Induced fit or conformational selection for RNA/U1A folding

Qin, Fang; Chen, Yue; Wu, Maoying; Li, Yixue; Zhang, Jian; Chen, Haifeng

doi:10.1261/rna.2008110

Cited by 48 publications

(58 citation statements)

References 67 publications

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“…More recently, Qin et al have reported kinetic and freeenergy landscape analyses of a set of MD simulations, which suggested that the SL2 RNA associates with U1A by a process that involves an initial association followed by folding of the RNA into the bound conformation. 90 The three-step dissociation model proposed by Tang and Nilsson was supported by studies of association and dissociation by SPR and computational modeling studies. 41,44,81 The results of these investigations suggested that the U1A complex is formed by at least two steps that were termed the "lure and lock" mechanism.…”

Section: Discussionmentioning

confidence: 84%

Multistep Kinetics of the U1A–SL2 RNA Complex Dissociation

Anunciado

Dhar

Gruebele

et al. 2011

Journal of Molecular Biology

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Section: Discussionmentioning

confidence: 84%

Multistep Kinetics of the U1A–SL2 RNA Complex Dissociation

Anunciado

Dhar

Gruebele

et al. 2011

Journal of Molecular Biology

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“…63–65 Most RNA binding proteins contain large numbers of basic amino acid residues, and electrostatic attraction to the RNA may drive the initial formation of non-specific and dynamic encounter complexes, as suggested for the RNA recognition motif (RRM) protein U1A. 66,67 …”

Section: Induced Fit In Rna-protein Recognitionmentioning

confidence: 99%

RNA Folding Pathways and the Self-Assembly of Ribosomes

Woodson

2011

Acc. Chem. Res.

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Conspectus Many non-protein coding RNAs fold into intricate three-dimensional shapes in order to act in protein synthesis, splicing, and many other facets of gene regulation and expression. Hydroxyl radical footprinting probes the solvent accessibility of the RNA backbone at each residue in as little as 10 ms, providing detailed views of RNA folding pathways in real time. Time-resolved footprinting of ribozymes showed, in conjunction with other methods such as solution scattering and single-molecule FRET, that stable domains of RNA tertiary structure fold in less than 1 s. However, the free energy landscapes for RNA folding are rugged, and individual molecules kinetically partition into folding pathways that lead through metastable intermediates, stalling the folding or assembly process. Time-resolved footprinting was used to follow the formation of tertiary structure and protein interactions in the 16S rRNA during the assembly of 30S ribosomes. As previously observed in much simpler ribozymes, assembly occurs in stages, with individual molecules taking different routes to the final complex. Interactions occur concurrently in all domains of the 16S rRNA, and multi-stage protection of binding sites of individual proteins suggests initial encounter complexes between the rRNA and ribosomal proteins are remodeled during assembly. Equilibrium footprinting experiments showed that one primary binding protein was sufficient to stabilize the tertiary structure of the entire 16S 5′ domain. The rich detail available from the footprinting data showed that the secondary assembly protein S16 suppresses non-native structures in the 16S 5′ domain. In doing so, S16 enables a conformational switch distant from its own binding site, that may play a role in establishing interactions with other domains of the 30S subunit. Together, the footprinting results show how protein-induced changes in RNA structure are communicated over long distances, ensuring cooperative assembly of even very large RNA-protein complexes such as the ribosome.

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“…The mechanism of the binding reaction could entail trapping a single loop structure that can be bound by the protein (conformational capture) (Williamson 2000) or making one RNA:protein contact that facilitates subsequent rearrangements of RNA and protein to form the final complex (induced fit) (Frankel and Smith 1998); of course, the reality is likely to be more complicated. Indeed, several possible mechanisms and schemes for U1A binding to SLII have been proposed (Katsamba et al 2001;Pitici et al 2002;Hall 2002, 2004;Kormos et al 2007;Qin et al 2010;1 These authors contributed equally to this work.…”

Section: Introductionmentioning

confidence: 99%

Intrinsic flexibility of snRNA hairpin loops facilitates protein binding

Rau

Stump

Hall

2012

RNA

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Stem-loop II of U1 snRNA and Stem-loop IV of U2 snRNA typically have 10 or 11 nucleotides in their loops. The fluorescent nucleobase 2-aminopurine was used as a substitute for the adenines in each loop to probe the local and global structures and dynamics of these unusually long loops. Using steady-state and time-resolved fluorescence, we find that, while the bases in the loops are stacked, they are able to undergo significant local motion on the picosecond/nanosecond timescale. In addition, the loops have a global conformational change at low temperatures that occurs on the microsecond timescale, as determined using laser T-jump experiments. Nucleobase and loop motions are present at temperatures far below the melting temperature of the hairpin stem, which may facilitate the conformational change required for specific protein binding to these RNA loops.

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Induced fit or conformational selection for RNA/U1A folding

Cited by 48 publications

References 67 publications

Multistep Kinetics of the U1A–SL2 RNA Complex Dissociation

Multistep Kinetics of the U1A–SL2 RNA Complex Dissociation

RNA Folding Pathways and the Self-Assembly of Ribosomes

Intrinsic flexibility of snRNA hairpin loops facilitates protein binding

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