(Q38229513)

31 August 2017

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

1 reference

31 August 2017

2

Darrin M York

1 reference

31 August 2017

Daniel L Kellerman

1

1 reference

31 August 2017

Joseph A Piccirilli

series ordinal

3

1 reference

31 August 2017

Michael E Harris

series ordinal

4

1 reference

31 August 2017

12 July 2014

1 reference

Current Opinion in Chemical Biology

31 August 2017

1 reference

31 August 2017

21

1 reference

31 August 2017

96-102

1 reference

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

31 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Why nature really chose phosphate

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Bovine pancreatic ribonuclease: fifty years of the first enzymatic reaction mechanism

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Charged nucleobases and their potential for RNA catalysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Biological phosphoryl-transfer reactions: understanding mechanism and catalysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Nucleases: diversity of structure, function and mechanism.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

6 September 2017

Artificial ribonucleases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

6 September 2017

Ribozyme speed limits

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Isotope effects in the study of phosphoryl and sulfuryl transfer reactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Binding Energy, Specificity, and Enzymic Catalysis: The Circe Effect

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Altered transition state for the reaction of an RNA model catalyzed by a dinuclear zinc(II) catalyst

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Phosphate binding energy and catalysis by small and large molecules

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

QM/MM simulation (B3LYP) of the RNase A cleavage-transesterification reaction supports a triester A(N) + D(N) associative mechanism with an O2' H internal proton transfer

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

There is no universal mechanism for the cleavage of RNA model compounds in the presence of metal ion catalysts.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Dinuclear Zn(II) complex catalyzed phosphodiester cleavage proceeds via a concerted mechanism: a density functional theory study.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Kinetic Isotope Effects for RNA Cleavage by 2′-O- Transphosphorylation: Nucleophilic Activation by Specific Base

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

Parameters for the Description of Transition States

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4149925

The Mechanism of Cleavage and Isomerisation of RNA Promoted by an Efficient Dinuclear Zn2+ Complex

1 October 2018

1 reference

12 December 2020

Reactions of phosphate and phosphorothiolate diesters with nucleophiles: comparison of transition state structures

1 reference

12 December 2020

The mechanism of RNA strand scission: an experimental measure of the Brønsted coefficient, beta nuc

1 reference

12 December 2020

Kinetics and Mechanisms for the Cleavage and Isomerization of the Phosphodiester Bonds of RNA by Brønsted Acids and Bases

1 reference

12 December 2020

Kinetic Isotope Effects and Stereochemical Studies on a Ribonuclease Model: Hydrolysis Reactions of Uridine 3'-Nitrophenyl Phosphate

1 reference

12 December 2020

10.1016/J.CBPA.2014.06.010

Identifiers

DOI

1 reference

31 August 2017

1 reference

31 August 2017

PubMed publication ID

25023967

1 reference