(Q33867466)

29 July 2017

title

Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways (English)

1 reference

29 July 2017

1

Paul C Whitford

1 reference

29 July 2017

5

José N Onuchic

1 reference

29 July 2017

6

Karissa Y Sanbonmatsu

1 reference

29 July 2017

Peter Geggier

2

1 reference

29 July 2017

Roger B Altman

series ordinal

3

1 reference

29 July 2017

Scott C Blanchard

series ordinal

4

1 reference

29 July 2017

language of work or name

English

0 references

publication date

28 April 2010

1 reference

29 July 2017

1 reference

29 July 2017

volume

16

1 reference

29 July 2017

issue

6

1 reference

29 July 2017

page(s)

1196-1204

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Single ribosome dynamics and the mechanism of translation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Regulation of the Protein-Conducting Channel by a Bound Ribosome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

The Crystal Structure of the Ribosome Bound to EF-Tu and Aminoacyl-tRNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Structures of the ribosome in intermediate states of ratcheting

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Formation of the First Peptide Bond: The Structure of EF-P Bound to the 70S Ribosome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Insights from coarse-grained Gō models for protein folding and dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Long-timescale molecular dynamics simulations of protein structure and function.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

GTPase activation of elongation factor EF-Tu by the ribosome during decoding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Single-molecule observations of ribosome function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Specificity of the ribosomal A site for aminoacyl-tRNAs.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Minimal models for proteins and RNA from folding to function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Crystal structure of a translation termination complex formed with release factor RF2

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Side-chain recognition and gating in the ribosome exit tunnel.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Molecular signatures of ribosomal evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Identification of two distinct hybrid state intermediates on the ribosome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Molecular dynamics: survey of methods for simulating the activity of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Simulating movement of tRNA into the ribosome during decoding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Symmetry at the active site of the ribosome: structural and functional implications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Exploring global motions and correlations in the ribosome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

An active role for tRNA in decoding beyond codon:anticodon pairing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Crystal structure of the ribosome at 5.5 A resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Use of TLS parameters to model anisotropic displacements in macromolecular refinement

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Funnels, pathways, and the energy landscape of protein folding: a synthesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

A quantitative model of the Escherichia coli 16 S RNA in the 30 S ribosomal subunit.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Prediction of the three-dimensional structure of Escherichia coli 30S ribosomal subunit: a molecular mechanics approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Molecular mechanism of drug-dependent ribosome stalling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Global ribosome motions revealed with elastic network model

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

tRNA selection and kinetic proofreading in translation

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874171

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20427512

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Variations on a theme by Debye and Waller: from simple crystals to proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20427512

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20427512

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1261/RNA.2035410

1 reference

29 July 2017

1 reference

29 July 2017

1 reference