(Q44428737)

2 December 2017

Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. (English)

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2 December 2017

1

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2 December 2017

3

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2 December 2017

4

Steven Chu

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2 December 2017

2

Xiaowei Zhuang

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2 December 2017

Daniel Herschlag

5

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PubMed ID

12729738

2 December 2017

language of work or name

English

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publication date

1 May 2003

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Journal of Molecular Biology

2 December 2017

16

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based on heuristic

inferred from page(s)

published in

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2 December 2017

328

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2 December 2017

5

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2 December 2017

1011-1026

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Exposing the kinetic traps in RNA folding

2 December 2017

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Beyond kinetic traps in RNA folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Recent insights on RNA folding mechanisms from catalytic RNA.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Mg2+-dependent folding of a large ribozyme without kinetic traps

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Fingerprinting the folding of a group I precursor RNA

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Kinetic intermediates in RNA folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Folding of RNA involves parallel pathways

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Kinetic intermediates trapped by native interactions in RNA folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

RNA Folding at Millisecond Intervals by Synchrotron Hydroxyl Radical Footprinting

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

New pathways in folding of the Tetrahymena group I RNA enzyme

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Energetics and cooperativity of tertiary hydrogen bonds in RNA structure

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Multiple folding pathways for the P4-P6 RNA domain

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

An early transition state for folding of the P4-P6 RNA domain

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli)

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Mg2+-induced tRNA folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Correlating structural dynamics and function in single ribozyme molecules

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Defining the inside and outside of a catalytic RNA molecule

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Visualizing the higher order folding of a catalytic RNA molecule

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Exploring the folding landscape of a structured RNA

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Rapid compaction during RNA folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Folding intermediates of a self-splicing RNA: mispairing of the catalytic core

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Quantifying the energetic interplay of RNA tertiary and secondary structure interactions

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

In vitro genetic analysis of the hinge region between helical elements P5-P4-P6 and P7-P3-P8 in the sunY group I self-splicing intron

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Dissection of the role of the conserved G.U pair in group I RNA self-splicing

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Mechanical devices of the spliceosome: motors, clocks, springs, and things

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A ratchet-like inter-subunit reorganization of the ribosome during translocation

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Molecular movement inside the translational engine

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

X-ray crystal structures of 70S ribosome functional complexes

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: intrinsic binding energy in an RNA enzyme

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: evidence for ribozyme specific interactions with 2' OH groups

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Characterization of a local folding event of the Tetrahymena group I ribozyme: effects of oligonucleotide substrate length, pH, and temperature on the two substrate binding steps

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Ribozyme recognition of RNA by tertiary interactions with specific ribose 2′-OH groups

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Contributions of 2'-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme. An energetic picture of an active site composed of RNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Minor groove recognition of the conserved G.U pair at the Tetrahymena ribozyme reaction site

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Exocyclic amine of the conserved G.U pair at the cleavage site of the Tetrahymena ribozyme contributes to 5'-splice site selection and transition state stabilization

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A minor groove RNA triple helix within the catalytic core of a group I intron

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Joining the two domains of a group I ribozyme to form the catalytic core

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A preorganized active site in the crystal structure of the Tetrahymena ribozyme

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Function of tyrosyl-tRNA synthetase in splicing group I introns: an induced-fit model for binding to the P4-P6 domain based on analysis of mutations at the junction of the P4-P6 stacked helices

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Characterisation of the transition states for protein folding: towards a new level of mechanistic detail in protein engineering analysis

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Mapping the transition state and pathway of protein folding by protein engineering

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

The folding of an enzyme. III. Structure of the transition state for unfolding of barnase analysed by a protein engineering procedure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

P22 Arc Repressor: Transition State Properties Inferred from Mutational Effects on the Rates of Protein Unfolding and Refolding

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

The energy landscape of a fast-folding protein mapped by Ala-->Gly substitutions

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Contribution of a buried hydrogen bond to lambda repressor folding kinetics

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A specific transition state for S-peptide combining with folded S-protein and then refolding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Rough energy landscapes in protein folding: dimeric E. coli Trp repressor folds through three parallel channels

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Kinetic epitope mapping of the chicken lysozyme.HyHEL-10 Fab complex: delineation of docking trajectories

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Experimental assignment of the structure of the transition state for the association of barnase and barstar

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A Single-Molecule Study of RNA Catalysis and Folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Guanosine binding to the Tetrahymena ribozyme: thermodynamic coupling with oligonucleotide binding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A positive entropy change for guanosine binding and for the chemical step in the Tetrahymena ribozyme reaction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Effects of Mg2+ and the 2' OH of guanosine on steps required for substrate binding and reactivity with the Tetrahymena ribozyme reveal several local folding transitions

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Isolation of a local tertiary folding transition in the context of a globally folded RNA.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Use of duplex rigidity for stability and specificity in RNA tertiary structure

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Single versus parallel pathways of protein folding and fractional formation of structure in the transition state

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Determination and analysis of urea and guanidine hydrochloride denaturation curves

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

From snapshot to movie: phi analysis of protein folding transition states taken one step further

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A collapsed non-native RNA folding state

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

7 January 2021

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

inferred from DOI database lookup

7 January 2021

based on heuristic

From Levinthal to pathways to funnels

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Kinetics of conformational fluctuations in DNA hairpin-loops

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

New roles for structure in biology and drug discovery

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Limited internal friction in the rate-limiting step of a two-state protein folding reaction

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

The topomer search model: A simple, quantitative theory of two-state protein folding kinetics

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

The role of solvent viscosity in the dynamics of protein conformational changes

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A complete conformational map for RNA

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Direct kinetic evidence for folding via a highly compact, misfolded state

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

RNA chaperones and the RNA folding problem

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Kinetic traps in lysozyme folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Acceleration of the folding of hen lysozyme by trifluoroethanol

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Fluorescence quenching: A tool for single-molecule protein-folding study

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: docking is not diffusion-controlled and is driven by a favorable entropy change

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Loop length, intramolecular diffusion and protein folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A quantitative study of the flexibility contributed to RNA structures by nicks and single-stranded gaps

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Bypassing the kinetic trap of serpin protein folding by loop extension

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Movement of the guide sequence during RNA catalysis by a group I ribozyme

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

A phosphoramidate substrate analog is a competitive inhibitor of the Tetrahymena group I ribozyme

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Mutations in a nonconserved sequence of the Tetrahymena ribozyme increase activity and specificity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Induced folding in RNA-protein recognition: more than a simple molecular handshake

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Structure, recognition and adaptive binding in RNA aptamer complexes

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Joining of RNAs by splinted ligation

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

Direct demonstration of the catalytic role of binding interactions in an enzymatic reaction

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900272-9

10.1016/S0022-2836(03)00272-9

7 January 2021

Identifiers

DOI

1 reference

2 December 2017

1 reference

PubMed ID

12729738