An integrated perspective on RNA aptamer ligand-recognition models: clearing muddy waters

Abstract

Riboswitches are short RNA motifs that sensitively and selectively bind cognate ligands to modulate gene expression. Like protein receptor-ligand pairs, their binding dynamics are traditionally categorized as following one of two paradigmatic mechanisms: conformational selection and induced fit. In conformational selection, ligand binding stabilizes a particular state already present in the receptor's dynamic ensemble. In induced fit, ligand-receptor interactions enable the system to overcome the energetic barrier into a previously inaccessible state. In this article, we question whether a polarized division of RNA binding mechanisms truly meets the conceptual needs of the field. We will review the history behind this classification of RNA-ligand interactions, and the way induced fit in particular has been rehabilitated by single-molecule studies of RNA aptamers. We will highlight several recent results from single-molecule experimental studies of riboswitches that reveal gaps or even contradictions between common definitions of the two terms, and we will conclude by proposing a more robust framework that considers the range of RNA behaviors unveiled in recent years as a reality to be described, rather than an increasingly unwieldy set of exceptions to the traditional models.

Unprecedented tunability of riboswitch structure and regulatory function by sub-millimolar variations in physiological Mg2+

“…Ligand-binding mechanisms are broadly classified as following either a ‘conformational selection’ or an ‘induced fit’ folding pathway (48,49). These pathways can be defined either structurally, in terms of whether the ligand binds after or before folding of the holo state; or kinetically, in terms of whether ligand binding reduces the unfolding rate of the holo state (selection) or increases the folding rate (induction).…”

“…These pathways can be defined either structurally, in terms of whether the ligand binds after or before folding of the holo state; or kinetically, in terms of whether ligand binding reduces the unfolding rate of the holo state (selection) or increases the folding rate (induction). Many of the riboswitches studied using single-molecule microscopy to date have been shown to pre-organize into a native or native-like state in the presence of Mg 2+ but the absence of ligand (47,49–58).…”

Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit

“…[26] In certain systems ac ombination mechanism is observed. [26] In certain systems ac ombination mechanism is observed.…”

“…In the conformational selection mechanism, conformational rearrangement precedes ligand binding,whereas in the induced fit mechanism binding induces the conformational change. [26] In certain systems ac ombination mechanism is observed. [27] Fort he FMN system, the apo conformation, which is more disordered in PEG200 than in Mg 2+ ,undergoes as ignificant conformational change upon FMN binding to form the holo A ( Figure 4);t hus,u nder crowding conditions ligand binding occurs through an induced fit mechanism.…”

Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit

“…In the conformational selection mechanism, conformational rearrangement precedes ligand binding, whereas in the induced fit mechanism binding induces the conformational change . In certain systems a combination mechanism is observed .…”