(Q36564863)

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Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings

scientific article published on 26 August 2015

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scholarly article

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Europe PubMed Central

PMC publication ID

15 August 2017

Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings (English)

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15 August 2017

1

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1 June 2020

George M Giambasu

2

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1 June 2020

Evgenia N Nikolova

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1 June 2020

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1 June 2020

Akash Bhattacharya

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1 June 2020

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David A Case

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1 June 2020

Hashim M Al-Hashimi

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1 June 2020

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26 August 2015

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15 August 2017

Journal of the American Chemical Society

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1 June 2020

137

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1 June 2020

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1 June 2020

12954-12965

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1 June 2020

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

1 reference

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Multiple conformational states of riboswitches fine-tune gene regulation

1 reference

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Measuring similarity between dynamic ensembles of biomolecules

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Chemical exchange in biomacromolecules: past, present, and future

1 reference

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Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges

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Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

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30 September 2017

Advances in the determination of nucleic acid conformational ensembles

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Recognition modes of RNA tetraloops and tetraloop-like motifs by RNA-binding proteins

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Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations

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A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.

1 reference

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30 September 2017

Utility of 1H NMR chemical shifts in determining RNA structure and dynamics

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30 September 2017

Visualizing transient low-populated structures of RNA.

1 reference

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30 September 2017

Multi-timescale conformational dynamics of the SH3 domain of CD2-associated protein using NMR spectroscopy and accelerated molecular dynamics

1 reference

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30 September 2017

Functional complexity and regulation through RNA dynamics

1 reference

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30 September 2017

New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation

1 reference

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Prospects for riboswitch discovery and analysis

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

1 reference

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30 September 2017

Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4748170

30 September 2017

Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein

1 reference

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30 September 2017

Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain

1 reference

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30 September 2017

RNA dynamics by design: biasing ensembles towards the ligand-bound state.

1 reference

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30 September 2017

Protein NMR using paramagnetic ions

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30 September 2017

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4748170

30 September 2017

Toward a unified representation of protein structural dynamics in solution.

1 reference

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30 September 2017

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4748170

30 September 2017

Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4748170

30 September 2017

Comparison of alignment tensors generated for native tRNA(Val) using magnetic fields and liquid crystalline media.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4748170

30 September 2017

Deciphering protein dynamics from NMR data using explicit structure sampling and selection

1 reference

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30 September 2017

The Amber biomolecular simulation programs

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30 September 2017

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

1 reference

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30 September 2017

Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic "hot spots"

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4748170

30 September 2017

Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4748170

30 September 2017

Partial alignment of biomolecules: an aid to NMR characterization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4748170

30 September 2017

Resonance assignment and structure determination for RNA.

1 reference

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30 September 2017

Structural and dynamic analysis of residual dipolar coupling data for proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4748170

30 September 2017

Structures of helical junctions in nucleic acids

1 reference

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Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions

1 reference

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30 September 2017

Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium

1 reference

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30 September 2017

NMR evidence for slow collective motions in cyanometmyoglobin

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30 September 2017

Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge

1 reference

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30 September 2017

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

1 reference

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30 September 2017

Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution

1 reference

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30 September 2017

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

1 reference

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28 June 2018

Variable helix elongation as a tool to modulate RNA alignment and motional couplings

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28 June 2018

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

1 reference

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28 June 2018

Probing Na(+)-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition

1 reference

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28 June 2018

Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4748170

28 June 2018

Order matrix analysis of residual dipolar couplings using singular value decomposition.

1 reference

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28 June 2018

Topology links RNA secondary structure with global conformation, dynamics, and adaptation

1 reference

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21 September 2018

Quantitative description of backbone conformational sampling of unfolded proteins at amino acid resolution from NMR residual dipolar couplings.

1 reference

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21 September 2018

RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis

1 reference

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21 September 2018

Protein conformational flexibility from structure-free analysis of NMR dipolar couplings: quantitative and absolute determination of backbone motion in ubiquitin.

1 reference

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21 September 2018

Ultrahigh resolution characterization of domain motions and correlations by multialignment and multireference residual dipolar coupling NMR.

1 reference

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21 September 2018

Resolving the motional modes that code for RNA adaptation

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21 September 2018

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1 reference

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Residue specific ribose and nucleobase dynamics of the cUUCGg RNA tetraloop motif by MNMR 13C relaxation.

1 reference

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21 September 2018

R(1rho) relaxation for two-site chemical exchange: general approximations and some exact solutions

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21 September 2018

A suite of 2H NMR spin relaxation experiments for the measurement of RNA dynamics

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21 September 2018

Anisotropic small amplitude Peptide plane dynamics in proteins from residual dipolar couplings

1 reference

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21 September 2018

Magnetic susceptibility tensor anisotropies for a lanthanide ion series in a fixed protein matrix.

1 reference

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21 September 2018

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1 reference

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21 September 2018

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1 reference

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21 September 2018

Quantitative Molecular Ensemble Interpretation of NMR Dipolar Couplings without Restraints

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mapping the population of protein conformational energy sub-states from NMR dipolar couplings

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Paramagnetically Induced Residual Dipolar Couplings for Solution Structure Determination of Lanthanide Binding Proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The global conformation of the hammerhead ribozyme determined using residual dipolar couplings

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RNA bulges and the helical periodicity of double-stranded RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modulating protein alignment in a liquid-crystalline medium through conservative mutagenesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Visualizing spatially correlated dynamics that directs RNA conformational transitions

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

NMR-based protein potentials

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extending the Range of Microsecond-to-Millisecond Chemical Exchange Detected in Labeled and Unlabeled Nucleic Acids by Selective Carbon R1ρNMR Spectroscopy

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Model-Free Analysis of Protein Backbone Motion from Residual Dipolar Couplings

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure-independent cross-validation between residual dipolar couplings originating from internal and external orienting media

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DNA bend direction by phase sensitive detection

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Independent alignment of RNA for dynamic studies using residual dipolar couplings

1 reference

https://pubmed.ncbi.nlm.nih.gov/26306428

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JACS.5B07229

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26306428%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26306428%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26306428%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

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