Literature DB >> 21379373

Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme.

Kin-Yiu Wong1, Tai-Sung Lee, Darrin M York.   

Abstract

Entities:  

Year:  2011        PMID： 21379373      PMCID： PMC3046872          DOI： 10.1021/ct100467t

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN： 1549-9618            Impact factor:   6.006


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  21 in total

1.  Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate.

Authors:  S Wang; K Karbstein; A Peracchi; L Beigelman; D Herschlag
Journal:  Biochemistry       Date:  1999-10-26       Impact factor: 3.162

2.  Characterization of a native hammerhead ribozyme derived from schistosomes.

Authors:  Edith M Osborne; Janell E Schaak; Victoria J Derose
Journal:  RNA       Date:  2005-02       Impact factor: 4.942

3.  Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis.

Authors:  Jennifer A Nelson; Olke C Uhlenbeck
Journal:  RNA       Date:  2007-11-12       Impact factor: 4.942

Review 4.  Ribozymes.

Authors:  William G Scott
Journal:  Curr Opin Struct Biol       Date:  2007-06-14       Impact factor: 6.809

5.  Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation.

Authors:  Tai-Sung Lee; Carlos Silva López; George M Giambasu; Monika Martick; William G Scott; Darrin M York
Journal:  J Am Chem Soc       Date:  2008-02-14       Impact factor: 15.419

6.  Insight into the role of Mg in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation.

Authors:  Tai-Sung Lee; Carlos Silva López; Monika Martick; William G Scott; Darrin M York
Journal:  J Chem Theory Comput       Date:  2007-03       Impact factor: 6.006

7.  NMR-spectroscopic characterization of phosphodiester bond cleavage catalyzed by the minimal hammerhead ribozyme.

Authors:  Boris Fürtig; Christian Richter; Peter Schell; Philipp Wenter; Stefan Pitsch; Harald Schwalbe
Journal:  RNA Biol       Date:  2008-02-06       Impact factor: 4.652

8.  Solvent structure and hammerhead ribozyme catalysis.

Authors:  Monika Martick; Tai-Sung Lee; Darrin M York; William G Scott
Journal:  Chem Biol       Date:  2008-04

9.  Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms.

Authors:  Kwangho Nam; Qiang Cui; Jiali Gao; Darrin M York
Journal:  J Chem Theory Comput       Date:  2007-03       Impact factor: 6.006

10.  Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.

Authors:  In Suk Joung; Thomas E Cheatham
Journal:  J Phys Chem B       Date:  2008-07-02       Impact factor: 2.991
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  26 in total

1.  Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment.

Authors:  Kin-Yiu Wong; Hong Gu; Shuming Zhang; Joseph A Piccirilli; Michael E Harris; Darrin M York
Journal:  Angew Chem Int Ed Engl       Date:  2011-11-11       Impact factor: 15.336

2.  Mapping L1 ligase ribozyme conformational switch.

Authors:  George M Giambaşu; Tai-Sung Lee; William G Scott; Darrin M York
Journal:  J Mol Biol       Date:  2012-07-03       Impact factor: 5.469

3.  Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations.

Authors:  Erich R Kuechler; Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2015-12-21       Impact factor: 3.488

4.  Multiscale methods for computational RNA enzymology.

Authors:  Maria T Panteva; Thakshila Dissanayake; Haoyuan Chen; Brian K Radak; Erich R Kuechler; George M Giambaşu; Tai-Sung Lee; Darrin M York
Journal:  Methods Enzymol       Date:  2015-01-22       Impact factor: 1.600

Review 5.  Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction.

Authors:  Barbara L Golden
Journal:  Biochemistry       Date:  2011-10-17       Impact factor: 3.162

6.  A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.

Authors:  Tai-Sung Lee; Brian K Radak; Michael E Harris; Darrin M York
Journal:  ACS Catal       Date:  2016-02-01       Impact factor: 13.084

7.  Exact Relation between Potential of Mean Force and Free-Energy Profile.

Authors:  Kin-Yiu Wong; Darrin M York
Journal:  J Chem Theory Comput       Date:  2012-09-06       Impact factor: 6.006

8.  Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models.

Authors:  Kin-Yiu Wong; Yuqing Xu; Darrin M York
Journal:  J Comput Chem       Date:  2014-05-20       Impact factor: 3.376

9.  A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations.

Authors:  Tai-Sung Lee; Brian K Radak; Anna Pabis; Darrin M York
Journal:  J Chem Theory Comput       Date:  2012-12-12       Impact factor: 6.006

10.  Active-site monovalent cations revealed in a 1.55-Å-resolution hammerhead ribozyme structure.

Authors:  Michael Anderson; Eric P Schultz; Monika Martick; William G Scott
Journal:  J Mol Biol       Date:  2013-05-25       Impact factor: 5.469
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