A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET. (Q34094042)

31 July 2017

1 reference

title

A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET. (English)

1 reference

31 July 2017

1 reference

Andrea Vaiana

2

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Scott C Blanchard

object named as

Scott C Blanchard

series ordinal

4

0 references

Karissa Sanbonmatsu

series ordinal

3

object named as

Kevin Y Sanbonmatsu

1 reference

31 July 2017

James B Munro

1

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31 July 2017

publication date

1 July 2008

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31 July 2017

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31 July 2017

volume

89

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31 July 2017

issue

7

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31 July 2017

page(s)

565-577

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Single-molecule experiments in biological physics: methods and applications

31 July 2017

cites work

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Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data

5 July 2018

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The ribosome in focus: new structures bring new insights

5 July 2018

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The role of fluctuations in tRNA selection by the ribosome

5 July 2018

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Fluctuations of transfer RNAs between classical and hybrid states

5 July 2018

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Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome

5 July 2018

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The ribosomal peptidyl transferase

5 July 2018

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Protein free energy landscapes remodeled by ligand binding

5 July 2018

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Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation

5 July 2018

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High-resolution, single-molecule measurements of biomolecular motion

5 July 2018

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Kinetically competent intermediates in the translocation step of protein synthesis

5 July 2018

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Identification of two distinct hybrid state intermediates on the ribosome

5 July 2018

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Ribosome recycling factor and release factor 3 action promotes TnaC-peptidyl-tRNA Dropoff and relieves ribosome stalling during tryptophan induction of tna operon expression in Escherichia coli

5 July 2018

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5 July 2018

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Structural basis for mRNA and tRNA positioning on the ribosome

5 July 2018

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Physical and functional interaction of the p14ARF tumor suppressor with ribosomes

5 July 2018

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

5 July 2018

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Structure of the 70S ribosome complexed with mRNA and tRNA

5 July 2018

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Real-time observation of RecA filament dynamics with single monomer resolution.

5 July 2018

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Analysis of single-molecule FRET trajectories using hidden Markov modeling

5 July 2018

1 reference

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Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps

5 July 2018

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Single-molecule fluorescence studies of protein folding and conformational dynamics

5 July 2018

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Bridging conformational dynamics and function using single-molecule spectroscopy.

5 July 2018

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Conformational heterogeneity in RNA polymerase observed by single-pair FRET microscopy.

5 July 2018

1 reference

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The hybrid state of tRNA binding is an authentic translation elongation intermediate

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited

5 July 2018

1 reference

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Fluctuating enzymes: lessons from single-molecule studies.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

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=2930612

Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Single-molecule RNA science

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Site-specific labeling of the ribosome for single-molecule spectroscopy

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

tRNA dynamics on the ribosome during 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=2930612

Single-molecule fluorescence spectroscopy and microscopy of biomolecular motors.

5 July 2018

1 reference

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Restoration of single-channel currents using the segmental k-means method based on hidden Markov modeling

5 July 2018

1 reference

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Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation

5 July 2018

1 reference

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Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme

5 July 2018

1 reference

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EF-G-independent reactivity of a pre-translocation-state ribosome complex with the aminoacyl tRNA substrate puromycin supports an intermediate (hybrid) state of tRNA binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

The role of dynamics in allosteric regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Cytoplasmic complex of p53 and eEF2

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Single-molecule transition-state analysis of RNA folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Locking and unlocking of ribosomal motions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Mechanism of elongation factor G function in tRNA translocation 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=2930612

Semisynthesis of proteins by expressed protein ligation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Does the ribosome translate cancer?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Protein synthesis at atomic resolution: mechanistics of translation in the light of highly resolved structures for 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=2930612

Correlating structural dynamics and function in single ribozyme molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Ribosome structure 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=2930612

Translocation of tRNA during protein 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=2930612

Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation 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=2930612

Single-molecule fluorescence resonance energy 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=2930612

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=2930612

Crystal structure of the ribosome at 5.5 A resolution

5 July 2018

1 reference

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Approaching translation at atomic resolution.

5 July 2018

1 reference

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

5 July 2018

1 reference

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Solution structure of the E. coli 70S ribosome at 11.5 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=2930612

Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

A structural change in the kinesin motor protein that drives motility

5 July 2018

1 reference

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X-ray crystal structures of 70S ribosome functional complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Ligand-induced conformational changes observed in single RNA molecules

5 July 2018

1 reference

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EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome

5 July 2018

1 reference

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Fluorescence spectroscopy of single biomolecules.

5 July 2018

1 reference

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Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Ribosomes and 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=2930612

Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Hydrolysis of GTP by elongation factor G drives tRNA movement 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=2930612

Estimating single-channel kinetic parameters from idealized patch-clamp data containing missed events

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

A base pair between tRNA and 23S rRNA in the peptidyl transferase centre 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=2930612

Characterisation of a new, fully active fluorescent derivative of E. coli tRNA Phe.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

The control of ribonucleic acid synthesis in Escherichia coli. IV. Relevance of unusual phosphorylated compounds from amino acid-starved stringent strains

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Conformational substates in 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=2930612

Intermediate states in the movement of transfer RNA 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=2930612

Errors and alternatives in reading the universal genetic code.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Binding of the 3' terminus of tRNA to 23S rRNA in the ribosomal exit site actively promotes translocation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Sites of interaction of the CCA end of peptidyl-tRNA with 23S rRNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

The Energy Landscapes and Motions 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=2930612

Factor-free ("non-enzymic") and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Single-molecule structural dynamics of EF-G--ribosome interaction during translocation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Observation of intersubunit movement of the ribosome in solution using FRET.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Dynamic polymorphism of Ras observed by single molecule FRET is the basis for molecular recognition

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Rapid ribosomal translocation depends on the conserved 18-55 base pair in P-site transfer RNA.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Single-molecule FRET study of denaturant induced unfolding of RNase H.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Repetitive shuttling of a motor protein on DNA.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Affinity purification of in vivo-assembled ribosomes for in vitro biochemical analysis

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

tRNA selection and kinetic proofreading in translation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Peptidyl-tRNA regulates the GTPase activity of translation factors

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Catalysis of ribosomal translocation by sparsomycin

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Rapid kinetic analysis of EF-G-dependent mRNA translocation in the ribosome

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Coupling of GTP hydrolysis by elongation factor G to translocation and factor recycling on the ribosome

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Maximum likelihood estimation of aggregated Markov processes

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

tRNA structure and ribosomal function. II. Interaction between anticodon helix and other tRNA mutations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930612

Direct Visualization of A-, P-, and E-Site Transfer RNAs in the Escherichia coli Ribosome

28 October 2018

1 reference

12 December 2020

Nonblinking and long-lasting single-molecule fluorescence imaging

1 reference

12 December 2020

Effect of buffer conditions on the position of tRNA on the 70 S ribosome as visualized by cryoelectron microscopy

1 reference

12 December 2020

Base-pairing between 23S rRNA and tRNA in the ribosomal A site

1 reference

12 December 2020

Single molecule FRET for the study on structural dynamics of biomolecules

1 reference

12 December 2020

Nonenzymic translocation and spontaneous release of noncognate peptidyl transfer ribonucleic acid from Escherichia coli ribosomes

1 reference

12 December 2020

Expanding the Genetic Code

1 reference

12 December 2020

Spontaneous, elongation factor G independent translocation of Escherichia coli ribosomes

1 reference

12 December 2020

Macromolecular arrangement in the aminoacyl-tRNA.elongation factor Tu.GTP ternary complex. A fluorescence energy transfer study

1 reference

12 December 2020

Programmed translational frameshifting

1 reference

12 December 2020

Optical studies of single molecules at room temperature

1 reference

12 December 2020

A Single-Molecule Study of RNA Catalysis and Folding

1 reference

12 December 2020

Identifiers

DOI

10.1002/BIP.20961

1 reference

31 July 2017

1 reference

31 July 2017

1 reference