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  • COMPUTER PROGRAMMING AND SOFTWARE  (5)
  • Superfluidity and superconductivity  (4)
  • Binding Sites  (2)
  • 1
    Publication Date: 2013-02-16
    Description: Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which-together with molecular dynamics simulations-suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586787/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586787/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Sangjin -- Brostromer, Erik -- Xing, Dong -- Jin, Jianshi -- Chong, Shasha -- Ge, Hao -- Wang, Siyuan -- Gu, Chan -- Yang, Lijiang -- Gao, Yi Qin -- Su, Xiao-dong -- Sun, Yujie -- Xie, X Sunney -- DP1 OD000277/OD/NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 15;339(6121):816-9. doi: 10.1126/science.1229223.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23413354" target="_blank"〉PubMed〈/a〉
    Keywords: *Allosteric Regulation ; Base Sequence ; Binding Sites ; DNA, B-Form/*chemistry ; DNA-Binding Proteins/*chemistry ; DNA-Directed RNA Polymerases/chemistry ; Escherichia coli/genetics/metabolism ; Gene Expression ; *Gene Expression Regulation, Bacterial ; Lac Repressors/chemistry ; Molecular Dynamics Simulation ; Nucleosomes/chemistry ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Glucocorticoid/chemistry ; Transcription Factors/*chemistry ; Viral Proteins/chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-08-19
    Description: Invasion of host erythrocytes is essential to the life cycle of Plasmodium parasites and development of the pathology of malaria. The stages of erythrocyte invasion, including initial contact, apical reorientation, junction formation, and active invagination, are directed by coordinated release of specialized apical organelles and their parasite protein contents. Among these proteins, and central to invasion by all species, are two parasite protein families, the reticulocyte-binding protein homologue (RH) and erythrocyte-binding like proteins, which mediate host-parasite interactions. RH5 from Plasmodium falciparum (PfRH5) is the only member of either family demonstrated to be necessary for erythrocyte invasion in all tested strains, through its interaction with the erythrocyte surface protein basigin (also known as CD147 and EMMPRIN). Antibodies targeting PfRH5 or basigin efficiently block parasite invasion in vitro, making PfRH5 an excellent vaccine candidate. Here we present crystal structures of PfRH5 in complex with basigin and two distinct inhibitory antibodies. PfRH5 adopts a novel fold in which two three-helical bundles come together in a kite-like architecture, presenting binding sites for basigin and inhibitory antibodies at one tip. This provides the first structural insight into erythrocyte binding by the Plasmodium RH protein family and identifies novel inhibitory epitopes to guide design of a new generation of vaccines against the blood-stage parasite.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4240730/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4240730/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wright, Katherine E -- Hjerrild, Kathryn A -- Bartlett, Jonathan -- Douglas, Alexander D -- Jin, Jing -- Brown, Rebecca E -- Illingworth, Joseph J -- Ashfield, Rebecca -- Clemmensen, Stine B -- de Jongh, Willem A -- Draper, Simon J -- Higgins, Matthew K -- 089455/2/09/z/Wellcome Trust/United Kingdom -- 101020/Wellcome Trust/United Kingdom -- 101020/Z/13/Z/Wellcome Trust/United Kingdom -- G1000527/Medical Research Council/United Kingdom -- MR/K025554/1/Medical Research Council/United Kingdom -- England -- Nature. 2014 Nov 20;515(7527):427-30. doi: 10.1038/nature13715. Epub 2014 Aug 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. ; Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK. ; ExpreS2ion Biotechnologies, SCION-DTU Science Park, Agern Alle 1, DK-2970 Horsholm, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25132548" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Blocking/*chemistry/immunology ; Antigens, CD147/*chemistry/immunology ; Antigens, Protozoan/chemistry/immunology ; Binding Sites ; Crystallography, X-Ray ; Epitopes/chemistry/immunology ; Erythrocytes/*chemistry ; Host-Parasite Interactions/immunology ; Humans ; *Malaria/parasitology ; Models, Molecular ; Plasmodium falciparum/*chemistry/immunology ; Protozoan Proteins/chemistry/immunology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2017-02-04
    Description: Author(s): Meng Wang, S. J. Jin, Ming Yi, Yu Song, H. C. Jiang, W. L. Zhang, H. L. Sun, H. Q. Luo, A. D. Christianson, E. Bourret-Courchesne, D. H. Lee, Dao-Xin Yao, and R. J. Birgeneau Inelastic neutron scattering measurements have been performed to investigate the spin waves of the quasi-one-dimensional antiferromagnetic ladder compound BaFe 2 S 3 , where a superconducting transition was observed under pressure [H. Takahashi et al. , Nat. Mater. 14 , 1008 (2015) ; T. Yamauchi et al. , … [Phys. Rev. B 95, 060502(R)] Published Fri Feb 03, 2017
    Keywords: Superfluidity and superconductivity
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 4
    Publication Date: 2016-07-26
    Description: Author(s): Y. Q. Wang, P. C. Lu, J. J. Wu, J. Liu, X. C. Wang, J. Y. Zhao, W. Bi, E. E. Alp, C. Y. Park, D. Popov, C. Q. Jin, J. Sun, and J. F. Lin To help our understanding of the structural and superconducting transitions in ferropnictides, partial phonon density of states (PDOS) of iron in a single-crystal SrF e 2 A s 2 pnictide have been investigated from both out-of-plane and in-plane polarizations with respect to the basal plane of the crystal… [Phys. Rev. B 94, 014516] Published Mon Jul 25, 2016
    Keywords: Superfluidity and superconductivity
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 5
    Publication Date: 2013-07-26
    Description: Author(s): J.-G. Cheng, J.-S. Zhou, K. Matsubayashi, P. P. Kong, Y. Kubo, Y. Kawamura, C. Sekine, C. Q. Jin, J. B. Goodenough, and Y. Uwatoko We have studied the pressure dependence of the superconducting transition temperature T c of the filled skutterudite YFe 4 P 12 under various quasihydrostatic pressures up to 8 GPa. DC magnetization measurements up to 1.2 GPa in a piston-cylinder cell yields a linear increase of T c with a positive coeff... [Phys. Rev. B 88, 024514] Published Thu Jul 25, 2013
    Keywords: Superfluidity and superconductivity
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 6
    Publication Date: 2016-09-08
    Description: Author(s): Wensen Wei, G. J. Zhao, D. R. Kim, Chiming Jin, J. L. Zhang, Langsheng Ling, Lei Zhang, Haifeng Du, T. Y. Chen, Jiadong Zang, Mingliang Tian, C. L. Chien, and Yuheng Zhang R h 2 M o 3 N , with a noncentrosymmetric β -manganese structure, has been found to be superconducting with critical temperature T c ≈ 4.3 K . Magnetic field dependence of resistivity, magnetization, and specific heat measurements show that its upper critical field of μ 0 H c 2 * ∼ 7.41 T comes close to, but does not ex… [Phys. Rev. B 94, 104503] Published Wed Sep 07, 2016
    Keywords: Superfluidity and superconductivity
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 7
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    Unknown
    In:  Other Sources
    Publication Date: 2011-08-24
    Description: A geometric method is proposed for fitting rational cubic B-spline curves to data that represent smooth curves including intersection or silhouette lines. The algorithm is based on the convex hull and the variation diminishing properties of Bezier/B-spline curves. The algorithm has the following structure: it tries to fit one Bezier segment to the entire data set and if it is impossible it subdivides the data set and reconsiders the subset. After accepting the subset the algorithm tries to find the longest run of points within a tolerance and then approximates this set with a Bezier cubic segment. The algorithm uses this procedure repeatedly to the rest of the data points until all points are fitted. It is concluded that the algorithm delivers fitting curves which approximate the data with high accuracy even in cases with large tolerances.
    Keywords: COMPUTER PROGRAMMING AND SOFTWARE
    Type: IEEE Computer Graphics and Applications (ISSN 0272-1716); 12; 3, Ma; 60-68
    Format: text
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  • 8
    facet.materialart.
    Unknown
    In:  CASI
    Publication Date: 2013-08-31
    Description: NASA-IGES Translator (NIGEStranslator) is a batch program that translates a general IGES (Initial Graphics Exchange Specification) file to a NASA-IGES-Nurbs-Only (NINO) file. IGES is the most popular geometry exchange standard among Computer Aided Geometric Design (CAD) systems. NINO format is a subset of IGES, implementing the simple and yet the most popular NURBS (Non-Uniform Rational B-Splines) representation. NIGEStranslator converts a complex IGES file to the simpler NINO file to simplify the tasks of CFD grid generation for models in CAD format. The NASA-IGES Viewer (NIGESview) is an Open-Inventor-based, highly interactive viewer/ editor for NINO files. Geometry in the IGES files can be viewed, copied, transformed, deleted, and inquired. Users can use NIGEStranslator to translate IGES files from CAD systems to NINO files. The geometry then can be examined with NIGESview. Extraneous geometries can be interactively removed, and the cleaned model can be written to an IGES file, ready to be used in grid generation.
    Keywords: COMPUTER PROGRAMMING AND SOFTWARE
    Type: NASA. Lewis Research Center, Surface Modeling, Grid Generation, and Related Issues in Computational Fluid Dynamic (CFD) Solutions; p 845-855
    Format: application/pdf
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  • 9
    facet.materialart.
    Unknown
    In:  CASI
    Publication Date: 2019-06-28
    Description: A design model geometry file format with topology information used for model geometry exchange in Computational Fluid Dynamics (CFD) grid generation is described. The first part describes the reason why this file format is necessary and what we want to achieve through the file format. The second part provides the information stored in the file format. The purpose of the publication is for broad dissemination of this file format and for the wide participation of testing.
    Keywords: COMPUTER PROGRAMMING AND SOFTWARE
    Type: NASA-CR-177627 , A-94010 , NAS 1.26:177627
    Format: application/pdf
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  • 10
    Publication Date: 2019-06-28
    Description: NIGESview, an interactive software tool for reading, viewing, and translating geometry data available in the Initial Graphics Exchange Specification (IGES) format, is described. NIGESview is designed to read a variety of IGES entities, translate some of the entities, graphically view the data, and output a file in a specific IGES format. The software provides a modern graphical user interface and is designed in a modular fashion so developers can utilize all or part of the code in their grid generation software for computational fluid dynamics.
    Keywords: COMPUTER PROGRAMMING AND SOFTWARE
    Type: NASA. Langley Research Center, Software Surface Modeling and Grid Generation Steering Committee; p 315-318
    Format: application/pdf
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