Folding of the Tetrahymena Ribozyme by Polyamines: Importance of Counterion Valence and Size

Koculi, Eda; Lee, Nam Kyung; Thirumalai, D.; Woodson, Sarah A.

doi:10.1016/j.jmb.2004.06.008

Cited by 62 publications

(77 citation statements)

References 47 publications

(58 reference statements)

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“…In solution, the presence of positively charged counterions modulates these electrostatic effects. Under low-salt conditions, extended and roughly collinear helical conformations minimize repulsive electrostatic forces; the increased presence of counterions at higher salt concentrations ameliorates this repulsion, allowing the helices to sample more ''relaxed conformations'' (e.g., bent and side-by-side conformations) (Russell and Herschlag 2001;Russell et al 2002;Das et al 2003;Koculi et al 2004;Takamoto et al 2004;Bai et al 2005Bai et al , 2008.…”

Section: Saxs Probes the Electrostatically Induced Changes In The Conmentioning

confidence: 99%

“…Repulsive electrostatic forces between the negatively charged phosphate moieties push the helices apart, favoring the extended and collinear helical configurations of the unfolded ensemble. In sufficient concentrations, solution counterions greatly reduce this electrostatic penalty, allowing the motif to ''relax'' and gradually adopt more folded configurations, where the helices are arranged side by side (Russell and Herschlag 2001;Russell et al 2002;Das et al 2003;Koculi et al 2004;Bai et al 2005). Opposing electrostatic repulsion, tertiary interactions formed from the dense tangle of hydrogen bonds and stacking interactions between specific regions on the helices, loops, and junctions can act as the ''molecular glue'' that, in conjunction with the junction, stabilize the folded structure (Tamura et al 2004).…”

Section: Introductionmentioning

confidence: 99%

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Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

Chu¹,

Lipfert²,

Bai³

et al. 2009

RNA

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Structured RNAs must fold into their native structures and discriminate against a large number of alternative ones, an especially difficult task given the limited information content of RNA's nucleotide alphabet. The simplest motifs within structured RNAs are two helices joined by nonhelical junctions. To uncover the fundamental behavior of these motifs and to elucidate the underlying physical forces and challenges faced by structured RNAs, we computationally and experimentally studied a tethered duplex model system composed of two helices joined by flexible single-or double-stranded polyethylene glycol tethers, whose lengths correspond to those typically observed in junctions from structured RNAs. To dissect the thermodynamic properties of these simple motifs, we computationally probed how junction topology, electrostatics, and tertiary contact location influenced folding stability. Small-angle X-ray scattering was used to assess our predictions. Single-or double-stranded junctions, independent of sequence, greatly reduce the space of allowed helical conformations and influencing the preferred location and orientation of their adjoining helices. A double-stranded junction guides the helices along a hinge-like pathway. In contrast, a single-stranded junction samples a broader set of conformations and has different preferences than the double-stranded junction. In turn, these preferences determine the stability and distinct specificities of tertiary structure formation. These sequence-independent effects suggest that properties as simple as a junction's topology can generally define the accessible conformational space, thereby stabilizing desired structures and assisting in discriminating against misfolded structures. Thus, junction topology provides a fundamental strategy for transcending the limitations imposed by the low information content of RNA primary sequence.

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Section: Saxs Probes the Electrostatically Induced Changes In The Conmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

Chu¹,

Lipfert²,

Bai³

et al. 2009

RNA

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show abstract

“…Moreover, recent studies have shown valence, size, and shape of counterions profoundly influence RNA folding. [147][148][149][150][151] Despite the complexity, it is possible to devise physics-based models that capture the essential aspects of RNA folding and dynamics. In order to provide a framework for understanding and anticipating the outcomes of increasingly sophisticated experiments involving RNA we have developed two classes of models.…”

Section: Rna Foldingmentioning

confidence: 99%

Minimal Models for Proteins and RNA: From Folding to Function

Pincus

Cho

Hyeon

et al. 2008

Progress in Molecular Biology and Translational Science

Self Cite

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We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key applications ranging from folding of proteins with disulfide bonds to functions of molecular machines. After presenting the theoretical basis that justifies the use of CG models, we explore the biophysical basis for the emergence of a finite number of folds from lattice models. The lattice model simulations of approach to the folded state show that non-native interactions are relevant only early in the folding process -a finding that rationalizes the success of structure-based models that emphasize native interactions. Applications of off-lattice C α and models that explicitly consider side chains (C α -SCM) to folding of β-hairpin and effects of macromolecular crowding are briefly discussed. Successful applications of a new class of off-lattice models, referred to as the Self- We also present two distinct models for RNA, namely, the Three Site Interaction (TIS) model and the SOP model, that probe forced unfolding and force quench refolding of a simple hairpin and Azoarcus ribozyme. The unfolding pathways of Azoarcus ribozyme depend on the loading rate, while constant force and constant loading rate simulations of the hairpin show that both forced-unfolding and force-quench refolding pathways are heterogeneous. The location of the transition state moves as force is varied. The predictions based on the SOP model show that force-induced unfolding pathways of the ribozyme can be dramatically changed by varying the loading rate. We conclude with a discussion of future prospects for the use of coarse-grained models in addressing problems of outstanding interest in biology.

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“…However, a comparison of activities among a series of ribozyme variants in 4 M Li + and in 10 mM Mg 2+ suggested that important interactions were absent in the monovalent reactions (O'Rear et al 2001). Polyamines are abundant inside cells, where they influence gene expression, DNA condensation, and RNA folding (Koculi et al 2004). In ribozyme catalysis, they are primarily used to augment self-cleavage or substrate cleavage in the presence of divalent cations (Dahm and Uhlenbeck 1991;Suh et al 1993;Earnshaw and Gait 1998;Akashi et al 2002).…”

Section: Introductionmentioning

confidence: 99%

Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme

Roychowdhury-Saha¹,

Burke²

2007

RNA

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Divalent ion sensitivity of hammerhead ribozymes is significantly reduced when the RNA structure includes appropriate tertiary stabilization. Therefore, we investigated the activity of the tertiary stabilized ''RzB'' hammerhead ribozyme in several nondivalent ions. Ribozyme RzB is active in spermidine and Na + alone, although the cleavage rates are reduced by more than 1,000-fold relative to the rates observed in Mg 2+ and in transition metal ions. The trivalent cobalt hexammine (CoHex) ion is often used as an exchange-inert analog of hydrated magnesium ion. Trans-cleavage rates exceeded 8 min À1 in 20 mM CoHex, which promoted cleavage through outersphere interactions. The stimulation of catalysis afforded by the tertiary structural interactions within RzB does not require Mg 2+ , unlike other extended hammerhead ribozymes. Site-specific interaction with at least one Mg 2+ ion is suggested by CoHex competition experiments. In the presence of a constant, low concentration of Mg 2+ , low concentrations of CoHex decreased the rate by two to three orders of magnitude relative to the rate in Mg 2+ alone. Cleavage rates increased as CoHex concentrations were raised further, but the final fraction cleaved was lower than what was observed in CoHex or Mg 2+ alone. These observations suggest that Mg 2+ and CoHex compete for binding and that they cause misfolded structures when they are together. The results of this study support the existence of an alternate catalytic mechanism used by nondivalent ions (especially CoHex) that is distinct from the one promoted by divalent metal ions, and they imply that divalent metals influence catalysis through a specific nonstructural role.

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Folding of the Tetrahymena Ribozyme by Polyamines: Importance of Counterion Valence and Size

Cited by 62 publications

References 47 publications

Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

Minimal Models for Proteins and RNA: From Folding to Function

Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme

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