Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures. (Q38375897)

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2 March 2020

review article

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title

Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures (English)

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X-ray scattering techniques

2 March 2020

main subject

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4

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2 March 2020

author name string

Xianyang Fang

1

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2 March 2020

Jason R Stagno

2

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2 March 2020

Yuba R Bhandari

3

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2 March 2020

Yun-Xing Wang

5

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2 March 2020

publication date

1 February 2015

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Current Opinion in Structural Biology

2 March 2020

published in

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volume

30

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2 March 2020

page(s)

147-160

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Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing

2 March 2020

cites work

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Small angle X-ray scattering reveals a compact intermediate in RNA folding

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Determination of domain structure of proteins from X-ray solution scattering

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Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme

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Rapid compaction during RNA folding

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Resolving the motional modes that code for RNA adaptation

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A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data

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Small-angle X-ray scattering from RNA, proteins, and protein complexes

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Structural characterization of flexible proteins using small-angle X-ray scattering

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X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution

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Visualizing spatially correlated dynamics that directs RNA conformational transitions

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Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data

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RNA secondary structure prediction

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RNA dynamics: it is about time.

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Structural principles from large RNAs

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Human immunodeficiency virus type 1 regulator of virion expression, rev, forms nucleoprotein filaments after binding to a purine-rich "bubble" located within the rev-responsive region of viral mRNAs

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The complete VS ribozyme in solution studied by small-angle X-ray scattering

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

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A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA

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

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Comparison and functional implications of the 3D architectures of viral tRNA-like structures

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The centrality of RNA.

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The dynamic landscapes of RNA architecture

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X-ray imaging beyond the limits

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Riboswitch conformations revealed by small-angle X-ray scattering

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Structure and flexibility within proteins as identified through small angle X-ray scattering

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A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements

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Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold

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Structural analysis of the interaction between the human immunodeficiency virus Rev protein and the Rev response element

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12 December 2020

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

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12 December 2020

Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus

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12 December 2020

Improving small-angle X-ray scattering data for structural analyses of the RNA world

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12 December 2020

Implications of the HIV-1 Rev dimer structure at 3.2 A resolution for multimeric binding to the Rev response element

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12 December 2020

Riboswitch function: flipping the switch or tuning the dimmer?

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12 December 2020

FoXS: a web server for rapid computation and fitting of SAXS profiles

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Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering

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12 December 2020

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

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12 December 2020

Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules

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12 December 2020

Time-resolved X-ray scattering and RNA folding

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12 December 2020

Structural basis for cooperative RNA binding and export complex assembly by HIV Rev

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12 December 2020

NMR and small-angle scattering-based structural analysis of protein complexes in solution

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12 December 2020

Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data

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12 December 2020

Time resolved SAXS and RNA folding

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12 December 2020

SAXS studies of ion-nucleic acid interactions

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12 December 2020

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

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12 December 2020

Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law.

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12 December 2020

The dynamic nature of RNA as key to understanding riboswitch mechanisms

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12 December 2020

Predicting coaxial helical stacking in RNA junctions

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12 December 2020

Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy.

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12 December 2020

Visualizing large RNA molecules in solution.

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12 December 2020

Structure of the yeast U2/U6 snRNA complex

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12 December 2020

Functional complexity and regulation through RNA dynamics

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12 December 2020

Structural flexibility of RNA as molecular basis for Hfq chaperone function

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12 December 2020

Nucleic acid structure characterization by small angle X-ray scattering (SAXS)

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12 December 2020

Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex

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12 December 2020

Structure of the full-length HCV IRES in solution.

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12 December 2020

Comprehensive macromolecular conformations mapped by quantitative SAXS analyses

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12 December 2020

Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray microbeam

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12 December 2020

An unusual topological structure of the HIV-1 Rev response element

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12 December 2020

Small-angle X-ray scattering-derived structure of the HIV-1 5' UTR reveals 3D tRNA mimicry

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12 December 2020

Quaternary arrangement of an active, native group II intron ribonucleoprotein complex revealed by small-angle X-ray scattering

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12 December 2020

Global analysis of riboswitches by small-angle X-ray scattering and calorimetry

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12 December 2020

Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser.

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12 December 2020

RNA-guided assembly of Rev-RRE nuclear export complexes

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12 December 2020

New developments in the ATSAS program package for small-angle scattering data analysis

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12 December 2020

Functional analysis of CAR, the target sequence for the Rev protein of HIV-1.

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12 December 2020

DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering

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12 December 2020

Structure of yeast phenylalanine tRNA at 3 Å resolution

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12 December 2020

Yeast Transfer RNA: A Small-Angle X-Ray Study

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12 December 2020

A molecular rheostat. Co-operative rev binding to stem I of the rev-response element modulates human immunodeficiency virus type-1 late gene expression

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12 December 2020

Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex

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12 December 2020

Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm

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12 December 2020

10.1016/J.SBI.2015.02.010

Identifiers

DOI

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25765781%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25765781%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

PubMed publication ID

25765781

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