Transition Metal Binding Drives Folding of a Metalloregulatory Riboswitch by Modulating Conformational Flexibility at Helical Junctions

Transition metal ions are crucial for bacteria survival. Bacteria employ metalloregulatory riboswitches to respond to varying metal ion concentrations. The czcD (NiCo) transcription riboswitch specifically senses Co²⁺, Ni²⁺, and Fe²⁺ ions at micromolar concentrations amid millimolar amounts of Mg²⁺. We used computer simulations with multiresolution RNA models to understand how global conformational changes in the NiCo riboswitch are coupled to the remarkable specific binding of Co²⁺. We show that the riboswitch folds through an intermediate state, where a partially folded four-way junction (4WJ) creates an anionic pocket large enough to accommodate the binding of solvated divalent ions. The binding of Co²⁺ is coupled to the stability of the weak noncanonical G·A base pairs at the helical junction that drive the formation of native-like coaxial stacking of four helices. The Co²⁺ binding further twists 4WJ, which locks the ions in the bound state. Electronic structure calculations show that enhanced orbital interactions between conserved guanines in the 4WJ and Co²⁺ are responsible for the high specificity of the riboswitch in binding to Co²⁺ over Mg²⁺. We provide a framework for understanding and engineering tunable RNA-based biosensors and developing antimicrobials, as metal intoxication is an evolutionary strategy to inhibit bacterial growth.