Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs
| Autor: | Daniel P. Aalberts |
|---|---|
| Rok vydání: | 2015 |
| Předmět: |
Loop (graph theory)
Base pair Stacking General Physics and Astronomy lcsh:Astrophysics Context (language use) multibranch loops 01 natural sciences Article 03 medical and health sciences Loop entropy lcsh:QB460-466 0103 physical sciences coaxial stacking Statistical physics lcsh:Science 010306 general physics Protein secondary structure 030304 developmental biology Physics 0303 health sciences Quantitative Biology::Biomolecules business.industry secondary structure lcsh:QC1-999 Protein tertiary structure polymer simulations RNA lcsh:Q tertiary structure Artificial intelligence business Hairpin loops lcsh:Physics Energy (signal processing) |
| Zdroj: | Entropy (Basel, Switzerland) Entropy Volume 13 Issue 11 Pages: 1958-1966 Entropy, Vol 13, Iss 11, Pp 1958-1966 (2011) |
| ISSN: | 1099-4300 |
| Popis: | The free energy of an RNA fold is a combination of favorable base pairing and stacking interactions competing with entropic costs of forming loops. Here we show how loop entropy, surprisingly, can promote tertiary order. A general formula for the free energy of forming multibranch and other RNA loops is derived with a polymer-physics based theory. We also derive a formula for the free energy of coaxial stacking in the context of a loop. Simulations support the analytic formulas. The effects of stacking of unpaired bases are also studied with simulations. |
| Databáze: | OpenAIRE |
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