(Q38312449)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

title

Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

Giovanni Bussi

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

Francesco Di Palma

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

author name string

Francesco Di Palma

series ordinal

1

1 reference

2 September 2017

language of work or name

English

0 references

publication date

19 September 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

volume

19

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

issue

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

page(s)

1517-1524

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

22 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=3851719

Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

RNA under tension: Folding Landscapes, Kinetic partitioning Mechanism, and Molecular Tensegrity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

6 September 2017

A decade of riboswitches

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Structure and mechanism of purine-binding riboswitches

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Metabolite recognition principles and molecular mechanisms underlying riboswitch function

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

6 September 2017

ViennaRNA Package 2.0

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Role of ligand binding in structural organization of add A-riboswitch aptamer: a molecular dynamics simulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Effects of Mg2+ on the free energy landscape for folding a purine riboswitch RNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Riboswitches and the RNA world

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Real-time multidimensional NMR follows RNA folding with second resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

A switch in time: detailing the life of a riboswitch

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

The structural and functional diversity of metabolite-binding riboswitches

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Relative Stability of Helices Determines the Folding Landscape of Adenine Riboswitch Aptamers

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Purine sensing by riboswitches

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Single-molecule experiments in vitro and in silico

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Canonical sampling through velocity rescaling

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Core requirements of the adenine riboswitch aptamer for ligand binding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Riboswitches as antibacterial drug targets

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Structure of the S-adenosylmethionine riboswitch regulatory mRNA element

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Gene regulation by riboswitches

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Development and testing of a general amber force field

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Adenine riboswitches and gene activation by disruption of a transcription terminator

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

The non-Watson-Crick base pairs and their associated isostericity matrices

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

RNA Unwinding from Reweighted Pulling Simulations

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3851719

3 December 2018

Identifiers

DOI

10.1261/RNA.040493.113

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

1 reference

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

PubMed publication ID

24051105

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24051105%20AND%20SRC:MED&resulttype=core&format=json