(Q41037740)

25 September 2017

Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome (English)

1 reference

25 September 2017

Hisashi Ishida

1

1 reference

25 September 2017

Steven Hayward

series ordinal

2

1 reference

25 September 2017

language of work or name

English

0 references

publication date

20 October 2008

1 reference

25 September 2017

1 reference

25 September 2017

95

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25 September 2017

12

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25 September 2017

5962-5973

1 reference

describes a project that uses

25 September 2017

molecular dynamics simulation

1 reference

A structural understanding of the dynamic ribosome machine

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=2599861

High performance computing in biology: multimillion atom simulations of nanoscale systems

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Structure of the 70S ribosome complexed with mRNA and tRNA

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Structures of the bacterial ribosome at 3.5 A resolution

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Simulating movement of tRNA into the ribosome during decoding

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Exploring global motions and correlations in the ribosome

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

UCSF Chimera--a visualization system for exploratory research and analysis

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent peptide exit path in the ribosome

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Locking and unlocking of ribosomal motions

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

The chemistry of protein synthesis and voyage through the ribosomal tunnel

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Structural insight into the role of the ribosomal tunnel in cellular regulation

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

The ribosomal exit tunnel functions as a discriminating gate

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Regulatory nascent peptides in the ribosomal tunnel

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Recognition of cognate transfer RNA by the 30S ribosomal subunit

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Steered molecular dynamics and mechanical functions of proteins

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Crystal structure of the ribosome at 5.5 A resolution

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

The structural basis of ribosome activity in peptide bond synthesis

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Collective protein dynamics in relation to function

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Essential dynamics of proteins

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Energy landscape of the ribosomal decoding center.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Features of ribosome-peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Global ribosome motions revealed with elastic network model

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

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

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

All-atom homology model of the Escherichia coli 30S ribosomal subunit.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Instruction of translating ribosome by nascent peptide

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

L23 protein functions as a chaperone docking site on the ribosome

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Mapping the electrostatic potential within the ribosomal exit tunnel

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

The Geometry of the Ribosomal Polypeptide Exit Tunnel

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Translational Operator of mRNA on the Ribosome: How Repressor Proteins Exclude Ribosome Binding

2 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599861

Large-amplitude nonlinear motions in proteins

2 December 2018

1 reference

12 December 2020

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

1 reference

12 December 2020

A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center

1 reference

12 December 2020

Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50

1 reference

12 December 2020

The ribosomal stalk binds to translation factors IF2, EF-Tu, EF-G and RF3 via a conserved region of the L12 C-terminal domain

1 reference

12 December 2020

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

1 reference

12 December 2020

10.1529/BIOPHYSJ.108.134890

Identifiers

DOI

1 reference

25 September 2017

1 reference

25 September 2017

PubMed publication ID

18936244

1 reference