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  • 1
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    Computational design of a protein crystal [Chemistry] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-05-09
    Description: Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which has a “honeycomb-like” structure and hexameric channels that span the crystal. The approach involves: (i) creating an ensemble of crystalline structures consistent with the targeted symmetry; (ii) characterizing this ensemble to identify “designable” structures from minima in the sequence-structure energy landscape and designing sequences for these structures; (iii) experimentally characterizing candidate proteins. A 2.1 Å resolution X-ray crystal structure of one such designed protein exhibits sub-Å agreement [backbone root mean square deviation (rmsd)] with the computational model of the crystal. This approach to crystal design has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    O-GlcNAcylation of histone deacetylases 1 in hepatocellular carcinoma promotes cancer progression (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-11
    Description: Hepatocellular carcinoma (HCC) is a malignant tumor originating in the liver. Previous studies have indicated that O-GlcNAc transferase (OGT) and histone deacetylase-1 (HDAC1) play important roles in the pathogenesis of HCC. In the present study, we investigated the physical link between OGT and HDAC1. The O-GlcNAcylation of HDAC1 is overexpressed in HCC. We found that HDAC1 has two major sites of O-GlcNAcylation in its histone deacetylase domain. HDAC1 O-GlcNAcylation increases the activated phosphorylation of HDAC1, which enhances its enzyme activity. HDAC1 O-GlcNAc mutants promote the p21 transcription regulation through affecting the acetylation levels of histones from chromosome, and then influence the proliferation of HCC cells. We also found that mutants of O-GlcNAcylation site of HDAC1 affect invasion and migration of HepG2 cells. E-cadherin level is highly up-regulated in HDAC1 O-GlcNAc mutant-treated liver cancer cells, which inhibit the occurrence and development of HCC. Our findings suggest that OGT promotes the O-GlcNAc modification of HDAC1in the development of HCC. Therefore, inhibiting O-GlcNAcylation of HDAC1 may repress the progression of HCC.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    Numerical Modeling and Mechanical Analysis of Flexible Risers (2015)
    Hindawi
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    Publication Date: 2015-05-20
    Description: ABAQUS is used to create a detailed finite element model for a 10-layer unbonded flexible riser to simulate the riser’s mechanical behavior under three load conditions: tension force and internal and external pressure. It presents a technique to create detailed finite element model and to analyze flexible risers. In FEM model, all layers are modeled separately with contact interfaces; interaction between steel trips in certain layers has been considered as well. FEM model considering contact interaction, geometric nonlinearity, and friction has been employed to accurately simulate the structural behavior of riser. The model includes the main features of the riser geometry with very little simplifying assumptions. The model was solved using a fully explicit time-integration scheme implemented in a parallel environment on an eight-processor cluster and 24 G memory computer. There is a very good agreement obtained from numerical and analytical comparisons, which validates the use of numerical model here. The results from the numerical simulation show that the numerical model takes into account various details of the riser. It has been shown that the detailed finite element model can be used to predict riser’s mechanics behavior under various load cases and bound conditions.
    Print ISSN: 1024-123X
    Electronic ISSN: 1563-5147
    Topics: Mathematics , Technology
    Published by Hindawi
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  • 4
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    Genetic control of gene expression at novel and established chronic obstructive pulmonary disease loci (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-25
    Description: Genetic risk loci have been identified for a wide range of diseases through genome-wide association studies (GWAS), but the relevant functional mechanisms have been identified for only a small proportion of these GWAS-identified loci. By integrating results from the largest current GWAS of chronic obstructive disease (COPD) with expression quantitative trait locus (eQTL) analysis in whole blood and sputum from 121 subjects with COPD from the ECLIPSE Study, this analysis identifies loci that are simultaneously associated with COPD and the expression of nearby genes (COPD eQTLs). After integrative analysis, 19 COPD eQTLs were identified, including all four previously identified genome-wide significant loci near HHIP , FAM13A , and the 15q25 and 19q13 loci. For each COPD eQTL, fine mapping and colocalization analysis to identify causal shared eQTL and GWAS variants identified a subset of sites with moderate-to-strong evidence of harboring at least one shared variant responsible for both the eQTL and GWAS signals. Transcription factor binding site (TFBS) analysis confirms that multiple COPD eQTL lead SNPs disrupt TFBS, and enhancer enrichment analysis for loci with the strongest colocalization signals showed enrichment for blood-related cell types (CD3 and CD4+ T cells, lymphoblastoid cell lines). In summary, integrative eQTL and GWAS analysis confirms that genetic control of gene expression plays a key role in the genetic architecture of COPD and identifies specific blood-related cell types as likely participants in the functional pathway from GWAS-associated variant to disease phenotype.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    A New Prenylated Isoflavone and a New Flavonol Glycoside from Flemingia philippinensis (2012)
    Wiley
    Details
    Publication Date: 2012-04-12
    Description: A new prenylated isoflavonoid, flemiphilippinin G ( 1 ), and a new flavonol glycoside, flemiphilippininside ( 2 ), along with eleven known isoflavonoids were obtained from the roots of Flemingia philippinensis ( Merr. et Rolfe) Li . Their structures were elucidated on the basis of spectroscopic data. The in vitro cytotoxicities of compounds 1 – 13 against MCF-7, A549, and Hep-G2 cell lines were determined by using the MTT (=3-(4,5-dimethylthazol-2-yl)-2,5-diphenyl-2 H -tetrazolium bromide) colorimetric assay, and their antioxidant activities were evaluated by ferric-reducing antioxidant power (FRAP) method. Compound 1 exhibited significant cytotoxicity against all the tested cell lines with IC 50 values of 4.8–7.3 μ M , and compound 2 was found to be inactive. Both compounds 1 and 2 showed weak antioxidant activities with FRAP values of 110±15 and 124±16 μmol/g, respectively.
    Print ISSN: 0018-019X
    Electronic ISSN: 1522-2675
    Topics: Chemistry and Pharmacology
    Published by Wiley
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  • 6
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    A New Prenylated Isoflavone and a New Flavonol Glycoside from Flemingia philippinensis (2012)
    Wiley
    Details
    Publication Date: 2012-04-15
    Description: A new prenylated isoflavonoid, flemiphilippinin G ( 1 ), and a new flavonol glycoside, flemiphilippininside ( 2 ), along with eleven known isoflavonoids were obtained from the roots of Flemingia philippinensis ( Merr. et Rolfe) Li . Their structures were elucidated on the basis of spectroscopic data. The in vitro cytotoxicities of compounds 1 – 13 against MCF-7, A549, and Hep-G2 cell lines were determined by using the MTT (=3-(4,5-dimethylthazol-2-yl)-2,5-diphenyl-2 H -tetrazolium bromide) colorimetric assay, and their antioxidant activities were evaluated by ferric-reducing antioxidant power (FRAP) method. Compound 1 exhibited significant cytotoxicity against all the tested cell lines with IC 50 values of 4.8–7.3 μ M , and compound 2 was found to be inactive. Both compounds 1 and 2 showed weak antioxidant activities with FRAP values of 110±15 and 124±16 μmol/g, respectively.
    Print ISSN: 0018-019X
    Electronic ISSN: 1522-2675
    Topics: Chemistry and Pharmacology
    Published by Wiley
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  • 7
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    Two New Prenylated Xanthones from the Pericarp of Garcinia mangostana (Mangosteen) (2011)
    Wiley
    Details
    Publication Date: 2011-11-15
    Description: Two new prenylated xanthones (=9 H -xanthen-9-ones), garcimangosxanthones D ( 1 ) and E ( 2 ), together with the six known xanthones 3 – 8 , were isolated from the pericarp of Garcinia mangostana. Their structures were determined by analysis of their spectroscopic data. All of the isolated compounds were biologically evaluated for their in vitro cytotoxic activity against A549, Hep-G2, and MCF-7 human-cancer cell lines and antioxidant activity. Compound 1 exhibited moderate cytotoxicity against Hep-G2 ( IC 50 =19.2 μ M ) and weak cytotoxicity against MCF-7 ( IC 50 =62.8 μ M ) cell lines, and compound 2 showed moderate cytotoxicity against A549, Hep-G2, and MCF-7 cell lines with IC 50 values of 12.5–20.0 μ M ( Table 2 ). Both compounds 1 and 2 demonstrated a weak antioxidant activity with ferric reducing antioxidant power (FRAP) values of 41±7 and 130±4 μmol/g, respectively ( Table 3 ).
    Print ISSN: 0018-019X
    Electronic ISSN: 1522-2675
    Topics: Chemistry and Pharmacology
    Published by Wiley
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  • 8
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    Robust Nodal Superconductivity Induced by Isovalent Doping in Ba(Fe_{1-x}Ru_{x})_{2}As_{2} and BaFe_{2}(As_{1-x}P_{x})_{2} (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-02-29
    Description: Author(s): X. Qiu, S. Y. Zhou, H. Zhang, B. Y. Pan, X. C. Hong, Y. F. Dai, Man Jin Eom, Jun Sung Kim, Z. R. Ye, Y. Zhang, D. L. Feng, and S. Y. Li Superconductivity arises from pairing of mobile electrons. The symmetry of the electron-pair wave function contains important clues about the mechanism underlying the pairing. A Chinese-Korean experimental collaboration carries out element-selective substitutional doping of BaFe 2 As 2 and searches for the pairing symmetry of the resulting iron-based superconductors. [Phys. Rev. X 2, 011010] Published Tue Feb 28, 2012
    Keywords: Research Articles
    Electronic ISSN: 2160-3308
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    Terahertz field-induced ferroelectricity in quantum paraelectric SrTiO3 (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉"Hidden phases" are metastable collective states of matter that are typically not accessible on equilibrium phase diagrams. These phases can host exotic properties in otherwise conventional materials and hence may enable novel functionality and applications, but their discovery and access are still in early stages. Using intense terahertz electric field excitation, we found that an ultrafast phase transition into a hidden ferroelectric phase can be dynamically induced in quantum paraelectric strontium titanate (SrTiO〈sub〉3〈/sub〉). The induced lowering in crystal symmetry yields substantial changes in the phonon excitation spectra. Our results demonstrate collective coherent control over material structure, in which a single-cycle field drives ions along the microscopic pathway leading directly to their locations in a new crystalline phase on an ultrafast time scale.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    IFITM3 and H7N9 disease [Immunology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-01-15
    Description: A unique avian-origin A/H7N9 influenza virus has so far caused 134 cases with 44 deaths. Probing the host factors contributing to disease severity, we found that lower levels of plasma inflammatory cytokines on hospital admission correlated with faster recovery in 18 patients with A/H7N9 influenza virus, whereas high concentrations of...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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