Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path (Q34045461)

30 July 2017

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

1 reference

30 July 2017

136

1 reference

30 July 2017

22

1 reference

30 July 2017

7789-7792

1 reference

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

30 July 2017

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

1 reference

Fatcat

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

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

4132952

1 reference

30 July 2017

1 reference