205 related articles for article (PubMed ID: 22014231)
1. 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]
2. Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.
Mlýnský V; Banás P; Hollas D; Réblová K; Walter NG; Sponer J; Otyepka M
J Phys Chem B; 2010 May; 114(19):6642-52. PubMed ID: 20420375
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. 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]
5. Mechanistic role of nucleobases in self-cleavage catalysis of hairpin ribozyme at ambient versus high-pressure conditions.
Kumar N; Marx D
Phys Chem Chem Phys; 2018 Aug; 20(32):20886-20898. PubMed ID: 30067263
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. Deciphering the Self-Cleavage Reaction Mechanism of Hairpin Ribozyme.
Kumar N; Marx D
J Phys Chem B; 2020 Jun; 124(24):4906-4918. PubMed ID: 32453954
[TBL] [Abstract][Full Text] [Related]
8. Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage.
Dubecký M; Walter NG; Šponer J; Otyepka M; Banáš P
Biopolymers; 2015 Oct; 103(10):550-62. PubMed ID: 25858644
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path.
Heldenbrand H; Janowski PA; Giambaşu G; Giese TJ; Wedekind JE; York DM
J Am Chem Soc; 2014 Jun; 136(22):7789-92. PubMed ID: 24842535
[TBL] [Abstract][Full Text] [Related]
11. Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis.
Nam K; Gao J; York DM
J Am Chem Soc; 2008 Apr; 130(14):4680-91. PubMed ID: 18345664
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.
Kath-Schorr S; Wilson TJ; Li NS; Lu J; Piccirilli JA; Lilley DM
J Am Chem Soc; 2012 Oct; 134(40):16717-24. PubMed ID: 22958171
[TBL] [Abstract][Full Text] [Related]
14. Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes.
Hegg LA; Fedor MJ
Biochemistry; 1995 Dec; 34(48):15813-28. PubMed ID: 7495813
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. Catalytic strategies of self-cleaving ribozymes.
Cochrane JC; Strobel SA
Acc Chem Res; 2008 Aug; 41(8):1027-35. PubMed ID: 18652494
[TBL] [Abstract][Full Text] [Related]
17. An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis.
Nesbitt S; Hegg LA; Fedor MJ
Chem Biol; 1997 Aug; 4(8):619-30. PubMed ID: 9281529
[TBL] [Abstract][Full Text] [Related]
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; 112(35):11177-87. PubMed ID: 18686993
[TBL] [Abstract][Full Text] [Related]
19. Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation.
Gaines CS; York DM
J Am Chem Soc; 2016 Mar; 138(9):3058-65. PubMed ID: 26859432
[TBL] [Abstract][Full Text] [Related]
20. Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ force field reparametrizations.
Mlýnský V; Kührová P; Zgarbová M; Jurečka P; Walter NG; Otyepka M; Šponer J; Banáš P
J Phys Chem B; 2015 Mar; 119(11):4220-9. PubMed ID: 25692537
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
