(Q35197136)

7 August 2017

title

Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations (English)

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7 August 2017

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2

Darrin M York

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7 August 2017

Ming Huang

1

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7 August 2017

language of work or name

English

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publication date

1 August 2014

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Physical Chemistry Chemical Physics

7 August 2017

published in

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7 August 2017

volume

16

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7 August 2017

issue

30

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7 August 2017

page(s)

15846-15855

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Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation

7 August 2017

cites work

1 reference

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Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces

13 July 2018

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

13 July 2018

1 reference

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

13 July 2018

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An active-site guanine participates in glmS ribozyme catalysis in its protonated state

13 July 2018

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Biological phosphoryl-transfer reactions: understanding mechanism and catalysis

13 July 2018

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Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data

13 July 2018

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Small Self-cleaving Ribozymes

13 July 2018

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A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage

13 July 2018

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Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes

13 July 2018

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Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme

13 July 2018

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Solvent Structure and Hammerhead Ribozyme Catalysis

13 July 2018

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An important role of G638 in the cis-cleavage reaction of the Neurospora VS ribozyme revealed by a novel nucleotide analog incorporation method

13 July 2018

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Essential role of an active-site guanine in glmS ribozyme catalysis

13 July 2018

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Structural basis of glmS ribozyme activation by glucosamine-6-phosphate

13 July 2018

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NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site

13 July 2018

1 reference

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Transition state stabilization by a catalytic RNA

13 July 2018

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13 July 2018

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Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme

13 July 2018

1 reference

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Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data?

13 July 2018

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Crystal structure of a hepatitis delta virus ribozyme

13 July 2018

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Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4366550

Experimental charge measurement at leaving oxygen in the bovine ribonuclease A catalyzed cyclization of uridine 3'-phosphate aryl esters

13 July 2018

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Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage.

13 July 2018

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Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping

13 July 2018

1 reference

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Continuous surface charge polarizable continuum models of solvation. I. General formalism.

26 September 2018

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Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4366550

Parameters for the Description of Transition States

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4366550

Quantum mechanical continuum solvation models.

26 September 2018

1 reference

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A concerted mechanism for the transfer of the thiophosphinoyl group from aryl dimethylphosphinothioate esters to oxyanionic nucleophiles in aqueous solution

26 September 2018

1 reference

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A mechanistic study of the alkaline hydrolysis of diaryl sulfate diesters

26 September 2018

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Compelling evidence for a stepwise mechanism of the alkaline cyclisation of uridine 3'-phosphate esters

26 September 2018

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Application of Brønsted-type LFER in the study of the phospholipase C mechanism

26 September 2018

1 reference

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The nature of the transition state for enzyme-catalyzed phosphoryl transfer. Hydrolysis of O-aryl phosphorothioates by alkaline phosphatase

26 September 2018

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A primer for the Bema Hapothle. An empirical approach to the characterization of changing transition-state structures

26 September 2018

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The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other fun

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01050G

21 January 2018

Natural hybrid orbitals

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01050G

Natural population analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01050G

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01050G

A Correlation of Reaction Rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01050G

Acid Ionization Constants of Alcohols. II. Acidities of Some Substituted Methanols and Related Compounds 1,2

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01050G

The Activated Complex in Chemical Reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01050G

Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01050G

Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis

21 January 2018

1 reference

12 December 2020

Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems

1 reference

12 December 2020

1 reference

12 December 2020

The pKaof the Internucleotidic 2‘-Hydroxyl Group in Diribonucleoside (3‘→5‘) Monophosphates

1 reference

12 December 2020

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

1 reference

12 December 2020

The hairpin ribozyme: structure, assembly and catalysis

1 reference

12 December 2020

Mutation of Arg-166 of Alkaline Phosphatase Alters the Thio Effect but Not the Transition State for Phosphoryl Transfer. Implications for the Interpretation of Thio Effects in Reactions of Phosphatases†

1 reference

12 December 2020

Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory

1 reference

12 December 2020

Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification

1 reference

12 December 2020

Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

1 reference

12 December 2020

Identifiers

DOI

10.1039/C4CP01050G

1 reference

7 August 2017

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7 August 2017

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