Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch (Q30540399)

17 August 2017

Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch (English)

1 reference

17 August 2017

0 references

6

José N Onuchic

1 reference

17 August 2017

7

Karissa Y Sanbonmatsu

1 reference

17 August 2017

5

Scott P Hennelly

1 reference

17 August 2017

Ryan L Hayes

1

1 reference

17 August 2017

Jeffrey K Noel

series ordinal

2

1 reference

17 August 2017

Udayan Mohanty

series ordinal

3

1 reference

17 August 2017

Paul C Whitford

series ordinal

4

1 reference

17 August 2017

language of work or name

English

0 references

publication date

16 July 2012

1 reference

Journal of the American Chemical Society

17 August 2017

1 reference

17 August 2017

134

1 reference

17 August 2017

29

1 reference

17 August 2017

12043-12053

1 reference

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

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Evidence for a thermodynamically distinct Mg2+ ion associated with formation of an RNA tertiary structure

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Tertiary contacts control switching of the SAM-I riboswitch

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Dependence of RNA tertiary structural stability on Mg2+ concentration: interpretation of the Hill equation and coefficient

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Salt-dependent folding energy landscape of RNA three-way junction

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Direct quantitation of Mg2+-RNA interactions by use of a fluorescent dye.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

RNA folding: conformational statistics, folding kinetics, and ion electrostatics.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Riboswitches: emerging themes in RNA structure and function

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Charge density of divalent metal cations determines RNA stability

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Structure of the S-adenosylmethionine riboswitch regulatory mRNA element

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Simulating movement of tRNA into the ribosome during decoding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Mechanical unfolding of RNA hairpins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Development and testing of a general amber force field

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

A guide to ions and RNA structure

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

A thermodynamic framework for the magnesium-dependent folding of RNA.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

The old problems of glass and the glass transition, and the many new twists

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Essential dynamics of proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Classical electrostatics in biology and chemistry

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Dynamics of a small globular protein in terms of low-frequency vibrational modes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Conformational changes of transfer RNA. The role of magnesium(II)

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Magnesium-dependent active-site conformational selection in the Diels-Alderase ribozyme

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Stochastic gating and drug-ribosome interactions.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Importance of partially unfolded conformations for Mg(2+)-induced folding of RNA tertiary structure: structural models and free energies of Mg2+ interactions.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

The linkage between magnesium binding and RNA folding.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Shear viscosity of strongly coupled Yukawa systems on finite length scales.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675279

tRNA Conformation and Magnesium Binding. A Study of Yeast Phenylalanine-Specific tRNA by a Fluorescent Indicator and Differential Melting Curves

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22612276

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Counterion distribution around DNA probed by solution X-ray scattering

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22612276

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JA301454U

1 reference

17 August 2017

1 reference

17 August 2017

PubMed publication ID

22612276

1 reference