Literature DB >> 22076983

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

Kin-Yiu Wong1, Hong Gu, Shuming Zhang, Joseph A Piccirilli, Michael E Harris, Darrin M York.   

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Year:  2011        PMID： 22076983      PMCID： PMC3448066          DOI： 10.1002/anie.201104147

Source DB:  PubMed          Journal:  Angew Chem Int Ed Engl        ISSN： 1433-7851            Impact factor:   15.336


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  23 in total

Review 1.  Advances in methods and algorithms in a modern quantum chemistry program package.

Authors:  Yihan Shao; Laszlo Fusti Molnar; Yousung Jung; Jörg Kussmann; Christian Ochsenfeld; Shawn T Brown; Andrew T B Gilbert; Lyudmila V Slipchenko; Sergey V Levchenko; Darragh P O'Neill; Robert A DiStasio; Rohini C Lochan; Tao Wang; Gregory J O Beran; Nicholas A Besley; John M Herbert; Ching Yeh Lin; Troy Van Voorhis; Siu Hung Chien; Alex Sodt; Ryan P Steele; Vitaly A Rassolov; Paul E Maslen; Prakashan P Korambath; Ross D Adamson; Brian Austin; Jon Baker; Edward F C Byrd; Holger Dachsel; Robert J Doerksen; Andreas Dreuw; Barry D Dunietz; Anthony D Dutoi; Thomas R Furlani; Steven R Gwaltney; Andreas Heyden; So Hirata; Chao-Ping Hsu; Gary Kedziora; Rustam Z Khalliulin; Phil Klunzinger; Aaron M Lee; Michael S Lee; Wanzhen Liang; Itay Lotan; Nikhil Nair; Baron Peters; Emil I Proynov; Piotr A Pieniazek; Young Min Rhee; Jim Ritchie; Edina Rosta; C David Sherrill; Andrew C Simmonett; Joseph E Subotnik; H Lee Woodcock; Weimin Zhang; Alexis T Bell; Arup K Chakraborty; Daniel M Chipman; Frerich J Keil; Arieh Warshel; Warren J Hehre; Henry F Schaefer; Jing Kong; Anna I Krylov; Peter M W Gill; Martin Head-Gordon
Journal:  Phys Chem Chem Phys       Date:  2006-06-12       Impact factor: 3.676

Review 2.  RNA catalysis: ribozymes, ribosomes, and riboswitches.

Authors:  Scott A Strobel; Jesse C Cochrane
Journal:  Curr Opin Chem Biol       Date:  2007-11-05       Impact factor: 8.822

3.  An automated integration-free path-integral method based on Kleinert's variational perturbation theory.

Authors:  Kin-Yiu Wong; Jiali Gao
Journal:  J Chem Phys       Date:  2007-12-07       Impact factor: 3.488

Review 4.  Ribozymes.

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

5.  Deprotonation mechanism of NH4+ in the Escherichia coli ammonium transporter AmtB: insight from QM and QM/MM calculations.

Authors:  Zexing Cao; Yirong Mo; Walter Thiel
Journal:  Angew Chem Int Ed Engl       Date:  2007       Impact factor: 15.336

Review 6.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

Review 7.  Small self-cleaving ribozymes.

Authors:  Adrian R Ferré-D'Amaré; William G Scott
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-09-15       Impact factor: 10.005

8.  Kinetic isotope effects for RNA cleavage by 2'-O- transphosphorylation: nucleophilic activation by specific base.

Authors:  Michael E Harris; Qing Dai; Hong Gu; Daniel L Kellerman; Joseph A Piccirilli; Vernon E Anderson
Journal:  J Am Chem Soc       Date:  2010-08-25       Impact factor: 15.419

9.  The effects of sulfur substitution for the nucleophile and bridging oxygen atoms in reactions of hydroxyalkyl phosphate esters.

Authors:  Subashree Iyer; Alvan C Hengge
Journal:  J Org Chem       Date:  2008-06-06       Impact factor: 4.354

10.  Theoretical analysis of kinetic isotope effects on proton transfer reactions between substituted alpha-methoxystyrenes and substituted acetic acids.

Authors:  Kin-Yiu Wong; John P Richard; Jiali Gao
Journal:  J Am Chem Soc       Date:  2009-10-07       Impact factor: 15.419
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  24 in total

1.  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 2.  Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism.

Authors:  Michael E Harris; Joseph A Piccirilli; Darrin M York
Journal:  Biochim Biophys Acta       Date:  2015-04-30

3.  Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology.

Authors:  Colin S Gaines; Timothy J Giese; Darrin M York
Journal:  ACS Catal       Date:  2019-05-22       Impact factor: 13.084

4.  Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects.

Authors:  Haoyuan Chen; Joseph A Piccirilli; Michael E Harris; Darrin M York
Journal:  Biochim Biophys Acta       Date:  2015-03-23

5.  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

6.  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

Review 7.  Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation.

Authors:  Daniel L Kellerman; Darrin M York; Joseph A Piccirilli; Michael E Harris
Journal:  Curr Opin Chem Biol       Date:  2014-07-12       Impact factor: 8.822

8.  Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations.

Authors:  Ming Huang; Darrin M York
Journal:  Phys Chem Chem Phys       Date:  2014-08-14       Impact factor: 3.676

Review 9.  Why nature really chose phosphate.

Authors:  Shina C L Kamerlin; Pankaz K Sharma; Ram B Prasad; Arieh Warshel
Journal:  Q Rev Biophys       Date:  2013-01-15       Impact factor: 5.318

10.  Molecular simulations of RNA 2'-O-transesterification reaction models in solution.

Authors:  Brian K Radak; Michael E Harris; Darrin M York
Journal:  J Phys Chem B       Date:  2012-12-24       Impact factor: 2.991
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