(Q27656362)

22 June 2017

title

Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping (English)

1 reference

22 June 2017

Vincenzo Venditti

1

1 reference

22 June 2017

Lawrence Clos

series ordinal

2

1 reference

22 June 2017

Neri Niccolai

series ordinal

3

1 reference

22 June 2017

Samuel E Butcher

series ordinal

4

1 reference

22 June 2017

language of work or name

English

0 references

publication date

8 July 2009

1 reference

Journal of Molecular Biology

22 June 2017

published in

1 reference

22 June 2017

volume

391

1 reference

22 June 2017

issue

5

1 reference

22 June 2017

page(s)

894-905

1 reference

The N- and C-terminal RNA recognition motifs of splicing factor Prp24 have distinct functions in U6 RNA binding

22 June 2017

cites work

1 reference

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Structure of the U6 RNA intramolecular stem–loop harboring an SP-phosphorothioate modification

20 March 2017

1 reference

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Structural Basis for a Lethal Mutation in U6 RNA † , ‡

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Solution structure of an RNA duplex including a C-U base pair

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

The Amber biomolecular simulation programs

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

MOLMOL: a program for display and analysis of macromolecular structures

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

A stem/loop in U6 RNA defines a conformational switch required for pre-mRNA splicing

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Allosteric cascade of spliceosome activation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Characterization of the catalytic activity of U2 and U6 snRNAs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Structural and dynamic analysis of residual dipolar coupling data for proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Dynamics and metal ion binding in the U6 RNA intramolecular stem-loop as analyzed by NMR.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

The relative stabilities of base pair stacking interactions and single mismatches in long RNA measured by temperature gradient gel electrophoresis.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

A periodic table of symmetric tandem mismatches in RNA.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Proximity of conserved U6 and U2 snRNA elements to the 5' splice site region in activated spliceosomes

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

U2–U6 RNA folding reveals a group II intron-like domain and a four-helix junction

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2799254

Theory and applications of the generalized Born solvation model in macromolecular simulations

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19591840

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Measurement of dipolar couplings for methylene and methyl sites in weakly oriented macromolecules and their use in structure determination

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19591840

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Thermodynamic characterization of RNA duplexes containing naturally occurring 1 x 2 nucleotide internal loops

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19591840

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.JMB.2009.07.003

1 reference

22 June 2017

0 references

1 reference