(Q41788002)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

title

Measurement of average decoding rates of the 61 sense codons in vivo (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Bruce Futcher

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

author name string

Rukhsana Yeasmin

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Alisa Yurovsky

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Ying Cai

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Steve Skiena

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

language of work or name

English

0 references

publication date

27 October 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

volume

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation

21 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Evaluating bias-reducing protocols for RNA sequencing library preparation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Effects of the yeast RNA-binding protein Whi3 on the half-life and abundance of CLN3 mRNA and other targets

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Translation elongation can control translation initiation on eukaryotic mRNAs

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Biases in small RNA deep sequencing data

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

eIF5A promotes translation of polyproline motifs.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

The ribosome as a versatile catalyst: reactions at the peptidyl transferase center

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Positively charged residues are the major determinants of ribosomal velocity

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Decoding properties of tRNA leave a detectable signal in codon usage bias

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Speeding with control: codon usage, tRNAs, and ribosomes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Mechanisms of SecM-mediated stalling in the ribosome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Balanced codon usage optimizes eukaryotic translational efficiency

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

A new understanding of the decoding principle on the ribosome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Arginine changes the conformation of the arginine attenuator peptide relative to the ribosome tunnel

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Nascent peptide side chains induce rearrangements in distinct locations of the ribosomal tunnel

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Synonymous but not the same: the causes and consequences of codon bias

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Gene optimization mechanisms: a multi-gene study reveals a high success rate of full-length human proteins expressed in Escherichia coli

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Quantification of the yeast transcriptome by single-molecule sequencing

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

A signal-anchor sequence stimulates signal recognition particle binding to ribosomes from inside the exit tunnel

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Slow peptide bond formation by proline and other N-alkylamino acids in translation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Electrostatics in the ribosomal tunnel modulate chain elongation rates

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Association of protein biogenesis factors at the yeast ribosomal tunnel exit is affected by the translational status and nascent polypeptide sequence

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

The ribosome's response to codon-anticodon mismatches.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

A sampling of the yeast proteome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

6 June 2018

Codon selection in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Contextual constraints on synonymous codon choice

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

An evolutionary perspective on synonymous codon usage in unicellular organisms

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Coevolution of codon usage and transfer RNA abundance

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Codon preferences in free-living microorganisms

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Is there selection against wobble in codon-anticodon pairing?

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Secondary structure of MS2 phage RNA and bias in code word usage

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

The preferential codon usages in variable and constant regions of immunoglobulin genes are quite distinct from each other

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

EF-P is essential for rapid synthesis of proteins containing consecutive proline residues

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Messenger RNA interactions in the decoding center control the rate of translocation.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Peptidyl-prolyl-tRNA at the ribosomal P-site reacts poorly with puromycin

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Energetic contribution of tRNA hybrid state formation to translocation catalysis on the ribosome.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Mapping the electrostatic potential within the ribosomal exit tunnel

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4371865

Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting tran

3 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25347064

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Peptide bond formation does not involve acid-base catalysis by ribosomal residues

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25347064

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.7554/ELIFE.03735

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

PubMed publication ID

25347064

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25347064%20AND%20SRC:MED&resulttype=core&format=json