(Q35972956)

11 August 2017

Coupling of fast and slow modes in the reaction pathway of the minimal hammerhead ribozyme cleavage (English)

1 reference

11 August 2017

0 references

Ravi Radhakrishnan

1

1 reference

PMCID

1965431

11 August 2017

language of work or name

English

0 references

publication date

1 June 2007

1 reference

11 August 2017

9

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inferred from page(s)

published in

Biophysical Journal

1 reference

11 August 2017

93

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11 August 2017

2391-2399

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11 August 2017

7

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Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

When to believe what you see.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Tertiary contacts distant from the active site prime a ribozyme for catalysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Efficient substrate cleavage catalyzed by hammerhead ribozymes derivatized with selenium for X-ray crystallography

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Relating protein motion to catalysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Role of protein dynamics in reaction rate enhancement by enzymes.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Structural evidence for a two-metal-ion mechanism of group I intron splicing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Single-molecule RNA folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Structure, folding and mechanisms of ribozymes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Linkage between proton binding and folding in RNA: implications for RNA catalysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Ribozyme catalysis: not different, just worse

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

The structure-function dilemma of the hammerhead ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

A small molecule-kinase interaction map for clinical kinase inhibitors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Protein dynamics and enzymatic catalysis: investigating the peptidyl-prolyl cis-trans isomerization activity of cyclophilin A.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Importance in catalysis of a magnesium ion with very low affinity for a hammerhead ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

The origins of RNA catalysis in ribozymes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

A perspective on enzyme catalysis.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

2 October 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=1965431

Single-molecule transition-state analysis of RNA folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Metal ion binding to catalytic RNA molecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Zinc-dependent cleavage in the catalytic core of the hammerhead ribozyme: evidence for a pH-dependent conformational change

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

2 October 2017

The hammerhead ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Hairpin and hammerhead ribozymes: how different are they?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Folding and activity of the hammerhead ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

The chemical repertoire of natural ribozymes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Network of coupled promoting motions in enzyme catalysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Ribozyme structures and mechanisms

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Dissection of the ion-induced folding of the hammerhead ribozyme using 19F NMR.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Thermodynamics of ion-induced RNA folding in the hammerhead ribozyme: an isothermal titration calorimetric study.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Molecular dynamics simulation of nucleic acids

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Ribozyme structures and mechanisms

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Conformational deformability of RNA: a harmonic mode analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Origins of the temperature dependence of hammerhead ribozyme catalysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

The structural basis of hammerhead ribozyme self-cleavage

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

A second catalytic metal ion in group I ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Observations on catalysis by hammerhead ribozymes are consistent with a two-divalent-metal-ion mechanism

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

VMD: visual molecular dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

A general two-metal-ion mechanism for catalytic RNA

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Essential dynamics of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Role of divalent metal ions in the hammerhead RNA cleavage reaction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Biochemistry. Enzyme motions inside and out.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Analysis of the conserved P9-G10.1 metal-binding motif in hammerhead ribozymes with an extra nucleotide inserted between A9 and G10.1 residues

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Structural polymorphism of a marginally stable 4-alpha-helical bundle. Images of a trapped molten globule?

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

24 September 2018

RNA finds a simpler way.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Catalytic roles for proton transfer and protonation in ribozymes

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Identification and characterization of a divalent metal ion-dependent cleavage site in the hammerhead ribozyme

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Mechanisms of signaling and related enzymes

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

EPR Spectroscopic Analysis of U7 Hammerhead Ribozyme Dynamics during Metal Ion Induced Folding†

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Fast Cleavage Kinetics of a Natural Hammerhead Ribozyme

14 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1965431

Training ribozymes to switch

14 November 2018

1 reference

12 December 2020

A Single-Molecule Study of RNA Catalysis and Folding

1 reference

12 December 2020

Comparison of molecular dynamics and harmonic mode calculations on RNA

1 reference

12 December 2020

The hammerhead ribozyme

1 reference

12 December 2020

Detection of a proton-transfer process by kinetic solvent isotope effects in NH(4)(+)-mediated reactions catalyzed by a hammerhead ribozyme

1 reference

12 December 2020

A reappraisal, based on (31)P NMR, of the direct coordination of a metal ion with the phosphoryl oxygen at the cleavage site of a hammerhead ribozyme

1 reference

12 December 2020

Ribozymes: the first 20 years

1 reference

12 December 2020

Ribozymes--a snip too far?

1 reference

12 December 2020

Importance of magnesium ions in the mechanism of catalysis by a hammerhead ribozyme: strictly linear relationship between the ribozyme activity and the concentration of magnesium ions

1 reference

12 December 2020

Analysis of global conformational transitions in ribozymes

1 reference

12 December 2020

Differential binding of Mg2+, Zn2+, and Cd2+ at two sites in a hammerhead ribozyme motif, determined by 15N NMR

1 reference

12 December 2020

Analysis on a cooperative pathway involving multiple cations in hammerhead reactions

1 reference

12 December 2020

NMR-based reappraisal of the coordination of a metal ion at the pro-Rp oxygen of the A9/G10.1 site in a hammerhead ribozyme

1 reference

12 December 2020

Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

1 reference

12 December 2020

Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

1 reference

12 December 2020

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

12 December 2020

A unified polymerase mechanism for nonhomologous DNA and RNA polymerases

1 reference

12 December 2020

RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin

1 reference

12 December 2020

The hairpin ribozyme: structure, assembly and catalysis

1 reference

12 December 2020

The hairpin ribozyme: structure, assembly and catalysis

1 reference

12 December 2020

Designing ribozymes for the inhibition of gene expression

1 reference

12 December 2020

10.1529/BIOPHYSJ.107.104661

Identifiers

DOI

1 reference

11 August 2017

1 reference

11 August 2017

1 reference

PMCID

1965431