Literature DB >> 18158891

Ribozyme catalysis revisited: is water involved?

Nils G Walter1.   

Abstract

Enzymatic catalysis by RNA was discovered 25 years ago, yet mechanistic insights are emerging only slowly. Thought to be metalloenzymes at first, some ribozymes proved more versatile than anticipated when shown to utilize their own functional groups for catalysis. Recent evidence suggests that some may also judiciously place structural water molecules to shuttle protons in acid-base catalyzed reactions.

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Year:  2007        PMID: 18158891      PMCID: PMC2575846          DOI: 10.1016/j.molcel.2007.12.001

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  74 in total

1.  Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis.

Authors:  P B Rupert; A R Ferré-D'Amaré
Journal:  Nature       Date:  2001-04-12       Impact factor: 49.962

2.  General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme.

Authors:  S Nakano; D M Chadalavada; P C Bevilacqua
Journal:  Science       Date:  2000-02-25       Impact factor: 47.728

3.  The structural basis of ribosome activity in peptide bond synthesis.

Authors:  P Nissen; J Hansen; N Ban; P B Moore; T A Steitz
Journal:  Science       Date:  2000-08-11       Impact factor: 47.728

Review 4.  Ribozyme speed limits.

Authors:  Gail Mitchell Emilsson; Shingo Nakamura; Adam Roth; Ronald R Breaker
Journal:  RNA       Date:  2003-08       Impact factor: 4.942

5.  In vitro selection of RNAs that undergo autolytic cleavage with Pb2+.

Authors:  T Pan; O C Uhlenbeck
Journal:  Biochemistry       Date:  1992-04-28       Impact factor: 3.162

6.  Sequential proton transfer through water bridges in acid-base reactions.

Authors:  Omar F Mohammed; Dina Pines; Jens Dreyer; Ehud Pines; Erik T J Nibbering
Journal:  Science       Date:  2005-10-07       Impact factor: 47.728

Review 7.  The ribosomal peptidyl transferase.

Authors:  Malte Beringer; Marina V Rodnina
Journal:  Mol Cell       Date:  2007-05-11       Impact factor: 17.970

Review 8.  Role of metal ions in ribozymes.

Authors:  A M Pyle
Journal:  Met Ions Biol Syst       Date:  1996

9.  Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy.

Authors:  Florian Garczarek; Klaus Gerwert
Journal:  Nature       Date:  2005-11-09       Impact factor: 49.962

Review 10.  Ribozymes: a distinct class of metalloenzymes.

Authors:  A M Pyle
Journal:  Science       Date:  1993-08-06       Impact factor: 47.728

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  26 in total

1.  Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.

Authors:  Pavel Banás; Nils G Walter; Jirí Sponer; Michal Otyepka
Journal:  J Phys Chem B       Date:  2010-07-08       Impact factor: 2.991

2.  Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.

Authors:  Vojtech Mlýnský; Pavel Banás; Daniel Hollas; Kamila Réblová; Nils G Walter; Jirí Sponer; Michal Otyepka
Journal:  J Phys Chem B       Date:  2010-05-20       Impact factor: 2.991

3.  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

4.  Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme.

Authors:  Chamaree de Silva; Nils G Walter
Journal:  RNA       Date:  2008-11-24       Impact factor: 4.942

5.  QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.

Authors:  Vojtěch Mlýnský; Pavel Banáš; Nils G Walter; Jiří Šponer; Michal Otyepka
Journal:  J Phys Chem B       Date:  2011-11-08       Impact factor: 2.991

Review 6.  Metal ions: supporting actors in the playbook of small ribozymes.

Authors:  Alexander E Johnson-Buck; Sarah E McDowell; Nils G Walter
Journal:  Met Ions Life Sci       Date:  2011

7.  The shape-shifting quasispecies of RNA: one sequence, many functional folds.

Authors:  Matthew S Marek; Alexander Johnson-Buck; Nils G Walter
Journal:  Phys Chem Chem Phys       Date:  2011-05-20       Impact factor: 3.676

8.  Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.

Authors:  Mark A Ditzler; Michal Otyepka; Jirì Sponer; Nils G Walter
Journal:  Acc Chem Res       Date:  2010-01-19       Impact factor: 22.384

9.  Identification of an imino group indispensable for cleavage by a small ribozyme.

Authors:  Robert C Spitale; Rosaria Volpini; Moriah G Heller; Jolanta Krucinska; Gloria Cristalli; Joseph E Wedekind
Journal:  J Am Chem Soc       Date:  2009-05-06       Impact factor: 15.419

10.  Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation.

Authors:  Man Guo; Robert C Spitale; Rosaria Volpini; Jolanta Krucinska; Gloria Cristalli; Paul R Carey; Joseph E Wedekind
Journal:  J Am Chem Soc       Date:  2009-09-16       Impact factor: 15.419

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