Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure.

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TitleProtonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure.
Publication TypeJournal Article
Year of Publication2013
AuthorsDenning, EJ, Thirumalai, D, Mackerell, AD
JournalBiophys Chem
Volume184
Pagination8-16
Date Published2013 Dec 31
ISSN1873-4200
KeywordsHydrogen-Ion Concentration, Methylamines, Models, Molecular, Nucleic Acid Conformation, Protons, RNA
Abstract

The osmolyte trimethylamine N-oxide (TMAO) stabilizes the tertiary but not the secondary structures of RNA. However, molecular dynamics simulations performed on the PreQ1 riboswitch showed that TMAO destabilizes the tertiary riboswitch structure, leading us to hypothesize that the presence of RNA could result in enhanced population of the protonated form, TMAOP. Constant pH replica exchange simulations showed that a percentage of TMAO is indeed protonated, thus contributing to the stability of the tertiary but not the secondary structure of PreQ1. TMAOP results in an unfavorable dehydration of phosphodiester backbone, which is compensated by electrostatic attraction between TMAOP and the phosphate groups. In addition, TMAOP interacts with specific sites in the tertiary RNA structure, mimicking the behavior of positively charged ions and of the PreQ1 ligand in stabilizing RNA. Finally, we predict that TMAO-induced stabilization of RNA tertiary structures should be strongly pH dependent.

DOI10.1016/j.bpc.2013.08.002
Alternate JournalBiophys. Chem.
PubMed ID24012912
PubMed Central IDPMC3842377
Grant ListR01 GM051501 / GM / NIGMS NIH HHS / United States
R29 GM051501 / GM / NIGMS NIH HHS / United States
GM051501 / GM / NIGMS NIH HHS / United States