Understanding the role of three-dimensional topology in determining the folding intermediates of group i introns

Chunxia Chen, Somdeb Mitra, Magdalena Jonikas, Joshua Martin, Michael D. Brenowitz, Alain Laederach

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Many RNA molecules exert their biological function only after folding to unique three-dimensional structures. For long, noncoding RNA molecules, the complexity of finding the native topology can be a major impediment to correct folding to the biologically active structure. An RNA molecule may fold to a near-native structure but not be able to continue to the correct structure due to a topological barrier such as crossed strands or incorrectly stacked helices. Achieving the native conformation thus requires unfolding and refolding, resulting in a long-lived intermediate. We investigate the role of topology in the folding of two phylogenetically related catalytic group I introns, the Twort and Azoarcus group I ribozymes. The kinetic models describing the Mg 2+ -mediated folding of these ribozymes were previously determined by time-resolved hydroxyl (̇OH) radical footprinting. Two intermediates formed by parallel intermediates were resolved for each RNA. These data and analytical ultracentrifugation compaction analyses are used herein to constrain coarse-grained models of these folding intermediates as we investigate the role of nonnative topology in dictating the lifetime of the intermediates. Starting from an ensemble of unfolded conformations, we folded the RNA molecules by progressively adding native constraints to subdomains of the RNA defined by the ̇OH timeprogress curves to simulate folding through the different kinetic pathways. We find that nonnative topologies (arrangement of helices) occur frequently in the folding simulations despite using only native constraints to drive the reaction, and that the initial conformation, rather than the folding pathway, is the major determinant of whether the RNA adopts nonnative topology during folding. From these analyses we conclude that biases in the initial conformation likely determine the relative flux through parallel RNA folding pathways.

Original languageEnglish (US)
Pages (from-to)1326-1337
Number of pages12
JournalBiophysical Journal
Volume104
Issue number6
DOIs
StatePublished - 2013

Fingerprint

Introns
RNA
Azoarcus
RNA Folding
Long Noncoding RNA
Nucleic Acid Conformation
Catalytic RNA
Ultracentrifugation
Hydroxyl Radical

ASJC Scopus subject areas

  • Biophysics

Cite this

Understanding the role of three-dimensional topology in determining the folding intermediates of group i introns. / Chen, Chunxia; Mitra, Somdeb; Jonikas, Magdalena; Martin, Joshua; Brenowitz, Michael D.; Laederach, Alain.

In: Biophysical Journal, Vol. 104, No. 6, 2013, p. 1326-1337.

Research output: Contribution to journalArticle

Chen, Chunxia ; Mitra, Somdeb ; Jonikas, Magdalena ; Martin, Joshua ; Brenowitz, Michael D. ; Laederach, Alain. / Understanding the role of three-dimensional topology in determining the folding intermediates of group i introns. In: Biophysical Journal. 2013 ; Vol. 104, No. 6. pp. 1326-1337.
@article{f6744eb9dcbf40b08c1bb22d6625c72c,
title = "Understanding the role of three-dimensional topology in determining the folding intermediates of group i introns",
abstract = "Many RNA molecules exert their biological function only after folding to unique three-dimensional structures. For long, noncoding RNA molecules, the complexity of finding the native topology can be a major impediment to correct folding to the biologically active structure. An RNA molecule may fold to a near-native structure but not be able to continue to the correct structure due to a topological barrier such as crossed strands or incorrectly stacked helices. Achieving the native conformation thus requires unfolding and refolding, resulting in a long-lived intermediate. We investigate the role of topology in the folding of two phylogenetically related catalytic group I introns, the Twort and Azoarcus group I ribozymes. The kinetic models describing the Mg 2+ -mediated folding of these ribozymes were previously determined by time-resolved hydroxyl (̇OH) radical footprinting. Two intermediates formed by parallel intermediates were resolved for each RNA. These data and analytical ultracentrifugation compaction analyses are used herein to constrain coarse-grained models of these folding intermediates as we investigate the role of nonnative topology in dictating the lifetime of the intermediates. Starting from an ensemble of unfolded conformations, we folded the RNA molecules by progressively adding native constraints to subdomains of the RNA defined by the ̇OH timeprogress curves to simulate folding through the different kinetic pathways. We find that nonnative topologies (arrangement of helices) occur frequently in the folding simulations despite using only native constraints to drive the reaction, and that the initial conformation, rather than the folding pathway, is the major determinant of whether the RNA adopts nonnative topology during folding. From these analyses we conclude that biases in the initial conformation likely determine the relative flux through parallel RNA folding pathways.",
author = "Chunxia Chen and Somdeb Mitra and Magdalena Jonikas and Joshua Martin and Brenowitz, {Michael D.} and Alain Laederach",
year = "2013",
doi = "10.1016/j.bpj.2013.02.007",
language = "English (US)",
volume = "104",
pages = "1326--1337",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "6",

}

TY - JOUR

T1 - Understanding the role of three-dimensional topology in determining the folding intermediates of group i introns

AU - Chen, Chunxia

AU - Mitra, Somdeb

AU - Jonikas, Magdalena

AU - Martin, Joshua

AU - Brenowitz, Michael D.

AU - Laederach, Alain

PY - 2013

Y1 - 2013

N2 - Many RNA molecules exert their biological function only after folding to unique three-dimensional structures. For long, noncoding RNA molecules, the complexity of finding the native topology can be a major impediment to correct folding to the biologically active structure. An RNA molecule may fold to a near-native structure but not be able to continue to the correct structure due to a topological barrier such as crossed strands or incorrectly stacked helices. Achieving the native conformation thus requires unfolding and refolding, resulting in a long-lived intermediate. We investigate the role of topology in the folding of two phylogenetically related catalytic group I introns, the Twort and Azoarcus group I ribozymes. The kinetic models describing the Mg 2+ -mediated folding of these ribozymes were previously determined by time-resolved hydroxyl (̇OH) radical footprinting. Two intermediates formed by parallel intermediates were resolved for each RNA. These data and analytical ultracentrifugation compaction analyses are used herein to constrain coarse-grained models of these folding intermediates as we investigate the role of nonnative topology in dictating the lifetime of the intermediates. Starting from an ensemble of unfolded conformations, we folded the RNA molecules by progressively adding native constraints to subdomains of the RNA defined by the ̇OH timeprogress curves to simulate folding through the different kinetic pathways. We find that nonnative topologies (arrangement of helices) occur frequently in the folding simulations despite using only native constraints to drive the reaction, and that the initial conformation, rather than the folding pathway, is the major determinant of whether the RNA adopts nonnative topology during folding. From these analyses we conclude that biases in the initial conformation likely determine the relative flux through parallel RNA folding pathways.

AB - Many RNA molecules exert their biological function only after folding to unique three-dimensional structures. For long, noncoding RNA molecules, the complexity of finding the native topology can be a major impediment to correct folding to the biologically active structure. An RNA molecule may fold to a near-native structure but not be able to continue to the correct structure due to a topological barrier such as crossed strands or incorrectly stacked helices. Achieving the native conformation thus requires unfolding and refolding, resulting in a long-lived intermediate. We investigate the role of topology in the folding of two phylogenetically related catalytic group I introns, the Twort and Azoarcus group I ribozymes. The kinetic models describing the Mg 2+ -mediated folding of these ribozymes were previously determined by time-resolved hydroxyl (̇OH) radical footprinting. Two intermediates formed by parallel intermediates were resolved for each RNA. These data and analytical ultracentrifugation compaction analyses are used herein to constrain coarse-grained models of these folding intermediates as we investigate the role of nonnative topology in dictating the lifetime of the intermediates. Starting from an ensemble of unfolded conformations, we folded the RNA molecules by progressively adding native constraints to subdomains of the RNA defined by the ̇OH timeprogress curves to simulate folding through the different kinetic pathways. We find that nonnative topologies (arrangement of helices) occur frequently in the folding simulations despite using only native constraints to drive the reaction, and that the initial conformation, rather than the folding pathway, is the major determinant of whether the RNA adopts nonnative topology during folding. From these analyses we conclude that biases in the initial conformation likely determine the relative flux through parallel RNA folding pathways.

UR - http://www.scopus.com/inward/record.url?scp=84877029089&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84877029089&partnerID=8YFLogxK

U2 - 10.1016/j.bpj.2013.02.007

DO - 10.1016/j.bpj.2013.02.007

M3 - Article

C2 - 23528092

AN - SCOPUS:84877029089

VL - 104

SP - 1326

EP - 1337

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 6

ER -