(Q35571390)

8 August 2017

title

Excited states of ribosome translocation revealed through integrative molecular modeling (English)

1 reference

8 August 2017

7

José N Onuchic

1 reference

8 August 2017

8

Karissa Y Sanbonmatsu

1 reference

8 August 2017

4

Scott P Hennelly

1 reference

8 August 2017

Paul C Whitford

1

1 reference

8 August 2017

Aqeel Ahmed

2

1 reference

8 August 2017

Yanan Yu

3

1 reference

8 August 2017

Florence Tama

5

1 reference

8 August 2017

Christian M T Spahn

6

1 reference

8 August 2017

language of work or name

English

0 references

publication date

11 November 2011

1 reference

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

8 August 2017

published in

1 reference

8 August 2017

volume

108

1 reference

8 August 2017

issue

47

1 reference

8 August 2017

page(s)

18943-18948

1 reference

Structures of the bacterial ribosome in classical and hybrid states of tRNA binding

8 August 2017

cites work

1 reference

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Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center

12 July 2018

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Dynamics of the translational machinery

12 July 2018

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Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

12 July 2018

1 reference

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Crystal structure of the eukaryotic ribosome

12 July 2018

1 reference

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Overlap between folding and functional energy landscapes for adenylate kinase conformational change

12 July 2018

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12 July 2018

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Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit

12 July 2018

1 reference

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Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution

12 July 2018

1 reference

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Applications of the molecular dynamics flexible fitting method

12 July 2018

1 reference

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Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome

12 July 2018

1 reference

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Proteins at work: a combined small angle X-RAY scattering and theoretical determination of the multiple structures involved on the protein kinase functional landscape

12 July 2018

1 reference

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Multidomain assembled states of Hck tyrosine kinase in solution

12 July 2018

1 reference

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The role of L1 stalk-tRNA interaction in the ribosome elongation cycle

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Structural aspects of messenger RNA reading frame maintenance by the ribosome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Interactions of the ribosome with mRNA and tRNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Free energy profile of RNA hairpins: a molecular dynamics simulation study

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

High-resolution protein complexes from integrating genomic information with molecular simulation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Spontaneous formation of the unlocked state of the ribosome is a multistep process

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Experimental and computational determination of tRNA dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

The Structure of the Ribosome with Elongation Factor G Trapped in the Posttranslocational State

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Structures of the ribosome in intermediate states of ratcheting

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Navigating the ribosome's metastable energy landscape

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Single-molecule observations of ribosome function

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Ligand-induced global transitions in the catalytic domain of protein kinase A.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

The eukaryotic ribosome: current status and challenges

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Structure of ratcheted ribosomes with tRNAs in hybrid states

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Translation at the single-molecule level

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

The molecular architecture of the nuclear pore complex

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

The process of mRNA-tRNA translocation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Analysis of structural dynamics in the ribosome by TLS crystallographic refinement

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Conformational transitions of adenylate kinase: switching by cracking

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

The transition state for formation of the peptide bond in the ribosome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Ribosomal crystallography: peptide bond formation, chaperone assistance and antibiotics activity.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions

12 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

12 July 2018

https://api.crossref.org/works/10.1073%2FPNAS.1108363108

Crystal structure of the ribosome at 5.5 A resolution

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Structure of the 30S ribosomal subunit

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Folding funnels and conformational transitions via hinge-bending motions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Dynamics of translation on the ribosome: molecular mechanics of translocation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Intermediate states in the movement of transfer RNA in the ribosome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

The Energy Landscapes and Motions of Proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Modeling of proteins and their assemblies with the integrative modeling platform

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Stochastic gating and drug-ribosome interactions.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

The antibiotic viomycin traps the ribosome in an intermediate state of translocation.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

The native energy landscape for interleukin-1beta. Modulation of the population ensemble through native-state topology

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

Global ribosome motions revealed with elastic network model

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223460

The ribosome and the mechanism of protein synthesis

26 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1108363108

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22080606

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Large-amplitude nonlinear motions in proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22080606

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1108363108

1 reference

8 August 2017

0 references

1 reference

8 August 2017

1 reference