Folding kinetics of riboswitch transcriptional terminators and sequesterers

DOI10.3390/E15083088MaRDI QIDQ280477zbMATH OpenOpenAlexFDO

Authors Ben Sauerwine, Michael Widom

Publication date 10 May 2016

Published in Entropy (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1307.3961

zbMATH Keywords

Monte Carlosimulationfoldinghairpinkineticnucleic acids

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Monte Carlo methods (65C05) Protein sequences, DNA sequences (92D20)

Abstract: To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales. We employ kinetic Monte Carlo simulation to model the time-dependent folding during transcription of TPP riboswitch expression platforms. According to our simulations, riboswitch transcriptional terminators, which must adopt a specific hairpin configuration by the time they have been transcribed, fold with higher efficiency than Shine-Dalgarno sequesterers, whose proper structure is required only at the time of ribosomal binding. Our findings suggest both that riboswitch transcriptional terminator sequences have been naturally selected for high folding efficiency, and that sequesterers can maintain their function even in the presence of significant misfolding.

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Cites work

• Arrhenius lifetimes of RNA structures from free energy landscapes

Cited in

(4)

• Quantitative modeling of the function of kinetically driven transcriptional riboswitches
• Determination of hammerhead ribozyme kinetic constants at high molar ratio ribozyme-substrate
• Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation
• Counting infinitely by oritatami co-transcriptional folding

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