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Statistical mechanical prediction of ligand perturbation to RNA secondary structure and application to riboswitches
Author(s) -
Alaidi Osama,
Aboulela Fareed
Publication year - 2020
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.26195
Subject(s) - riboswitch , rna , chemistry , nucleic acid structure , biophysics , folding (dsp implementation) , terminator (solar) , nucleic acid secondary structure , ligand (biochemistry) , computational biology , crystallography , non coding rna , biology , physics , biochemistry , gene , receptor , ionosphere , astronomy , electrical engineering , engineering
The realization that noncoding RNA is implicated in numerous cellular processes, 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, perturbations to equilibrium secondary structure conformational distributions for two riboswitches are calculated in the presence of bound cognate ligands. This work incorporates a key factor coupling ligand binding to RNA conformation but not considered in most previous calculations: the differential affinity of the ligand for a range of RNA‐folding intermediates. Significant shifts in the free energy landscape (FEL) due to the ligand occur for transcripts of lengths corresponding to the “decision window,” following transcription of the so‐called anti‐terminator helix. The results suggest how ligand perturbation can stabilize the formation of an intermediate conformation, readily facilitating terminator hairpin formation in the full‐length riboswitch.