(Q36800450)

English

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

scientific article published on 19 June 2008

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scholarly article

1 reference

Europe PubMed Central

16 August 2017

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

1 reference

Europe PubMed Central

16 August 2017

0 references

0 references

3

object named as

Darrin M York

1 reference

Europe PubMed Central

16 August 2017

author name string

Kwangho Nam

1

1 reference

Europe PubMed Central

16 August 2017

Jiali Gao

2

1 reference

Europe PubMed Central

16 August 2017

language of work or name

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publication date

19 June 2008

1 reference

Europe PubMed Central

16 August 2017

1 reference

Europe PubMed Central

16 August 2017

14

1 reference

Europe PubMed Central

16 August 2017

8

1 reference

Europe PubMed Central

16 August 2017

1501-1507

1 reference

Europe PubMed Central

16 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Trapped water molecules are essential to structural dynamics and function of a ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Chemical models for ribozyme action

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

The catalytic diversity of RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Role of an active site adenine in hairpin ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

The hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Transition state stabilization by a catalytic RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Comparative analysis of hairpin ribozyme structures and interference data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Functional involvement of G8 in the hairpin ribozyme cleavage mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Ribozyme structures and mechanisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Structure and function of the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Structure, folding and catalysis of the small nucleolytic ribozymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Use of intrinsic binding energy for catalysis by an RNA enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

29 September 2017

Nucleobase catalysis in the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

27 June 2018

Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

27 June 2018

Functional analysis of hairpin ribozyme active site architecture

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

5 September 2018

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

5 September 2018

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

5 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

5 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2491468

5 September 2018

The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects

1 reference

https://pubmed.ncbi.nlm.nih.gov/18566190

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Hydrolysis of RNA: From Theoretical Calculations to the Hammerhead Ribozyme-Mediated Cleavage of RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/18566190

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Variational electrostatic projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/18566190

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

1 reference

https://pubmed.ncbi.nlm.nih.gov/18566190

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations.

1 reference

https://pubmed.ncbi.nlm.nih.gov/18566190

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage

1 reference

https://pubmed.ncbi.nlm.nih.gov/18566190

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The hairpin ribozyme: structure, assembly and catalysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/18566190

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1261/RNA.863108

1 reference

Europe PubMed Central

16 August 2017

1 reference

Europe PubMed Central

16 August 2017

1 reference

Europe PubMed Central

16 August 2017

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