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273 related items for PubMed ID: 20643139

  • 1. Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments.
    Veeraraghavan N, Bevilacqua PC, Hammes-Schiffer S.
    J Mol Biol; 2010 Sep 10; 402(1):278-91. PubMed ID: 20643139
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  • 3. Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.
    Sripathi KN, Banáš P, Réblová K, Šponer J, Otyepka M, Walter NG.
    Phys Chem Chem Phys; 2015 Feb 28; 17(8):5887-900. PubMed ID: 25631765
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  • 4. pK(a) perturbation in genomic Hepatitis Delta Virus ribozyme catalysis evidenced by nucleotide analogue interference mapping.
    Oyelere AK, Kardon JR, Strobel SA.
    Biochemistry; 2002 Mar 19; 41(11):3667-75. PubMed ID: 11888283
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  • 5. A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage.
    Chen JH, Yajima R, Chadalavada DM, Chase E, Bevilacqua PC, Golden BL.
    Biochemistry; 2010 Aug 10; 49(31):6508-18. PubMed ID: 20677830
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  • 6. Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme.
    Tinsley RA, Harris DA, Walter NG.
    Biochemistry; 2004 Jul 20; 43(28):8935-45. PubMed ID: 15248751
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  • 7. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.
    Sripathi KN, Tay WW, Banáš P, Otyepka M, Šponer J, Walter NG.
    RNA; 2014 Jul 20; 20(7):1112-28. PubMed ID: 24854621
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  • 9. A conformational switch controls hepatitis delta virus ribozyme catalysis.
    Ke A, Zhou K, Ding F, Cate JH, Doudna JA.
    Nature; 2004 May 13; 429(6988):201-5. PubMed ID: 15141216
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  • 11. Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation.
    Veeraraghavan N, Ganguly A, Golden BL, Bevilacqua PC, Hammes-Schiffer S.
    J Phys Chem B; 2011 Jun 30; 115(25):8346-57. PubMed ID: 21644800
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  • 12. The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.
    Mlýnský V, Walter NG, Šponer J, Otyepka M, Banáš P.
    Phys Chem Chem Phys; 2015 Jan 07; 17(1):670-9. PubMed ID: 25412464
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  • 14. New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
    Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS.
    Nucleic Acids Res; 2014 Nov 10; 42(20):12833-46. PubMed ID: 25326328
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  • 15. Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction.
    Golden BL.
    Biochemistry; 2011 Nov 08; 50(44):9424-33. PubMed ID: 22003985
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  • 16. Characterization of the trans Watson-Crick GU base pair located in the catalytic core of the antigenomic HDV ribozyme.
    Lévesque D, Reymond C, Perreault JP.
    PLoS One; 2012 Nov 08; 7(6):e40309. PubMed ID: 22768274
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  • 18. General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility.
    Banás P, Rulísek L, Hánosová V, Svozil D, Walter NG, Sponer J, Otyepka M.
    J Phys Chem B; 2008 Sep 04; 112(35):11177-87. PubMed ID: 18686993
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  • 19. Site-specific modification of functional groups in genomic hepatitis delta virus (HDV) ribozyme.
    Nishikawa F, Shirai M, Nishikawa S.
    Eur J Biochem; 2002 Dec 04; 269(23):5792-803. PubMed ID: 12444967
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  • 20. A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses.
    Tanner NK, Schaff S, Thill G, Petit-Koskas E, Crain-Denoyelle AM, Westhof E.
    Curr Biol; 1994 Jun 01; 4(6):488-98. PubMed ID: 7922369
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