(Q34045461)

30 July 2017

title

Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path (English)

1 reference

30 July 2017

0 references

6

Darrin M York

1 reference

30 July 2017

Hugh Heldenbrand

1

1 reference

30 July 2017

Pawel A Janowski

2

1 reference

30 July 2017

George Giambaşu

3

1 reference

30 July 2017

Timothy J Giese

4

1 reference

30 July 2017

Joseph E Wedekind

5

1 reference

30 July 2017

language of work or name

English

0 references

publication date

23 May 2014

1 reference

Journal of the American Chemical Society

30 July 2017

published in

1 reference

30 July 2017

volume

136

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30 July 2017

issue

22

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30 July 2017

page(s)

7789-7792

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A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis

30 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Comparative enzymology and structural biology of RNA self-cleavage

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

'In-line attack' conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Active site labeling of G8 in the hairpin ribozyme: implications for structure and mechanism

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Nucleobase catalysis in ribozyme mechanism

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Nucleobase catalysis in the hairpin ribozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Scalable molecular dynamics with NAMD

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Role of an active site adenine in hairpin ribozyme catalysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Ribozyme structures and mechanisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Relationship between internucleotide linkage geometry and the stability of RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132952

An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24842535

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JA500180Q

1 reference

release_2qmeysky4jakras5gujb57nyiq

30 July 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/2qmeysky4jakras5gujb57nyiq

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

4132952

1 reference

30 July 2017

1 reference