(Q52591449)

21 June 2018

title

Stochastic gating and drug-ribosome interactions. (English)

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21 June 2018

2

Kevin Y Sanbonmatsu

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21 June 2018

author name string

Andrea C Vaiana

series ordinal

1

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21 June 2018

language of work or name

English

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publication date

24 December 2008

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21 June 2018

Journal of Molecular Biology

published in

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21 June 2018

volume

386

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21 June 2018

issue

3

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21 June 2018

page(s)

648-661

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21 June 2018

Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae

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

22 June 2018

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Structure of the 70S ribosome complexed with mRNA and tRNA

22 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns

22 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

The ribosome's response to codon-anticodon mismatches.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Aminoglycoside-induced reduction in nucleotide mobility at the ribosomal RNA A-site as a potentially key determinant of antibacterial activity.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Structures of the bacterial ribosome at 3.5 A resolution

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

GROMACS: fast, flexible, and free

22 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Direct calculation of the binding free energies of FKBP ligands

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Structural insights into translational fidelity

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Defining the basis for the specificity of aminoglycoside-rRNA recognition: a comparative study of drug binding to the A sites of Escherichia coli and human rRNA.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Atomistic view of base flipping in DNA.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

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

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Peptide folding simulations

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Selection of tRNA by the ribosome requires a transition from an open to a closed form

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

How common is the funnel-like energy landscape in protein-protein interactions?

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

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

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Recognition of cognate transfer RNA by the 30S ribosomal subunit

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Structure of the 30S ribosomal subunit

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Recognition of the codon-anticodon helix by ribosomal RNA.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Structural origins of gentamicin antibiotic action

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Picosecond dynamics of tyrosine side chains in proteins

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Antibiotic blocks mRNA path on the ribosome.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Effective stochastic dynamics on a protein folding energy landscape

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Energy landscape of the ribosomal decoding center.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Convergence of replica exchange molecular dynamics.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Coarse-grained kinetic computations for rare events: application to micelle formation.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Atomic simulations of protein folding, using the replica exchange algorithm.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5970275

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

13 August 2018

1 reference

12 December 2020

Exploring the energy landscape of a beta hairpin in explicit solvent

1 reference

12 December 2020

Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer

1 reference

12 December 2020

Major groove binding of the tRNA/mRNA complex to the 16 S ribosomal RNA decoding site

1 reference

12 December 2020

Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs

1 reference

12 December 2020

Energetics of codon-anticodon recognition on the small ribosomal subunit

1 reference

12 December 2020

10.1016/J.JMB.2008.12.035

Identifiers

DOI

1 reference

21 June 2018

PMC publication ID

5970275

1 reference

21 June 2018

PubMed publication ID

19146858

1 reference

21 June 2018