Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation (Q37088641)

18 August 2017

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

1 reference

18 August 2017

1 reference

10

Darrin M York

1 reference

18 August 2017

Kin-Yiu Wong

3

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author name string

Hong Gu

1

1 reference

18 August 2017

Shuming Zhang

2

1 reference

18 August 2017

Brian K Radak

4

1 reference

18 August 2017

Thakshila Dissanayake

5

1 reference

18 August 2017

Daniel L Kellerman

6

1 reference

18 August 2017

Qing Dai

7

1 reference

18 August 2017

Masaru Miyagi

8

1 reference

18 August 2017

Vernon E Anderson

9

1 reference

18 August 2017

Joseph A Piccirilli

11

1 reference

18 August 2017

Michael E Harris

12

1 reference

18 August 2017

language of work or name

English

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publication date

22 July 2013

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18 August 2017

6

1 reference

Proceedings of the National Academy of Sciences of the United States of America

inferred from page(s)

published in

1 reference

18 August 2017

110

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18 August 2017

32

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18 August 2017

13002-13007

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

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

The mechanism of peptidyl transfer catalysis by the ribosome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Biological phosphoryl-transfer reactions: understanding mechanism and catalysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Comparison of multiple Amber force fields and development of improved protein backbone parameters

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Transition states and inhibitors of the purine nucleoside phosphorylase family

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Scalable molecular dynamics with NAMD

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

The use of isotope effects to determine enzyme mechanisms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Isotope effects in the study of phosphoryl and sulfuryl transfer reactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Mechanisms of phosphoryl and acyl transfer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Secondary 18O isotope effects as a tool for studying reactions of phosphate mono-, di-, and triesters.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Limits to Catalysis by Ribonuclease A.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Transition state analysis of thymidine hydrolysis by human thymidine phosphorylase

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Transition State Structure for the Hydrolysis of NAD Catalyzed by Diphtheria Toxin

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Transition-state structures for N-glycoside hydrolysis of AMP by acid and by AMP nucleosidase in the presence and absence of allosteric activator.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

A two-step chemical mechanism for ribosome-catalysed peptide bond formation

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

A dianionic phosphorane intermediate and transition states in an associative A(N)+D(N) mechanism for the ribonucleaseA hydrolysis reaction

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Efficient synthesis of [2'-18O]uridine and its incorporation into oligonucleotides: a new tool for mechanistic study of nucleotidyl transfer reactions by isotope effect analysis

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Altered mechanisms of reactions of phosphate esters bridging a dinuclear metal center

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

Evidence for direct attack by hydroxide in phosphodiester hydrolysis

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740856

His···Asp Catalytic Dyad of Ribonuclease A: Conformational Stability of the Wild-Type, D121N, D121A, and H119A Enzymes†

3 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1215086110

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23878223

12 December 2020

inferred from PubMed ID database lookup

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23878223

12 December 2020

inferred from PubMed ID database lookup

A designed peptide ligase for total synthesis of ribonuclease A with unnatural catalytic residues

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23878223

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1073/PNAS.1215086110

1 reference

18 August 2017

0 references

1 reference

18 August 2017

PubMed publication ID

23878223

1 reference