to interpenetrating net in 3D MOFs.
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Fluorescent single-ion magnets: molecular hybrid (HNEt?)[DyxYb1-x(bpyda)?] (x = 0.135-1).
Dalton Trans
PUBLISHED: 07-02-2013
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Four single-phase isostructural mononuclear complexes (HNEt?)[DyxYb1-x(bpyda)2]·3H?O (x = 1 (1), 0 (2), 0.367 (3), 0.135 (4), bpyda = 2,2-bipyridine-6,6-dicarboxylate) show characteristics of controllable slow relaxation and photoluminescence. The molecular hybrids 3 and 4 exhibit the Orbach process for the DyIII component and a mixture of direct and Raman processes for the YbIII component. The presence of paramagnetic YbIII enhances the relaxation time of the DyIII component, originating from the suppression of the direct process/QTM. The correlation between photoluminescence, static susceptibilities and dynamic magnetic relaxation in the hybrid species was also analysed by comparing the energy gap between the ground and first excited states to the energy barrier.
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Two 3d-4f nanomagnets formed via a two-step in situ reaction of picolinaldehyde.
Chem. Commun. (Camb.)
PUBLISHED: 06-14-2013
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Two 3d-4f nanomagnets, [Dy(III)2Cu(II)7] (1) and [Gd(III)6Cu(II)12] (2), are synthesized under a two-step in situ reaction of picolinaldehyde. Not only the final adduct (hemiacetal), but also the intermediate (gem-diol) are "visualized" by X-ray single crystal diffraction. The Dy complex behaves as a single-molecule magnet, while the Gd complex exhibits a significant magnetocaloric effect. Theoretical calculations are employed to obtain the orientation of the magnetic moments and the magnetic exchange.
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Anion-Templated Assembly and Magnetocaloric Properties of a Nanoscale {Gd38 } Cage versus a {Gd48 } Barrel.
Chemistry
PUBLISHED: 06-01-2013
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The comprehensive study reported herein provides compelling evidence that anion templates are the main driving force in the formation of two novel nanoscale lanthanide hydroxide clusters, {Gd38 (ClO4 )6 } (1) and {Gd48 Cl2 (NO3 )} (2), characterized by single-crystal X-ray crystallography, infrared spectroscopy, and magnetic measurements. {Gd38 (ClO4 )6 }, encapsulating six ClO4 (-) ions, features a cage core composed of twelve vertex-sharing {Gd4 } tetrahedrons and one Gd???Gd pillar. When Cl(-) and NO3 (-) were incorporated in the reaction instead of ClO4 (-) , {Gd48 Cl2 (NO3 )} is obtained with a barrel shape constituted by twelve vertex-sharing {Gd4 } tetrahedrons and six {Gd5 } pyramids. What is more, the cage-like {Gd38 } can be dynamically converted into the barrel-shaped {Gd48 } upon Cl(-) and NO3 (-) stimulus. To our knowledge, it is the first time that the linear M-O-M fashion and the unique ?8 -ClO4 (-) mode have been crystallized in pure lanthanide complex, and complex 2 represents the largest gadolinium cluster. Both of the complexes display large magnetocaloric effect in units of J?kg(-1) ?K(-1) and mJ?cm(-3) ?K(-1) on account of the weak antiferromagnetic exchange, the high NGd /MW ratio (magnetic density), and the relatively compact crystal lattice (mass density).
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Locomotion mode classification using a wearable capacitive sensing system.
IEEE Trans Neural Syst Rehabil Eng
PUBLISHED: 05-17-2013
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Locomotion mode classification is one of the most important aspects for the control of powered lower-limb prostheses. We propose a wearable capacitive sensing system for recognizing locomotion modes as an alternative solution to popular electromyography (EMG)-based systems, aiming to overcome drawbacks of the latter. Eight able-bodied subjects and five transtibial amputees were recruited for automatic classification of six common locomotion modes. The system measured ten channels of capacitance signals from the shank, the thigh, or both. With a phase-dependent linear discriminant analysis classifier and selected time-domain features, the system can achieve a satisfactory classification accuracy of 93.6% ±0.9% and 93.4% ±0.8% for able-bodied subjects and amputee subjects, respectively. The classification accuracy is comparable with that of EMG-based systems. More importantly, we verify that neuro-mechanical delay inherent in capacitive sensing does not affect the timeliness of classification decisions as the system, similar to EMG-based systems, can make multiple judgments during a gait cycle. Experimental results also indicate that capacitance signals from the thigh alone are sufficient for mode classification for both able-bodied and transtibial subjects. Our investigations demonstrate that capacitive sensing is a promising alternative to myoelectric sensing for real-time control of powered lower-limb prostheses.
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High symmetry superoctahedron cluster [Mn(III)18O14]26+ from the use of N,N,N,N-tetrakis(2-hydroxyethyl)ethylenediamine.
Dalton Trans
PUBLISHED: 05-17-2013
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The use of flexible N,N,N,N-tetrakis(2-hydroxyethyl)ethylenediamine has provided one new high symmetry superoctahedron with unprecedented aesthetically-pleasing Mn(III)18 clusters, which exhibits out-of-phase signals indicative of the slow magnetic relaxation.
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Programmed self-assembly of heterometallic [3 × 3] grid [M(II)Cu(II)4Cu(I)4] (M = Fe, Ni, Cu, and Zn).
Inorg Chem
PUBLISHED: 05-14-2013
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A series of heterometallic [3 × 3] grids have been synthesized readily through a one-pot solvothermal reaction. Given metal ions carrying distinct electronic, magnetic, and optical information can be addressed precisely at specific locations in the array.
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Computational design of a protein-based enzyme inhibitor.
J. Mol. Biol.
PUBLISHED: 04-23-2013
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While there has been considerable progress in designing protein-protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.
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Lanthanide oxide clusters: from tetrahedral [Dy4(?4-O)](10+) to supertetrahedral [Ln20(?4-O)11]38+ (Ln = Tb, Dy, Ho, Er).
Chemistry
PUBLISHED: 04-12-2013
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Supertetrahedral clusters: A family of lanthanide oxide supertetrahedral T3{Ln20} clusters (Ln = Tb, Dy, Ho, Er; see figure) were obtained from the solvothermal reaction of lanthanide(III) salts with polytriazolate ligands that could be methylated and oxidized in situ.
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[The role of occlusal factors in the occurrence of vertical root fracture].
Shanghai Kou Qiang Yi Xue
PUBLISHED: 04-05-2013
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To investigate the occlusal characteristics and the condition of tooth abrasion in patients with vertical root fracture and to discuss the etiology of the vertical root fracture and the relationships between occlusal disorder, tooth abrasion and vertical root fracture of molars.
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Gadolinium(III)-hydroxy ladders trapped in succinate frameworks with optimized magnetocaloric effect.
Chemistry
PUBLISHED: 03-31-2013
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Two kinds of inorganic gadolinium(III)-hydroxy "ladders", [2×n] and [3×n], were successfully trapped in succinate (suc) coordination polymers, [Gd2(OH)2(suc)2(H2O)]n·2nH2O (1) and [Gd6(OH)8(suc)5(H2O)2 ]n·4n H2O (2), respectively. Such coordination polymers could be regarded as alternating inorganic-organic hybrid materials with relatively high density. Magnetic and heat capacity studies reveal a large cryogenic magnetocaloric effect (MCE) in both compounds, namely (?H=70 kG) 42.8 J kg(-1) K(-1) for complex 1 and 48.0 J kg(-1) K(-1) for complex 2. The effect of the high density is evident, which gives very large volumetric MCEs up to 120 and 144 mJ cm(-3) K(-1) for complexes 1 and 2, respectively.
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C2-symmetrical hexaazatriphenylene derivatives as colorimetric and ratiometric fluorescence chemsensors for Zn2+.
Talanta
PUBLISHED: 02-21-2013
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Two C2-symmetrical hexaazatriphenylene (HAT) derivatives, 2,3-diphenyl-6,7,10,11-tetra(pyridin-2-yl)dipyrazino[2,3-f:2,3-h]quinoxaline (1) and 2,3,6,7-tetraphenyl-10,11-di(pyridin-2-yl)dipyrazino[2,3-f:2,3-h]quinoxaline (2), were designed and synthesized by the condensation reaction of 1,2-diamines and 1,2-diketones. Both compounds 1 and 2 exhibit sensitive, ratiometric and colorimetric fluorescence selectivity for Zn(2+) ion over alkali ions, alkaline earth ions and a wide range of transition metal ions upon excitation at 350 nm in acetonitrile/water. The interactions between 1 or 2 and Zn(2+) can be observed by naked eyes with an obvious color change of the solution from colorless to yellow. For fluorescence intensity of 2 toward Zn(2+), a good linearity (correlation coefficient R(2)=0.993) was established with a detection limit of 0.095 ?M, which is more sensitive than that of 1 (0.2 ?M). The binding modes of the free ligands 1 and 2 with Zn(2+) are discussed in context to their photophysical and electrochemical properties as well as single X-ray crystallographic structures of 1, 2 and 1-Zn.
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Crystal structures of malonyl-coenzyme A decarboxylase provide insights into its catalytic mechanism and disease-causing mutations.
Structure
PUBLISHED: 02-06-2013
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Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2.3 Å resolution. The MCD monomer contains an N-terminal helical domain involved in oligomerization and a C-terminal catalytic domain. The four structures exhibit substantial differences in the organization of the helical domains and, consequently, the oligomeric states and intersubunit interfaces. Unexpectedly, the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis. Our structures, along with mutagenesis and kinetic studies, provide a molecular basis for understanding pathogenic mutations and catalysis, as well as a template for structure-based drug design.
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Caulerprenylols A and B, two rare antifungal prenylated para-xylenes from the green alga Caulerpa racemosa.
Bioorg. Med. Chem. Lett.
PUBLISHED: 02-02-2013
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Two new prenylated para-xylenes, named caulerprenylols A (1) and B (2), were isolated from the green alga Caulerpa racemosa, collected from the Zhanjiang coastline, China. The structures of the two metabolites were elucidated on the basis of detailed spectroscopic analysis. This is the first report of prenylated para-xylenes from marine algae and from marine organisms as well. Moreover, caulerprenylol B (2) is also characterized by an uncommon indane ring system. In in vitro bioassays, the new compounds exhibited a broad spectrum of antifungal activity against Candida glabrata (537), Trichophyton rubrum (Cmccftla), and Cryptococcus neoformans (32609) with MIC80 values between 4 and 64 ?g/mL when compared to amphotericin B (MIC80 values of 2.0, 1.0, and 4.0 ?g/mL, respectively) as a positive control and showed no growth inhibition activity against the tumor cells HL60 and A549.
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A mammalian pre-mRNA 5 end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing.
Mol. Cell
PUBLISHED: 01-24-2013
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Recently, we reported that two homologous yeast proteins, Rai1 and Dxo1, function in a quality control mechanism to clear cells of incompletely 5 end-capped messenger RNAs (mRNAs). Here, we report that their mammalian homolog, Dom3Z (referred to as DXO), possesses pyrophosphohydrolase, decapping, and 5-to-3 exoribonuclease activities. Surprisingly, we found that DXO preferentially degrades defectively capped pre-mRNAs in cells. Additional studies show that incompletely capped pre-mRNAs are inefficiently spliced at all introns, a fact that contrasts with current understanding, and are also poorly cleaved for polyadenylation. Crystal structures of DXO in complex with substrate mimic and products at a resolution of up to 1.5Å provide elegant insights into the catalytic mechanism and molecular basis for their three apparently distinct activities. Our data reveal a pre-mRNA 5 end capping quality control mechanism in mammalian cells, indicating DXO as the central player for this mechanism, and demonstrate an unexpected intimate link between proper 5 end capping and subsequent pre-mRNA processing.
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Structure of histone mRNA stem-loop, human stem-loop binding protein, and 3hExo ternary complex.
Science
PUBLISHED: 01-19-2013
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Metazoan replication-dependent histone messenger RNAs (mRNAs) have a conserved stem-loop (SL) at their 3-end. The stem-loop binding protein (SLBP) specifically recognizes the SL to regulate histone mRNA metabolism, and the 3-5 exonuclease 3hExo trims its 3-end after processing. We report the crystal structure of a ternary complex of human SLBP RNA binding domain, human 3hExo, and a 26-nucleotide SL RNA. Only one base of the SL is recognized specifically by SLBP, and the two proteins primarily recognize the shape of the RNA. SLBP and 3hExo have no direct contact with each other, and induced structural changes in the loop of the SL mediate their cooperative binding. The 3 flanking sequence is positioned in the 3hExo active site, but the ternary complex limits the extent of trimming.
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Characterizing the importance of the biotin carboxylase domain dimer for Staphylococcus aureus pyruvate carboxylase catalysis.
Biochemistry
PUBLISHED: 01-09-2013
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Biotin carboxylase (BC) is a conserved component among biotin-dependent carboxylases and catalyzes the MgATP-dependent carboxylation of biotin, using bicarbonate as the CO? donor. Studies with Escherichia coli BC have suggested long-range communication between the two active sites of a dimer, although its mechanism is not well understood. In addition, mutations in the dimer interface can produce stable monomers that are still catalytically active. A homologous dimer for the BC domain is observed in the structure of the tetrameric pyruvate carboxylase (PC) holoenzyme. We have introduced site-specific mutations into the BC domain dimer interface of Staphylococcus aureus PC (SaPC), equivalent to those used for E. coli BC, and also made chimeras replacing the SaPC BC domain with the E. coli BC subunit (EcBC chimera) or the yeast ACC BC domain (ScBC chimera). We assessed the catalytic activities of these mutants and characterized their oligomerization states by gel filtration and analytical ultracentrifugation experiments. The K442E mutant and the ScBC chimera disrupted the BC dimer and were catalytically inactive, while the F403A mutant and the EcBC chimera were still tetrameric and retained catalytic activity. The R54E mutant was also tetrameric but was catalytically inactive. Crystal structures of the R54E, F403A, and K442E mutants showed that they were tetrameric in the crystal, with conformational changes near the mutation site as well as in the tetramer organization. We have also produced the isolated BC domain of SaPC. In contrast to E. coli BC, the SaPC BC domain is monomeric in solution and catalytically inactive.
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Spherical assemblies from ?-conjugated alternating copolymers: toward optoelectronic colloidal crystals.
J. Am. Chem. Soc.
PUBLISHED: 01-08-2013
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Self-assembly of conducting polymers, which are often used as photoabsorbing, charge-transporting, and photoemission layers of organic photovoltaic and light-emitting devices, were comprehensively studied by means of slow precipitation from polymer solutions upon addition of a vapor of nonsolvents. Polymers such as polyfluorene and polythiophene having a single monomer component hardly formed defined and discrete objects but only gave ill-defined aggregates. In contrast, alternating copolymers typically having both fluorene and thiophene components in their repeating unit self-assembled into well-shaped spheres with diameters ranging from several hundreds of nanometers to several micrometers. Such clear differences in terms of the assembling geometries derive from the rigidity and crystallinity of the polymers, where the copolymers possess large steric hindrance on their backbone that reduces planarity of the polymers and inhibits anisotropic crystal growth, leading to the formation of structurally isotropic spheres. Changing the assembling parameters can systematically control diameter and deviation of the spheres. Furthermore, photocarrier lifetimes of the spheres were markedly enhanced by more than 3 orders of magnitude in comparison with those of cast films from their solutions. This research gives a useful guide for preparation of colloidal crystals from ?-conjugated polymers toward their optoelectronic applications.
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Structure determination and biochemical characterization of a putative HNH endonuclease from Geobacter metallireducens GS-15.
PLoS ONE
PUBLISHED: 01-01-2013
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The crystal structure of a putative HNH endonuclease, Gmet_0936 protein from Geobacter metallireducens GS-15, has been determined at 2.6 Å resolution using single-wavelength anomalous dispersion method. The structure contains a two-stranded anti-parallel ?-sheet that are surrounded by two helices on each face, and reveals a Zn ion bound in each monomer, coordinated by residues Cys38, Cys41, Cys73, and Cys76, which likely plays an important structural role in stabilizing the overall conformation. Structural homologs of Gmet_0936 include Hpy99I endonuclease, phage T4 endonuclease VII, and other HNH endonucleases, with these enzymes sharing 15-20% amino acid sequence identity. An overlay of Gmet_0936 and Hpy99I structures shows that most of the secondary structure elements, catalytic residues as well as the zinc binding site (zinc ribbon) are conserved. However, Gmet_0936 lacks the N-terminal domain of Hpy99I, which mediates DNA binding as well as dimerization. Purified Gmet_0936 forms dimers in solution and a dimer of the protein is observed in the crystal, but with a different mode of dimerization as compared to Hpy99I. Gmet_0936 and its N77H variant show a weak DNA binding activity in a DNA mobility shift assay and a weak Mn²?-dependent nicking activity on supercoiled plasmids in low pH buffers. The preferred substrate appears to be acid and heat-treated DNA with AP sites, suggesting Gmet_0936 may be a DNA repair enzyme.
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