Simulating movement of tRNA into the ribosome during decoding (Q30476304)

3 November 2017

Simulating movement of tRNA into the ribosome during decoding (English)

1 reference

3 November 2017

1

Kevin Y Sanbonmatsu

1 reference

3 November 2017

Simpson Joseph

2

1 reference

PMCID

1266076

3 November 2017

Chang-Shung Tung

series ordinal

3

1 reference

PMCID

1266076

3 November 2017

language of work or name

English

0 references

publication date

25 October 2005

1 reference

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

3 November 2017

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3 November 2017

102

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3 November 2017

44

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3 November 2017

15854-15859

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Exploring global motions and correlations in the ribosome

3 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Atomic model of the Thermus thermophilus 70S ribosome developed in silico

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

The molecular basis of electroporation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

A twisted tRNA intermediate sets the threshold for decoding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Selection of tRNA by the ribosome requires a transition from an open to a closed form

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Molecular dynamics simulations of biomolecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Structural insights into peptide bond formation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and validates molecular dynamics simulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Control of the selectivity of the aquaporin water channel family by global orientational tuning

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Recognition of cognate transfer RNA by the 30S ribosomal subunit

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Crystal structure of the ribosome at 5.5 A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Movement of the decoding region of the 16 S ribosomal RNA accompanies tRNA translocation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

A dynamic model for the allosteric mechanism of GroEL

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Molecular dynamics simulations of solvated yeast tRNA(Asp).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

VMD: visual molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Mutations at U2555, a tRNA-protected base in 23S rRNA, affect translational fidelity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Intermediate states in the movement of transfer RNA in the ribosome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

The allosteric three-site model for the ribosomal elongation cycle: features and future

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Novel mutants of 23S RNA: characterization of functional properties

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Proofreading of the codon-anticodon interaction on ribosomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Dynamics of folded proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1266076

Kinetic determinants of high-fidelity tRNA discrimination on the ribosome

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0503456102

Visualization of elongation factor Tu on the Escherichia coli ribosome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0503456102

tRNA selection and kinetic proofreading in translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0503456102

Ribosome motions modulate electrostatic properties

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0503456102

Energetics of ion conduction through the K+ channel.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0503456102

The involvement of two distinct regions of 23 S ribosomal RNA in tRNA selection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0503456102

Mega-Dalton Biomolecular Motion Captured from Electron Microscopy Reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0503456102

Animation of the dynamical events of the elongation cycle based on cryoelectron microscopy of functional complexes of the ribosome

21 January 2018

1 reference

12 December 2020

Modeling a minimal ribosome based on comparative sequence analysis

1 reference

12 December 2020

Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs

1 reference

12 December 2020

A semi-quantitative treatment of missense and nonsense suppression in the strA and ram ribosomal mutants of Escherichia coli Evaluation of some molecular parameters of translation in vivo

1 reference

12 December 2020

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

1 reference

12 December 2020

Major groove binding of the tRNA/mRNA complex to the 16 S ribosomal RNA decoding site

1 reference

12 December 2020

In search of the hair-cell gating spring elastic properties of ankyrin and cadherin repeats

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0503456102

1 reference

3 November 2017

0 references

1 reference

3 November 2017

1 reference

PMCID

1266076