A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm (Q30491321)

12 October 2017

A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm (English)

1 reference

12 October 2017

Wei Huang

1

1 reference

12 October 2017

Joohyun Kim

series ordinal

2

1 reference

12 October 2017

Shantenu Jha

series ordinal

3

1 reference

12 October 2017

Fareed Aboul-ela

series ordinal

4

1 reference

12 October 2017

language of work or name

English

0 references

publication date

31 August 2009

1 reference

12 October 2017

Nucleic Acids Research

1 reference

12 October 2017

37

1 reference

12 October 2017

19

1 reference

12 October 2017

6528-6539

1 reference

Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch

12 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Long-timescale molecular dynamics simulations of protein structure and function.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Riboswitch RNAs: using RNA to sense cellular metabolism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Riboswitches: ancient and promising genetic regulators

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

A repulsive field: advances in the electrostatics of the ion atmosphere

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Annotation of tertiary interactions in RNA structures reveals variations and correlations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

A short guide for molecular dynamics simulations of RNA systems.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Riboswitches: emerging themes in RNA structure and function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

RNA dynamics: it is about time.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Molecular dynamics simulations of nucleic acid-protein complexes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Molecular simulations of protein dynamics: new windows on mechanisms in biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Direct observation of hierarchical folding in single riboswitch aptamers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Dynamic personalities of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

The distributions, mechanisms, and structures of metabolite-binding riboswitches

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Abundance and functional diversity of riboswitches in microbial communities

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Riboswitches as antibacterial drug targets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Molecular dynamics simulations of RNA: an in silico single molecule approach.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Structure of the S-adenosylmethionine riboswitch regulatory mRNA element

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Automatic atom type and bond type perception in molecular mechanical calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Scalable molecular dynamics with NAMD

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

The Amber biomolecular simulation programs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Gene regulation by riboswitches

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Development and testing of a general amber force field

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Regulation of gene expression by effectors that bind to RNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

An mRNA structure that controls gene expression by binding S-adenosylmethionine

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Tools for the automatic identification and classification of RNA base pairs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

The riboswitch-mediated control of sulfur metabolism in bacteria

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

A detailed view of a ribosomal active site: the structure of the L11-RNA complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Crystal structure of a conserved ribosomal protein-RNA complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Essential dynamics of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Dynamics of folded proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770654

Molecular-recognition characteristics of SAM-binding riboswitches

20 June 2018

1 reference

The kinetics of ligand binding by an adenine-sensing riboswitch

21 January 2018

1 reference

Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field.

21 January 2018

1 reference

Prediction of drug solubility from Monte Carlo simulations.

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

A Detailed View of a Ribosomal Active Site

21 January 2018

1 reference

Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach.

21 January 2018

1 reference

Monitoring structural changes in nucleic acids with single residue spatial and millisecond time resolution by quantitative hydroxyl radical footprinting

21 January 2018

1 reference

Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA.

21 January 2018

1 reference

The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch

21 January 2018

1 reference

The Mg2 binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19720737

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The dynamic landscapes of RNA architecture

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19720737

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19720737

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKP664

1 reference

12 October 2017

1 reference

12 October 2017

PubMed publication ID

19720737

1 reference