DOI: 10.1101/461749Nov 5, 2018Paper

Statistical Mechanical Prediction of Ligand Perturbation to RNA Secondary Structure and Application to the SAM-I Riboswitch

BioRxiv : the Preprint Server for Biology
O. Alaidi, Fareed Aboul-ela

Abstract

The realization that non protein-coding RNA (ncRNA) is implicated in an increasing number of cellular processes, many related to human disease, makes it imperative to understand and predict RNA folding. RNA secondary structure prediction is more tractable than tertiary structure or protein structure. Yet insights into RNA structure-function relationships are complicated by coupling between RNA folding and ligand binding. Here, we introduce a simple statistical mechanical formalism to calculate perturbations to equilibrium secondary structure conformational distributions for RNA, in the presence of bound cognate ligands. For the first time, this formalism incorporates a key factor in coupling ligand binding to RNA conformation: the differential affinity of the ligand for a range of RNA-folding intermediates. We apply the approach to the SAM-I riboswitch, for which binding data is available for analogs of intermediate secondary structure conformers. Calculations of equilibrium secondary structure distributions during the transcriptional \"decision window\" predict subtle shifts due to the ligand, rather than an on/off switch. The results suggest how ligand perturbation can release a kinetic block to the formation of a terminator ...Continue Reading

Software Mentioned

Aptamer
RNAsubop t
Vienna package
TS
SAM
RNAsubopt

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