Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM (Q33700051)

28 July 2017

title

Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM (English)

1 reference

cryogenic electron microscopy

28 July 2017

main subject

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5

Joachim Frank

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Jirí Sponer

object named as

Jirí Sponer

6

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author name string

Kamila Réblová

1

1 reference

28 July 2017

Filip Rázga

2

1 reference

28 July 2017

Wen Li

3

1 reference

28 July 2017

Haixiao Gao

4

1 reference

28 July 2017

language of work or name

English

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publication date

1 December 2009

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28 July 2017

published in

Nucleic Acids Research

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28 July 2017

volume

38

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28 July 2017

issue

4

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28 July 2017

page(s)

1325-1340

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describes a project that uses

28 July 2017

molecular dynamics simulation

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Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations

inferred from title

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

A repulsive field: advances in the electrostatics of the ion atmosphere

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

The UA_handle: a versatile submotif in stable RNA 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=2831300

Molecular dynamics study of the ribosomal A-site.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

A short guide for molecular dynamics simulations of RNA systems.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large 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=2831300

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

The process of mRNA-tRNA translocation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Molecular dynamics simulations and their application to four-stranded DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by 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=2831300

Nucleic acid solvation: from outside to insight.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn 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=2831300

Molecular dynamics simulations of RNA: an in silico single molecule approach.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Structure of the 70S ribosome complexed with mRNA and tRNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Multiple stages in codon-anticodon recognition: double-trigger mechanisms and geometric constraints

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Functional conformations of the L11-ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Structures of the bacterial ribosome at 3.5 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=2831300

Simulating movement of tRNA into the ribosome during decoding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Molecular basis for RNA kink-turn recognition by the h15.5K small RNP protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Site-specific labeling of the ribosome for single-molecule spectroscopy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Ion motions in molecular dynamics simulations on DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein 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=2831300

tRNA dynamics on the ribosome during translation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

The kink-turn motif in RNA is dimorphic, and metal ion-dependent

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Theoretical methods for the simulation 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=2831300

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Biochemical characterization of the kink-turn RNA motif.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Locking and unlocking of ribosomal motions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Study of the structural dynamics of the E coli 70S ribosome using real-space refinement

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Ribosome as a molecular machine

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

The kink-turn: a new RNA secondary structure motif

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Crystal structure of the ribosome at 5.5 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=2831300

A ratchet-like inter-subunit reorganization of the ribosome during translocation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

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=2831300

A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Essential dynamics of proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2831300

Mutations in the intersubunit bridge regions of 23 S rRNA.

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

Potential new antibiotic sites in the ribosome revealed by deleterious mutations in RNA of the large ribosomal subunit.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

The A-site finger in 23 S rRNA acts as a functional attenuator for translocation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

tRNA selection and kinetic proofreading in translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

Molecular Dynamics and Free Energy Study of the Conformational Equilibria in the UUUU RNA Hairpin

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

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/10.1093%2FNAR%2FGKP1057

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/10.1093%2FNAR%2FGKP1057

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

Interactive essential dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

Dynamics of B-DNA on the microsecond time scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1057

Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge

21 January 2018

1 reference

12 December 2020

The conserved A-site finger of the 23S rRNA: just one of the intersubunit bridges or a part of the allosteric communication pathway?

1 reference

12 December 2020

The importance of G.A hydrogen bonding in the metal ion- and protein-induced folding of a kink turn RNA

1 reference

12 December 2020

Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?

1 reference

12 December 2020

Nanosecond Molecular Dynamics Simulations of Parallel and Antiparallel Guanine Quadruplex DNA Molecules

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1093/NAR/GKP1057

Identifiers

DOI

10.1093/NAR/GKP1057

1 reference

28 July 2017

1 reference

28 July 2017

1 reference