Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers
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...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2013-07-01
|
| Series: | Entropy |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1099-4300/15/8/3088 |
| _version_ | 1811301470292672512 |
|---|---|
| author | Ben Sauerwine Michael Widom |
| author_facet | Ben Sauerwine Michael Widom |
| author_sort | Ben Sauerwine |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T07:09:23Z |
| format | Article |
| id | doaj.art-c64cac10a1ff4bfea9ea4daf66bc098d |
| institution | Directory Open Access Journal |
| issn | 1099-4300 |
| language | English |
| last_indexed | 2024-04-13T07:09:23Z |
| publishDate | 2013-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Entropy |
| spelling | doaj.art-c64cac10a1ff4bfea9ea4daf66bc098d2022-12-22T02:56:55ZengMDPI AGEntropy1099-43002013-07-011583088309910.3390/e15083088Folding Kinetics of Riboswitch Transcriptional Terminators and SequesterersBen SauerwineMichael WidomTo 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.http://www.mdpi.com/1099-4300/15/8/3088nucleic acidshairpinfoldingMonte Carlokineticsimulation |
| spellingShingle | Ben Sauerwine Michael Widom Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers Entropy nucleic acids hairpin folding Monte Carlo kinetic simulation |
| title | Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers |
| title_full | Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers |
| title_fullStr | Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers |
| title_full_unstemmed | Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers |
| title_short | Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers |
| title_sort | folding kinetics of riboswitch transcriptional terminators and sequesterers |
| topic | nucleic acids hairpin folding Monte Carlo kinetic simulation |
| url | http://www.mdpi.com/1099-4300/15/8/3088 |
| work_keys_str_mv | AT bensauerwine foldingkineticsofriboswitchtranscriptionalterminatorsandsequesterers AT michaelwidom foldingkineticsofriboswitchtranscriptionalterminatorsandsequesterers |