(Q33206283)

23 July 2017

title

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

1 reference

23 July 2017

Neocles B Leontis

4

0 references

Jaroslav Koča

object named as

Jaroslav Koca

3

0 references

Jirí Sponer

object named as

Jirí Sponer

5

0 references

author name string

Kamila Réblová

1

1 reference

23 July 2017

Nad'a Spacková

2

1 reference

23 July 2017

language of work or name

English

0 references

publication date

31 August 2004

1 reference

23 July 2017

number of pages

16

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

23 July 2017

volume

87

1 reference

23 July 2017

issue

5

1 reference

23 July 2017

page(s)

3397-3412

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MD studies of the DIS/DIS kissing complex solution and x-ray structures

23 July 2017

cites work

1 reference

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21 June 2018

1 reference

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

21 June 2018

1 reference

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21 June 2018

Analysis of RNA motifs

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

21 June 2018

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

21 June 2018

1 reference

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The solution structure of the loop E region of the 5S rRNA from spinach chloroplasts

21 June 2018

1 reference

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Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

21 June 2018

1 reference

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Structure of the L1 protuberance in the ribosome

21 June 2018

1 reference

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

21 June 2018

1 reference

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21 June 2018

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Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

21 June 2018

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The free energy landscape for beta hairpin folding in explicit water

21 June 2018

1 reference

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High resolution structure of the large ribosomal subunit from a mesophilic eubacterium

21 June 2018

1 reference

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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

21 June 2018

1 reference

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

21 June 2018

1 reference

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Crystal structure of the ribosome at 5.5 A resolution

21 June 2018

1 reference

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

21 June 2018

1 reference

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Structure of the 30S ribosomal subunit

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

21 June 2018

1 reference

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Structural motifs in RNA.

21 June 2018

1 reference

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Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family

21 June 2018

1 reference

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Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain

21 June 2018

1 reference

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Conserved geometrical base-pairing patterns in RNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

Stitching together RNA tertiary architectures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

The NMR structure of the 5S rRNA E-domain–protein L25 complex shows preformed and induced recognition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

A detailed view of a ribosomal active site: the structure of the L11-RNA complex

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

Simulations of the molecular dynamics of nucleic acids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

VMD: visual molecular dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

Hydration and solution structure of nucleic acids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

Anion binding to nucleic acids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304806

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

31 October 2018

1 reference

12 December 2020

Singly and bifurcated hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes

1 reference

12 December 2020

Simulation of the structure and dynamics of nonhelical RNA motifs

1 reference

12 December 2020

Molecular dynamics investigations of hammerhead ribozyme RNA

1 reference

12 December 2020

10.1529/BIOPHYSJ.104.047126

Identifiers

DOI

1 reference

23 July 2017

1 reference

23 July 2017

1 reference