(Q35037250)

5 August 2017

title

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

1 reference

5 August 2017

0 references

Maria M Rhodes

1

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5 August 2017

Kamila Réblová

series ordinal

2

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5 August 2017

Jirí Sponer

series ordinal

3

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5 August 2017

Nils G Walter

series ordinal

4

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5 August 2017

language of work or name

English

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publication date

24 August 2006

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5 August 2017

number of pages

6

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

inferred from page(s)

published in

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5 August 2017

volume

103

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5 August 2017

issue

36

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5 August 2017

page(s)

13380-13385

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

5 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Nucleobase catalysis in the hairpin ribozyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Molecular dynamics simulations of sarcin-ricin rRNA motif.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

The transcriptional landscape of the mammalian genome

8 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Ribo-gnome: the big world of small RNAs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

The RNA world on ice: a new scenario for the emergence of RNA information

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Ribozyme catalysis: not different, just worse

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Does water play a structural role in the folding of small nucleic acids?

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

A perspective on enzyme catalysis.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Single-molecule transition-state analysis of RNA folding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Transition state stabilization by a catalytic RNA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Investigation of Overhauser effects between pseudouridine and water protons in RNA helices

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Correlating structural dynamics and function in single ribozyme molecules

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Functional involvement of G8 in the hairpin ribozyme cleavage mechanism

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Autoionization in liquid water

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Nucleic acids: theory and computer simulation, Y2K.

8 July 2018

1 reference

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Energetics and cooperativity of tertiary hydrogen bonds in RNA structure

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Hydration of transfer RNA molecules: a crystallographic study

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569172

Role of Solvent Dynamics in Stabilizing the Transition State of RNA Hydrolysis by Hairpin Ribozyme.

8 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605090103

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605090103

Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605090103

Observation of a dewetting transition in the collapse of the melittin tetramer

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605090103

A molecular switch and proton wire synchronize the active sites in thiamine enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605090103

Sequential proton transfer through water bridges in acid-base reactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605090103

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605090103

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605090103

Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605090103

Novel guanosine requirement for catalysis by the hairpin ribozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605090103

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

21 January 2018

1 reference

12 December 2020

RNA solvation: a molecular dynamics simulation perspective

1 reference

12 December 2020

Observation of internal cleavage and ligation reactions of a ribozyme

1 reference

12 December 2020

The solvent-protected core of the hairpin ribozyme-substrate complex

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0605090103

1 reference

5 August 2017

0 references

1 reference

5 August 2017

1 reference