These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
226 related articles for article (PubMed ID: 24383543)
1. Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme. Ganguly A; Thaplyal P; Rosta E; Bevilacqua PC; Hammes-Schiffer S J Am Chem Soc; 2014 Jan; 136(4):1483-96. PubMed ID: 24383543 [TBL] [Abstract][Full Text] [Related]
2. Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM. Radak BK; Lee TS; Harris ME; York DM RNA; 2015 Sep; 21(9):1566-77. PubMed ID: 26170378 [TBL] [Abstract][Full Text] [Related]
3. Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density. Thaplyal P; Ganguly A; Hammes-Schiffer S; Bevilacqua PC Biochemistry; 2015 Mar; 54(12):2160-75. PubMed ID: 25799319 [TBL] [Abstract][Full Text] [Related]
4. 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; 17(1):670-9. PubMed ID: 25412464 [TBL] [Abstract][Full Text] [Related]
5. 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; 112(35):11177-87. PubMed ID: 18686993 [TBL] [Abstract][Full Text] [Related]
6. Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations. Zhang S; Ganguly A; Goyal P; Bingaman JL; Bevilacqua PC; Hammes-Schiffer S J Am Chem Soc; 2015 Jan; 137(2):784-98. PubMed ID: 25526516 [TBL] [Abstract][Full Text] [Related]
7. Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction. Golden BL Biochemistry; 2011 Nov; 50(44):9424-33. PubMed ID: 22003985 [TBL] [Abstract][Full Text] [Related]
8. Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme. Thaplyal P; Ganguly A; Golden BL; Hammes-Schiffer S; Bevilacqua PC Biochemistry; 2013 Sep; 52(37):6499-514. PubMed ID: 24001219 [TBL] [Abstract][Full Text] [Related]
9. Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. Krasovska MV; Sefcikova J; Spacková N; Sponer J; Walter NG J Mol Biol; 2005 Aug; 351(4):731-48. PubMed ID: 16045932 [TBL] [Abstract][Full Text] [Related]
10. Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. Nakano S; Proctor DJ; Bevilacqua PC Biochemistry; 2001 Oct; 40(40):12022-38. PubMed ID: 11580278 [TBL] [Abstract][Full Text] [Related]
11. Quantum Mechanical/Molecular Mechanical Study of the HDV Ribozyme: Impact of the Catalytic Metal Ion on the Mechanism. Ganguly A; Bevilacqua PC; Hammes-Schiffer S J Phys Chem Lett; 2011 Nov; 2(22):2906-2911. PubMed ID: 22163069 [TBL] [Abstract][Full Text] [Related]
12. Structural roles of monovalent cations in the HDV ribozyme. Ke A; Ding F; Batchelor JD; Doudna JA Structure; 2007 Mar; 15(3):281-7. PubMed ID: 17355864 [TBL] [Abstract][Full Text] [Related]
13. QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms. Mlýnský V; Banáš P; Walter NG; Šponer J; Otyepka M J Phys Chem B; 2011 Dec; 115(47):13911-24. PubMed ID: 22014231 [TBL] [Abstract][Full Text] [Related]
14. Competition between Co(NH(3)(6)3+ and inner sphere Mg2+ ions in the HDV ribozyme. Gong B; Chen JH; Bevilacqua PC; Golden BL; Carey PR Biochemistry; 2009 Dec; 48(50):11961-70. PubMed ID: 19888753 [TBL] [Abstract][Full Text] [Related]
15. 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; 49(31):6508-18. PubMed ID: 20677830 [TBL] [Abstract][Full Text] [Related]
17. Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Veeraraghavan N; Ganguly A; Chen JH; Bevilacqua PC; Hammes-Schiffer S; Golden BL Biochemistry; 2011 Apr; 50(13):2672-82. PubMed ID: 21348498 [TBL] [Abstract][Full Text] [Related]
18. 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; 402(1):278-91. PubMed ID: 20643139 [TBL] [Abstract][Full Text] [Related]
19. Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. Krasovska MV; Sefcikova J; Réblová K; Schneider B; Walter NG; Sponer J Biophys J; 2006 Jul; 91(2):626-38. PubMed ID: 16617077 [TBL] [Abstract][Full Text] [Related]
20. Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid. Cerrone-Szakal AL; Siegfried NA; Bevilacqua PC J Am Chem Soc; 2008 Nov; 130(44):14504-20. PubMed ID: 18842044 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]