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For: Leclerc F. Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from? Molecules 2010;15:5389-407. [PMID: 20714304 DOI: 10.3390/molecules15085389] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/29/2010] [Accepted: 08/04/2010] [Indexed: 11/17/2022]  Open
Number Cited by Other Article(s)
1
Giese TJ, Ekesan Ş, McCarthy E, Tao Y, York DM. Surface-Accelerated String Method for Locating Minimum Free Energy Paths. J Chem Theory Comput 2024;20:2058-2073. [PMID: 38367218 PMCID: PMC11059188 DOI: 10.1021/acs.jctc.3c01401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
2
Roy P, Bhattacharyya D. MetBP: A Software Tool for Detection of Interaction between Metal Ion-RNA Base Pairs. Bioinformatics 2022;38:3833-3834. [PMID: 35695777 DOI: 10.1093/bioinformatics/btac392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/09/2022] [Accepted: 06/10/2022] [Indexed: 11/14/2022]  Open
3
Maurel MC, Leclerc F, Hervé G. Ribozyme Chemistry: To Be or Not To Be under High Pressure. Chem Rev 2019;120:4898-4918. [DOI: 10.1021/acs.chemrev.9b00457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
4
Maurel MC, Leclerc F, Vergne J, Zaccai G. RNA Back and Forth: Looking through Ribozyme and Viroid Motifs. Viruses 2019;11:E283. [PMID: 30901893 PMCID: PMC6466107 DOI: 10.3390/v11030283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 12/28/2022]  Open
5
Kolev SK, Petkov PS, Rangelov MA, Trifonov DV, Milenov TI, Vayssilov GN. Interaction of Na+, K+, Mg2+ and Ca2+ counter cations with RNA. Metallomics 2018;10:659-678. [DOI: 10.1039/c8mt00043c] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
6
Mlýnský V, Kührová P, Jurečka P, Šponer J, Otyepka M, Banáš P. Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis. J Phys Chem B 2017;121:10828-10840. [DOI: 10.1021/acs.jpcb.7b09129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
7
Chen H, Giese TJ, Golden BL, York DM. Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations. Biochemistry 2017;56:2985-2994. [PMID: 28530384 DOI: 10.1021/acs.biochem.6b01192] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
8
Auffinger P, D'Ascenzo L, Ennifar E. Sodium and Potassium Interactions with Nucleic Acids. Met Ions Life Sci 2016;16:167-201. [PMID: 26860302 DOI: 10.1007/978-3-319-21756-7_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
9
Radak BK, Lee TS, Harris ME, York DM. Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM. RNA (NEW YORK, N.Y.) 2015;21:1566-1577. [PMID: 26170378 PMCID: PMC4536318 DOI: 10.1261/rna.051466.115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
10
Review of computer simulations of isotope effects on biochemical reactions: From the Bigeleisen equation to Feynman's path integral. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015;1854:1782-94. [PMID: 25936775 DOI: 10.1016/j.bbapap.2015.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/13/2015] [Accepted: 04/22/2015] [Indexed: 12/18/2022]
11
Chen H, Giese TJ, Huang M, Wong KY, Harris ME, York DM. Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions. Chemistry 2014;20:14336-43. [PMID: 25223953 DOI: 10.1002/chem.201403862] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Indexed: 11/10/2022]
12
Wong KY, Xu Y, York DM. Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models. J Comput Chem 2014;35:1302-16. [PMID: 24841935 PMCID: PMC4096342 DOI: 10.1002/jcc.23628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/06/2014] [Indexed: 12/16/2022]
13
Kolev S, Petkov PS, Rangelov M, Vayssilov GN. Ab initio molecular dynamics of Na⁺ and Mg²⁺ countercations at the backbone of RNA in water solution. ACS Chem Biol 2013;8:1576-89. [PMID: 23642311 DOI: 10.1021/cb300463h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
14
Chapman EG, DeRose VJ. Site-specific platinum(II) cross-linking in a ribozyme active site. J Am Chem Soc 2012;134:256-62. [PMID: 22070373 PMCID: PMC3257396 DOI: 10.1021/ja206455t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
15
Ions in Molecular Dynamics Simulations of RNA Systems. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2012. [DOI: 10.1007/978-3-642-25740-7_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
16
Kaddour H, Vergne J, Hervé G, Maurel MC. High-pressure analysis of a hammerhead ribozyme from Chrysanthemum chlorotic mottle viroid reveals two different populations of self-cleaving molecule. FEBS J 2011;278:3739-47. [PMID: 21824288 DOI: 10.1111/j.1742-4658.2011.08291.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
17
Chval Z, Chvalová D, Leclerc F. Modeling the RNA 2'OH activation: possible roles of metal ion and nucleobase as catalysts in self-cleaving ribozymes. J Phys Chem B 2011;115:10943-56. [PMID: 21823619 DOI: 10.1021/jp200970d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
18
Wong KY, Lee TS, York DM. Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme. J Chem Theory Comput 2010;7:1-3. [PMID: 21379373 DOI: 10.1021/ct100467t] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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