(Q36908415)

English

Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis

scientific article published on 11 July 2008

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scholarly article

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18621815%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis (English)

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18621815%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

Alexandar L Hansen

2

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10 January 2020

Catherine Musselman

3

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10 January 2020

4

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10 January 2020

author name string

Elizabeth A Dethoff

1

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10 January 2020

Ioan Andricioaei

5

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10 January 2020

Hashim M Al-Hashimi

6

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10 January 2020

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11 July 2008

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10 January 2020

Biophysical Journal

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10 January 2020

95

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10 January 2020

8

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10 January 2020

3906-3915

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Europe PubMed Central

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10 January 2020

Role of the 5' TAR stem--loop and the U5-AUG duplex in dimerization of HIV-1 genomic RNA.

1 reference

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29 September 2017

NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

NMR studies of RNA dynamics and structural plasticity 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=2553144

29 September 2017

Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings

1 reference

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29 September 2017

iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation

1 reference

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29 September 2017

Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy

1 reference

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29 September 2017

HIV-1 TAR RNA: the target of molecular interactions between the virus and its host

1 reference

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29 September 2017

Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance

1 reference

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29 September 2017

Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 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=2553144

29 September 2017

NMR spectroscopy of RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

The apical loop of the HIV-1 TAR RNA hairpin is stabilized by a cross-loop base pair

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Electron paramagnetic resonance dynamic signatures of TAR RNA-small molecule complexes provide insight into RNA structure and recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 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=2553144

29 September 2017

Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

TAR RNA loop: a scaffold for the assembly of a regulatory switch in HIV replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Development and current status of the CHARMM force field for nucleic acids.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 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=2553144

29 September 2017

Recent advances in RNA-protein recognition.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Induced fit in RNA-protein recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Aminoglycoside-arginine conjugates that bind TAR RNA: synthesis, characterization, and antiviral activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Recognition of 5'-terminal TAR structure in human immunodeficiency virus-1 mRNA by eukaryotic translation initiation factor 2.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Transcriptional regulation by targeted recruitment of cyclin-dependent CDK9 kinase in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Canonical dynamics: Equilibrium phase-space distributions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Solution structure of the HIV-2 TAR-argininamide complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Modeling and solution structure probing of the HIV-1 TAR stem-loop

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

Direct interactions between autoantigen La and human immunodeficiency virus leader RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553144

29 September 2017

The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein

1 reference

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29 September 2017

Two- and three-dimensional HCN experiments for correlating base and sugar resonances in 15N,13C-labeled RNA oligonucleotides

1 reference

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29 September 2017

Solid-state deuterium NMR studies reveal micros-ns motions in the HIV-1 transactivation response RNA recognition site.

1 reference

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27 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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27 June 2018

TAR-RNA recognition by a novel cyclic aminoglycoside analogue.

1 reference

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27 June 2018

Role of the trans-activation response element in dimerization of HIV-1 RNA.

1 reference

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27 June 2018

Evidence for a base triple in the free HIV-1 TAR RNA.

1 reference

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27 June 2018

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

1 reference

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27 June 2018

Inhibitors of protein-RNA complexation that target the RNA: specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules

1 reference

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27 June 2018

Taking a new TAK on tat transactivation

1 reference

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27 June 2018

Fragments of the HIV-1 Tat protein specifically bind TAR RNA.

1 reference

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27 June 2018

Dynamics of large elongated RNA by NMR carbon relaxation.

1 reference

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4 September 2018

Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme

1 reference

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4 September 2018

Resolving the motional modes that code for RNA adaptation

1 reference

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4 September 2018

Insight into the CSA tensors of nucleobase carbons in RNA polynucleotides from solution measurements of residual CSA: towards new long-range orientational constraints.

1 reference

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4 September 2018

Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility

1 reference

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4 September 2018

Specific interactions between HIV-1 nucleocapsid protein and the TAR element

1 reference

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4 September 2018

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

1 reference

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4 September 2018

Triple resonance experiments for the simultaneous correlation of H6/H5 and exchangeable protons of pyrimidine nucleotides in 13C,15N-labeled RNA applicable to larger RNA molecules

1 reference

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4 September 2018

Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-Tat-TAR ternary complex formation

1 reference

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4 September 2018

Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation

1 reference

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4 September 2018

Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

1 reference

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4 September 2018

An Arg/Lys-rich core peptide mimics TRBP binding to the HIV-1 TAR RNA upper-stem/loop

1 reference

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4 September 2018

Regulation of mRNA accumulation by a human immunodeficiency virus trans-activator protein

1 reference

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4 September 2018

Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/18621815

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/18621815

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

EPR spectroscopic analysis of TAR RNA–metal ion interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/18621815

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The role of coherence transfer efficiency in design of TROSY-type multidimensional NMR experiments

1 reference

https://pubmed.ncbi.nlm.nih.gov/18621815

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Specific recognition of HIV TAR RNA by the dsRNA binding domains (dsRBD1-dsRBD2) of PKR

1 reference

https://pubmed.ncbi.nlm.nih.gov/18621815

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Conformation of the TAR RNA-Arginine Complex by NMR Spectroscopy

1 reference

https://pubmed.ncbi.nlm.nih.gov/18621815

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/18621815

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Bulge-induced bends in RNA: quantification by transient electric birefringence

1 reference

https://pubmed.ncbi.nlm.nih.gov/18621815

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1529/BIOPHYSJ.108.140285

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18621815%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18621815%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18621815%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

ResearchGate publication ID

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