folding kinetics of riboswitch transcriptional terminators and sequesterers

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ID: 254023
2013
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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 thiamine pyrophosphate (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.
Reference Key
sauerwine2013entropyfolding Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Ben Sauerwine;Michael Widom
Journal European journal of medicinal chemistry
Year 2013
DOI
10.3390/e15083088
URL
http://www.mdpi.com/1099-4300/15/8/3088
Keywords
Monte Carlo nucleic acids folding kinetic simulationscienceastrophysicsphysics

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