Apr 15, 2016

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension

BioRxiv : the Preprint Server for Biology
Naoto HoriDave Thirumalai

Abstract

Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed ribosomal frameshifting. Motivated in part by these experiments, we performed simulations using a coarse-grained model of RNA to describe the response of a PK over a range of mechanical forces ( f s) and monovalent salt concentrations ( C s). The coarse-grained simulations quantitatively reproduce the multistep thermal melting observed in experiments, thus validating our model. The free energy changes obtained in simulations are in excellent agreement with experiments. By varying f and C , we calculated the phase diagram that shows a sequence of structural transitions, populating distinct intermediate states. As f and C are changed, the stem-loop tertiary interactions rupture first, followed by unfolding of the 3'-end hairpin (I-F). Finally, the 5'-end hairpin unravels, producing an extended state (E-I). A theoretical analysis of the phase boundaries shows that the critical force for rupture scales as (log C )α with α = 1 (0.5) for E-I (I-F) transition. This relation is used to obtain the pref...Continue Reading

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Mentioned in this Paper

Rupture
Human neutrophil peptide 3
Concentrate Dosage Form
Blood group antigen S
Hairpin Loop Sequence
Ions
Theoretical Study
Protein Biosynthesis
Cocaine
Ribosomes

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