(Q34698713)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

main subject

ribozyme

0 references

hepatitis delta virus

object named as

hepatitis delta virus

1 reference

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Jirí Sponer

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

author name string

Maryna V Krasovska

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Jana Sefcikova

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Kamila Réblová

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Bohdan Schneider

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

language of work or name

English

0 references

publication date

14 April 2006

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

number of pages

13

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

volume

91

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

page(s)

626-638

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

Molecular dynamics simulations of sarcin-ricin rRNA motif.

19 January 2020

cites work

1 reference

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Crystal structure of a luteoviral RNA pseudoknot and model for a minimal ribosomal frameshifting motif

7 July 2018

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7 July 2018

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Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases

7 July 2018

1 reference

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

7 July 2018

1 reference

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Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

7 July 2018

1 reference

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DNA and its counterions: a molecular dynamics study

7 July 2018

1 reference

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Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

7 July 2018

1 reference

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Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

RNA conformational classes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

A crystallographic study of the binding of 13 metal ions to two related RNA duplexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Metal ions in the structure and function of RNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

The non-Watson-Crick base pairs and their associated isostericity matrices

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Catalytic strategies of the hepatitis delta virus ribozymes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Molecular dynamics simulation of the human U2B" protein complex with U2 snRNA hairpin IV in aqueous solution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

RNA tertiary interactions in the large ribosomal subunit: the A-minor motif

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Metal ions in ribozyme folding and catalysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Presence of a coordinated metal ion in a trans-acting antigenomic delta ribozyme

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Sequential Folding of the Genomic Ribozyme of the Hepatitis Delta Virus: Structural Analysis of RNA Transcription Intermediates

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

On the role of magnesium ions in RNA stability

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Hydration of the phosphate group in double-helical DNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Crystal structure of a hepatitis delta virus ribozyme

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

A general module for RNA crystallization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

VMD: visual molecular dynamics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Hydration of the DNA bases is local

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Identification of important bases in a single-stranded region (SSrC) of the hepatitis delta (delta) virus ribozyme

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

The molecular biology of hepatitis delta virus

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Water: an integral part of nucleic acid structure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

The self-cleaving domain from the genomic RNA of hepatitis delta virus: sequence requirements and the effects of denaturant

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

General acid catalysis by the hepatitis delta virus ribozyme

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Terbium-mediated footprinting probes a catalytic conformational switch in the antigenomic hepatitis delta virus ribozyme

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

A conformational switch controls hepatitis delta virus ribozyme catalysis

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Anion binding to nucleic acids

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Trans-acting hepatitis delta virus ribozyme: catalytic core and global structure are dependent on the 5' substrate sequence

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

The linkage between magnesium binding and RNA folding.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Proton inventory of the genomic HDV ribozyme in Mg(2+)-containing solutions.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1483112

The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations

26 October 2018

1 reference

12 December 2020

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

1 reference

12 December 2020

Principles of RNA Base Pairing: Structures and Energies of the Trans Watson−Crick/Sugar Edge Base Pairs

1 reference

12 December 2020

A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion

1 reference

12 December 2020

RNA solvation: a molecular dynamics simulation perspective

1 reference

12 December 2020

Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge

1 reference

12 December 2020

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

1 reference

12 December 2020

Structural Requirement for Mg2+ Binding in the Group I Intron Core

1 reference

12 December 2020

10.1529/BIOPHYSJ.105.079368

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16617077%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

PubMed publication ID

16617077

1 reference